From issues at mygrid.org.uk Mon Jun 6 09:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 6 Jun 2011 14:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-596) Monitoring should work on services with untrusted certificates Message-ID: <2660401.936.1307368495434.JavaMail.jira@rosalind.cs.man.ac.uk> Monitoring should work on services with untrusted certificates -------------------------------------------------------------- Key: BIOCAT-596 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596 Project: BioCatalogue Issue Type: Bug Components: Service Monitoring Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 Take for example: http://www.biocatalogue.org/service_tests/4870... ... monitoring should still be able to monitor this endpoint even if it has an untrusted certificate. Check the code to see what exactly it is doing here! -- This 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 Jun 7 04:29:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 09:29:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-597) Investigate monitoring for archived services Message-ID: <16684682.944.1307435395526.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Reporter: Mannie Tagarira Assignee: Jiten Bhagat 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 Jun 7 10:22:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 15:22:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-598) Figure out what to do with service providers with no services Message-ID: <22732435.949.1307456575352.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Service Provider Management Reporter: Mannie Tagarira Assignee: Mannie Tagarira As of June 7th 2011, 4 providers exist with no services. IDs: 333, 314, 304, 322 -- This 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 Jun 7 10:41:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 15:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-599) Identify a way to reduce the number of service providers whose name is the default (derived from the hostname) Message-ID: <13022427.950.1307457715368.JavaMail.jira@rosalind.cs.man.ac.uk> Identify a way to reduce the number of service providers whose name is the default (derived from the hostname) -------------------------------------------------------------------------------------------------------------- Key: BIOCAT-599 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-599 Project: BioCatalogue Issue Type: Task Components: Service Provider Management Reporter: Mannie Tagarira Assignee: Mannie Tagarira The latest 3 pages on the service provider index contain service providers whose name is in the format www-domain-name-com. The provider "Bio2RDF" has a number of such instances. Consider automatically updating these names when a new service is registered into the catalogue where no provider matching the hostname already exists. Check the hostname of the new service against existing hostnames. For instance, the hostname "new.service.bio2rdf.com" should identify with "x.bio2rdf.com", "y.bio2rdf.com", and "z.bio2rdf.com" based on the domain component of the hostname (ie "bio2rdf.com"). Since the db just sees the hostnames as strings, this process will have linear complexity as each db entry is compared for a match. What if there is no match? This should therefore be a background process, which will trigger the sending of an email to the provider informing them of any changes/merges to be made. For hostnames that do not match any instance in the DB, consider matching against the submitting user's email address. If the user has an "affiliation" value set, and an email address whose domain matches the service's hostname, rename the provider's name to the submitter's affiliation. This will not take care of all the cases but will take care of at least 35-40% of existing nameless providers. -- This 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 Jun 7 11:32:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 16:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-385) Implement annotation support for REST Services In-Reply-To: <29346203.5237.1276599015355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9185560.951.1307460775378.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-385?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-385. ------------------------------------ Resolution: Fixed This was done just before I left for final year. > Implement annotation support for REST Services > ---------------------------------------------- > > Key: BIOCAT-385 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-385 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > > Only the annotation of SOAP Services is currently supported; extend the app to allow for REST Services as well... -- This 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 Jun 7 11:41:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 16:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <14762518.953.1307461315397.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 updated BIOCAT-413: ----------------------------------- Description: 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 was:For example, "support at genouest.org" does not link to that email address, it links to "genouest.org" ("support@" is shown as is). > 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 > Reporter: Sergejs Aleksejevs > Assignee: Mannie Tagarira > Priority: Critical > > 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 Tue Jun 7 11:39:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 16:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-600) Some web services (which are not archived) have incorrect monitoring information Message-ID: <2567019.952.1307461195351.JavaMail.jira@rosalind.cs.man.ac.uk> 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 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 Jun 7 11:55:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 7 Jun 2011 16:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-462) Expose archived services and service components in the API In-Reply-To: <9943135.8517.1283874555417.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16053693.954.1307462155394.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-462?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16752#comment-16752 ] Mannie Tagarira commented on BIOCAT-462: ---------------------------------------- This has been done for JSON but not for XML. > Expose archived services and service components in the API > ---------------------------------------------------------- > > Key: BIOCAT-462 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-462 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > -- This 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 Jun 8 05:07:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 8 Jun 2011 10:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-39) Add soap_operations to search results web UI Message-ID: <31050437.955.1307524075508.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-39?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-39. ----------------------------------- Resolution: Fixed > Add soap_operations to search results web UI > -------------------------------------------- > > Key: BIOCAT-39 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-39 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > Currently, soap_operations are available in the search via the API. > Build this into the web UI for search too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 8 05:39:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 8 Jun 2011 10:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-150) Add admin features for curation, like delete Message-ID: <30293141.956.1307525995404.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-150?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16753#comment-16753 ] Mannie Tagarira commented on BIOCAT-150: ---------------------------------------- Consider curation assertions and linking related services (e.g service X is the REST variant to SOAP service Y) > Add admin features for curation, like delete > -------------------------------------------- > > Key: BIOCAT-150 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-150 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > Add features to allow admins and curators to curate/administrate the catalogue through the UI. This will permit people like Franck to go in and delete services and so on. -- This 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 Jun 8 11:39:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 16:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-596) Monitoring should work on services with untrusted certificates In-Reply-To: <2660401.936.1307368495434.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22962208.957.1307547595421.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16754#comment-16754 ] Jiten Bhagat commented on BIOCAT-596: ------------------------------------- Looking at the code, it does: {code} @response = %x[curl -I --max-time 20 -X GET #{url}] {code} ... which fails whenever during certificate verification if the certificate is not from a trusted set of CAs. > Monitoring should work on services with untrusted certificates > -------------------------------------------------------------- > > Key: BIOCAT-596 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Take for example: http://www.biocatalogue.org/service_tests/4870... > ... monitoring should still be able to monitor this endpoint even if it has an untrusted certificate. > Check the code to see what exactly it is doing here! -- This 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 Jun 8 11:39:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 16:39:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-596) Monitoring should work on services with untrusted certificates In-Reply-To: <2660401.936.1307368495434.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18575340.958.1307547598173.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16755#comment-16755 ] Jiten Bhagat commented on BIOCAT-596: ------------------------------------- For now we'll use the {{--inecure}} option in curl to ignore the verification process. > Monitoring should work on services with untrusted certificates > -------------------------------------------------------------- > > Key: BIOCAT-596 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Take for example: http://www.biocatalogue.org/service_tests/4870... > ... monitoring should still be able to monitor this endpoint even if it has an untrusted certificate. > Check the code to see what exactly it is doing here! -- This 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 Jun 8 12:01:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 17:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-596) Monitoring should work on services with untrusted certificates In-Reply-To: <2660401.936.1307368495434.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5121873.959.1307548915376.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16755#comment-16755 ] Jiten Bhagat edited comment on BIOCAT-596 at 08/06/11 17:00: ------------------------------------------------------------- For now we'll use the {{--insecure}} option in curl to ignore the verification process. was (Author: jbhagat): For now we'll use the {{--inecure}} option in curl to ignore the verification process. > Monitoring should work on services with untrusted certificates > -------------------------------------------------------------- > > Key: BIOCAT-596 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Take for example: http://www.biocatalogue.org/service_tests/4870... > ... monitoring should still be able to monitor this endpoint even if it has an untrusted certificate. > Check the code to see what exactly it is doing here! -- 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 Jun 8 12:21:18 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Jun 2011 12:21:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2389] trunk/lib/bio_catalogue/availability_check.rb: [BIOCAT-596] Fixed a couple of issues with monitoring HTTPS URLs. Message-ID: <20110608162118.532A51858363@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 8 12:23:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 17:23:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-596) Monitoring should work on services with untrusted certificates In-Reply-To: <2660401.936.1307368495434.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14338742.960.1307550235384.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-596. --------------------------------- Resolution: Fixed Fixed in revision 2389. Note: another, highly related, bug was also found and fixed in this commit - HTTPS responses that involved redirects were not being followed. > Monitoring should work on services with untrusted certificates > -------------------------------------------------------------- > > Key: BIOCAT-596 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-596 > Project: BioCatalogue > Issue Type: Bug > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Take for example: http://www.biocatalogue.org/service_tests/4870... > ... monitoring should still be able to monitor this endpoint even if it has an untrusted certificate. > Check the code to see what exactly it is doing here! -- This 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 Jun 8 12:27:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 17:27:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-589) Google Analytics is broken on the live site!! In-Reply-To: <6813614.166.1302690055358.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1026082.961.1307550475378.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-589?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-589. --------------------------------- Resolution: Fixed This was due to the configuration setup on the EBI servers; the switch for GA was off (!) > Google Analytics is broken on the live site!! > --------------------------------------------- > > Key: BIOCAT-589 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-589 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 8 12:27:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 17:27:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <4231210.962.1307550477659.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-568?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16758#comment-16758 ] Jiten Bhagat commented on BIOCAT-568: ------------------------------------- The consensus now is to just make all routes run on HTTPS, always! > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Application issues a double rendering error when ssl is switched on. This has a major impact on all secure pages like loggin -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 8 12:37:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 8 Jun 2011 17:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-584) Stop monitoring of the test site In-Reply-To: <18223488.107.1300357107911.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14374455.963.1307551075381.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-584: -------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: 1.0.1 (was: 1.0.0) Looks like the monitoring has been switched on the test site already. When doing releases we need this to be switched back on (even if just temporarily or manually running it) so that we can check that the monitoring system is working. > Stop monitoring of the test site > -------------------------------- > > Key: BIOCAT-584 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > Stop monitoring of the test site as no one is really checking these and they are redundant given the live site monitoring -- This 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 Jun 9 05:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-537) Get this app working for the Dec 2010 release (or maybe post release) In-Reply-To: <20412778.568.1289922569170.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25202034.971.1307612695425.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-537?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-537. --------------------------------- Resolution: No longer relevant The app is now being rewritten purely in Java, so this task is no longer relevant. > Get this app working for the Dec 2010 release (or maybe post release) > --------------------------------------------------------------------- > > Key: BIOCAT-537 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-537 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.0 > > > Currently the app doesn't work properly and needs to be fixed, hopefully for the Dec 2010 release, but if not then for soon after. > One of the errors experienced is from Mahmut: > {quote} > On 15/11/2010 14:36, Mahmut Uludag wrote: > > > > i just have noticed the following messages where i started the curator > > > > program. > > > > > > > > -- mahmut > > > > > > > > > > > > A, [2010-11-15T14:30:25.224000 #8913] ANY -- : Errno::EACCES - > > > > Permission denied - > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `initialize' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/modules/Application.rb:97:in `writeConfigFile' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:56:in `stateChanged' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `initialize' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `new' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `stateChanged' > > > > :1 > > > > A, [2010-11-15T14:30:25.334000 #8913] ANY -- : Errno::EACCES - > > > > Permission denied - > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `initialize' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/modules/Application.rb:97:in `writeConfigFile' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:56:in `stateChanged' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `initialize' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `new' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `stateChanged' > > > > :1 > > > > > > > > > > > > > > > > On Mon, 2010-11-15 at 14:34 +0000, Mahmut Uludag wrote: > >> > >> Hi Eric, > >> > >> > >> > >> After i started the curator program, i made a 'soaplab' search and > >> > >> selected few applications, when i try top export them, a file name is > >> > >> asked but no file is not generated after a file name is provided. > >> > >> > >> > >> Mahmut > {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 Thu Jun 9 05:44:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:44:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-537) Get this app working for the Dec 2010 release (or maybe post release) In-Reply-To: <20412778.568.1289922569170.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25019104.972.1307612698244.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-537?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-537. ------------------------------- > Get this app working for the Dec 2010 release (or maybe post release) > --------------------------------------------------------------------- > > Key: BIOCAT-537 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-537 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.0 > > > Currently the app doesn't work properly and needs to be fixed, hopefully for the Dec 2010 release, but if not then for soon after. > One of the errors experienced is from Mahmut: > {quote} > On 15/11/2010 14:36, Mahmut Uludag wrote: > > > > i just have noticed the following messages where i started the curator > > > > program. > > > > > > > > -- mahmut > > > > > > > > > > > > A, [2010-11-15T14:30:25.224000 #8913] ANY -- : Errno::EACCES - > > > > Permission denied - > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `initialize' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/modules/Application.rb:97:in `writeConfigFile' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:56:in `stateChanged' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `initialize' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `new' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `stateChanged' > > > > :1 > > > > A, [2010-11-15T14:30:25.334000 #8913] ANY -- : Errno::EACCES - > > > > Permission denied - > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `initialize' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > file:/data2/uludag/myGrid-BioCatalogue-Mass-Curator/lib/jruby-complete-1.5.1.jar!/META-INF/jruby.home/lib/ruby/1.8/open-uri.rb:32:in `open' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/modules/Application.rb:97:in `writeConfigFile' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:56:in `stateChanged' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `initialize' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `new' > > > > /data2/uludag/myGrid-BioCatalogue-Mass-Curator/src/events/AppCheckBoxListener.rb:45:in `stateChanged' > > > > :1 > > > > > > > > > > > > > > > > On Mon, 2010-11-15 at 14:34 +0000, Mahmut Uludag wrote: > >> > >> Hi Eric, > >> > >> > >> > >> After i started the curator program, i made a 'soaplab' search and > >> > >> selected few applications, when i try top export them, a file name is > >> > >> asked but no file is not generated after a file name is provided. > >> > >> > >> > >> Mahmut > {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 Thu Jun 9 05:46:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:46:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20746601.973.1307612816757.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-536: -------------------------------- Fix Version/s: 1.0.1 (was: 1.0.0) > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the API docs and wiki (http://www.biocatalogue.org/wiki/doku.php?id=development:annotation) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 05:46:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:46:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-564) Set up new sandbox server In-Reply-To: <14703282.195.1296477429427.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32975668.974.1307612819236.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-564?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-564: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.0) > Set up new sandbox server > ------------------------- > > Key: BIOCAT-564 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-564 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Set up, and migrate to, a new sandbox server for http://sandbox.biocatalogue.org -- This 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 Jun 9 05:47:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:47:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <6664369.975.1307612821464.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 updated BIOCAT-551: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.0) > 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: 1.0.2 > > > 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 Thu Jun 9 05:48:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:48:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-525) Remove ratings mechanism In-Reply-To: <22388840.543.1289909491708.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23203290.976.1307612935415.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-525?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16763#comment-16763 ] Jiten Bhagat commented on BIOCAT-525: ------------------------------------- This has been disabled, now all code needs to be removed (but make sure to archive code somewhere as it is useful from a code point of view). > Remove ratings mechanism > ------------------------ > > Key: BIOCAT-525 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-525 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.0 > > > Remove/disable the current ratings mechanism from the UI as it has proven to be not very useful -- This 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 Jun 9 05:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 10:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-532) Inform Alan or Alex how they should update the BioCat plugin for Taverna to take into account archived things In-Reply-To: <32074650.559.1289921549163.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3655584.977.1307613295396.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-532?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16455#comment-16455 ] Jiten Bhagat edited comment on BIOCAT-532 at 09/06/11 10:53: ------------------------------------------------------------- Had an initial chat with Alex about this and she will look at the Sergey's code to see what would be the quickest thing to do. was (Author: jbhagat): Has an initial chat with Alex about this and she will look at the Sergey's code to see what would be the quickest thing to do. > Inform Alan or Alex how they should update the BioCat plugin for Taverna to take into account archived things > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-532 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-532 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.0 > > > The inclusion of archived status in the API should be used by the BioCatalogue plugin for Taverna. > Meet with Alan or Alex to discuss how this could be done. -- This 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 Jun 9 06:12:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-535) After release, update API docs and data model diagram In-Reply-To: <24641103.566.1289922271996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27049218.978.1307614375381.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-535?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-535: -------------------------------- Fix Version/s: (was: 1.0.0) > After release, update API docs and data model diagram > ----------------------------------------------------- > > Key: BIOCAT-535 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-535 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > After the release has been carried out and before announcing, update the API docs and data model diagram using the material provided by Mannie (as a starting point). -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:12:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:12:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-532) Inform Alan or Alex how they should update the BioCat plugin for Taverna to take into account archived things In-Reply-To: <32074650.559.1289921549163.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25478607.979.1307614378622.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-532?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-532: -------------------------------- Fix Version/s: 1.0.1 (was: 1.0.0) > Inform Alan or Alex how they should update the BioCat plugin for Taverna to take into account archived things > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-532 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-532 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > The inclusion of archived status in the API should be used by the BioCatalogue plugin for Taverna. > Meet with Alan or Alex to discuss how this could be done. -- This 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 Jun 9 06:13:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:13:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-525) Remove ratings mechanism In-Reply-To: <22388840.543.1289909491708.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5826418.980.1307614380705.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-525?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-525: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Remove ratings mechanism > ------------------------ > > Key: BIOCAT-525 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-525 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Remove/disable the current ratings mechanism from the UI as it has proven to be not very useful -- This 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 Jun 9 06:13:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:13:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-525) Remove ratings mechanism In-Reply-To: <22388840.543.1289909491708.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26340407.981.1307614382785.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-525?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-525: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.0) > Remove ratings mechanism > ------------------------ > > Key: BIOCAT-525 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-525 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Remove/disable the current ratings mechanism from the UI as it has proven to be not very useful -- This 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 Jun 9 06:15:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:15:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-508) Look to changing the style of field names in ALL JSON outputs in the REST API In-Reply-To: <18306186.10446.1288560005033.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21189811.982.1307614555385.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-508. --------------------------------- Resolution: Won't Fix Changing the current outputs is deemed to be too impactful, so for now we will keep it as it is. > Look to changing the style of field names in ALL JSON outputs in the REST API > ----------------------------------------------------------------------------- > > Key: BIOCAT-508 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Original Estimate: 6 hours > Remaining Estimate: 6 hours > > Currently field names in the JSON outputs use Ruby naming conventions (eg: "service_type"), but the XML outputs of the API uses camel casing (eg: "serviceType"). Need to standardise on one if possible. So the proposal is to change all the JSON outputs to use camel case. > Need to take into consideration how this affects Sergey's BioCatalogue plugin (which is being polished up by Alex now) AND Mannie's BioCatalogue Mass Curator app. It might be that it's not worth changing the current outputs because they will have too much of an impact. -- This 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 Jun 9 06:15:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:15:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-508) Look to changing the style of field names in ALL JSON outputs in the REST API In-Reply-To: <18306186.10446.1288560005033.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13680189.983.1307614557712.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-508. ------------------------------- > Look to changing the style of field names in ALL JSON outputs in the REST API > ----------------------------------------------------------------------------- > > Key: BIOCAT-508 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Original Estimate: 6 hours > Remaining Estimate: 6 hours > > Currently field names in the JSON outputs use Ruby naming conventions (eg: "service_type"), but the XML outputs of the API uses camel casing (eg: "serviceType"). Need to standardise on one if possible. So the proposal is to change all the JSON outputs to use camel case. > Need to take into consideration how this affects Sergey's BioCatalogue plugin (which is being polished up by Alex now) AND Mannie's BioCatalogue Mass Curator app. It might be that it's not worth changing the current outputs because they will have too much of an impact. -- This 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 Jun 9 06:17:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:17:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-468) Do not show archived items in BLJSON In-Reply-To: <24041041.9044.1284113539275.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25121070.984.1307614675445.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-468?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-468. --------------------------------- Resolution: Won't Fix Archived items need to be shown in the API otherwise it breaks the API contract we have laid down. What is needed is a way of seeing whether a service is archived or not (done), and filtering of archived services (pending). > Do not show archived items in BLJSON > ------------------------------------ > > Key: BIOCAT-468 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-468 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > 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 Thu Jun 9 06:17:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:17:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-468) Do not show archived items in BLJSON In-Reply-To: <24041041.9044.1284113539275.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22496970.985.1307614677590.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-468?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-468. ------------------------------- > Do not show archived items in BLJSON > ------------------------------------ > > Key: BIOCAT-468 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-468 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > 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 Thu Jun 9 06:19:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:19:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make ALL routes/pages HTTPS Message-ID: <20054118.986.1307614795386.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 (was: Make important pages HTTPS) Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 Priority: Critical (was: Blocker) Description: The decision now is to make the WHOLE site run on HTTPS. This simplifies things greatly. (was: ... like log in, register etc etc) > Make ALL routes/pages HTTPS > --------------------------- > > 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: 1.0.2 > > > 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 Jun 9 06:19:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:19:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-243) Make ALL routes/pages HTTPS Message-ID: <29470922.987.1307614797575.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=16766#comment-16766 ] Jiten Bhagat commented on BIOCAT-243: ------------------------------------- Ian has done this for MethodBox and would be a valuable ally here! > Make ALL routes/pages HTTPS > --------------------------- > > 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: 1.0.2 > > > 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 Jun 9 06:19:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:19:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-447) Test SSL on the BioCatalogue main site In-Reply-To: <337413.7600.1280153355313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27326300.988.1307614799861.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-447?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-447: -------------------------------- Fix Version/s: 1.0.2 > Test SSL on the BioCatalogue main site > -------------------------------------- > > Key: BIOCAT-447 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-447 > Project: BioCatalogue > Issue Type: Sub-task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.2 > > -- This 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 Jun 9 06:21:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-594) Investigate: service test scripts are not currently running on the live site In-Reply-To: <13934139.782.1305900595406.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16834150.989.1307614915379.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-594?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-594. --------------------------------- Resolution: Fixed This was due a jammed delayed_job! > Investigate: service test scripts are not currently running on the live site > ---------------------------------------------------------------------------- > > Key: BIOCAT-594 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-594 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > Test scripts (for service monitoring) are not currently running on the live site and have been down since beginning of May. Need to investigate this and get it back up running. -- This 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 Jun 9 06:21:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:21:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-585) WSDLUtils service not working in Debian 5/6 In-Reply-To: <23216200.9.1301072635381.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3630802.990.1307614918616.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-585?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-585. --------------------------------- Resolution: Won't Fix The WSDLUtils service has now been fixed for *PHP 5.3* and it's not worth spending more time on this. > WSDLUtils service not working in Debian 5/6 > ------------------------------------------- > > Key: BIOCAT-585 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-585 > Project: BioCatalogue > Issue Type: Bug > Components: SOAP Services Support > Environment: Debian 5, PHP 5.2.6 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > WSDL files are failing to parse when using a WSDLUtils service running on Debian 5. > More investigation is required into this. > Example URL: > {code} > http://localhost/WSDLUtils/WSDLUtils.php?method=parse&wsdl_uri=http://www.biocatalogue.org/soap_services/2709/latest_wsdl > {code} > Error report: > {code} > Warning: DOMDocument::load(): supplied argument is not a valid Stream-Context resource in /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php on line 24 > Warning: Cannot modify header information - headers already sent by (output started at /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php:24) in /var/www/WSDLUtils/WSDLUtils.php on line 247 > 2Retrieving document at 'http://www.biocatalogue.org/soap_services/2709/latest_wsdl'. Retrieving document at 'http://www.biocatalogue.org/soap_services/2709/latest_wsdl'. Analyzer Stopped By Exception: Version null of the "null" document is not compatible with this version of the test tools. 1http://www.bioinf.manchester.ac.uk/http://schemas.xmlsoap.org/soap/httphttp://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/minotaur/services/minotaurPrecis.cgiTakes a UniProt ID list as input; returns the associated PRECIS report. > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:22:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:22:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-585) WSDLUtils service not working in Debian 5/6 In-Reply-To: <23216200.9.1301072635381.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31697876.991.1307614920740.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-585?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-585. ------------------------------- > WSDLUtils service not working in Debian 5/6 > ------------------------------------------- > > Key: BIOCAT-585 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-585 > Project: BioCatalogue > Issue Type: Bug > Components: SOAP Services Support > Environment: Debian 5, PHP 5.2.6 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > WSDL files are failing to parse when using a WSDLUtils service running on Debian 5. > More investigation is required into this. > Example URL: > {code} > http://localhost/WSDLUtils/WSDLUtils.php?method=parse&wsdl_uri=http://www.biocatalogue.org/soap_services/2709/latest_wsdl > {code} > Error report: > {code} > Warning: DOMDocument::load(): supplied argument is not a valid Stream-Context resource in /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php on line 24 > Warning: Cannot modify header information - headers already sent by (output started at /var/www/WSDLUtils/WSDLParser/WSDLXmlSchemaParser.php:24) in /var/www/WSDLUtils/WSDLUtils.php on line 247 > 2Retrieving document at 'http://www.biocatalogue.org/soap_services/2709/latest_wsdl'. Retrieving document at 'http://www.biocatalogue.org/soap_services/2709/latest_wsdl'. Analyzer Stopped By Exception: Version null of the "null" document is not compatible with this version of the test tools. 1http://www.bioinf.manchester.ac.uk/http://schemas.xmlsoap.org/soap/httphttp://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/minotaur/services/minotaurPrecis.cgiTakes a UniProt ID list as input; returns the associated PRECIS report. > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:22:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:22:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-594) Investigate: service test scripts are not currently running on the live site In-Reply-To: <13934139.782.1305900595406.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12270644.992.1307614922855.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-594?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16767#comment-16767 ] Jiten Bhagat edited comment on BIOCAT-594 at 09/06/11 11:20: ------------------------------------------------------------- This was due to a jammed delayed_job! Back up now. was (Author: jbhagat): This was due a jammed delayed_job! > Investigate: service test scripts are not currently running on the live site > ---------------------------------------------------------------------------- > > Key: BIOCAT-594 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-594 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > Test scripts (for service monitoring) are not currently running on the live site and have been down since beginning of May. Need to investigate this and get it back up running. -- This 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 Jun 9 06:23:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:23:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <13391979.993.1307615035391.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-499?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16769#comment-16769 ] Jiten Bhagat commented on BIOCAT-499: ------------------------------------- Alex also needs this for SCAPE! > 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 > > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > 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 Thu Jun 9 06:23:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:23:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-500) Document how to use and update the VM In-Reply-To: <16227861.9965.1286463195301.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18738917.994.1307615037724.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-500: -------------------------------- Fix Version/s: 1.0.1 > Document how to use and update the VM > ------------------------------------- > > Key: BIOCAT-500 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Document how to set up, use and update the BioCatalogue VM. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:23:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:23:59 +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: <17030031.995.1307615039838.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 > 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 > > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > 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 Thu Jun 9 06:27:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:27:55 +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: <931094.996.1307615275375.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: -------------------------------- Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 > 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: Jiten Bhagat > Priority: Critical > Fix For: 1.0.2 > > -- This 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 Jun 9 06:27:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:27:57 +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: <1125723.997.1307615277515.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: 1.0.2 > 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: 1.0.2 > > -- This 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 Jun 9 06:29:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:29:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-423) Fix Service Provider name autocomplete to show escaped names In-Reply-To: <29360194.6732.1277733735420.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6648439.998.1307615395377.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-423: -------------------------------- Priority: Major (was: Critical) > Fix Service Provider name autocomplete to show escaped names > ------------------------------------------------------------ > > Key: BIOCAT-423 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.2 > > > When a Service Provider has a name like "my provider ", it is shown as "my provider" in the autocomplete. When it has been selected, it will fill in the text box with "my provider alert("warning...");". > The autocomplete should show the name as is... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:29:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:29:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <7222639.999.1307615397529.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 ] Jiten Bhagat updated BIOCAT-413: -------------------------------- Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 Priority: Major (was: Critical) > 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: 1.0.2 > > > 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 Thu Jun 9 06:30:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:30:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-423) Fix Service Provider name autocomplete to show escaped names In-Reply-To: <29360194.6732.1277733735420.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9734459.1000.1307615400164.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-423: -------------------------------- Fix Version/s: 1.0.2 > Fix Service Provider name autocomplete to show escaped names > ------------------------------------------------------------ > > Key: BIOCAT-423 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.2 > > > When a Service Provider has a name like "my provider ", it is shown as "my provider" in the autocomplete. When it has been selected, it will fill in the text box with "my provider alert("warning...");". > The autocomplete should show the name as is... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:30:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:30:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-112) Integrate a rich text editor Message-ID: <30688336.1001.1307615402482.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-112?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-112: -------------------------------- Fix Version/s: 1.2.0 Priority: Minor (was: Major) > Integrate a rich text editor > ---------------------------- > > Key: BIOCAT-112 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-112 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > ... for things like the announcement text box and annotations. > CKEditor and TinyMCE are both copyleft licenced, so try something like: http://github.com/80beans/wysihat-engine|wysihat-engine -- This 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 Jun 9 06:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-303) Investigate database timout errors when deleting entries Message-ID: <5450861.1003.1307615635368.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-303?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-303: -------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: 1.1.0 More investigation is required for this. Especially, need's some testing under stress/bulk conditions. > 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 Thu Jun 9 06:35:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:35:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-294) Migrate the test script descriptions from main table to annotations Message-ID: <9086244.1004.1307615755357.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-294?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-294. --------------------------------- Resolution: Waiting For Info It's not certain how we can go about doing this now. > Migrate the test script descriptions from main table to annotations > ------------------------------------------------------------------- > > Key: BIOCAT-294 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-294 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations (in App), Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Critical > > When the test script were imported, the description were imported into the main test script table. This gives these descriptions the weighting of trust & reliability associated with provider but that may not necessarily be the case. Moving them to annotations would associate them with the user that supplied the description. -- This 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 Jun 9 06:37:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-285) Search should take into account special characters Message-ID: <11710012.1005.1307615875364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-285?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-285: -------------------------------- Fix Version/s: 1.2.0 Affects Version/s: 1.0.0 Priority: Major (was: Critical) > Search should take into account special characters > -------------------------------------------------- > > Key: BIOCAT-285 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-285 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Certain characters are special characters to the search engine. Ie: > \, +, -, !, (, ), :, ^, ], {, }, ~, *, ? > Sometimes these need to be escaped (eg: for WSDL URLs). Need to have a way to tackle this in both the Web AND API in a consistent way. > Eg: in API, queries with double quotes on either side will get escaped. Otherwise it will be pattern matched etc by Solr. In Web API we need special cases like for when a URL is pasted in. > For Web interface, Alan and Stian suggest a separation in results such as "Exact matched", "Pattern matched", 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 Jun 9 06:37:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:37:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-200) Need to import the Soaplab services metadata from Feta Message-ID: <29031446.1006.1307615877617.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16772#comment-16772 ] Jiten Bhagat commented on BIOCAT-200: ------------------------------------- This needs to be picked up again! > Need to import the Soaplab services metadata from Feta > ------------------------------------------------------ > > Key: BIOCAT-200 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > ... as these could not be imported in the first instance. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:39:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-200) Need to import the Soaplab services metadata from Feta Message-ID: <22220322.1007.1307615995369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-200: -------------------------------- Fix Version/s: 1.1.0 Priority: Major (was: Critical) > Need to import the Soaplab services metadata from Feta > ------------------------------------------------------ > > Key: BIOCAT-200 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > ... as these could not be imported in the first instance. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:39:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:39:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-135) Fix WSDL parsing - not picking up all descriptions Message-ID: <3207.1008.1307615997480.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: -------------------------------- Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 Priority: Major (was: Critical) > 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: Eric Nzuobontane > Fix For: 1.1.0 > > > 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 Thu Jun 9 06:39:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:39:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-142) Search needs to handle pluralisations Message-ID: <13461860.1009.1307615999618.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-142?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-142: -------------------------------- Fix Version/s: Future Affects Version/s: 1.0.0 Priority: Major (was: Critical) > Search needs to handle pluralisations > ------------------------------------- > > Key: BIOCAT-142 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-142 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > From Sam Schmidt - "The other thing was; there doesn't appear to be LIKE searching? Searching for "Phylogenetics" returns 0 results, where "Phylogenetic" returns 5." -- This 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 Jun 9 06:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-373) Issue with < and > characters within annotations when rendered in the UI In-Reply-To: <2931027.2646.1275987497061.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6771264.1002.1307615515379.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-373?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-373: -------------------------------- Fix Version/s: 1.2.0 Priority: Major (was: Critical) > Issue with < and > characters within annotations when rendered in the UI > ------------------------------------------------------------------------ > > Key: BIOCAT-373 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-373 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Currently, if users add annotations like: > bq. usage: iprscan [-appl ...] [-nocrc] [-seqtype p|n] [-trlen ] [-trtable ]\r\n [-iprlookup] [-goterms] -i [-o ]\r\n\r\n -i > ... then the annotation is displayed incorrectly and breaks the page layout. > This is not good! > It seems that only a rich text editor will solve this particular issue. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:41:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-133) Move normalisation of URLs to the specific models Message-ID: <33536754.1010.1307616115370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-133?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-133: -------------------------------- Fix Version/s: Future Affects Version/s: 1.0.0 Priority: Minor (was: Critical) > Move normalisation of URLs to the specific models > ------------------------------------------------- > > Key: BIOCAT-133 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-133 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Currently, the normalisation of URLs (ie: using: Addressable::URI.parse(..).normalise.to_s) is done in various places like the controllers and in import scripts (feta, seekda etc). Instead, they should be done in the models, in places like the check_duplicate method and when setting URL based fields. -- This 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 Jun 9 06:41:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:41:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-107) Implement descriptions pages for annotation attributes Message-ID: <17404580.1011.1307616117595.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-107?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-107: -------------------------------- Fix Version/s: 1.1.0 Priority: Major (was: Critical) > Implement descriptions pages for annotation attributes > ------------------------------------------------------ > > Key: BIOCAT-107 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-107 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App), Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > Annotation Attributes have "identifiers" such as: "http://biocatalogue.org/attribute/description" so that they can be referenced uniquely from outside the BioCatalogue. > Some have identifiers from known vocabularies, eg: Dublin Core, but by default they have an identifier like: > http://biocatalogue.org/attribute/{processed_name} > Make these into dereferenceable URIs (ie: a URL to a web page) so that people can find out more information about the Annotation Attribute. In other words, implement pages for Annotation Attributes with the BioCatalogue based URI. -- This 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 Jun 9 06:42:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:42:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-117) Investigate how rollbacks in transactions affect Solr Message-ID: <22501746.1012.1307616121409.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-117?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-117: -------------------------------- Fix Version/s: Future (was: 1.2.0) > Investigate how rollbacks in transactions affect Solr > ----------------------------------------------------- > > Key: BIOCAT-117 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-117 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > When transactions rollback, what happens to anything that was indexed in Solr during the transaction??? -- This 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 Jun 9 06:42:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:42:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-117) Investigate how rollbacks in transactions affect Solr Message-ID: <17885563.1013.1307616123433.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-117?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-117: -------------------------------- Fix Version/s: 1.2.0 Priority: Major (was: Critical) > Investigate how rollbacks in transactions affect Solr > ----------------------------------------------------- > > Key: BIOCAT-117 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-117 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > When transactions rollback, what happens to anything that was indexed in Solr during the transaction??? -- This 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 Jun 9 06:43:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:43:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-67) Unique identifiers for annotation attributes Message-ID: <8795903.1014.1307616235357.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-67?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-67. -------------------------------- Resolution: Fixed > Unique identifiers for annotation attributes > -------------------------------------------- > > Key: BIOCAT-67 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-67 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App) > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > Possibility to have unique URI for the annotation predicates such as description, publication, example. > e.g www.biocatalogue.org/annotation#description -- This 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 Jun 9 06:43:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:43:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-67) Unique identifiers for annotation attributes Message-ID: <28715785.1015.1307616238038.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-67?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-67. ------------------------------ > Unique identifiers for annotation attributes > -------------------------------------------- > > Key: BIOCAT-67 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-67 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App) > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > Possibility to have unique URI for the annotation predicates such as description, publication, example. > e.g www.biocatalogue.org/annotation#description -- This 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 Jun 9 06:45:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:45:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-601) Annotation attributes need to store descriptions, labels, etc about themselves Message-ID: <23929179.1016.1307616355378.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Affects Versions: 1.0.0 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 Thu Jun 9 06:46:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:46:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-107) Implement descriptions pages for annotation attributes Message-ID: <23275928.1018.1307616360107.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-107?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-107: -------------------------------- Assignee: Jiten Bhagat (was: Mannie Tagarira) > Implement descriptions pages for annotation attributes > ------------------------------------------------------ > > Key: BIOCAT-107 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-107 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App), Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Annotation Attributes have "identifiers" such as: "http://biocatalogue.org/attribute/description" so that they can be referenced uniquely from outside the BioCatalogue. > Some have identifiers from known vocabularies, eg: Dublin Core, but by default they have an identifier like: > http://biocatalogue.org/attribute/{processed_name} > Make these into dereferenceable URIs (ie: a URL to a web page) so that people can find out more information about the Annotation Attribute. In other words, implement pages for Annotation Attributes with the BioCatalogue based URI. -- This 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 Jun 9 06:45:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:45:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-107) Implement descriptions pages for annotation attributes Message-ID: <15470637.1017.1307616357665.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-107?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-107: -------------------------------- Fix Version/s: 1.2.0 (was: 1.1.0) > Implement descriptions pages for annotation attributes > ------------------------------------------------------ > > Key: BIOCAT-107 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-107 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App), Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Annotation Attributes have "identifiers" such as: "http://biocatalogue.org/attribute/description" so that they can be referenced uniquely from outside the BioCatalogue. > Some have identifiers from known vocabularies, eg: Dublin Core, but by default they have an identifier like: > http://biocatalogue.org/attribute/{processed_name} > Make these into dereferenceable URIs (ie: a URL to a web page) so that people can find out more information about the Annotation Attribute. In other words, implement pages for Annotation Attributes with the BioCatalogue based URI. -- This 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 Jun 9 06:49:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:49:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-599) Identify a way to reduce the number of service providers whose name is the default (derived from the hostname) In-Reply-To: <13022427.950.1307457715368.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1954805.1019.1307616595364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-599?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16773#comment-16773 ] Jiten Bhagat commented on BIOCAT-599: ------------------------------------- Nice proposal outlined. Need's more discussion in the future. > Identify a way to reduce the number of service providers whose name is the default (derived from the hostname) > -------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-599 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-599 > Project: BioCatalogue > Issue Type: Task > Components: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: Future > > > The latest 3 pages on the service provider index contain service providers whose name is in the format www-domain-name-com. The provider "Bio2RDF" has a number of such instances. > Consider automatically updating these names when a new service is registered into the catalogue where no provider matching the hostname already exists. Check the hostname of the new service against existing hostnames. For instance, the hostname "new.service.bio2rdf.com" should identify with "x.bio2rdf.com", "y.bio2rdf.com", and "z.bio2rdf.com" based on the domain component of the hostname (ie "bio2rdf.com"). Since the db just sees the hostnames as strings, this process will have linear complexity as each db entry is compared for a match. What if there is no match? This should therefore be a background process, which will trigger the sending of an email to the provider informing them of any changes/merges to be made. > For hostnames that do not match any instance in the DB, consider matching against the submitting user's email address. If the user has an "affiliation" value set, and an email address whose domain matches the service's hostname, rename the provider's name to the submitter's affiliation. > This will not take care of all the cases but will take care of at least 35-40% of existing nameless providers. -- This 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 Jun 9 06:49:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:49:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-599) Identify a way to reduce the number of service providers whose name is the default (derived from the hostname) In-Reply-To: <13022427.950.1307457715368.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5761024.1020.1307616597478.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-599?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-599: -------------------------------- Fix Version/s: Future > Identify a way to reduce the number of service providers whose name is the default (derived from the hostname) > -------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-599 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-599 > Project: BioCatalogue > Issue Type: Task > Components: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: Future > > > The latest 3 pages on the service provider index contain service providers whose name is in the format www-domain-name-com. The provider "Bio2RDF" has a number of such instances. > Consider automatically updating these names when a new service is registered into the catalogue where no provider matching the hostname already exists. Check the hostname of the new service against existing hostnames. For instance, the hostname "new.service.bio2rdf.com" should identify with "x.bio2rdf.com", "y.bio2rdf.com", and "z.bio2rdf.com" based on the domain component of the hostname (ie "bio2rdf.com"). Since the db just sees the hostnames as strings, this process will have linear complexity as each db entry is compared for a match. What if there is no match? This should therefore be a background process, which will trigger the sending of an email to the provider informing them of any changes/merges to be made. > For hostnames that do not match any instance in the DB, consider matching against the submitting user's email address. If the user has an "affiliation" value set, and an email address whose domain matches the service's hostname, rename the provider's name to the submitter's affiliation. > This will not take care of all the cases but will take care of at least 35-40% of existing nameless providers. -- This 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 Jun 9 06:49:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:49:59 +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: <17396934.1021.1307616599670.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: -------------------------------- Fix Version/s: 1.0.2 > 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: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.2 > > > As of June 7th 2011, 4 providers exist with no services. > IDs: 333, 314, 304, 322 -- This 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 Jun 9 06:51:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:51:55 +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: <5659567.1022.1307616715362.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: 1.0.2 Affects Version/s: 1.0.0 > 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: 1.0.2 > > > 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 Thu Jun 9 06:51:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:51:57 +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: <26331433.1023.1307616717679.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: 1.1.0 > 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: 1.1.0 > > > 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 Thu Jun 9 06:51:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:51:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-593) Look to moving to a JRuby based stack to possibly simplify the process and make it fit in better with the EBI setup In-Reply-To: <15403048.781.1305819175347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7748332.1024.1307616719746.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-593?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-593: -------------------------------- Fix Version/s: Future > Look to moving to a JRuby based stack to possibly simplify the process and make it fit in better with the EBI setup > ------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-593 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-593 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > -- This 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 Jun 9 06:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-591) Investigate running multiple delayed_job workers on the live EBI setup In-Reply-To: <14672693.779.1305818395351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <681882.1025.1307616835356.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-591?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-591: -------------------------------- Fix Version/s: 1.0.2 Need's some initial investigation to figure out how it currently works; what needs to be done to have multiple workers; what needs to be documented; and what needs to change for the release procedure (ie: now we would need to restart more workers on every release). > Investigate running multiple delayed_job workers on the live EBI setup > ---------------------------------------------------------------------- > > Key: BIOCAT-591 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-591 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > Having only one delayed_job worker running means that if it get's clogged up or freezes then all jobs stop getting processed. > Look into having multiple (at least 2 delayed_job workers) running. Possibly one per node. > This needs to be done in a careful manner so as not to break the current set up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:55:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-583) Possible resource of interest! In-Reply-To: <13325920.102.1299672507778.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8334960.1026.1307616955379.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-583?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16775#comment-16775 ] Jiten Bhagat commented on BIOCAT-583: ------------------------------------- http://vadlo.com/ seems to be down. > Possible resource of interest! > ------------------------------ > > Key: BIOCAT-583 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-583 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: Future > > > EMAIL: maya.kennard at yahoo.com > QUERY TYPE: EBI HELP: BioCatalogue Support > DATE: Wednesday 11 February 2009, 17:24 > Hello, > I wanted to bring to your attention a web-resource for your resources list. > VADLO - Biomedical & Life Sciences Search Engine > Vadlo is an academic, open-access, life sciences search engine created by two biology scientists. In addition to other biology research related categories, it is also a good resource for academic lectures/powerpoints. > References: vadlo.com/VADLO_References.html > Daily Research Cartoons: vadlo.com/Daily_Research_Cartoon.html > Website: vadlo.com > Thanks. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 06:55:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:55:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-582) Send a reminders to maintainers of services with tests that have been failing for a while to update their services/tests In-Reply-To: <27093980.101.1299669447777.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6809668.1027.1307616957763.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-582?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-582: -------------------------------- Affects Version/s: Future Priority: Minor (was: Major) > Send a reminders to maintainers of services with tests that have been failing for a while to update their services/tests > ------------------------------------------------------------------------------------------------------------------------ > > Key: BIOCAT-582 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-582 > Project: BioCatalogue > Issue Type: Task > Affects Versions: Future > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > > As the monitoring only sends out mail when there is a status change, some tests might fail for a while without the service owner noticing. A manual prompt could/should be made once in a while to remind service owners of services that need attention. -- This 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 Jun 9 06:56:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 11:56:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-583) Possible resource of interest! In-Reply-To: <13325920.102.1299672507778.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6156917.1028.1307616962638.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-583?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-583: -------------------------------- Fix Version/s: Future Priority: Minor (was: Major) > Possible resource of interest! > ------------------------------ > > Key: BIOCAT-583 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-583 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > EMAIL: maya.kennard at yahoo.com > QUERY TYPE: EBI HELP: BioCatalogue Support > DATE: Wednesday 11 February 2009, 17:24 > Hello, > I wanted to bring to your attention a web-resource for your resources list. > VADLO - Biomedical & Life Sciences Search Engine > Vadlo is an academic, open-access, life sciences search engine created by two biology scientists. In addition to other biology research related categories, it is also a good resource for academic lectures/powerpoints. > References: vadlo.com/VADLO_References.html > Daily Research Cartoons: vadlo.com/Daily_Research_Cartoon.html > Website: vadlo.com > Thanks. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 07:01:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-602) Implement support for importing WADL documents for REST services Message-ID: <26673191.1029.1307617315358.JavaMail.jira@rosalind.cs.man.ac.uk> Implement support for importing WADL documents for REST services ---------------------------------------------------------------- Key: BIOCAT-602 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-602 Project: BioCatalogue Issue Type: New Feature Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor Fix For: Future WADL - http://wadl.java.net/ - is a specification for describing REST based services. It is gaining in popularity. Some valuable info from Shoaib: {quote} Hi Jits, I remembered we discussed description documents for REST services earlier this week and the fact that there was no clear momentum around description of services in REST at all (let alone WADL or WSDL 2) at the moment. I thought anecdotal evidence might be interesting to mention: I downloaded and installed netbeans 6.8 (as do earlier versions) and it comes pre-configured with access to a number of web services (in the services tab) it was interesting to note what it had pre-loaded and how these were described. (disclaimer - I am not sure whether the WADL is being done auto-magically or provided by the original service provider or provided by the netbeans team) Service Description document format ---------- ------------------------------------------ Amazon WADL Delicious WADL Facebook WADL Flick WADL Google WADL/WSDL(seems to be not available)/some not described StrikeIron WSDL(seems to be not available) Twitter WADL WeatherBug WADL Yahoo WADL Zillow WADL Zvents WADL Worth considering when thinking about REST support for BioCatalogue and Taverna ? - I will leave that for you chaps to judge but I thought it interesting none the less. Best Regards, Shoaib {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 Thu Jun 9 07:01:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:01:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-582) Send a reminders to maintainers of services with tests that have been failing for a while to update their services/tests In-Reply-To: <27093980.101.1299669447777.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27634831.1030.1307617318227.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-582?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-582: -------------------------------- Fix Version/s: Future Affects Version/s: (was: Future) > Send a reminders to maintainers of services with tests that have been failing for a while to update their services/tests > ------------------------------------------------------------------------------------------------------------------------ > > Key: BIOCAT-582 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-582 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > As the monitoring only sends out mail when there is a status change, some tests might fail for a while without the service owner noticing. A manual prompt could/should be made once in a while to remind service owners of services that need attention. -- This 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 Jun 9 07:02:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:02:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-581) Service to look at as an example of a REST service with a WADL In-Reply-To: <10076359.100.1299667407766.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6589415.1031.1307617320744.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-581?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-581: -------------------------------- Summary: Service to look at as an example of a REST service with a WADL (was: Service to look at as an example of a rest service with a wadl) Fix Version/s: Future > Service to look at as an example of a REST service with a WADL > -------------------------------------------------------------- > > Key: BIOCAT-581 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-581 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > For a service with wadl to look at > http://www.ebi.ac.uk/QuickGO/WebServices.html > http://www.ebi.ac.uk/QuickGO/clients/QuickGO.wadl -- This 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 Jun 9 07:02:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:02:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-581) Service to look at as an example of a rest service with a wadl In-Reply-To: <10076359.100.1299667407766.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20441963.1032.1307617322833.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-581?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-581: -------------------------------- Parent: BIOCAT-602 Issue Type: Sub-task (was: Task) > Service to look at as an example of a rest service with a wadl > -------------------------------------------------------------- > > Key: BIOCAT-581 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-581 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > For a service with wadl to look at > http://www.ebi.ac.uk/QuickGO/WebServices.html > http://www.ebi.ac.uk/QuickGO/clients/QuickGO.wadl -- This 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 Jun 9 07:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-570) Admins should be able to assign services to other users In-Reply-To: <29445705.597.1297417629501.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17965559.1033.1307617435388.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-570?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-570: -------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: Future Priority: Minor (was: Major) For now we can ask people to do the service responsibility requests directly. > Admins should be able to assign services to other users > ------------------------------------------------------- > > Key: BIOCAT-570 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-570 > Project: BioCatalogue > Issue Type: Task > Components: Curation Dashboard > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > Original Estimate: 1 day > Remaining Estimate: 1 day > > The service responsibility request mechanism permits user to actively seek to take responsibility of a service. This has to be initiated from the end of the person wanting to take responsibility. This is OK in most cases. Sometimes however, an admin/curator just needs to assign the service to some user in a curation exercise. -- This 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 Jun 9 07:03:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:03:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-566) Add archived status to ResourceLink (in API) In-Reply-To: <32851271.372.1296838509410.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2873196.1034.1307617437671.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-566?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-566: -------------------------------- Fix Version/s: Future > Add archived status to ResourceLink (in API) > -------------------------------------------- > > Key: BIOCAT-566 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-566 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Add archived="false|true" to the ResourceLink element in the relevant API outputs. -- This 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 Jun 9 07:03:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:03:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-566) Add archived status to ResourceLink (in API) In-Reply-To: <32851271.372.1296838509410.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <436459.1035.1307617439800.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-566?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16777#comment-16777 ] Jiten Bhagat commented on BIOCAT-566: ------------------------------------- Need to consider this a bit more, as we don't want to make the ResourceLink schema to bloated. > Add archived status to ResourceLink (in API) > -------------------------------------------- > > Key: BIOCAT-566 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-566 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Add archived="false|true" to the ResourceLink element in the relevant API outputs. -- This 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 Jun 9 07:04:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:04:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-567) Review steps for updating life site for release of Feb 2011 In-Reply-To: <4889087.378.1297064109494.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24003372.1036.1307617441969.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-567?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-567. ------------------------------- Resolution: No longer relevant > Review steps for updating life site for release of Feb 2011 > ----------------------------------------------------------- > > Key: BIOCAT-567 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-567 > Project: BioCatalogue > Issue Type: Task > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > Update the release notes and the server update 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 Thu Jun 9 07:22:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:22:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-565) Move shell scripts for launching cron jobs into repository In-Reply-To: <9599295.196.1296480609416.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7885560.1037.1307618575391.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-565. --------------------------------- Resolution: Implemented This has been done. Scripts are in: {{script/biocatalogue/bin}} > Move shell scripts for launching cron jobs into repository > ---------------------------------------------------------- > > Key: BIOCAT-565 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Remove any local configs in the various cron scripts and add them to repository -- This 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 Jun 9 07:22:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:22:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-562) Make the default listing of services in BioCatalogue configurable In-Reply-To: <653900.189.1296227769402.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26616647.1038.1307618578569.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-562: -------------------------------- Fix Version/s: 1.2.0 > Make the default listing of services in BioCatalogue configurable > ----------------------------------------------------------------- > > Key: BIOCAT-562 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current default listing is grid. This is fine for listing with a considerable number of entries. However, for a few entries, like when starting a new catalogue, the grid view might not be the most appropriate. Allowing the default listing setting to be configurable would help. -- This 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 Jun 9 07:23:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 12:23:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-565) Move shell scripts for launching cron jobs into repository In-Reply-To: <9599295.196.1296480609416.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30850154.1039.1307618581127.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-565. ------------------------------- > Move shell scripts for launching cron jobs into repository > ---------------------------------------------------------- > > Key: BIOCAT-565 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-565 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Remove any local configs in the various cron scripts and add them to repository -- This 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 Jun 9 08:21:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-603) Implement a configuration, branding and theming system Message-ID: <8756193.1040.1307622115358.JavaMail.jira@rosalind.cs.man.ac.uk> Implement a configuration, branding and theming system ------------------------------------------------------ Key: BIOCAT-603 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-603 Project: BioCatalogue Issue Type: New Feature Components: Misc Codebase, Web Interface Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.2.0 Currently, BioCatalogue instances are configured through multiple YAML and Ruby files with the main one being: {code} config/initializers/biocat_local.rb {code} We need a better, more robust and customisable system for doing this as this affects the whole configuring, branding and theming of other instances of the catalogue software. Emory have already done some work on this that we can build on. [rails_config|https://github.com/railsjedi/rails_config] is used in some of our newer projects and provides a very good platform for configuration to build on. Though it is only for Rails 3 apps. -- This 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 Jun 9 08:21:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:21:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-562) Make the default listing of services in BioCatalogue configurable In-Reply-To: <653900.189.1296227769402.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25616392.1041.1307622118490.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-562: -------------------------------- Parent: BIOCAT-603 Issue Type: Sub-task (was: Task) > Make the default listing of services in BioCatalogue configurable > ----------------------------------------------------------------- > > Key: BIOCAT-562 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current default listing is grid. This is fine for listing with a considerable number of entries. However, for a few entries, like when starting a new catalogue, the grid view might not be the most appropriate. Allowing the default listing setting to be configurable would help. -- This 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 Jun 9 08:22:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:22:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-562) Make the default listing of services in BioCatalogue configurable In-Reply-To: <653900.189.1296227769402.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3363576.1042.1307622120782.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-562 stopped by Jiten Bhagat. > Make the default listing of services in BioCatalogue configurable > ----------------------------------------------------------------- > > Key: BIOCAT-562 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current default listing is grid. This is fine for listing with a considerable number of entries. However, for a few entries, like when starting a new catalogue, the grid view might not be the most appropriate. Allowing the default listing setting to be configurable would help. -- This 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 Jun 9 08:22:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:22:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-562) Make the default listing of services in BioCatalogue configurable In-Reply-To: <653900.189.1296227769402.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10177939.1043.1307622123225.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-562 started by Jiten Bhagat. > Make the default listing of services in BioCatalogue configurable > ----------------------------------------------------------------- > > Key: BIOCAT-562 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-562 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current default listing is grid. This is fine for listing with a considerable number of entries. However, for a few entries, like when starting a new catalogue, the grid view might not be the most appropriate. Allowing the default listing setting to be configurable would help. -- This 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 Jun 9 08:27:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:27:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-59) Secure delete actions Message-ID: <7176408.1044.1307622475361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-59?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16779#comment-16779 ] Jiten Bhagat commented on BIOCAT-59: ------------------------------------ We need an audit of ALL delete actions in the system, to make sure they are all secured. > Secure delete actions > --------------------- > > Key: BIOCAT-59 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-59 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > Need to secure/disable all delete actions on resources -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:29:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:29:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-59) Secure delete actions Message-ID: <9107205.1045.1307622595362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-59?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-59: ------------------------------- Fix Version/s: 1.1.0 Priority: Major (was: Critical) Component/s: Misc Codebase > Secure delete actions > --------------------- > > Key: BIOCAT-59 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-59 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Need to secure/disable all delete actions on resources -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:29:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:29:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-30) Rank services based on their availability Message-ID: <30153878.1046.1307622597482.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-30?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-30: ------------------------------- Fix Version/s: 1.2.0 Priority: Major (was: Critical) Description: We need the ability to rank the services index and search results based on the monitoring status of services. (was: Possibility to rank search result based on service availability test.) > Rank services based on their availability > ----------------------------------------- > > Key: BIOCAT-30 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-30 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > We need the ability to rank the services index and search results based on the monitoring status of 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 Thu Jun 9 08:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-6) Search By Data menu item needs to be more prominent Message-ID: <18233201.1047.1307622715359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-6?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-6. ------------------------------- Resolution: No longer relevant > Search By Data menu item needs to be more prominent > --------------------------------------------------- > > Key: BIOCAT-6 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-6 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jerzy Orlowski > Assignee: Jiten Bhagat > Priority: Critical > > Need to revisit the Nav bar to ensure that links like the Search By Data are visible -- This 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 Jun 9 08:31:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:31:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-6) Search By Data menu item needs to be more prominent Message-ID: <29716453.1048.1307622717571.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-6?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-6. ----------------------------- > Search By Data menu item needs to be more prominent > --------------------------------------------------- > > Key: BIOCAT-6 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-6 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jerzy Orlowski > Assignee: Jiten Bhagat > Priority: Critical > > Need to revisit the Nav bar to ensure that links like the Search By Data are visible -- This 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 Jun 9 08:33:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:33:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-561) Update the public facing BioCatalogue Roadmap In-Reply-To: <5092817.172.1296128110712.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29464819.1050.1307622837536.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-561: -------------------------------- Fix Version/s: 1.0.2 Priority: Critical (was: Major) Component/s: Wiki > Update the public facing BioCatalogue Roadmap > --------------------------------------------- > > Key: BIOCAT-561 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.2 > > > The BioCatalogue Roadmap needs to be updated with the 2011 plans. Current roadmap is for 2010! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:33:55 +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: <15979631.1049.1307622835372.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: 1.0.2 > 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: 1.0.2 > > > 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 Thu Jun 9 08:35:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:35:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-552) Rebuild patched gems and push them to rubygems.org In-Reply-To: <13349919.538.1291985512811.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3953024.1052.1307622957573.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-552?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-552. ------------------------------- > Rebuild patched gems and push them to rubygems.org > -------------------------------------------------- > > Key: BIOCAT-552 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-552 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Patched: gem rubaidh-google_analytics (1.1.4) -- This 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 Jun 9 08:35:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:35:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-552) Rebuild patched gems and push them to rubygems.org In-Reply-To: <13349919.538.1291985512811.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8262918.1053.1307622959774.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-552?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-552. --------------------------------- Resolution: No longer relevant This doesn't seem to be an issue any more as it looks like it's still using the vendorised gems. > Rebuild patched gems and push them to rubygems.org > -------------------------------------------------- > > Key: BIOCAT-552 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-552 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Patched: gem rubaidh-google_analytics (1.1.4) -- This 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 Jun 9 08:37:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:37:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-548) Investigate why there is a huge number of search entries in the activity logs with empty search terms In-Reply-To: <9364871.312.1291218472813.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2113031.1054.1307623078540.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-548: -------------------------------- Summary: Investigate why there is a huge number of search entries in the activity logs with empty search terms (was: Investigate why there is a hughe number of search entries in the activity logs with empty search terms) Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 > Investigate why there is a huge number of search entries in the activity logs with empty search terms > ----------------------------------------------------------------------------------------------------- > > Key: BIOCAT-548 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548 > Project: BioCatalogue > Issue Type: Task > Components: Data > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > It appears that the activity logs indicate a high number of searches. However, the majority of these search are not associated with any search term. This needs to be investigated. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:38:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:38:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-518) Create wiki page to document the current server software(OS, gems+versions...) In-Reply-To: <4045820.524.1289906849197.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8743481.1055.1307623080728.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-518?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-518. ------------------------------- > Create wiki page to document the current server software(OS, gems+versions...) > ------------------------------------------------------------------------------ > > Key: BIOCAT-518 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-518 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > List all environment information for the BioCatalogue servers. That includes OS, mysql, passenger, all ruby gems installed -- This 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 Jun 9 08:38:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:38:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-518) Create wiki page to document the current server software(OS, gems+versions...) In-Reply-To: <4045820.524.1289906849197.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14480929.1056.1307623083108.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-518?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-518. --------------------------------- Resolution: Implemented Initial work on this is done. > Create wiki page to document the current server software(OS, gems+versions...) > ------------------------------------------------------------------------------ > > Key: BIOCAT-518 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-518 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > List all environment information for the BioCatalogue servers. That includes OS, mysql, passenger, all ruby gems installed -- This 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 Jun 9 08:38:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:38:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-538) Optimise calls to BLJSON formats In-Reply-To: <9686795.576.1289923829165.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2947018.1057.1307623085322.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-538?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-538: -------------------------------- Fix Version/s: Future > Optimise calls to BLJSON formats > -------------------------------- > > Key: BIOCAT-538 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-538 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Look at possible ways to further optimise the BLJSON calls. -- This 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 Jun 9 08:38:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:38:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-539) Add archived_xx associations to the Rest* models In-Reply-To: <5594945.588.1289924612840.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18734209.1058.1307623087574.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-539?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-539: -------------------------------- Fix Version/s: Future > Add archived_xx associations to the Rest* models > ------------------------------------------------ > > Key: BIOCAT-539 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-539 > Project: BioCatalogue > Issue Type: Task > Components: REST Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Just like in the SoapOperation model, add corresponding archived_xx associations to all the appropriate Rest models. -- This 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 Jun 9 08:38:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:38:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-542) After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user In-Reply-To: <20071148.102.1290181372807.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6588182.1059.1307623089755.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16781#comment-16781 ] Jiten Bhagat commented on BIOCAT-542: ------------------------------------- The last tab viewed *should* be remembered. > After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user > ---------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-542 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > -- This 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 Jun 9 08:38:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:38:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-542) After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user In-Reply-To: <20071148.102.1290181372807.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19685307.1060.1307623091867.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-542: -------------------------------- Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 Component/s: Web Interface > After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user > ---------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-542 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > -- This 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 Jun 9 08:39:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-516) Deactivate all duplicate accounts on www.BioCatalogue.org In-Reply-To: <401697.10513.1288785975324.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29831667.1061.1307623195735.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-516?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-516: -------------------------------- Summary: Deactivate all duplicate accounts on www.BioCatalogue.org (was: Deactivate all duplicate accounts in BioCatalogue) Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: Future Description: Some users have more than one account on www.BioCatalogue.org. Check if all accounts are used and disable any redundant ones. (was: Some users have more than one account on BioCatalogue. Check if all accounts are used and disable any redundant ones.) Component/s: Server Management > Deactivate all duplicate accounts on www.BioCatalogue.org > --------------------------------------------------------- > > Key: BIOCAT-516 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-516 > Project: BioCatalogue > Issue Type: Improvement > Components: Data, Server Management > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: Future > > > Some users have more than one account on www.BioCatalogue.org. Check if all accounts are used and disable any redundant ones. -- This 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 Jun 9 08:39:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:39:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-512) Seed annotation_attributes table with the default set of attributes In-Reply-To: <10281504.10458.1288624815371.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20187682.1062.1307623198228.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-512?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-512: -------------------------------- Fix Version/s: Future Priority: Minor (was: Major) > Seed annotation_attributes table with the default set of attributes > ------------------------------------------------------------------- > > Key: BIOCAT-512 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-512 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations (in App) > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > Original Estimate: 2 hours > Remaining Estimate: 2 hours > > Especially for new instances of the BioCatalogue system, we need to seed the annotation_attributes with all the default attributes being used in the system and with the appropriate identifiers, etc. This way all BioCatalogue instance then share the same common set of annotation attributes (and new ones can still be created on top of them). > This can be done at application start up or as a one off rake task / 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 Jun 9 08:35:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:35:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-555) Ability to search within collections of Services In-Reply-To: <27592347.592.1293808012808.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14494150.1051.1307622955374.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-555?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-555: -------------------------------- Fix Version/s: 1.2.0 Affects Version/s: 1.0.0 > Ability to search within collections of Services > ------------------------------------------------ > > Key: BIOCAT-555 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-555 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing, Web Interface > Affects Versions: 1.0.0 > Reporter: Carole Goble > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > When browsing collections of services, for example the 'Services' tab on the Service Provider or User pages, it is currently not possible to *search within* just that collection. Have the ability to browse within that set of services only. > This is an alternative way of browsing for services, similar to filtering. It may be possible to reuse the filtering mechanism here. -- This 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 Jun 9 08:41:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-510) BioCatalogue wsdl parsers should handle wsdl imports In-Reply-To: <17327464.10453.1288612695320.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7472176.1063.1307623315359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-510?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16783#comment-16783 ] Jiten Bhagat commented on BIOCAT-510: ------------------------------------- Need's further investigation. > BioCatalogue wsdl parsers should handle wsdl imports > ---------------------------------------------------- > > Key: BIOCAT-510 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-510 > Project: BioCatalogue > Issue Type: Improvement > Components: SOAP Services Support > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Some WSDL like those from caBIG have wsdl which import other wsdl using the element. BioCatalogue needs to be able to handle these as well. > See mail from Tod Jackson below: > ----------------------- > Greetings BioCataloguers, > My colleagues and I here at Emory University and the Atlanta Clinical & Translational Science Institute are attempting to register some services in our local Emory BioCatalogue deployment. These services are authored using caGrid tools and hosted in various caGrid deployments both internally and externally. I believe many of you are familiar with the caGrid project (http://cagrid.org). > It appears as though most, if not all of the WSDL definitions associated to these "grid services" leverage "wsdl:import" to fully resolve themselves. After some quick analysis, it does not appear as though BioCatalogue is able to fully resolve service definitions that use wsdl:import. I am able to load the services using soapUI and Taverna however. > So, my first question is, am I missing anything regarding BioCatalogue's support for this? i.e., is there a configuration setting or something that might make this work? Assuming the answer to that is "no", my second question is, are there any plans to add support for this in future versions of the application? > As always, thanks for any input you might have on this. > Best Regards, > Tod Jackson > ----------------------- -- This 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 Jun 9 08:45:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:45:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-510) BioCatalogue wsdl parsers should handle wsdl imports In-Reply-To: <17327464.10453.1288612695320.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30147377.1065.1307623555364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-510?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-510: -------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: Future Description: Some WSDL like those from caBIG have WSDL which import other WSDL using the element. BioCatalogue needs to be able to handle these as well. See mail from Tod Jackson below: {quote} Greetings BioCataloguers, My colleagues and I here at Emory University and the Atlanta Clinical & Translational Science Institute are attempting to register some services in our local Emory BioCatalogue deployment. These services are authored using caGrid tools and hosted in various caGrid deployments both internally and externally. I believe many of you are familiar with the caGrid project (http://cagrid.org). It appears as though most, if not all of the WSDL definitions associated to these "grid services" leverage "wsdl:import" to fully resolve themselves. After some quick analysis, it does not appear as though BioCatalogue is able to fully resolve service definitions that use wsdl:import. I am able to load the services using soapUI and Taverna however. So, my first question is, am I missing anything regarding BioCatalogue's support for this? i.e., is there a configuration setting or something that might make this work? Assuming the answer to that is "no", my second question is, are there any plans to add support for this in future versions of the application? As always, thanks for any input you might have on this. Best Regards, Tod Jackson {quote} was: Some WSDL like those from caBIG have wsdl which import other wsdl using the element. BioCatalogue needs to be able to handle these as well. See mail from Tod Jackson below: ----------------------- Greetings BioCataloguers, My colleagues and I here at Emory University and the Atlanta Clinical & Translational Science Institute are attempting to register some services in our local Emory BioCatalogue deployment. These services are authored using caGrid tools and hosted in various caGrid deployments both internally and externally. I believe many of you are familiar with the caGrid project (http://cagrid.org). It appears as though most, if not all of the WSDL definitions associated to these "grid services" leverage "wsdl:import" to fully resolve themselves. After some quick analysis, it does not appear as though BioCatalogue is able to fully resolve service definitions that use wsdl:import. I am able to load the services using soapUI and Taverna however. So, my first question is, am I missing anything regarding BioCatalogue's support for this? i.e., is there a configuration setting or something that might make this work? Assuming the answer to that is "no", my second question is, are there any plans to add support for this in future versions of the application? As always, thanks for any input you might have on this. Best Regards, Tod Jackson ----------------------- > BioCatalogue wsdl parsers should handle wsdl imports > ---------------------------------------------------- > > Key: BIOCAT-510 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-510 > Project: BioCatalogue > Issue Type: Improvement > Components: SOAP Services Support > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: Future > > > Some WSDL like those from caBIG have WSDL which import other WSDL using the element. BioCatalogue needs to be able to handle these as well. > See mail from Tod Jackson below: > {quote} > Greetings BioCataloguers, > My colleagues and I here at Emory University and the Atlanta Clinical & Translational Science Institute are attempting to register some services in our local Emory BioCatalogue deployment. These services are authored using caGrid tools and hosted in various caGrid deployments both internally and externally. I believe many of you are familiar with the caGrid project (http://cagrid.org). > It appears as though most, if not all of the WSDL definitions associated to these "grid services" leverage "wsdl:import" to fully resolve themselves. After some quick analysis, it does not appear as though BioCatalogue is able to fully resolve service definitions that use wsdl:import. I am able to load the services using soapUI and Taverna however. > So, my first question is, am I missing anything regarding BioCatalogue's support for this? i.e., is there a configuration setting or something that might make this work? Assuming the answer to that is "no", my second question is, are there any plans to add support for this in future versions of the application? > As always, thanks for any input you might have on this. > Best Regards, > Tod Jackson > {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 Thu Jun 9 08:45:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:45:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-502) Update the fail controller to only allow it to process when an admin user hits it In-Reply-To: <14642526.9979.1287048375608.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21778514.1066.1307623557675.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-502?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-502. ------------------------------- > Update the fail controller to only allow it to process when an admin user hits it > --------------------------------------------------------------------------------- > > Key: BIOCAT-502 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-502 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > ... this is to prevent someone spamming us through our own error emails! > The solution is to add a before_filter in the fail controller to check that a user is logged in and that they are an admin. Only then should it actually go ahead with the failure and send out the error email. -- This 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 Jun 9 08:45:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:45:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-502) Update the fail controller to only allow it to process when an admin user hits it In-Reply-To: <14642526.9979.1287048375608.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23357213.1067.1307623559880.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-502?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-502. --------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Resolution: Fixed > Update the fail controller to only allow it to process when an admin user hits it > --------------------------------------------------------------------------------- > > Key: BIOCAT-502 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-502 > Project: BioCatalogue > Issue Type: Bug > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > ... this is to prevent someone spamming us through our own error emails! > The solution is to add a before_filter in the fail controller to check that a user is logged in and that they are an admin. Only then should it actually go ahead with the failure and send out the error email. -- This 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 Jun 9 08:46:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:46:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-503) Check the that services have the appropriate contacts, especially the ones that were registered by BioCatalogue team members In-Reply-To: <31281353.9991.1287060615323.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21383724.1068.1307623562021.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-503?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-503. ------------------------------- > Check the that services have the appropriate contacts, especially the ones that were registered by BioCatalogue team members > ---------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-503 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-503 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Franck Tanoh > > Many services were registered by BioCatalogue team members and other people that do not maintain the services. This means that notifications about the services may be sent to those people instead of the appropriate responsible persons. It is important to review the content and make sure we have appropriate contacts for the 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 Thu Jun 9 08:46:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:46:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-503) Check the that services have the appropriate contacts, especially the ones that were registered by BioCatalogue team members In-Reply-To: <31281353.9991.1287060615323.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13059032.1069.1307623564776.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-503?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-503. --------------------------------- Resolution: Implemented I believe this was done. > Check the that services have the appropriate contacts, especially the ones that were registered by BioCatalogue team members > ---------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-503 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-503 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Franck Tanoh > > Many services were registered by BioCatalogue team members and other people that do not maintain the services. This means that notifications about the services may be sent to those people instead of the appropriate responsible persons. It is important to review the content and make sure we have appropriate contacts for the 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 Thu Jun 9 08:46:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:46:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-510) BioCatalogue wsdl parsers should handle wsdl imports In-Reply-To: <17327464.10453.1288612695320.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12642548.1071.1307623569249.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-510?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-510: -------------------------------- Priority: Minor (was: Major) No one seems to be asking for this (though we might just not know!) > BioCatalogue wsdl parsers should handle wsdl imports > ---------------------------------------------------- > > Key: BIOCAT-510 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-510 > Project: BioCatalogue > Issue Type: Improvement > Components: SOAP Services Support > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Some WSDL like those from caBIG have WSDL which import other WSDL using the element. BioCatalogue needs to be able to handle these as well. > See mail from Tod Jackson below: > {quote} > Greetings BioCataloguers, > My colleagues and I here at Emory University and the Atlanta Clinical & Translational Science Institute are attempting to register some services in our local Emory BioCatalogue deployment. These services are authored using caGrid tools and hosted in various caGrid deployments both internally and externally. I believe many of you are familiar with the caGrid project (http://cagrid.org). > It appears as though most, if not all of the WSDL definitions associated to these "grid services" leverage "wsdl:import" to fully resolve themselves. After some quick analysis, it does not appear as though BioCatalogue is able to fully resolve service definitions that use wsdl:import. I am able to load the services using soapUI and Taverna however. > So, my first question is, am I missing anything regarding BioCatalogue's support for this? i.e., is there a configuration setting or something that might make this work? Assuming the answer to that is "no", my second question is, are there any plans to add support for this in future versions of the application? > As always, thanks for any input you might have on this. > Best Regards, > Tod Jackson > {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 Thu Jun 9 08:46:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:46:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-495) Implement similar searches feature - "people who searched for X searched for Y too" In-Reply-To: <9737834.9935.1286266995425.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18202043.1072.1307623571500.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-495?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-495: -------------------------------- Fix Version/s: Future > Implement similar searches feature - "people who searched for X searched for Y too" > ----------------------------------------------------------------------------------- > > Key: BIOCAT-495 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-495 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > We can use the information stored in the activity logs to build similar searches (and even similar filters) functionality. -- This 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 Jun 9 08:47:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-494) Harvest DAS services and all metadata from the central DAS registry In-Reply-To: <9402951.9924.1286189835300.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <202987.1073.1307623675367.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-494?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-494: -------------------------------- Fix Version/s: Future > Harvest DAS services and all metadata from the central DAS registry > ------------------------------------------------------------------- > > Key: BIOCAT-494 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-494 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Fix For: Future > > > Harvest all DAS services (together with their annotations/metadata) from the central DAS registry (http://www.dasregistry.org/) -- This 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 Jun 9 08:47:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:47:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-492) Implement support for DAS services In-Reply-To: <31286071.9922.1286189175303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10601446.1074.1307623677507.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-492?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-492: -------------------------------- Fix Version/s: Future > Implement support for DAS services > ---------------------------------- > > Key: BIOCAT-492 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-492 > Project: BioCatalogue > Issue Type: New Feature > Components: REST Services Support > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Fix For: Future > > > The current thinking is DAS services are just REST services but with the label "DAS" (much like how we do for Soaplab). -- This 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 Jun 9 08:47:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:47:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-493) Implement the ability to harvest DAS services from DAS registries In-Reply-To: <6791634.9923.1286189715307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3193432.1075.1307623679695.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-493: -------------------------------- Fix Version/s: Future > Implement the ability to harvest DAS services from DAS registries > ----------------------------------------------------------------- > > Key: BIOCAT-493 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493 > Project: BioCatalogue > Issue Type: New Feature > Components: REST Services Support, Service Submission > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Fix For: Future > > > We need the ability to harvest DAS services (and all annotations/metadata) from DAS registries, especially the central DAS registry. -- This 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 Jun 9 08:50:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-604) Improve the stats generation process Message-ID: <21474347.1076.1307623855384.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 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! -- This 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 Jun 9 08:50:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:50:57 +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: <7363613.1077.1307623857579.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: 1.1.0 > 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: 1.1.0 > > > 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 Thu Jun 9 08:52:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:52:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-488) Investigate the double rendering error generated by the login controller when ssl is switched on In-Reply-To: <16949619.9904.1285778415305.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16237482.1078.1307623975362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-488?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-488. --------------------------------- Resolution: No longer relevant The whole site will now run on SSL so this is not relevant anymore. > Investigate the double rendering error generated by the login controller when ssl is switched on > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-488 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-488 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Login fails with a double rendering error when ssl is switch on. Preliminary investigation shows that this may be cause by the redirects in "ensure_proper_protocol" method in the vendor/plugins/ssl_requirement/lib/ssl_requirement.rb. > Further investigation needed. -- This 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 Jun 9 08:52:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:52:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-486) Write up the requirements for the annotation level feature on the wiki page In-Reply-To: <31626901.9901.1285767975304.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15691351.1079.1307623977790.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-486?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-486. ------------------------------- Resolution: No longer relevant > Write up the requirements for the annotation level feature on the wiki page > --------------------------------------------------------------------------- > > Key: BIOCAT-486 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-486 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Environment: Wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Add the Requirements & documentation for the annotation level feature to the existing wiki page. > http://www.biocatalogue.org/wiki/doku.php?id=development:software_development:annotation_models -- This 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 Jun 9 08:52:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:52:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-487) Exception generated by linked_data handler In-Reply-To: <18811203.9902.1285777575311.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28879471.1080.1307623979923.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-487: -------------------------------- Priority: Minor (was: Major) > Exception generated by linked_data handler > ------------------------------------------ > > Key: BIOCAT-487 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.2 > > > LinkedDataHandler metal app... > Intial URL: /services/10 > undefined method `to_sym' for nil:NilClass > /rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' > rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' > lib/ruby/1.8/benchmark.rb:293:in `measure' -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:53:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:53:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-487) Exception generated by linked_data handler In-Reply-To: <18811203.9902.1285777575311.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3769364.1081.1307623982492.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-487: -------------------------------- Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 > Exception generated by linked_data handler > ------------------------------------------ > > Key: BIOCAT-487 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > LinkedDataHandler metal app... > Intial URL: /services/10 > undefined method `to_sym' for nil:NilClass > /rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' > rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' > lib/ruby/1.8/benchmark.rb:293:in `measure' -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:53:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:53:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-488) Investigate the double rendering error generated by the login controller when ssl is switched on In-Reply-To: <16949619.9904.1285778415305.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14596198.1082.1307623984806.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-488?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-488. ------------------------------- > Investigate the double rendering error generated by the login controller when ssl is switched on > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-488 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-488 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Login fails with a double rendering error when ssl is switch on. Preliminary investigation shows that this may be cause by the redirects in "ensure_proper_protocol" method in the vendor/plugins/ssl_requirement/lib/ssl_requirement.rb. > Further investigation needed. -- This 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 Jun 9 08:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-475) Rendering problem in safari when rendering search results In-Reply-To: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19978892.1083.1307624095370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16788#comment-16788 ] Jiten Bhagat commented on BIOCAT-475: ------------------------------------- This seems to be a common problem across WebKit powered browsers (ie: Chrome too!). Needs more investigation. > Rendering problem in safari when rendering search results > --------------------------------------------------------- > > Key: BIOCAT-475 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > Attachments: screenshot-1.jpg > > > buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:54:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:54:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-475) Rendering problem in safari when rendering search results In-Reply-To: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4887706.1084.1307624097562.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-475: -------------------------------- Fix Version/s: 1.0.2 Affects Version/s: 1.0.0 > Rendering problem in safari when rendering search results > --------------------------------------------------------- > > Key: BIOCAT-475 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > Attachments: screenshot-1.jpg > > > buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 08:59:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:59:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-470) Reindex the live data and restart the tomcat server In-Reply-To: <26696124.9321.1284382275368.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25346721.1085.1307624395383.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-470?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-470. ------------------------------- Resolution: No longer relevant > Reindex the live data and restart the tomcat server > --------------------------------------------------- > > Key: BIOCAT-470 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-470 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Environment: Solr & tomcat > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This 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 Jun 9 08:59:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 13:59:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-467) Enhanced write support for the REST API In-Reply-To: <28646784.9004.1284043335312.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25823009.1086.1307624398107.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-467?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-467: -------------------------------- Fix Version/s: Future > Enhanced write support for the REST API > --------------------------------------- > > Key: BIOCAT-467 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-467 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > - user registration and update > - extended rest support (submission and update of rest methods, rest parameters, and rest representations) > - service update and deletion > - annotation update and deletion > - other -- This 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 Jun 9 09:00:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:00:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-467) Enhanced write support for the REST API In-Reply-To: <28646784.9004.1284043335312.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15781794.1087.1307624400194.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-467?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16789#comment-16789 ] Jiten Bhagat commented on BIOCAT-467: ------------------------------------- Need to break out the various requirements/tasks into sub-tasks. > Enhanced write support for the REST API > --------------------------------------- > > Key: BIOCAT-467 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-467 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > - user registration and update > - extended rest support (submission and update of rest methods, rest parameters, and rest representations) > - service update and deletion > - annotation update and deletion > - other -- This 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 Jun 9 09:01:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-464) Exclude archived items from the API index RestMethods if sorted by name In-Reply-To: <29023845.8998.1284038835382.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20891679.1088.1307624515362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-464?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-464. --------------------------------- Resolution: No longer relevant Archived services MUST be shown in the API > Exclude archived items from the API index RestMethods if sorted by name > ----------------------------------------------------------------------- > > Key: BIOCAT-464 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-464 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > -- This 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 Jun 9 09:01:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:01:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-463) Allow test scripts to be run on demand In-Reply-To: <16413607.8521.1283937195300.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2461421.1089.1307624519047.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-463?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-463: -------------------------------- Fix Version/s: Future > Allow test scripts to be run on demand > -------------------------------------- > > Key: BIOCAT-463 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-463 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > At the moment, tests are run as background processes after a given time interval. It would be nice for users (via external tools such as Taverna) to check the monitoring status of a service on demand... -- This 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 Jun 9 09:02:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:02:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-464) Exclude archived items from the API index RestMethods if sorted by name In-Reply-To: <29023845.8998.1284038835382.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27455325.1090.1307624521175.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-464?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-464. ------------------------------- > Exclude archived items from the API index RestMethods if sorted by name > ----------------------------------------------------------------------- > > Key: BIOCAT-464 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-464 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > -- This 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 Jun 9 09:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-462) Expose archived services and service components in the API In-Reply-To: <9943135.8517.1283874555417.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1291191.1091.1307624635380.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-462?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-462. --------------------------------- Resolution: Implemented Done > Expose archived services and service components in the API > ---------------------------------------------------------- > > Key: BIOCAT-462 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-462 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > -- This 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 Jun 9 09:03:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:03:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-459) Implement lookup functionality for REST Methods In-Reply-To: <32920953.8161.1282752075507.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23829821.1092.1307624637454.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-459?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-459: -------------------------------- Fix Version/s: Future > Implement lookup functionality for REST Methods > ----------------------------------------------- > > Key: BIOCAT-459 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-459 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > Consider this email snippet: > The BioCatalogue plugin in Taverna would try to do a lookup (via the use of /lookup?...) for a REST Method entry in the main catalogue based on a URL template. This template could be, for demonstrative purposes, "http://example.com?service=ONE&method={METHOD}". The BioCatalogue could have some REST Services registered based on the following list of base URLs: > - "http://example.com?service=ONE" > - "http://example.com?service=TWO" > - "http://example.com?service=THREE" > At first glance this looks doable; then you start to think about cases where the user might enter the following templates: > - "http://example.com?service={SERVICE}&method={METHOD}&x={X}&y=Y&z=Z" > - "http://example.com/{API_VERSION}/rest/{database}/{id}?x={X}&y=Y" > - "http://example.com/{API_VERSION}/rest?x={X}&y=Y" > - and many other permutations > The BioCatalogue currently has no way of knowing what the base URL of the user provided template is, so this will have to be "intelligently" derived. This would involve getting all the services that have a base URL that contains the hostname of the provided template, "example.com" in this case. For each of these services, check that it is possible to create a template that matches the one provided by the user; the use of different combinations of required and optional parameters available is probable. This could result in long waiting times depending on the number of services matching the hostname, and the number of query (and template) parameters in the template being passed in; think DDBJ! > - "http://xml.nig.ac.jp/rest/Invoke?service={service}&method={method}&accession={accession}&..." > After intelligently filtering these services and REST methods in a "maintainable, manageable, and actually possible to squat bugs in the future" manner, which I'm sure is possible by the way, i am fairly certain that it will not always return *one and only one* REST method; again, think DDBJ! -- This 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 Jun 9 09:03:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:03:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-460) Document latest updates to the API In-Reply-To: <6899755.8166.1282752315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10944549.1093.1307624639669.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-460: -------------------------------- Fix Version/s: 1.0.1 Affects Version/s: (was: 1.0.1) > Document latest updates to the API > ---------------------------------- > > Key: BIOCAT-460 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460 > Project: BioCatalogue > Issue Type: Task > Components: REST API, Wiki > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:04:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:04:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-460) Document latest updates to the API In-Reply-To: <6899755.8166.1282752315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29744561.1094.1307624641773.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-460: -------------------------------- Summary: Document latest updates to the API (was: Document updates to the API) Affects Version/s: 1.0.1 > Document latest updates to the API > ---------------------------------- > > Key: BIOCAT-460 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460 > Project: BioCatalogue > Issue Type: Task > Components: REST API, Wiki > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:04:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:04:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-461) Fix inconsistencies with the "counts" of results between /soap_operations/filters and /soap_operations In-Reply-To: <22675401.8171.1283438655431.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32542551.1095.1307624645006.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-461?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-461: -------------------------------- Fix Version/s: Future > Fix inconsistencies with the "counts" of results between /soap_operations/filters and /soap_operations > ------------------------------------------------------------------------------------------------------ > > Key: BIOCAT-461 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-461 > Project: BioCatalogue > Issue Type: Bug > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > Using the tag "blast" as an example: > Under "Tags" in "/soap_operations/filters.format", the count for "blast" if 4 (for example) > The same tag used as a filter ("/soap_operations.format?tag=[blast]") returns 3 more results. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:05:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:05:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-455) Add XML support for the submission of annotations and services via the Write API In-Reply-To: <31779577.8064.1281956955306.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31920614.1097.1307624757563.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-455?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-455: -------------------------------- Summary: Add XML support for the submission of annotations and services via the Write API (was: Add XML support for the submission of annotations and services via the API) Fix Version/s: 1.2.0 > Add XML support for the submission of annotations and services via the Write API > -------------------------------------------------------------------------------- > > Key: BIOCAT-455 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-455 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Mannie Tagarira > 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 Thu Jun 9 09:06:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:06:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-458) Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application In-Reply-To: <27122381.8114.1282212375444.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16055979.1099.1307624762343.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-458?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-458: -------------------------------- Fix Version/s: Future > Investigate biocatalogue db encoding problems and fix any inconsistencies with the rails application > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-458 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-458 > Project: BioCatalogue > Issue Type: Task > Components: Data > Environment: MySQL, Rails > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Fix For: Future > > > From Mannie: > There is a concerning issue regarding database encodings in which some characters are stored in the database in an inconsistent way; most European character sets are not being handled properly. Accented characters, for example, will appear as symbols, which is clearly not the desired effect. Take for example, the user with ID 234 (not yet activated), whose name is "Jos? Mar?a Fern?ndez"; this may appear in the BioCatalogue as "Jos?? Mar? a Fern??ndez" or something similar depending on the database encoding used. > So far, this has been the case on my machine, Jits's machine, as well as the sandbox. Could you please look into this just to make sure this issue does not affect the test and live sites as well... -- This 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 Jun 9 09:07:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-445) Upgrade main packages/libraries use by BioCatalogue In-Reply-To: <3176667.7559.1279796355366.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11222091.1100.1307624875380.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-445?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-445. --------------------------------- Resolution: Fixed Most of this has been updated. See: http://www.biocatalogue.org/docs/biocatalogue-application-stack-specs for info on the new VMs set up. > Upgrade main packages/libraries use by BioCatalogue > --------------------------------------------------- > > Key: BIOCAT-445 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-445 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > It is desirable for performance and other reasons, to update the following libraries used by BioCatalogue > * MySQL - Server version: 5.0.41-log MySQL Community Server (GPL) > * Solr - 1.3.0 694707 - grantingersoll - 2008-09-12 11 > * Ruby - 1.8.5 > * passenger-2.2.2 > * PHP -5.1.6 > The desired versions are : > * MySQL - 5.1 > * Solr - 1.4.1 > * Ruby - 1.8.6 or 1.8.7 > * passenger - 2.2.15 > * PHP- 5.3 -- This 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 Jun 9 09:07:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:07:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-444) Optimize the code to retrieve display name annotations in BioCatalogue::Filtering::Annotations.get_filters_for_annotatables In-Reply-To: <754586.7519.1279628775436.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31072054.1101.1307624877534.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-444?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-444: -------------------------------- Fix Version/s: 1.1.0 > Optimize the code to retrieve display name annotations in BioCatalogue::Filtering::Annotations.get_filters_for_annotatables > ---------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-444 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-444 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations > Reporter: Mannie Tagarira > 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 Jun 9 09:09:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:09:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-443) Update the REST API's XML schema to account for the REST services support endpoints In-Reply-To: <8259919.7505.1279535115302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <147437.1102.1307624995370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16795#comment-16795 ] Jiten Bhagat commented on BIOCAT-443: ------------------------------------- I think this was done. Need to verify. > Update the REST API's XML schema to account for the REST services support endpoints > ------------------------------------------------------------------------------------ > > Key: BIOCAT-443 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443 > Project: BioCatalogue > Issue Type: Task > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:09:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:09:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-443) Update the REST API's XML schema to account for the REST services support endpoints In-Reply-To: <8259919.7505.1279535115302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1472878.1103.1307624997987.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-443: -------------------------------- Fix Version/s: 1.0.1 > Update the REST API's XML schema to account for the REST services support endpoints > ------------------------------------------------------------------------------------ > > Key: BIOCAT-443 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443 > Project: BioCatalogue > Issue Type: Task > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:10:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:10:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-442) Optimize BioCatalogue::Mapper.compound_ids_to_model_objects for better performance In-Reply-To: <23853784.7504.1279534995408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20076034.1104.1307625000138.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-442?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-442: -------------------------------- Fix Version/s: Future > Optimize BioCatalogue::Mapper.compound_ids_to_model_objects for better performance > ---------------------------------------------------------------------------------- > > Key: BIOCAT-442 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-442 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > BioCatalogue::Mapper.compound_ids_to_model_objects currently runs a separate database query for each compound id supplied. Hence, if the overall result yields 100 Service objects, and 20 User objects, 120 database queries would have been made; this can be done in 2 queries - one for Users and one for 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 Thu Jun 9 09:11:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:11:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-440) Implement rate limiting for REST API calls In-Reply-To: <483658.7233.1278603854488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10578201.1105.1307625115366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-440: -------------------------------- Summary: Implement rate limiting for REST API calls (was: Implement activity limits for REST API calls) Fix Version/s: Future > Implement rate limiting for REST API calls > ------------------------------------------ > > Key: BIOCAT-440 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > -- This 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 Jun 9 09:11:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:11:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-440) Implement rate limiting for REST API calls In-Reply-To: <483658.7233.1278603854488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30443701.1106.1307625117569.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-440: -------------------------------- Description: Could potentially use [rack-throttle|https://github.com/datagraph/rack-throttle] IF it works with Rails 2.x apps. > Implement rate limiting for REST API calls > ------------------------------------------ > > Key: BIOCAT-440 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > Could potentially use [rack-throttle|https://github.com/datagraph/rack-throttle] IF it works with Rails 2.x apps. -- This 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 Jun 9 09:13:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:13:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-440) Implement rate limiting for REST API calls In-Reply-To: <483658.7233.1278603854488.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19642361.1107.1307625235367.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-440: -------------------------------- Description: Could potentially use [rack-throttle|https://github.com/datagraph/rack-throttle] IF it works with Rails 2.x apps. This should use configuration settings provided by the new configuration management system. was:Could potentially use [rack-throttle|https://github.com/datagraph/rack-throttle] IF it works with Rails 2.x apps. > Implement rate limiting for REST API calls > ------------------------------------------ > > Key: BIOCAT-440 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-440 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: Future > > > Could potentially use [rack-throttle|https://github.com/datagraph/rack-throttle] IF it works with Rails 2.x apps. > This should use configuration settings provided by the new configuration management 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 Thu Jun 9 09:13:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:13:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-429) Update the protocol for updating the BioCatalogue website on EBI wiki In-Reply-To: <28477819.6994.1277977875320.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6257789.1108.1307625237519.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-429?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-429. ------------------------------- > Update the protocol for updating the BioCatalogue website on EBI wiki > --------------------------------------------------------------------- > > Key: BIOCAT-429 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-429 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Recently, it has been necessary to restart the tomcat instance running the solr server whenever a codebase update has been made and reindexing required. Review the server update protocol and update where necessary. -- This 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 Jun 9 09:13:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:13:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-421) create branch for better soaplab profiles and visuals for monitoring In-Reply-To: <8901030.6714.1277716095438.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27081226.1109.1307625239629.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-421?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-421. --------------------------------- Resolution: Implemented > create branch for better soaplab profiles and visuals for monitoring > -------------------------------------------------------------------- > > Key: BIOCAT-421 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-421 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This 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 Jun 9 09:14:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:14:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-429) Update the protocol for updating the BioCatalogue website on EBI wiki In-Reply-To: <28477819.6994.1277977875320.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <835928.1110.1307625241904.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-429?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-429. --------------------------------- Resolution: No longer relevant > Update the protocol for updating the BioCatalogue website on EBI wiki > --------------------------------------------------------------------- > > Key: BIOCAT-429 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-429 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Recently, it has been necessary to restart the tomcat instance running the solr server whenever a codebase update has been made and reindexing required. Review the server update protocol and update where necessary. -- This 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 Jun 9 09:14:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:14:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-421) create branch for better soaplab profiles and visuals for monitoring In-Reply-To: <8901030.6714.1277716095438.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16134553.1111.1307625244730.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-421?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-421. ------------------------------- > create branch for better soaplab profiles and visuals for monitoring > -------------------------------------------------------------------- > > Key: BIOCAT-421 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-421 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This 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 Jun 9 09:15:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:15:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-415) Item lookup via API - for SOAP services may need to add ports as another checking criteria In-Reply-To: <5200307.6611.1277371335311.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27577663.1112.1307625355386.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-415?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-415: -------------------------------- Fix Version/s: 1.2.0 Affects Version/s: 1.0.0 > Item lookup via API - for SOAP services may need to add ports as another checking criteria > ------------------------------------------------------------------------------------------ > > Key: BIOCAT-415 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-415 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Currently only WSDL location and the operation name determine the SOAP operation. In case there are identical operations on different SOAP ports, the one on the first known port is always returned by the lookup. -- This 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 Jun 9 09:15:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:15:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-407) Add BioCatalogue NAR reference to homepage In-Reply-To: <21597958.6378.1277124795309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13285600.1113.1307625357504.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-407?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-407. ------------------------------- > Add BioCatalogue NAR reference to homepage > ------------------------------------------ > > Key: BIOCAT-407 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-407 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > ... so people know what to use to cite the BioCatalogue. -- This 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 Jun 9 09:15:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:15:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-407) Add BioCatalogue NAR reference to homepage In-Reply-To: <21597958.6378.1277124795309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22596794.1114.1307625359821.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-407?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-407. --------------------------------- Resolution: Fixed > Add BioCatalogue NAR reference to homepage > ------------------------------------------ > > Key: BIOCAT-407 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-407 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > ... so people know what to use to cite the BioCatalogue. -- This 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 Jun 9 09:16:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:16:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-414) SOAP Service Views - Grouping of operations by port In-Reply-To: <25888115.6610.1277371155310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17200850.1115.1307625361919.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-414?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-414: -------------------------------- Fix Version/s: 1.2.0 > SOAP Service Views - Grouping of operations by port > --------------------------------------------------- > > Key: BIOCAT-414 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-414 > Project: BioCatalogue > Issue Type: Improvement > Components: SOAP Services Support > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Service like http://www.biocatalogue.org/services/2160 have identical operations available at different ports. The UI would be much clearer if the operations were grouped by ports, thus eliminating duplicates in the overall list of operations as it happens now. -- This 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 Jun 9 09:17:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:17:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-400) some example endpoints do not resolve to valid URI In-Reply-To: <31506485.6312.1276852635419.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <703405.1116.1307625475369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-400. --------------------------------- Resolution: No longer relevant > some example endpoints do not resolve to valid URI > --------------------------------------------------- > > Key: BIOCAT-400 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > > Some example endpoints seem to be displayed as relative to the base end point. This affects monitoring such endpoints as they would resolve to invalid URI. Example is http://www.biocatalogue.org/services/2705#monitoring -- This 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 Jun 9 09:17:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:17:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <32005422.1117.1307625477785.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 ] Jiten Bhagat updated BIOCAT-398: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Fix Version/s: 1.1.0 > 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 Jun 9 09:17:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:17:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-400) some example endpoints do not resolve to valid URI In-Reply-To: <31506485.6312.1276852635419.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27137370.1118.1307625479939.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-400. ------------------------------- > some example endpoints do not resolve to valid URI > --------------------------------------------------- > > Key: BIOCAT-400 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-400 > Project: BioCatalogue > Issue Type: Bug > Components: REST Services Support > Reporter: Eric Nzuobontane > Assignee: Mannie Tagarira > > Some example endpoints seem to be displayed as relative to the base end point. This affects monitoring such endpoints as they would resolve to invalid URI. Example is http://www.biocatalogue.org/services/2705#monitoring -- This 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 Jun 9 09:18:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:18:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-375) Find a way if indicating which fields have been updated in a model (updated_at field just indicates that something was updated) Message-ID: <5292568.1119.1307625482039.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-375?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-375. --------------------------------- Resolution: By Design > Find a way if indicating which fields have been updated in a model (updated_at field just indicates that something was updated) > ------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-375 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-375 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > When a field of a soap service is updated, any view which uses the updated at field will reflect this irrespective of whether it is referring to the updated field or not. For example, when the detailed descriptions from soaplab are updated, it gives the impression that the service description has also been updated which is might not always be true -- This 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 Jun 9 09:19:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:19:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-375) Find a way if indicating which fields have been updated in a model (updated_at field just indicates that something was updated) Message-ID: <5506136.1120.1307625595359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-375?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-375. ------------------------------- > Find a way if indicating which fields have been updated in a model (updated_at field just indicates that something was updated) > ------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-375 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-375 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > When a field of a soap service is updated, any view which uses the updated at field will reflect this irrespective of whether it is referring to the updated field or not. For example, when the detailed descriptions from soaplab are updated, it gives the impression that the service description has also been updated which is might not always be true -- This 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 Jun 9 09:19:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:19:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-371) Some easy ways to fill in the ID on the 'copy annotation page' will be useful. for example, auto-complete when I tick a service on the 'report' page. In-Reply-To: <8889938.2562.1275911657025.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7331817.1121.1307625599881.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-371?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-371: -------------------------------- Fix Version/s: Future Description: (Franck) > Some easy ways to fill in the ID on the 'copy annotation page' will be > useful. for example, auto-complete when I tick a service on the > 'report' page. (Jits) This is a very good idea, though slightly tricky to implement unfortunately (because the ID fields are dependant on the type of item you want to copy annotations on). was: (Franck) > Some easy ways to fill in the ID on the 'copy annotation page' will be > useful. for example, auto-complete when I tick a service on the > 'report' page. (Jits) This is a very good idea, but very tricky to implement unfortunately (because the ID fields are dependant on the type of item you want to copy annotations on). > Some easy ways to fill in the ID on the 'copy annotation page' will be useful. for example, auto-complete when I tick a service on the 'report' page. > ----------------------------------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-371 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-371 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > (Franck) > Some easy ways to fill in the ID on the 'copy annotation page' will be > > useful. for example, auto-complete when I tick a service on the > > 'report' page. > (Jits) This is a very good idea, though slightly tricky to implement unfortunately > (because the ID fields are dependant on the type of item you want to > copy annotations on). -- This 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 Jun 9 09:20:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:20:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-370) In the curation dashboard possibility to compare each archived soap operation to all existing soap operations of a service. In-Reply-To: <11617150.2514.1275907172502.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17742865.1122.1307625602476.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-370?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-370: -------------------------------- Fix Version/s: Future > In the curation dashboard possibility to compare each archived soap operation to all existing soap operations of a service. > ---------------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-370 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-370 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > In the curation dashboard possibility to compare each archived soap operation to all existing soap operations of a service. > If we can do a 1(archived operation) to all (existing operations) comparison, we can then easily transfer any descriptions from archived services that are still valid. -- This 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 Jun 9 09:20:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:20:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-374) Use teaser of the description from soaplab In-Reply-To: <9984711.2865.1276080977016.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30597677.1123.1307625604789.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-374: -------------------------------- Summary: Use teaser of the description from soaplab (was: use teaser of the description from soaplab) Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 Component/s: Web Interface > Use teaser of the description from soaplab > ------------------------------------------ > > Key: BIOCAT-374 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-374 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > As descriptions from soaplab can be long, a teaser is needed to show a bit of the description and the whole lot on click. -- This 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 Jun 9 09:22:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:22:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-366) Implement a "Most Popular Services" box In-Reply-To: <17734181.1836.1275470177015.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28748228.1124.1307625725425.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-366?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-366: -------------------------------- Fix Version/s: 1.2.0 > Implement a "Most Popular Services" box > --------------------------------------- > > Key: BIOCAT-366 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-366 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > Original Estimate: 2 days > Remaining Estimate: 2 days > > Need some way of seeing what the most popular services are in the catalogue. > This will require some work to cache viewings/stats counts 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 Jun 9 09:22:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:22:07 +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: <12653932.1125.1307625727644.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: -------------------------------- Summary: Add a "Users responsible for this service" section on the service's profile page (was: Add a "User responsible for this service" section on the service's profile page) Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 > 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 > 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 Jun 9 09:22:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:22:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-362) Add archive/unarchive events to the ActivityLogs and then the activity feed(s) In-Reply-To: <27841565.1720.1275053057051.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17964836.1126.1307625729780.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-362?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-362: -------------------------------- Fix Version/s: 1.0.2 > Add archive/unarchive events to the ActivityLogs and then the activity feed(s) > ------------------------------------------------------------------------------ > > Key: BIOCAT-362 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-362 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > Original Estimate: 5 hours > Remaining Estimate: 5 hours > > Currently, no ActivityLog events are being made when archive/unarchive services occur. Need to log these events and then show them 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 Thu Jun 9 09:22:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:22:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-364) The service update checker should also update ServiceDeployment locations In-Reply-To: <5338610.1723.1275135377283.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27889921.1127.1307625731843.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-364: -------------------------------- Fix Version/s: 1.0.1 > The service update checker should also update ServiceDeployment locations > ------------------------------------------------------------------------- > > Key: BIOCAT-364 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Currently, the service update checker process doesn't take into account updating of location info of service 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 Thu Jun 9 09:22:13 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:22:13 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-364) The service update checker should also update ServiceDeployment locations In-Reply-To: <5338610.1723.1275135377283.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10494747.1128.1307625733919.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16796#comment-16796 ] Jiten Bhagat commented on BIOCAT-364: ------------------------------------- Are we sure it doesn't do this? Need to investigate! > The service update checker should also update ServiceDeployment locations > ------------------------------------------------------------------------- > > Key: BIOCAT-364 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Currently, the service update checker process doesn't take into account updating of location info of service 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 Thu Jun 9 09:23:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:23:55 +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: <25706720.1129.1307625835362.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: -------------------------------- Fix Version/s: 1.0.2 (was: 1.1.0) > 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 > Fix For: 1.0.2 > > 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 Jun 9 09:23:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:23:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-345) Update the annotation counts mechanism to take into account new fields In-Reply-To: <32597963.524.1274181737002.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1517096.1130.1307625837526.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-345?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-345: -------------------------------- Summary: Update the annotation counts mechanism to take into account new fields (was: update the annotations counts mechanism to take into account these new fields) Fix Version/s: 1.1.0 Description: Update the annotation counts mechanism to take into account new fields (like soaplab_description and namespace) (was: update the annotations counts mechanism to take into account these new fields (like soaplab_description and namespace)) > Update the annotation counts mechanism to take into account new fields > ---------------------------------------------------------------------- > > Key: BIOCAT-345 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-345 > Project: BioCatalogue > Issue Type: Refinement > Components: Annotations (in App) > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Update the annotation counts mechanism to take into account new fields (like soaplab_description and namespace) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:23:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:23:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-353) Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs In-Reply-To: <31076462.1623.1274872997018.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13994725.1131.1307625839644.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-353: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Fix Version/s: 1.0.1 > Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-353 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, SOAP Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > When making calls via the REST API those 2 endpoints are shown in the related section; they do not work. > Example: > Calling: http://www.biocatalogue.org/soap_operations/15369.xml returns some XML but the key lookout points are: > > ... > > > ... > > > > ... > > -- This 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 Jun 9 09:24:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:24:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-353) Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs In-Reply-To: <31076462.1623.1274872997018.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27315590.1132.1307625841742.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16797#comment-16797 ] Jiten Bhagat commented on BIOCAT-353: ------------------------------------- This may have been done. Verify please! > Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-353 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, SOAP Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > When making calls via the REST API those 2 endpoints are shown in the related section; they do not work. > Example: > Calling: http://www.biocatalogue.org/soap_operations/15369.xml returns some XML but the key lookout points are: > > ... > > > ... > > > > ... > > -- This 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 Jun 9 09:25:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:25:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32947598.1133.1307625955362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=14965#comment-14965 ] Jiten Bhagat edited comment on BIOCAT-343 at 09/06/11 14:24: ------------------------------------------------------------- This now takes into account all annotations on the associated ServiceDeployment, ServiceVersion, SoapServices and RestServices of a service, but not on the operations/inputs/outputs, etc. was (Author: jbhagat): This now takes into account all annotations on the associated ServiceDeployment, ServiceVersion, SoapServices and RestServices of a service. > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > Original Estimate: 2 days > Time Spent: 1 day, 1 hour > Remaining Estimate: 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This 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 Jun 9 09:25:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:25:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-333) Paging does not work when a providers services are listed from service show page In-Reply-To: <7774406.91.1273726817082.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30944821.1134.1307625958086.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-333: -------------------------------- Summary: Paging does not work when a providers services are listed from service show page (was: paging does not work when a providers services are listed from service show page) Check that the correct tab is being shown after paging. > Paging does not work when a providers services are listed from service show page > -------------------------------------------------------------------------------- > > Key: BIOCAT-333 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > When a provider link is clicked from a service show page, the provider profile is shown with all the providers services. If provider has several pages of services, then clicking next or page number take you back to provider profile. -- This 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 Jun 9 09:26:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:26:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-339) Convert INBTester.pl templates to URL checks In-Reply-To: <12638841.476.1274024297139.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16751292.1136.1307625962338.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-339. --------------------------------- Resolution: No longer relevant > Convert INBTester.pl templates to URL checks > --------------------------------------------- > > Key: BIOCAT-339 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339 > Project: BioCatalogue > Issue Type: Refinement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > INBTester.pl scripts basically contruct a URL and parse the output from that URL. That can be converted to URL checks which would make them runnable on the main servers. -- This 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 Jun 9 09:26:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:26:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-343) Implement a "News" tab on a service's page In-Reply-To: <29654500.520.1274178676994.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12753749.1137.1307625964784.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-343: -------------------------------- Fix Version/s: 1.2.0 > Implement a "News" tab on a service's page > ------------------------------------------ > > Key: BIOCAT-343 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-343 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > Original Estimate: 2 days > Time Spent: 1 day, 1 hour > Remaining Estimate: 7 hours > > This should show a full activity list/feed for the service, showing events that have happened, like new annotations, WSDL changes, etc. > Maybe have the WSDL changes in a separate column on the right hand side? -- This 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 Jun 9 09:26:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:26:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-333) Paging does not work when a providers services are listed from service show page In-Reply-To: <7774406.91.1273726817082.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20602629.1138.1307625967181.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-333: -------------------------------- Fix Version/s: 1.0.1 > Paging does not work when a providers services are listed from service show page > -------------------------------------------------------------------------------- > > Key: BIOCAT-333 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > When a provider link is clicked from a service show page, the provider profile is shown with all the providers services. If provider has several pages of services, then clicking next or page number take you back to provider profile. -- This 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 Jun 9 09:26:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:26:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-339) Convert INBTester.pl templates to URL checks In-Reply-To: <12638841.476.1274024297139.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19292269.1135.1307625960253.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-339. ------------------------------- > Convert INBTester.pl templates to URL checks > --------------------------------------------- > > Key: BIOCAT-339 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-339 > Project: BioCatalogue > Issue Type: Refinement > Components: Service Monitoring > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > INBTester.pl scripts basically contruct a URL and parse the output from that URL. That can be converted to URL checks which would make them runnable on the main servers. -- This 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 Jun 9 09:27:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:27:55 +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: <2386480.1139.1307626075362.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: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Fix Version/s: 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: 1.1.0 > > 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 Thu Jun 9 09:27:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:27:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-327) Implement option in search results to ignore archived items In-Reply-To: <20298642.61.1273658419378.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28919816.1140.1307626078212.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-327?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-327: -------------------------------- Fix Version/s: 1.2.0 A simple check box to say "Include Archived Services" may work. > Implement option in search results to ignore archived items > ----------------------------------------------------------- > > Key: BIOCAT-327 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-327 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > 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 Thu Jun 9 09:28:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:28:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17537251.1141.1307626080544.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-329: -------------------------------- Fix Version/s: 1.0.1 > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 5 hours > Time Spent: 4 hours > Remaining Estimate: 1 hour > -- This 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 Jun 9 09:28:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:28:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22073851.1142.1307626082806.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16799#comment-16799 ] Jiten Bhagat commented on BIOCAT-329: ------------------------------------- Verify that this has been done. > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 5 hours > Time Spent: 4 hours > Remaining Estimate: 1 hour > -- This 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 Jun 9 09:29:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:29:55 +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: <13080394.1143.1307626195357.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: -------------------------------- Fix Version/s: 1.1.0 Description: A filter / check box to "Include Archived Services" may work. > 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 > 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 Thu Jun 9 09:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:31:55 +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: <3027886.1144.1307626315362.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: -------------------------------- Fix Version/s: 1.1.0 > 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 > 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 Thu Jun 9 09:31:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:31:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-297) Implement Service Families Message-ID: <28864959.1145.1307626317746.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-297?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-297: -------------------------------- Fix Version/s: 1.2.0 > Implement Service Families > -------------------------- > > Key: BIOCAT-297 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-297 > Project: BioCatalogue > Issue Type: Improvement > Components: REST Services Support, Search / Filtering / Browsing, Service Submission, SOAP Services Support, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > In order to cater for BioMoby, DAS, Soaplab, etc, we can introduce the notion of a "service family" that SOAP or REST services can belong to. -- This 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 Jun 9 09:31:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:31:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-313) post_tweet function should provide option for proxy setting Message-ID: <5901540.1146.1307626319915.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-313?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-313. ------------------------------- > post_tweet function should provide option for proxy setting > ----------------------------------------------------------- > > Key: BIOCAT-313 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-313 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR,Twitter > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This 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 Jun 9 09:32:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:32:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-313) post_tweet function should provide option for proxy setting Message-ID: <13977615.1147.1307626321995.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-313?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-313. --------------------------------- Resolution: No longer relevant > post_tweet function should provide option for proxy setting > ----------------------------------------------------------- > > Key: BIOCAT-313 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-313 > Project: BioCatalogue > Issue Type: Sub-task > Components: Server Management > Environment: RoR,Twitter > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This 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 Jun 9 09:32:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:32:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-315) Integrate fix for Hash#from_xml from Tod Jackson (Emory University) for the WSDL parsing Message-ID: <23828676.1148.1307626324733.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-315?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-315. --------------------------------- Resolution: Implemented This seems to be working now! > Integrate fix for Hash#from_xml from Tod Jackson (Emory University) for the WSDL parsing > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-315 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-315 > Project: BioCatalogue > Issue Type: Improvement > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Original Estimate: 2 hours > Time Spent: 1 hour > Remaining Estimate: 1 hour > > Tod Jackson, from Emory University, has found a way to solve the issues with Hash#from_xml that were causing major problems with the legacy WSDL Parser. > Below is the full text of his solution. > Integrate this into the codebase so at least the legacy WSDL parser can work better. > --- > First, after spending some time trying to narrow in on what I *thought* the issue was, I did some research and found a few references to what I thought were people having similar issues. The one that seemed most relevant to me was this blog by Peter Wagenet (http://in.finitu.de/2008/11/05/stop-hash-from_xml-from-killing-xml-attributes). It seemed like Peter was describing a very similar situation to what I thought we were seeing (losing attributes when you had an element with only attributes). > In the blog, Peter references a patch that he had submitted but after spending quite a bit of time trying to track the patch down and apply it (or parts of it anyway) I reverted to what is probably a complete hack. I was concerned with applying a "global patch" anyway because I thought it might introduce backward compatibility issues. So, I focussed my efforts on the things I knew about and thought I had at least some control over. Namely, the WsdlParser module (lib/bio_catalogue/wsdl_parser.rb). As you mentioned, this module is used when/if the new parser fails. In my case, that was happening so that's where I focussed. > Ultimately, I took snippets of the code from the blog I mention above and added a couple new methods to the Hash class which is defined in the vendor/rails/activesupport/lib/active_support/core_ext/hash/conversions.rb file (did I mention it's a hack?). Here are the methods I added (I took this code pretty much verbatim from Peter's blog but I didn't use everything he mentions, only these methods): > def hacked_from_xml(xml, options = {}) > Rails.logger.info("conversions.rb: hacked_from_xml called.") > end > private > def hacked_typecast_xml_value(value, options = {}) > options.symbolize_keys! > options.reverse_merge!(:preserve_attributes => false) > case value.class.to_s > when 'Hash' > if value['type'] == 'array' > child_key, entries = value.detect { |k,v| k != 'type' } # child_key is throwaway > if entries.nil? || (c = value['__content__'] && c.blank?) > [] > else > case entries.class.to_s # something weird with classes not matching here. maybe singleton methods breaking is_a? > when "Array" > entries.collect { |v| hacked_typecast_xml_value(v, options) } > when "Hash" > [hacked_typecast_xml_value(entries, options)] > else > raise "can't typecast #{entries.inspect}" > end > end > elsif value.has_key?("__content__") > content = value["__content__"] > if parser = XML_PARSING[value["type"]] > if parser.arity == 2 > XML_PARSING[value["type"]].call(content, value) > else > XML_PARSING[value["type"]].call(content) > end > elsif options[:preserve_attributes] && value.keys.size > 1 > value["content"] = value.delete("__content__") > value > else > content > end > elsif value['type'] == 'string' && value['nil'] != 'true' > "" > # blank or nil parsed values are represented by nil > elsif value.blank? || value['nil'] == 'true' > nil > # If the type is the only element which makes it then > # this still makes the value nil, except if type is > # a XML node(where type['value'] is a Hash) > elsif value['type'] && value.size == 1 && !value['type'].is_a?(::Hash) > nil > else > xml_value = value.inject({}) do |h,(k,v)| > h[k] = hacked_typecast_xml_value(v, options) > h > end > # Turn { :files => { :file => # } into { :files => # } so it is compatible with > # how multipart uploaded files from HTML appear > xml_value["file"].is_a?(StringIO) ? xml_value["file"] : xml_value > end > when 'Array' > value.map! { |i| hacked_typecast_xml_value(i, options) } > case value.length > when 0 then nil > when 1 then value.first > else value > end > when 'String' > value > else > raise "can't typecast #{value.class.name} - #{value.inspect}" > end > end > Then, I modified wsdl_parser.rb to use my new "hacked" version of these methods. I changed this: > wsdl_hash = Hash.from_xml(wsdl_file_contents) > to this: > wsdl_hash = Hash.hacked_from_xml(wsdl_file_contents, :preserve_attributes => true) > We haven't had any of the issues since putting these changes in. Since I thought I new where the issues were occurring, I felt somewhat okay with making the change this way because I could "hack" the foundation and only use that hack in the one place I knew were were having issues thereby avoiding the introduction of backward compatibility issue if there were other places throughout the app that was still using the original Hash.from_xml method. > --- -- This 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 Jun 9 09:32:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:32:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-318) Improve styling of "Part of Service..." Message-ID: <18506296.1149.1307626326904.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: -------------------------------- Fix Version/s: 1.0.2 > 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: Jiten Bhagat > Fix For: 1.0.2 > > 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 Thu Jun 9 09:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-293) Refactor filtering UI to use new filters code Message-ID: <15606497.1150.1307626435361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-293?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-293: -------------------------------- Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 > Refactor filtering UI to use new filters code > --------------------------------------------- > > Key: BIOCAT-293 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-293 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > A new mechanism has been implemented to load up all available filter groups for a resource type. See: > BioCatalogue::Filtering.get_all_filter_groups_for > The filtering in the services index needs to be updated to use this instead of loading up filters in the views. > That way caching, etc can be done in one place. -- This 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 Jun 9 09:33:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:33:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-289) Filters disappear when I switch between different views Message-ID: <3734890.1151.1307626437605.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-289?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-289: -------------------------------- Fix Version/s: 1.0.2 Description: When I filter services (e.g by provider, location etc.) and switch to simple view for example, it clears off all the selected filters. Need to remember the filters selected when switching views. was:when i filter services (e.g by provider, location etc.) and switch to simple view for example, it clears off all the selected filters. > Filters disappear when I switch between different views > ------------------------------------------------------- > > Key: BIOCAT-289 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-289 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > When I filter services (e.g by provider, location etc.) and switch to simple view for example, it clears off all the selected filters. > Need to remember the filters selected when switching views. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:33:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:33:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-290) Filtering after search results Message-ID: <22426555.1152.1307626439800.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-290?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-290: -------------------------------- Fix Version/s: Future > Filtering after search results > ------------------------------ > > Key: BIOCAT-290 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-290 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Potential idea: After a search is carried out, users can select 'filter these services' and they will be presented with a filter pop up dialog. They can then select the required filters and get taken to the filtered services index. -- This 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 Jun 9 09:34:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:34:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-287) Look to making the HTML pages more Linked Data compliant Message-ID: <25003566.1153.1307626441872.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-287?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-287: -------------------------------- Fix Version/s: Future > Look to making the HTML pages more Linked Data compliant > -------------------------------------------------------- > > Key: BIOCAT-287 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-287 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > 2 sub tasks: > 1. Use the 303 redirect way, via extensions way > eg: URIs like "http://www.biocatalogue.org/services/23" should become noon-information resource URIs and when a request is made to it a response should be given back redirecting to the appropriate URL, eg: http://www.biocatalogue.org/services/23.html). > 2. In the various documents that are outputted, ensure that a link to the non-information resource URI is there. For XML this is done. For HTML, look to using a <link> tag with foaf:primaryTopic through RDFa [1]. > An email thread with Sean: > --- > Jits > I started a thread on public-lod: > http://lists.w3.org/Archives/Public/public-lod/2010Feb/0118.html > It looks like a possible initial solution would be to use a <link> element with an appropriate attribute (possibly foaf:primaryTopic). > --- > --- > On 17 Feb 2010, at 10:20, Jiten Bhagat wrote: > > Sean Bechhofer wrote: > >> > >> On 17 Feb 2010, at 10:01, Jiten Bhagat wrote: > >> > >>> Thanks Sean, some useful responses there. I'll go with the > >>> foaf:primaryTopic <link> for now. > >> > >> The RDFa solution might also be worth considering -- it would provide > >> an route for migration in the future if you wanted to provide richer > >> information in the HTML (and is W3C Rec [1]). Happy to chat about this > >> if you want. > > > > Good point. I would prefer to do it the RDFa way as I can see a need for > > the future. I need to first check to ensure that we are generating XHTML > > compliant pages. Then I should be able to add the foaf:primarryTopic as > > starters. > Cool. It would be nice for us to be producing some RDFa pages. > > I'll run things past you when I have something to show :-) > Great. > Sean > --- -- This 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 Jun 9 09:35:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:35:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-278) Improve solr indexing by using the solr types config option Message-ID: <11554952.1154.1307626555362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-278?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-278: -------------------------------- Fix Version/s: Future > Improve solr indexing by using the solr types config option > ----------------------------------------------------------- > > Key: BIOCAT-278 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-278 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Currently all fields indexed are treated as solr "text" fields which have the full ngramtokenizer treatment applied to them. However we might want certain fields to be indexed as they are and not split into tokens (potentially fields like "category"). Look into doing this using syntax such as: > acts_as_solr :fields => [ { :price => :range_float } ] > The available field types are: > - :float > - :integer > - :boolean > - :date > - :string > - :range_integer > - :range_float -- This 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 Jun 9 09:35:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:35:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-262) Add meta keywords and meta descriptions to web pages Message-ID: <30483462.1155.1307626559149.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-262?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-262: -------------------------------- Fix Version/s: 1.2.0 > Add meta keywords and meta descriptions to web pages > ---------------------------------------------------- > > Key: BIOCAT-262 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-262 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > For better SEO!! -- This 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 Jun 9 09:36:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:36:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-267) In Annotations plugin - check the setting of "source" when creating annotations Message-ID: <28698061.1156.1307626561485.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: Future > 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 > Fix For: Future > > > 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 Jun 9 09:36:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:36:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-268) Upgrade to latest memcache-client Message-ID: <6744578.1157.1307626563601.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-268?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-268: -------------------------------- Fix Version/s: 1.2.0 > Upgrade to latest memcache-client > --------------------------------- > > Key: BIOCAT-268 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-268 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Some speed improvements have been promised for 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 Thu Jun 9 09:36:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:36:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-251) Registration email bounced back Message-ID: <17072813.1158.1307626565737.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-251?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-251. --------------------------------- Resolution: No longer relevant > Registration email bounced back > ------------------------------- > > Key: BIOCAT-251 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-251 > Project: BioCatalogue > Issue Type: Improvement > Components: User Management > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > This week we had some issues with some users from Southampton university registering to the biocat and not getting their activation email cause blocked by the university servers for unknown reasons. we should put in place an automate process so that when the activation mail is not delivered, it tries other means. -- This 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 Jun 9 09:36:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:36:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-268) Upgrade to latest memcache-client Message-ID: <4041317.1159.1307626567775.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-268?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16802#comment-16802 ] Jiten Bhagat commented on BIOCAT-268: ------------------------------------- Need to make sure we upgrade to a Rails 2 compatible version! > Upgrade to latest memcache-client > --------------------------------- > > Key: BIOCAT-268 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-268 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Some speed improvements have been promised for 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 Thu Jun 9 09:36:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:36:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-251) Registration email bounced back Message-ID: <18418371.1160.1307626571312.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-251?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-251. ------------------------------- > Registration email bounced back > ------------------------------- > > Key: BIOCAT-251 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-251 > Project: BioCatalogue > Issue Type: Improvement > Components: User Management > Reporter: Franck Tanoh > Assignee: Eric Nzuobontane > > This week we had some issues with some users from Southampton university registering to the biocat and not getting their activation email cause blocked by the university servers for unknown reasons. we should put in place an automate process so that when the activation mail is not delivered, it tries other means. -- This 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 Jun 9 09:36:13 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:36:13 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-270) Curation / statistics reports Message-ID: <6941667.1161.1307626573555.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-270?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-270: -------------------------------- Fix Version/s: 1.2.0 > Curation / statistics reports > ----------------------------- > > Key: BIOCAT-270 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-270 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Stats Dashboard > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > 1- New services added > 2- Recently updated services > 3- Services that don't work anymore > 4- Anything picks up by the monitor (notify me when amber or red) > 5- Most viewed services > 6- Less viewed services > 7- Most farourited services > 8- Most annotated services > 9- Services without any description > 10- List of services non-categorized > 11- New members > 12- Members detail and contact mail > 13- Member with the most annotation > 14- Member with the most submitted service > 15- New comments added > 16- Updated service description by members > 17- Service providers list > 18- Service submitter list > 19- Recently annotated services > 20- Recently deleted service -- This 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 Jun 9 09:37:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-249) error_to_home and other such should return appropriate HTTP codes Message-ID: <15757171.1162.1307626675359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16803#comment-16803 ] Jiten Bhagat commented on BIOCAT-249: ------------------------------------- Please verify > error_to_home and other such should return appropriate HTTP codes > ----------------------------------------------------------------- > > Key: BIOCAT-249 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > Methods like error_to_home etc should return appropriate HTTP status codes. Right now there's just a redirect, and no way of telling that a genuine error has occurred. > Need to rethink this whole thing. Maybe beef up the 404 etc error pages and have those served up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:37:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:37:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-234) Set expiry time for sessions Message-ID: <18376284.1163.1307626677473.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-234?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-234. ------------------------------- > Set expiry time for sessions > ---------------------------- > > Key: BIOCAT-234 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-234 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > set up expiry time for cookies and delete expired sessions from the db -- This 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 Jun 9 09:37:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:37:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-234) Set expiry time for sessions Message-ID: <5412791.1164.1307626679610.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-234?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-234. --------------------------------- Resolution: No longer relevant > Set expiry time for sessions > ---------------------------- > > Key: BIOCAT-234 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-234 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > set up expiry time for cookies and delete expired sessions from the db -- This 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 Jun 9 09:38:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:38:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-237) For search, allow scoping to particular types of objects Message-ID: <17497893.1165.1307626681875.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-237?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-237: -------------------------------- Fix Version/s: Future > For search, allow scoping to particular types of objects > -------------------------------------------------------- > > Key: BIOCAT-237 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-237 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > E.g: > query: "blast obj:SoapOperation" > Would give all services that have the word blast somewhere in a SoapOperation object. -- This 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 Jun 9 09:38:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:38:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-244) Refactor user mailer etc Message-ID: <28564426.1166.1307626684586.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-244?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-244: -------------------------------- Fix Version/s: 1.2.0 > Refactor user mailer etc > ------------------------ > > Key: BIOCAT-244 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-244 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > ... and move it to the new app/mailers and other appropriate directories. > Also add tests for these. -- This 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 Jun 9 09:38:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:38:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-248) Help text about cookies required for logging in Message-ID: <24738828.1167.1307626686667.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-248?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-248: -------------------------------- Fix Version/s: 1.2.0 > Help text about cookies required for logging in > ----------------------------------------------- > > Key: BIOCAT-248 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-248 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Via Pieter Neerincx: > I was trying yesterday from a machine, which had cookies disabled. I know many sites which require a login also require session cookies, so I knew what to look for, but for those who are less familiar with the tech behind websites it would be nice if BioCatalogue will show a warning that it cannot set a session cookie when you try to login... -- This 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 Jun 9 09:38:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:38:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-249) error_to_home and other such should return appropriate HTTP codes Message-ID: <21308455.1168.1307626689119.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-249: -------------------------------- Fix Version/s: 1.0.2 > error_to_home and other such should return appropriate HTTP codes > ----------------------------------------------------------------- > > Key: BIOCAT-249 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > Methods like error_to_home etc should return appropriate HTTP status codes. Right now there's just a redirect, and no way of telling that a genuine error has occurred. > Need to rethink this whole thing. Maybe beef up the 404 etc error pages and have those served up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:39:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-233) Need to take into account old/deprecated/deleted services Message-ID: <17054441.1169.1307626795367.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-233: -------------------------------- Fix Version/s: 1.2.0 > Need to take into account old/deprecated/deleted services > --------------------------------------------------------- > > Key: BIOCAT-233 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-233 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > Original Estimate: 3 days > Time Spent: 1 day > Remaining Estimate: 0 minutes > > From Steve: > "Perhaps a wikipedia-like approach, where something gets marked for > deletion and gets a big warning badge in the meantime, giving people a > chance to comment / complain before it goes in the bin. " -- This 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 Jun 9 09:39:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:39:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-223) Update auto_tagger script to do tags to categories Message-ID: <13290290.1170.1307626797510.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-223?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-223: -------------------------------- Affects Version/s: 1.1.0 > Update auto_tagger script to do tags to categories > -------------------------------------------------- > > Key: BIOCAT-223 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-223 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Affects Versions: 1.1.0 > Reporter: Katy Wolstencroft > Assignee: Jiten Bhagat > > For categories with unambiguous labels, we can find tags with those labels and add categories automatically. > (As suggested by Katy) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:39:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:39:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-224) Add caching to filters in filtering sidebar Message-ID: <27035165.1171.1307626799670.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-224?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-224: -------------------------------- Fix Version/s: 1.1.0 > Add caching to filters in filtering sidebar > ------------------------------------------- > > Key: BIOCAT-224 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-224 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Currently the filtering sidebar is generated on each request. This is not scalable. Some caching work is required. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:40:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:40:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-231) Enable tag filter not persisting Message-ID: <10894473.1172.1307626801951.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-231: -------------------------------- Fix Version/s: 1.0.2 > Enable tag filter not persisting > -------------------------------- > > Key: BIOCAT-231 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > the 'enable tag filter' doesn't stay. i have to keep on clicking on it anytime i want to browse for new services...very frustrating. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:40:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:40:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-231) Enable tag filter not persisting Message-ID: <21634171.1173.1307626804717.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16804#comment-16804 ] Jiten Bhagat commented on BIOCAT-231: ------------------------------------- Check this > Enable tag filter not persisting > -------------------------------- > > Key: BIOCAT-231 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > the 'enable tag filter' doesn't stay. i have to keep on clicking on it anytime i want to browse for new services...very frustrating. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:41:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-219) Search indexing for annotations Message-ID: <26528036.1174.1307626915363.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-219?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-219: -------------------------------- Fix Version/s: 1.1.0 > Search indexing for annotations > ------------------------------- > > Key: BIOCAT-219 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-219 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > 2 things here: > 1. Make sure that when you do the categories work, that the ID (which is what is stored as the value) is not what gets indexed, rather, the actual category label itself! > 2. Maybe certain types of annotations, like name aliases, should have a boost, when indexed. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:41:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:41:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-172) Optimise filtering sidebar Message-ID: <9175357.1175.1307626917996.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-172?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-172. ------------------------------- > Optimise filtering sidebar > -------------------------- > > Key: BIOCAT-172 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-172 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > The filtering sidebar takes a fair bit of time to render. Look into possibly optimising 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 Thu Jun 9 09:42:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:42:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-172) Optimise filtering sidebar Message-ID: <5141001.1176.1307626920102.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-172?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-172. --------------------------------- Resolution: Duplicate > Optimise filtering sidebar > -------------------------- > > Key: BIOCAT-172 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-172 > Project: BioCatalogue > Issue Type: Task > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > The filtering sidebar takes a fair bit of time to render. Look into possibly optimising 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 Thu Jun 9 09:42:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:42:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-174) Look into changing tag show URL scheme for ontology term tags Message-ID: <14112800.1177.1307626922298.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-174?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-174: -------------------------------- Fix Version/s: Future Priority: Minor (was: Major) > Look into changing tag show URL scheme for ontology term tags > ------------------------------------------------------------- > > Key: BIOCAT-174 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-174 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Currently the URL scheme for showing results for tags that are ontology terms might not be completely appropriate! > Look into how this can be more done more appropriately. -- This 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 Jun 9 09:42:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:42:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-170) Change metadata counts calcuation to a background task Message-ID: <5204149.1178.1307626924709.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-170?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-170: -------------------------------- Fix Version/s: 1.2.0 > Change metadata counts calcuation to a background task > ------------------------------------------------------ > > Key: BIOCAT-170 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-170 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Currently, metadata counts are calculated and cached for 60 mins. > Change this to have a table to store metadata counts, that get refreshed "offline" via a background task, so as not to affect user requests. -- This 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 Jun 9 09:42:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:42:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-185) Update filtering help text and write How To page Message-ID: <22292216.1179.1307626926781.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-185?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-185. ------------------------------- > Update filtering help text and write How To page > ------------------------------------------------ > > Key: BIOCAT-185 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-185 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Web Interface > Reporter: Jiten Bhagat > Assignee: Franck Tanoh > > Update the help text that explains what exactly the filtering does. > Also possibly write a How To page on the public wiki for 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 Thu Jun 9 09:42:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:42:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-185) Update filtering help text and write How To page Message-ID: <25522016.1180.1307626929026.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-185?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-185. --------------------------------- Resolution: No longer relevant > Update filtering help text and write How To page > ------------------------------------------------ > > Key: BIOCAT-185 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-185 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Web Interface > Reporter: Jiten Bhagat > Assignee: Franck Tanoh > > Update the help text that explains what exactly the filtering does. > Also possibly write a How To page on the public wiki for 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 Thu Jun 9 09:42:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:42:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-189) Improve search results ordering Message-ID: <15905943.1181.1307626931361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-189?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-189: -------------------------------- Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 > Improve search results ordering > ------------------------------- > > Key: BIOCAT-189 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-189 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Right now the ordering of search results isn't great. > Maybe use boosting to ensure that services that contain the word(s) in their names get higher up. > Also MUST look to using the scores directly from SOLR when doing the reordering of results. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:43:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:43:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-169) Add a note on VBI services about VBI out of funds Message-ID: <4894307.1182.1307627035365.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-169?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-169: -------------------------------- Fix Version/s: Future > Add a note on VBI services about VBI out of funds > ------------------------------------------------- > > Key: BIOCAT-169 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-169 > Project: BioCatalogue > Issue Type: Task > Reporter: Franck Tanoh > Assignee: Franck Tanoh > Fix For: Future > > > There are lots of VBI services in the catalogue which may not work anymore because the project is no more funded. We need to point to this for every VBI service in the catalogue: > http://pathport.vbi.vt.edu/main/home.php -- This 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 Jun 9 09:43:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:43:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-156) Remove beta from the biocat logo Message-ID: <8908491.1183.1307627037638.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-156: -------------------------------- Fix Version/s: 1.0.1 Affects Version/s: 1.0.0 > Remove beta from the biocat logo > -------------------------------- > > Key: BIOCAT-156 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Remove Beta from BioCatalogue logo on the main site. -- This 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 Jun 9 09:43:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:43:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-165) Show source of tags, categories and name aliases Message-ID: <7713987.1184.1307627039827.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-165?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-165: -------------------------------- Fix Version/s: Future > Show source of tags, categories and name aliases > ------------------------------------------------ > > Key: BIOCAT-165 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-165 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > When you hover over tags and name aliases, show who submitted that 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 Jun 9 09:44:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:44:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-166) Check that annotation popup and tag URLs are URL encoded Message-ID: <28957776.1185.1307627042077.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-166?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-166. ------------------------------- > Check that annotation popup and tag URLs are URL encoded > -------------------------------------------------------- > > Key: BIOCAT-166 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-166 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > In various places like the code for generating the add annotation popup, and tag cloud generation, the custom URLs generated might not be escaping the query string values appropriately. Look into 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 Thu Jun 9 09:44:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:44:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-166) Check that annotation popup and tag URLs are URL encoded Message-ID: <20519154.1186.1307627044673.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-166?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-166. --------------------------------- Resolution: No longer relevant > Check that annotation popup and tag URLs are URL encoded > -------------------------------------------------------- > > Key: BIOCAT-166 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-166 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > In various places like the code for generating the add annotation popup, and tag cloud generation, the custom URLs generated might not be escaping the query string values appropriately. Look into 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 Thu Jun 9 09:45:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:45:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-150) Add admin features for curation, like delete Message-ID: <22269962.1187.1307627155364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-150?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-150. --------------------------------- Fix Version/s: 1.0.0 Resolution: Fixed Done. More requirements around curation should be specified as a separate JIRA entries. > Add admin features for curation, like delete > -------------------------------------------- > > Key: BIOCAT-150 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-150 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.0 > > > Add features to allow admins and curators to curate/administrate the catalogue through the UI. This will permit people like Franck to go in and delete services and so on. -- This 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 Jun 9 09:45:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:45:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-223) Update auto_tagger script to do tags to categories Message-ID: <18960312.1188.1307627157633.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-223?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-223: -------------------------------- Fix Version/s: 1.1.0 Affects Version/s: (was: 1.1.0) > Update auto_tagger script to do tags to categories > -------------------------------------------------- > > Key: BIOCAT-223 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-223 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Katy Wolstencroft > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > For categories with unambiguous labels, we can find tags with those labels and add categories automatically. > (As suggested by Katy) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:46:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:46:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-150) Add admin features for curation, like delete Message-ID: <3410417.1189.1307627160118.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-150?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-150. ------------------------------- > Add admin features for curation, like delete > -------------------------------------------- > > Key: BIOCAT-150 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-150 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.0 > > > Add features to allow admins and curators to curate/administrate the catalogue through the UI. This will permit people like Franck to go in and delete services and so on. -- This 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 Jun 9 09:46:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:46:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-137) Investigate no values for min_occurs and max_occurs, from WSDL parsing Message-ID: <7958375.1190.1307627163658.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: -------------------------------- Assignee: Jiten Bhagat (was: Eric Nzuobontane) Fix Version/s: 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: 1.1.0 > > > 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 Thu Jun 9 09:47:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-124) Get recently registered or updated services Message-ID: <21607411.1191.1307627275367.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-124?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-124: -------------------------------- Summary: Get recently registered or updated services (was: Get reecently registered or updated services) The news feed caters for this to some extent. Is this enough? > Get recently registered or updated services > ------------------------------------------- > > Key: BIOCAT-124 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-124 > Project: BioCatalogue > Issue Type: New Feature > Components: Homepage, Search / Filtering / Browsing, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > From the 20Q's, Q4 - > "Which are the most recently updated services?", "Which are the most recently registered services?", "Most search services?" > - possibility to filter services based on these factors. -- This 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 Jun 9 09:47:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:47:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-122) Get number of submitters for a given provider Message-ID: <30308613.1192.1307627277582.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-122?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-122: -------------------------------- Fix Version/s: Future > Get number of submitters for a given provider > --------------------------------------------- > > Key: BIOCAT-122 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-122 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > From the 20Q's, Q2 - > "How many submitters does provider X have?" > - number of submitter from a provider must be clear. -- This 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 Jun 9 09:47:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:47:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-124) Get recently registered or updated services Message-ID: <29364712.1193.1307627279698.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-124?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-124: -------------------------------- Fix Version/s: Future > Get recently registered or updated services > ------------------------------------------- > > Key: BIOCAT-124 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-124 > Project: BioCatalogue > Issue Type: New Feature > Components: Homepage, Search / Filtering / Browsing, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > From the 20Q's, Q4 - > "Which are the most recently updated services?", "Which are the most recently registered services?", "Most search services?" > - possibility to filter services based on these factors. -- This 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 Jun 9 09:49:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:49:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-121) Get numbers and types of services for a given provider Message-ID: <16312902.1194.1307627395362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-121?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-121: -------------------------------- Fix Version/s: 1.2.0 > Get numbers and types of services for a given provider > ------------------------------------------------------ > > Key: BIOCAT-121 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-121 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > From the 20Q's, Q1 - > "How many services has provider X?" > - currently implemented but need to make sure it clear enough for users > "How many of those are REST?", "How many of those are SOAP?" > - different type of services should be clear on the site and users should know the number of each type after a search. -- This 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 Jun 9 09:49:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:49:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-120) Sourcing tags from myGrid ontology Message-ID: <2205322.1195.1307627397517.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-120?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-120. ------------------------------- > Sourcing tags from myGrid ontology > ---------------------------------- > > Key: BIOCAT-120 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-120 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App) > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > Sourcing tags from the myGrid ontology. This is the first step toward semantic annotation of web 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 Thu Jun 9 09:49:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:49:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-120) Sourcing tags from myGrid ontology Message-ID: <15538167.1196.1307627399703.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-120?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-120. --------------------------------- Resolution: No longer relevant > Sourcing tags from myGrid ontology > ---------------------------------- > > Key: BIOCAT-120 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-120 > Project: BioCatalogue > Issue Type: Task > Components: Annotations (in App) > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > Sourcing tags from the myGrid ontology. This is the first step toward semantic annotation of web 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 Thu Jun 9 09:51:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:51:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-119) Tag frequency count fix for tags_box partial Message-ID: <24927206.1197.1307627515364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-119?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-119: -------------------------------- Fix Version/s: Future The counter thinking here is that having this multi-size tag cloud is quite distracting! Does the frequency of the tag across the whole site matter in the context of a single service? > Tag frequency count fix for tags_box partial > -------------------------------------------- > > Key: BIOCAT-119 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-119 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations (in App) > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > The partial annotations/_tags_box will currently only get a count of 1 per tag so all tags will be of the same size. > In myexperiment, the size of the tag, even on individual tag clouds, always represents the frequency of that tag word on the whole site. Maybe this should be the same for the partial. > Maybe this could be done after the move to Annotation Values as compound objects (which would allow complex SQL queries for tags). -- This 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 Jun 9 09:51:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:51:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-102) Automatic testing of services based on sets of example inputs Message-ID: <19598164.1198.1307627517632.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-102?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-102: -------------------------------- Fix Version/s: Future > Automatic testing of services based on sets of example inputs > ------------------------------------------------------------- > > Key: BIOCAT-102 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-102 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Monitoring > Reporter: Jerzy Orlowski > Assignee: Eric Nzuobontane > Fix For: Future > > > Testing not only if service exists but if it works -- This 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 Jun 9 09:51:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:51:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-106) Allow the submitter to select a display name for a service Message-ID: <13581220.1199.1307627519723.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-106?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-106: -------------------------------- Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 > Allow the submitter to select a display name for a service > ---------------------------------------------------------- > > Key: BIOCAT-106 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-106 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > "I have a suggestion -- you allow people to add name aliases for services, but it would be really useful if you could tag one as the primary display name. > I wouldn't be surprised if quite a lot of the services out there have fairly unfriendly names in the WSDLs. > The EMBRACE Registry lets you enter a title for the service, which is what comes up in the human-readable web page, rather than the computer-readable name from the WSDL." > Posted by Andrew on the Biocat support list -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:52:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:52:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-111) Tags should only be allowed on top level Service resource Message-ID: <9782482.1200.1307627521836.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-111?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-111: -------------------------------- Fix Version/s: Future Affects Version/s: 1.0.0 Description: Currently, the tags box for a service combines all tags on the Service, ServiceDeployments, ServiceVersions and SoapService/RestService. This adds significant processing overheads to things! Need to consolidate this to only allow 'tag' annotations on the top level Service object. This will also make things like {{ServiceProvider#tags_from_services}} more accurate! (was: Currently, the tags box for a service combines all tags on the Service, ServiceDeployments, ServiceVersions and SoapService/RestService. This adds significant processing overheads to things! Need to consolidate this to only allow 'tag' annotations on the top level Service object. This will also make things like ServiceProvider#tags_from_services more accurate!) > Tags should only be allowed on top level Service resource > --------------------------------------------------------- > > Key: BIOCAT-111 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-111 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations (in App) > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Currently, the tags box for a service combines all tags on the Service, ServiceDeployments, ServiceVersions and SoapService/RestService. This adds significant processing overheads to things! Need to consolidate this to only allow 'tag' annotations on the top level Service object. This will also make things like {{ServiceProvider#tags_from_services}} more accurate! -- This 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 Jun 9 09:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-83) Allow users to link to their myExp profiles Message-ID: <8217756.1201.1307627635358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-83?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-83: ------------------------------- Fix Version/s: 1.2.0 > Allow users to link to their myExp profiles > ------------------------------------------- > > Key: BIOCAT-83 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-83 > Project: BioCatalogue > Issue Type: New Feature > Components: User Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > For now, at the very least we should allow users to submit their myExp user profile url or user id and then we fetch all the public info about them and cache it and show it in BioCatalogue -- This 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 Jun 9 09:53:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:53:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-69) Check usage of class_name_of_active_record... Message-ID: <2235005.1202.1307627637628.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-69?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-69: ------------------------------- Priority: Minor (was: Major) > Check usage of class_name_of_active_record... > --------------------------------------------- > > Key: BIOCAT-69 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-69 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Lines like: > obj_type = ActiveRecord::Base.send(:class_name_of_active_record_descendant, self).to_s > .. basically gets the parent class in a object hierarchy (after ActiveRecord::Base). But is this correct? Do we want the parent being stored or the actual child's type? > Need to investigate, based on Rail's STI thing... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:53:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:53:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-69) Check usage of class_name_of_active_record... Message-ID: <20250508.1203.1307627639790.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-69?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-69: ------------------------------- Fix Version/s: Future > Check usage of class_name_of_active_record... > --------------------------------------------- > > Key: BIOCAT-69 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-69 > Project: BioCatalogue > Issue Type: Task > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Lines like: > obj_type = ActiveRecord::Base.send(:class_name_of_active_record_descendant, self).to_s > .. basically gets the parent class in a object hierarchy (after ActiveRecord::Base). But is this correct? Do we want the parent being stored or the actual child's type? > Need to investigate, based on Rail's STI thing... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:54:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:54:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-77) Add sets of inputs for operations Message-ID: <13824956.1204.1307627642051.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-77?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-77. -------------------------------- Resolution: No longer relevant Superseded by the functional units work. > Add sets of inputs for operations > --------------------------------- > > Key: BIOCAT-77 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-77 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), SOAP Services Support > Reporter: Jerzy Orlowski > Assignee: Jiten Bhagat > > Add possibility to group example inputs for operations in sets. Each set will be a *working case* for this operation. -- This 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 Jun 9 09:54:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:54:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-82) Implement simple curation assertions Message-ID: <5598414.1205.1307627644702.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-82?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-82: ------------------------------- Fix Version/s: Future > Implement simple curation assertions > ------------------------------------ > > Key: BIOCAT-82 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-82 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), Annotations Plugin, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: Future > > > Need the ability to determine whether annotation are useful / approved etc. So have some simple curation assertions available on 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 Thu Jun 9 09:55:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-58) Service submission, annotation and monitoring through API Message-ID: <15675139.1206.1307627755362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-58?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-58. -------------------------------- Fix Version/s: 1.0.1 Resolution: Fixed This has largely been done. > Service submission, annotation and monitoring through API > --------------------------------------------------------- > > Key: BIOCAT-58 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-58 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > From PALs: service providers like GenOuest (http://www.genouest.org/) wants to submit service, add annotation (description, example), monitor services through the BioCatalogue 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 Thu Jun 9 09:55:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:55:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-54) Implement custom 404 etc pages Message-ID: <1869365.1207.1307627757454.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-54?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-54. ------------------------------ > Implement custom 404 etc pages > ------------------------------ > > Key: BIOCAT-54 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-54 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > Instead of using the default 404 page, implement a better, more dynamic 404 page that will guide users in a better way. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:55:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:55:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-54) Implement custom 404 etc pages Message-ID: <8396696.1208.1307627759641.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-54?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-54. -------------------------------- Resolution: Fixed > Implement custom 404 etc pages > ------------------------------ > > Key: BIOCAT-54 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-54 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > Instead of using the default 404 page, implement a better, more dynamic 404 page that will guide users in a better way. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 09:56:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:56:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-57) Soaplab badge is not clickable - build a services filter for this Message-ID: <5923125.1209.1307627761735.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-57: ------------------------------- Fix Version/s: 1.2.0 > Soaplab badge is not clickable - build a services filter for this > ----------------------------------------------------------------- > > Key: BIOCAT-57 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-57 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > Original Estimate: 1 day > Remaining Estimate: 1 day > > Soaplab badge not clickable... need to get to a filtered list. This relates to the "service families" work. > Note: this is about service filtering; we need to ensure the same consistent experience as when you click on the "SOAP" or "REST" badges. -- This 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 Jun 9 09:56:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:56:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-58) Service submission, annotation and monitoring through API Message-ID: <22188886.1210.1307627764697.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-58?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-58. ------------------------------ > Service submission, annotation and monitoring through API > --------------------------------------------------------- > > Key: BIOCAT-58 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-58 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > From PALs: service providers like GenOuest (http://www.genouest.org/) wants to submit service, add annotation (description, example), monitor services through the BioCatalogue 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 Thu Jun 9 09:57:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:57:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-605) Build more useful error pages with links/suggestions/etc Message-ID: <5021327.1211.1307627875379.JavaMail.jira@rosalind.cs.man.ac.uk> Build more useful error pages with links/suggestions/etc -------------------------------------------------------- Key: BIOCAT-605 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-605 Project: BioCatalogue Issue Type: Improvement Reporter: Jiten Bhagat Assignee: Jiten Bhagat The current set of error pages (404, 500, etc) are not very useful. Add link, suggestions, potential search results, etc so the user can go on with from there. For 404 pages in particular, need to say something like "the service you are looking for may have been removed from the BioCatalogue". -- This 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 Jun 9 09:57:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:57:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-47) Add OpenSearch feature Message-ID: <12526237.1212.1307627878162.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-47?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-47. -------------------------------- Resolution: Implemented > Add OpenSearch feature > ---------------------- > > Key: BIOCAT-47 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-47 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Implement full OpenSearch capabilities -- This 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 Jun 9 09:58:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:58:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-47) Add OpenSearch feature Message-ID: <18333016.1213.1307627880322.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-47?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-47. ------------------------------ > Add OpenSearch feature > ---------------------- > > Key: BIOCAT-47 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-47 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > > Implement full OpenSearch capabilities -- This 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 Jun 9 09:58:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:58:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-605) Build more useful error pages with links/suggestions/etc In-Reply-To: <5021327.1211.1307627875379.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22372237.1214.1307627882421.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-605?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-605: -------------------------------- Fix Version/s: 1.2.0 > Build more useful error pages with links/suggestions/etc > -------------------------------------------------------- > > Key: BIOCAT-605 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-605 > Project: BioCatalogue > Issue Type: Improvement > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current set of error pages (404, 500, etc) are not very useful. Add link, suggestions, potential search results, etc so the user can go on with from there. > For 404 pages in particular, need to say something like "the service you are looking for may have been removed from the BioCatalogue". -- This 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 Jun 9 09:59:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:59:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-606) Implement the ATOM results for OpenSearch Message-ID: <32802.1215.1307627995357.JavaMail.jira@rosalind.cs.man.ac.uk> Implement the ATOM results for OpenSearch ----------------------------------------- Key: BIOCAT-606 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-606 Project: BioCatalogue Issue Type: Improvement Components: Search / Filtering / Browsing Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.2.0 This will allow for deeper integration with OpenSearch clients. -- This 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 Jun 9 09:59:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 14:59:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-605) Build more useful error pages with links/suggestions/etc In-Reply-To: <5021327.1211.1307627875379.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4594554.1216.1307627997466.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-605?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-605: -------------------------------- Component/s: Web Interface > Build more useful error pages with links/suggestions/etc > -------------------------------------------------------- > > Key: BIOCAT-605 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-605 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > The current set of error pages (404, 500, etc) are not very useful. Add link, suggestions, potential search results, etc so the user can go on with from there. > For 404 pages in particular, need to say something like "the service you are looking for may have been removed from the BioCatalogue". -- This 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 Jun 9 10:01:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:01:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-19) Add link to "filter these services" on search Message-ID: <8883728.1218.1307628117636.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-19?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-19. -------------------------------- Resolution: No longer relevant > Add link to "filter these services" on search > --------------------------------------------- > > Key: BIOCAT-19 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-19 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > For services in the search results, add a button to "filter these services" so users can easily go from -- This 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 Jun 9 10:01:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-46) Which description to display in the simple view for service listings? Message-ID: <15314786.1217.1307628115356.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-46?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-46: ------------------------------- Fix Version/s: 1.2.0 > Which description to display in the simple view for service listings? > --------------------------------------------------------------------- > > Key: BIOCAT-46 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-46 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > If possible we should allow the curator to set per service which description to show in the simple view. -- This 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 Jun 9 10:01:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:01:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-19) Add link to "filter these services" on search Message-ID: <17427398.1219.1307628119884.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-19?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-19. ------------------------------ > Add link to "filter these services" on search > --------------------------------------------- > > Key: BIOCAT-19 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-19 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > For services in the search results, add a button to "filter these services" so users can easily go from -- This 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 Jun 9 10:02:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:02:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-22) Broken links in the feta imports Message-ID: <29640764.1220.1307628122127.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-22?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-22: ------------------------------- Fix Version/s: 1.0.2 > Broken links in the feta imports > -------------------------------- > > Key: BIOCAT-22 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-22 > Project: BioCatalogue > Issue Type: Bug > Components: Content Acquisition, Data > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > > Revisit links from the feta import. Some (example workflows listed in the other annotation in biocat) don't work anymore: > http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/extractPosition_workflow.xml (blast should be capital BLAST) > http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/getSupportDatabaseList_workflow.xml (doesn't exist) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:02:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:02:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-23) WSDL Parsers doesn't deal with WSDL attachments Message-ID: <19324802.1221.1307628124769.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-23?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-23: ------------------------------- Fix Version/s: Future > WSDL Parsers doesn't deal with WSDL attachments > ----------------------------------------------- > > Key: BIOCAT-23 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-23 > Project: BioCatalogue > Issue Type: Improvement > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Fix For: Future > > > The main WSDL parser needs to be able to deal with WSDL attachements -- This 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 Jun 9 10:02:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:02:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-27) Easy ways for members to contact providers Message-ID: <29075700.1222.1307628127069.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-27?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-27. ------------------------------ > Easy ways for members to contact providers > ------------------------------------------ > > Key: BIOCAT-27 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-27 > Project: BioCatalogue > Issue Type: Objective > Reporter: Franck Tanoh > Assignee: Franck Tanoh > > Make it easy for user of the BioCatalogue to contact service provider -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:02:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:02:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-27) Easy ways for members to contact providers Message-ID: <21072585.1223.1307628129206.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-27?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-27. -------------------------------- Resolution: No longer relevant > Easy ways for members to contact providers > ------------------------------------------ > > Key: BIOCAT-27 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-27 > Project: BioCatalogue > Issue Type: Objective > Reporter: Franck Tanoh > Assignee: Franck Tanoh > > Make it easy for user of the BioCatalogue to contact service provider -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:02:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:02:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-28) BioCatalogue approved annotation stamp(s) Message-ID: <26898673.1224.1307628131318.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-28?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-28: ------------------------------- Fix Version/s: Future > BioCatalogue approved annotation stamp(s) > ----------------------------------------- > > Key: BIOCAT-28 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-28 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations Plugin, Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > How do you know that the service is well annotated? Need a kind of BioCatalogue approved annotation stamp, with measures of how well things are annotated. -- This 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 Jun 9 10:02:13 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:02:13 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-42) Flag services/annotation for deletion Message-ID: <20231958.1225.1307628133435.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-42?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-42: ------------------------------- Fix Version/s: Future > Flag services/annotation for deletion > ------------------------------------- > > Key: BIOCAT-42 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-42 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: Future > > > Can we flag service or annotation before deletion? For example, keep them in the catalogue for 1 or week or 2 with the delete flag; then inform the submitter that his service/annotation is going to be deleted; -- This 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 Jun 9 10:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-17) Push annotations to the BioCatalogue Message-ID: <11903927.1226.1307628235355.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-17?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-17. -------------------------------- Resolution: No longer relevant > Push annotations to the BioCatalogue > ------------------------------------ > > Key: BIOCAT-17 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-17 > Project: BioCatalogue > Issue Type: Objective > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > BioCatalogue should import annotation from application using web services such as Taverna, myExperiment etc. > This can be done via mechanisms like the Annotations Write 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 Thu Jun 9 10:03:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:03:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-17) Push annotations to the BioCatalogue Message-ID: <4693748.1227.1307628237501.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-17?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-17. ------------------------------ > Push annotations to the BioCatalogue > ------------------------------------ > > Key: BIOCAT-17 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-17 > Project: BioCatalogue > Issue Type: Objective > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > > BioCatalogue should import annotation from application using web services such as Taverna, myExperiment etc. > This can be done via mechanisms like the Annotations Write 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 Thu Jun 9 10:08:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:08:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-13) Add filter to filtering sidebar for services from, or that were present in, the EMBRACE registry Message-ID: <11883881.1228.1307628535353.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-13?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16810#comment-16810 ] Jiten Bhagat commented on BIOCAT-13: ------------------------------------ Need to figure out how this fits in with the proposed work on "service families". > Add filter to filtering sidebar for services from, or that were present in, the EMBRACE registry > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-13 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-13 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Web Interface > Reporter: Carole Goble > Assignee: Jiten Bhagat > > Update the filtering sidebar to reflect ALL services that were present in the EMBRACE registry. > A general mechanism is also needed for other such sources. -- This 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 Jun 9 10:10:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:10:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-13) Add filter to filtering sidebar for services from, or that were present in, the EMBRACE registry Message-ID: <4647747.1229.1307628655362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-13?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-13: ------------------------------- Fix Version/s: 1.2.0 > Add filter to filtering sidebar for services from, or that were present in, the EMBRACE registry > ------------------------------------------------------------------------------------------------ > > Key: BIOCAT-13 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-13 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Web Interface > Reporter: Carole Goble > Assignee: Jiten Bhagat > Fix For: 1.2.0 > > > Update the filtering sidebar to reflect ALL services that were present in the EMBRACE registry. > A general mechanism is also needed for other such sources. -- This 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 Jun 9 10:10:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:10:57 +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: <19915760.1230.1307628657541.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: -------------------------------- Fix Version/s: 1.0.2 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: 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. 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: 0) 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: 1.0.2 > > > 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. -- This 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 Jun 9 10:10:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:10:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-547) Remove redundant branches from codebase In-Reply-To: <2469093.242.1290775012810.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29018264.1231.1307628659729.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-547?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-547. ------------------------------- > Remove redundant branches from codebase > --------------------------------------- > > Key: BIOCAT-547 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-547 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > -- This 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 Jun 9 10:11:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:11:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-547) Remove redundant branches from codebase In-Reply-To: <2469093.242.1290775012810.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19357847.1232.1307628661889.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-547?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-547. --------------------------------- Resolution: By Design > Remove redundant branches from codebase > --------------------------------------- > > Key: BIOCAT-547 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-547 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > -- This 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 Jun 9 10:12:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-497) Look into using the change logs (generated from the service update checker) to calculate service API stability In-Reply-To: <14812729.9946.1286378955308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18779840.1233.1307628775366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-497?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-497: -------------------------------- Fix Version/s: Future > Look into using the change logs (generated from the service update checker) to calculate service API stability > -------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-497 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-497 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Original query from Richard Adams: > {quote} > Hi Katy, > I've just been having a browse around Biocatalogue - it's really > useful! - as we're trying to enhance our support for webservices > within our SBSI project, by providing UI plugins to access some of the > SysBio services. > I was wondering if Biocatalogue would provide stats on API stability > of webservices (e.g., breaking API changes such as removal of a > method, for example)? > Clearly some services will be more experimental than others, for app > developers developing UI to access the plugins then stability of the > API ( as well as the % availability) is influential in deciding which > webservices to offer/support. > Perhaps I've missed something in the Help files, but couldn't see > anything directly related to API changes. > Cheers > Richard > {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 Thu Jun 9 10:12:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:12:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-490) Need a mechanism for activating the first user in the system in new deployments In-Reply-To: <29633402.9917.1285951395303.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31053386.1234.1307628777748.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-490: -------------------------------- Fix Version/s: 1.1.0 Priority: Major (was: Minor) This is a very important issue for people who set up their own instances. > Need a mechanism for activating the first user in the system in new deployments > ------------------------------------------------------------------------------- > > Key: BIOCAT-490 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490 > Project: BioCatalogue > Issue Type: Improvement > Components: User Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > When someone sets up a fresh instance of the BioCatalogue software they usually create a new user and then run into the issue of how to activate that user (in cases where a mail server wasn't set up). > Need a way of solving this issue. One potential solution is to always activate the first user in a system (and maybe automatically make them an admin too?) > OR when the app is first run have a "set up" wizard in which one of the tasks is to create an admin user. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:14:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:14:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-456) Potentially optimise the BioCatalogue::Util::display_name method In-Reply-To: <2178224.8102.1282139595466.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4666309.1235.1307628895364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-456. --------------------------------- Resolution: Not A Bug > Potentially optimise the BioCatalogue::Util::display_name method > ---------------------------------------------------------------- > > Key: BIOCAT-456 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Original Estimate: 2 hours > Time Spent: 30 minutes > Remaining Estimate: 1 hour, 30 minutes > > Currently, the BioCatalogue::Util::display_name method helper method (which is used everywhere to show display names of objects) makes heavy use of eval(). This is a potential performance hog, so look to optimise this and move away from using eval. -- This 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 Jun 9 10:14:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:14:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-319) Add /soap_services/wsdl_locations to XML Schema for REST API In-Reply-To: <32175098.1.1273582037157.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8917564.1236.1307628897718.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-319: -------------------------------- Fix Version/s: 1.0.1 > Add /soap_services/wsdl_locations to XML Schema for REST API > ------------------------------------------------------------ > > Key: BIOCAT-319 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:14:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:14:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-319) Add /soap_services/wsdl_locations to XML Schema for REST API In-Reply-To: <32175098.1.1273582037157.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1947887.1237.1307628899864.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16812#comment-16812 ] Jiten Bhagat commented on BIOCAT-319: ------------------------------------- Check > Add /soap_services/wsdl_locations to XML Schema for REST API > ------------------------------------------------------------ > > Key: BIOCAT-319 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:15:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:15:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-320) Add /soap_services/wsdl_locations to REST API documentation In-Reply-To: <5755038.2.1273582277250.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8583613.1238.1307628901950.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-320?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-320: -------------------------------- Fix Version/s: 1.0.1 Priority: Major (was: Minor) > Add /soap_services/wsdl_locations to REST API documentation > ----------------------------------------------------------- > > Key: BIOCAT-320 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-320 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:15:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:15:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-317) Allow for filtering of services using hostname Message-ID: <29016040.1239.1307628904813.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-317?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-317: -------------------------------- Fix Version/s: Future > Allow for filtering of services using hostname > ---------------------------------------------- > > Key: BIOCAT-317 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-317 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > -- This 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 Jun 9 10:15:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:15:06 +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: <13262205.1240.1307628906893.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: 1.0.2 > 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: 1.0.2 > > 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 Thu Jun 9 10:15:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:15:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-456) Potentially optimise the BioCatalogue::Util::display_name method In-Reply-To: <2178224.8102.1282139595466.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31312795.1241.1307628909228.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-456. ------------------------------- > Potentially optimise the BioCatalogue::Util::display_name method > ---------------------------------------------------------------- > > Key: BIOCAT-456 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-456 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Original Estimate: 2 hours > Time Spent: 30 minutes > Remaining Estimate: 1 hour, 30 minutes > > Currently, the BioCatalogue::Util::display_name method helper method (which is used everywhere to show display names of objects) makes heavy use of eval(). This is a potential performance hog, so look to optimise this and move away from using eval. -- This 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 Jun 9 10:16:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:16:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-299) Allow updating of the geolocation data for service deployments Message-ID: <10419210.1242.1307629015364.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: 1.1.0 Affects Version/s: 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 > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.0 > > > 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 Thu Jun 9 10:16:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:16:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-288) Reimplement the service filtering method for conditions/joining Message-ID: <26019765.1243.1307629017455.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-288?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-288: -------------------------------- Fix Version/s: 1.1.0 > Reimplement the service filtering method for conditions/joining > --------------------------------------------------------------- > > Key: BIOCAT-288 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-288 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.0 > > > A new way of doing it was done for BioCatalogue::Filtering::Annotations::generate_conditions_and_joins_from_filters > Possibly reimplement the services one to do it this way. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:16:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:16:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-291) Import myExperiment example data into the BioCatalogue Message-ID: <29929052.1244.1307629019556.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-291?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-291: -------------------------------- Fix Version/s: Future > Import myExperiment example data into the BioCatalogue > ------------------------------------------------------ > > Key: BIOCAT-291 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-291 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), Content Acquisition > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Find a way to automatically import all example data provide by the SPARQL query from George: > Here's the SPARQL query just put it on > http://rdf.myexperiment.org/sparql > I am working on a version that will go with xmlsplitters > George > ----------------- > #get all stringconstant input of wsdl processors > PREFIX mecomp: <http://rdf.myexperiment.org/ontologies/components/> > PREFIX mebase: <http://rdf.myexperiment.org/ontologies/base/> > PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> > select distinct ?output_processor_type, ?output_service, ?output_uri, ?output_port, ?input_processor_value where{ > ?link rdf:type mecomp:Link . > ?link mecomp:from-output ?output . > ?output mecomp:for-component ?input_processor . > ?input_processor mecomp:processor-type ?input_processor_type . > ?input_processor mecomp:processor-value ?input_processor_value . > ?link mecomp:to-input ?input . > ?input mecomp:for-component ?output_processor . > ?output_processor mecomp:processor-type ?output_processor_type . > ?output_processor mecomp:processor-uri ?output_uri . > ?output_processor mecomp:service-name ?output_service . > ?input dcterms:title ?output_port . > FILTER(REGEX(?input_processor_type,'stringconstant')) . > FILTER(REGEX(?output_processor_type,'wsdl')) . > } -- This 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 Jun 9 10:17:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:17:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-275) Implement mechanism and UI for "Recommended Services" Message-ID: <26126518.1245.1307629021663.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-275?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-275: -------------------------------- Fix Version/s: Future > Implement mechanism and UI for "Recommended Services" > ----------------------------------------------------- > > Key: BIOCAT-275 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-275 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Have Franck etc be able to set certain services as "Recommended for..... x y z" (where xyz are for specific tasks) and then those recommended services are highlighted in listings (much like they do on the FireFox and Thunderbird addons site). > Also have a "All recommended services" list. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:17:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:17:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-295) Investigate double render error with "error_to_back_or_home" helper Message-ID: <2369331.1246.1307629023804.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: -------------------------------- Fix Version/s: 1.0.2 > 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: Jiten Bhagat > Priority: Minor > Fix For: 1.0.2 > > > 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 Thu Jun 9 10:18:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:18:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-274) Possibly implement ordering based on curation of annotations Message-ID: <28055980.1247.1307629135403.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-274?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-274: -------------------------------- Fix Version/s: 1.2.0 > Possibly implement ordering based on curation of annotations > ------------------------------------------------------------ > > Key: BIOCAT-274 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-274 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Up/down buttons for people to specify where they think the annotation belongs in the list. Like votes. Like in ServerFault and StackOverflow. -- This 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 Jun 9 10:18:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:18:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-241) Being able to click on annotation values to find all services (or other things) with that annotation Message-ID: <31188193.1248.1307629137488.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-241?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-241: -------------------------------- Fix Version/s: Future > Being able to click on annotation values to find all services (or other things) with that annotation > ---------------------------------------------------------------------------------------------------- > > Key: BIOCAT-241 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-241 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App), Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Eg: being able to click on "free" for cost, or whatever annotations. > This is essentially a way of finding other services with the same (or maybe even similar 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 Thu Jun 9 10:19:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:19:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-253) Monitoring history limit should not be hard coded Message-ID: <7970674.1250.1307629141813.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: -------------------------------- Fix Version/s: 1.1.0 Affects Version/s: 1.0.0 > 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: Eric Nzuobontane > 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 Jun 9 10:19:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:19:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-260) Tooltip hover issues Message-ID: <13817922.1251.1307629144835.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-260?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-260: -------------------------------- Fix Version/s: 1.0.2 > Tooltip hover issues > -------------------- > > Key: BIOCAT-260 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-260 > Project: BioCatalogue > Issue Type: Bug > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.2 > > > As reported by Sergey: > "I've just noticed that the tooltips over 'Latest Services Feed' and > the 'Follow me on Twitter' icons in the action bar appear under these > icons themselves (this doesn't normally happen with other tooltips - at > least not that I've seen)." > Occurs in FF and IE apparently. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:20:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:20:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-239) Improve view of service description in the result page Message-ID: <6561625.1252.1307629255365.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-239?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-239. --------------------------------- Resolution: Not A Bug > Improve view of service description in the result page > ------------------------------------------------------ > > Key: BIOCAT-239 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-239 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > > at the moment you can just see part of the description which is not useful some time. so my idea is to be able to have a kind of 'click to view the entire description'. this will avoid having to select the service before you can see its full description. -- This 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 Jun 9 10:20:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:20:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-199) Implement messaging/networking between members Message-ID: <7769275.1253.1307629257613.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-199?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-199. ------------------------------- > Implement messaging/networking between members > ---------------------------------------------- > > Key: BIOCAT-199 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-199 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > > As requested by Frnack: > --- > Hi, > > Yesterday, I wanted to contact a biocat user about a service he submitted ??? but couldn???t. > I said to myself; how will a biocat user contact a provider about his services then? > Should he send us a mail first? Not a good idea??? we are not service providers. > We therefore need a way to enable communication between services provider/submitters/users/curators. > My solution is to have an internal messaging system (myExperiment style)??? leverage on existing technology :-) > I know you guys have already a long list of requirements but I think we should have this system in place before the public release. > > Cheers > Franck > --- > Should be able to drop in a plugin to achieve 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 Thu Jun 9 10:20:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:20:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-199) Implement messaging/networking between members Message-ID: <14585608.1254.1307629259760.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-199?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-199. --------------------------------- Resolution: No longer relevant > Implement messaging/networking between members > ---------------------------------------------- > > Key: BIOCAT-199 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-199 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > > As requested by Frnack: > --- > Hi, > > Yesterday, I wanted to contact a biocat user about a service he submitted ??? but couldn???t. > I said to myself; how will a biocat user contact a provider about his services then? > Should he send us a mail first? Not a good idea??? we are not service providers. > We therefore need a way to enable communication between services provider/submitters/users/curators. > My solution is to have an internal messaging system (myExperiment style)??? leverage on existing technology :-) > I know you guys have already a long list of requirements but I think we should have this system in place before the public release. > > Cheers > Franck > --- > Should be able to drop in a plugin to achieve 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 Thu Jun 9 10:21:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:21:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-213) All external links should open in a new tab/window Message-ID: <14852044.1255.1307629261998.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: 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: 1.1.0 > > > 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 Thu Jun 9 10:21:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:21:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-220) Ability to make announcements on services Message-ID: <29763847.1256.1307629264710.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-220?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-220: -------------------------------- Fix Version/s: 1.1.0 Priority: Major (was: Minor) > Ability to make announcements on services > ----------------------------------------- > > Key: BIOCAT-220 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-220 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Potentially using the annotations plugin, implement a way for users to make announcements on services, in order to inform people about things. -- This 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 Jun 9 10:21:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:21:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-222) Implement show category page Message-ID: <6391162.1257.1307629266797.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-222?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-222: -------------------------------- Fix Version/s: Future > Implement show category page > ---------------------------- > > Key: BIOCAT-222 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-222 > Project: BioCatalogue > Issue Type: New Feature > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > This page can allow users to easily traverse the category tree and get the results. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 10:21:08 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:21:08 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-239) Improve view of service description in the result page Message-ID: <6053570.1258.1307629268965.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-239?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-239. ------------------------------- > Improve view of service description in the result page > ------------------------------------------------------ > > Key: BIOCAT-239 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-239 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > > at the moment you can just see part of the description which is not useful some time. so my idea is to be able to have a kind of 'click to view the entire description'. this will avoid having to select the service before you can see its full description. -- This 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 Jun 9 10:21:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:21:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-194) Easily add "my tags" during service submission Message-ID: <4014504.1259.1307629271217.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-194?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-194: -------------------------------- Fix Version/s: 1.2.0 > Easily add "my tags" during service submission > ---------------------------------------------- > > Key: BIOCAT-194 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-194 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Submission, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Make it easy to add the tags that a user uses commonly. -- This 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 Jun 9 10:22:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:22:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-192) In Annotations plugin: better error handling for .create_annotations(..) Message-ID: <10387899.1260.1307629375363.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-192?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-192: -------------------------------- Fix Version/s: Future > In Annotations plugin: better error handling for .create_annotations(..) > ------------------------------------------------------------------------ > > Key: BIOCAT-192 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-192 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > The acts_as_annotatable#create_annotations method currently saves a bunch of data as annotation objects but there is no way to tell what has errored and why. > Need to do 2 things: > 1. Log all errors (probably in the Annotation model directly. > 2. Have a way to get any errors generated in the .create_annotations method. -- This 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 Jun 9 10:22:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:22:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-158) Service page loads very strangely Message-ID: <24139954.1261.1307629377691.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-158?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-158. ------------------------------- > Service page loads very strangely > --------------------------------- > > Key: BIOCAT-158 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-158 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > > when a service page is loading, it first shows the operation page then comes back to the service page...strange behaviour -- This 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 Jun 9 10:22:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:22:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-158) Service page loads very strangely Message-ID: <15458677.1262.1307629379811.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-158?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-158. --------------------------------- Resolution: Fixed > Service page loads very strangely > --------------------------------- > > Key: BIOCAT-158 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-158 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > > when a service page is loading, it first shows the operation page then comes back to the service page...strange behaviour -- This 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 Jun 9 10:23:01 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:23:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-178) Show correct datetimes to users in UI Message-ID: <990523.1263.1307629381883.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-178?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-178: -------------------------------- Fix Version/s: Future > Show correct datetimes to users in UI > ------------------------------------- > > Key: BIOCAT-178 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-178 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Currenly all datetime info is stored in UTC in the database and thus will be shown as UTC to users, in the UI. > Allow users to specify what timezone they are in and ensure that all rendered datetime info is in the user's current timezone. -- This 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 Jun 9 10:23:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:23:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-188) Look to changing the session store to memcache Message-ID: <2058713.1264.1307629384992.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-188?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-188: -------------------------------- Fix Version/s: Future > Look to changing the session store to memcache > ---------------------------------------------- > > Key: BIOCAT-188 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-188 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, Server Management > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Priority: Minor > Fix For: Future > > > Currently sessions are stored in the db. This is quite slow (but more secure than cookies). > The best solution is to use memcache as the session store. -- This 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 Jun 9 10:24:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:24:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-153) Refactor tag cloud expand/collapse Message-ID: <7971336.1265.1307629495364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-153?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-153: -------------------------------- Fix Version/s: Future Priority: Trivial (was: Minor) > Refactor tag cloud expand/collapse > ---------------------------------- > > Key: BIOCAT-153 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-153 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > 1. make the expand/collapse an option within the tag cloud render method. > 2. (maybe) use expand/collapse method from here: http://code.google.com/p/sysmo-db/source/browse/seek-hub/trunk/app/views/gadgets/_tag_cloud.html.erb -- This 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 Jun 9 10:24:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:24:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-134) Issue with popups on IE (when on operations tab) Message-ID: <16665092.1266.1307629497687.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-134?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-134: -------------------------------- Fix Version/s: Future > Issue with popups on IE (when on operations tab) > ------------------------------------------------ > > Key: BIOCAT-134 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-134 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > When using IE and when opening the popup on the operations tab of soap services, the background becomes fully grey, which is not good! -- This 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 Jun 9 10:25:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:25:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-148) Add search/by_data to stats dashboard Message-ID: <16830674.1268.1307629505232.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-148?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-148: -------------------------------- Fix Version/s: 1.2.0 > Add search/by_data to stats dashboard > ------------------------------------- > > Key: BIOCAT-148 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-148 > Project: BioCatalogue > Issue Type: New Feature > Components: Stats Dashboard > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Show number of search_by data queries (preferably by month) -- This 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 Jun 9 10:25:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:25:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-149) Stats dashboard filtered by time Message-ID: <27059813.1269.1307629507382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-149?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-149: -------------------------------- Fix Version/s: Future > Stats dashboard filtered by time > -------------------------------- > > Key: BIOCAT-149 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-149 > Project: BioCatalogue > Issue Type: Improvement > Components: Stats Dashboard > Reporter: Rodrigo Lopez > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > From Rodrigo: "Status during the last 24 hours - but I do realise you need to couple > this within the scope of present possibilities - for the near future? " -- This 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 Jun 9 10:25:10 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:25:10 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-132) Add cancel button to various forms Message-ID: <5192425.1270.1307629510693.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-132?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-132: -------------------------------- Fix Version/s: Future Priority: Trivial (was: Minor) > Add cancel button to various forms > ---------------------------------- > > Key: BIOCAT-132 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-132 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > Potentially using... > <input type="button" name="Cancel" value="Cancel" onclick="window.location = 'yourpage.html' " /> -- This 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 Jun 9 10:26:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:26:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-131) In the Annotatons plugin, any finder should be able to take a list of options Message-ID: <16554424.1271.1307629615366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-131?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-131: -------------------------------- Fix Version/s: Future > In the Annotatons plugin, any finder should be able to take a list of options > ----------------------------------------------------------------------------- > > Key: BIOCAT-131 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-131 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > For any finder method in the annotations plugin, it should be possible to provide a list of options as well as a single option. > E.g.: should be able to get a set of annotations for multiple attributes in one query. -- This 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 Jun 9 10:18:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:18:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-250) Investigate potential benchmarking of services Message-ID: <4384192.1249.1307629139751.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-250?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-250: -------------------------------- Fix Version/s: Future > Investigate potential benchmarking of services > ---------------------------------------------- > > Key: BIOCAT-250 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-250 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Priority: Minor > Fix For: Future > > > One suggestion, from Andrew Clegg: > " > Thought I'd put this idea in here for discussion after the lively > questions on Jiten's talk in Manchester just now... > Once functional testing (e.g. via soapUI scripting) is running, let > service owners specify how many instances of the functional test can > be run in parallel. > Then once a day, run that many copies of the test at once, with slight > random start delays, thereby simulating that number of simultaneous > users. > On completion, count how many of the sessions returned successfully, > and display this for each day. > Benefits: > Service owners can indicate how 'enterprisey' their services are by > how many sessions can be safely run. > Users know whether this is a realistic claim or not, by seeing how > many sessions actually completed (on each day and over history). > Owners of small services can indicate that by setting the parallelism > level low (or at 1), but still get judged for reliability *relative to > their own capacity*. > Users also avoid getting unrealistic expectations of small services. > Thoughts: > Let the service owner specify the time of day to run the test -- so > they can tell their users that the service will be slow at that time. > Comments? > Andrew. > " -- This 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 Jun 9 10:26:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:26:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-130) Add creditation mechanism for annotations Message-ID: <15419250.1272.1307629617520.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-130?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-130: -------------------------------- Fix Version/s: Future > Add creditation mechanism for annotations > ----------------------------------------- > > Key: BIOCAT-130 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-130 > Project: BioCatalogue > Issue Type: Bug > Components: Annotations (in App), Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Annotations may have a specific "source" but sometimes "credit" needs to be given to other people/entities for that annotation. So implement a creditation mechanism in the 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 Jun 9 10:26:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:26:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-116) Make complex type services parameter elements annotatable Message-ID: <19973039.1273.1307629619673.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-116?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16813#comment-16813 ] Jiten Bhagat commented on BIOCAT-116: ------------------------------------- This can only be done currently if the complex type is extracted out into objects in the app. > Make complex type services parameter elements annotatable > --------------------------------------------------------- > > Key: BIOCAT-116 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-116 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App) > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > > Make all element extracted from parameters of a complex type service annotatable by members. -- This 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 Jun 9 10:28:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:28:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-116) Make complex type services parameter elements annotatable Message-ID: <18934744.1274.1307629735369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-116?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-116: -------------------------------- Fix Version/s: Future > Make complex type services parameter elements annotatable > --------------------------------------------------------- > > Key: BIOCAT-116 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-116 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations (in App) > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Minor > Fix For: Future > > > Make all element extracted from parameters of a complex type service annotatable by members. -- This 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 Jun 9 10:28:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:28:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-84) Allow users to register links to other things as part of their profile Message-ID: <17602597.1275.1307629738045.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-84?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-84: ------------------------------- Fix Version/s: Future > Allow users to register links to other things as part of their profile > ---------------------------------------------------------------------- > > Key: BIOCAT-84 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-84 > Project: BioCatalogue > Issue Type: New Feature > Components: User Management > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Marco specifically wants to be able to link to his LinkedIn profile and such. > So in the meantime we can allow users to register the URL to your LinkedIn etc profiles and any other links, which will then get shown on their profile. -- This 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 Jun 9 10:29:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:29:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-105) Add more tweets Message-ID: <26085930.1276.1307629740309.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-105?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-105. ------------------------------- > Add more tweets > --------------- > > Key: BIOCAT-105 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-105 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > > Start tweeting more events, with more useful info shown, like: > - status change messages (DONE). > - other important messages. -- This 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 Jun 9 10:29:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:29:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-105) Add more tweets Message-ID: <7823109.1277.1307629742404.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-105?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-105. --------------------------------- Resolution: No longer relevant Twitter changed it's Auth, which broke our integration with it. > Add more tweets > --------------- > > Key: BIOCAT-105 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-105 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > > Start tweeting more events, with more useful info shown, like: > - status change messages (DONE). > - other important messages. -- This 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 Jun 9 10:29:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:29:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-113) Add "load from file" functionality in search by data Message-ID: <10232591.1278.1307629744715.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-113?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-113: -------------------------------- Fix Version/s: Future > Add "load from file" functionality in search by data > ---------------------------------------------------- > > Key: BIOCAT-113 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-113 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing > Reporter: Jerzy Orlowski > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Note to check if the file is binary and change encoding to unicode if needed. -- This 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 Jun 9 10:29:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:29:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-115) Make Biocatologue a scientific journal Message-ID: <17033981.1279.1307629746809.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-115?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-115: -------------------------------- Fix Version/s: Future > Make Biocatologue a scientific journal > -------------------------------------- > > Key: BIOCAT-115 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-115 > Project: BioCatalogue > Issue Type: Objective > Reporter: Jerzy Orlowski > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > With (if chosen by provider) > - peer-reviewing of the services > - pdf genation > - DOI > - affiliations, references citations 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 Jun 9 10:30:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:30:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-80) Add custom style sheet for annotation contents Message-ID: <828928.1280.1307629855355.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-80?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-80: ------------------------------- Fix Version/s: 1.2.0 Description: Currently the "value" of an annotation will be rendered in HTML using the default styles of the app. Need to have a custom stylesheet for the contents of annotations in the UI, otherwise things like headers and other styles will be picked up from the main CSS. (was: Currently the "value" of an annotation will be rendered in HTML using the default styles of the app. Need to have a custom stylesheet for the contents of annotations in the UI.) > Add custom style sheet for annotation contents > ---------------------------------------------- > > Key: BIOCAT-80 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-80 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Currently the "value" of an annotation will be rendered in HTML using the default styles of the app. Need to have a custom stylesheet for the contents of annotations in the UI, otherwise things like headers and other styles will be picked up from the main CSS. -- This 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 Jun 9 10:32:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-37) Add categories info to stats dashboard Message-ID: <1234033.1281.1307629975358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-37?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-37: ------------------------------- Fix Version/s: 1.2.0 > Add categories info to stats dashboard > -------------------------------------- > > Key: BIOCAT-37 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-37 > Project: BioCatalogue > Issue Type: New Feature > Components: Stats Dashboard > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Like the number of services that each category has, 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 Jun 9 10:34:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-34) Automatically check all the links in the data Message-ID: <19120900.1282.1307630095364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-34?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-34: ------------------------------- Fix Version/s: Future Description: Use existing tools to check the availability of all external links within the biocat. This can then be fed into the Curation Dashboard and brought to the attention of curators. It's possible that this is catered for by Eric's link checker script that generates an HTML report. was:Use existing tools to check the availability of all external links within the biocat. Then display an icon near those which don't exist anymore. > Automatically check all the links in the data > --------------------------------------------- > > Key: BIOCAT-34 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-34 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Use existing tools to check the availability of all external links within the biocat. This can then be fed into the Curation Dashboard and brought to the attention of curators. > It's possible that this is catered for by Eric's link checker script that generates an HTML report. -- This 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 Jun 9 10:34:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:34:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-15) Update prototype libraries (especially for IE8 support) Message-ID: <17403967.1283.1307630097605.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-15?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-15: ------------------------------- Fix Version/s: Future > Update prototype libraries (especially for IE8 support) > ------------------------------------------------------- > > Key: BIOCAT-15 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-15 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > At the moment the Prototype library we use is quite old and newer versions have better IE8 compatibility. -- This 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 Jun 9 10:34:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:34:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-16) Collapse tag cloud on the Service Provider page Message-ID: <17027755.1284.1307630099814.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-16?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-16: ------------------------------- Fix Version/s: Future > Collapse tag cloud on the Service Provider page > ----------------------------------------------- > > Key: BIOCAT-16 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-16 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > E.g.: on http://www.biocatalogue.org/service_providers/1 > Probably display the first 20 like the tag cloud on the service page, and the "similar services" box on a service's page. -- This 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 Jun 9 10:35:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:35:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-18) Add more Soaplab info Message-ID: <12238691.1285.1307630102155.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-18?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-18: ------------------------------- Fix Version/s: Future > Add more Soaplab info > --------------------- > > Key: BIOCAT-18 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-18 > Project: BioCatalogue > Issue Type: New Feature > Components: Stats Dashboard > Reporter: Carole Goble > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Specifically, how many actual services that are from Soaplab servers. So people can ask a simple question like: "how many services are soaplab based?" > This is related to the service family 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 Thu Jun 9 10:35:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:35:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-25) Monitor submitter contact details Message-ID: <6263404.1286.1307630104754.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-25?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-25: ------------------------------- Fix Version/s: Future > Monitor submitter contact details > --------------------------------- > > Key: BIOCAT-25 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-25 > Project: BioCatalogue > Issue Type: Task > Reporter: Franck Tanoh > Assignee: Franck Tanoh > Priority: Minor > Fix For: Future > > > Need to monitor submitter contact details. With time, some of them > will be out of date. For example when a service submitter leaves his > project. -- This 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 Jun 9 10:35:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:35:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-33) Better error handling in stats dashboard Message-ID: <17706.1287.1307630106900.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-33?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-33: ------------------------------- Fix Version/s: 1.2.0 > Better error handling in stats dashboard > ---------------------------------------- > > Key: BIOCAT-33 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-33 > Project: BioCatalogue > Issue Type: Improvement > Components: Stats Dashboard > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Since the stats are cached and only regenerated every now and then, the view that renders needs to take into account non-existent services etc 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 Jun 9 10:35:08 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:35:08 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-14) Add contributors to system stats and curation workbenches Message-ID: <31003454.1288.1307630108979.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-14?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-14: ------------------------------- Fix Version/s: 1.2.0 > Add contributors to system stats and curation workbenches > --------------------------------------------------------- > > Key: BIOCAT-14 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-14 > Project: BioCatalogue > Issue Type: New Feature > Components: Curation Dashboard, Stats Dashboard > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.2.0 > > > Same as the /latest#contributors page -- This 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 Jun 9 10:36:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:36:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-8) Add limit= to annotation finder methods Message-ID: <13243527.1289.1307630215369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-8?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-8: ------------------------------ Fix Version/s: Future > Add limit= to annotation finder methods > --------------------------------------- > > Key: BIOCAT-8 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-8 > Project: BioCatalogue > Issue Type: New Feature > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > Currently methods like annotations_with_attribute will return all objects. Sometimes you only want the last one or a subset. So add the option to have a limit. -- This 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 Jun 9 10:36:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:36:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-245) Potentially integrate the GetSatisfaction feedback service Message-ID: <23645304.1290.1307630217655.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-245?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-245: -------------------------------- Fix Version/s: Future > Potentially integrate the GetSatisfaction feedback service > ---------------------------------------------------------- > > Key: BIOCAT-245 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-245 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > http://getsatisfaction.com/ -- This 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 Jun 9 10:36:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:36:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-246) Use FeedBurner for the main ATOM feed Message-ID: <19228941.1291.1307630219879.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-246?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-246. ------------------------------- > Use FeedBurner for the main ATOM feed > ------------------------------------- > > Key: BIOCAT-246 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-246 > Project: BioCatalogue > Issue Type: Task > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > > ... in order to track how many people are subscribed etc 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 Jun 9 10:37:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-257) Move lib/country_codes.rb into a plugin Message-ID: <27479323.1293.1307630224831.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-257?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-257: -------------------------------- Fix Version/s: 1.0.0 > Move lib/country_codes.rb into a plugin > --------------------------------------- > > Key: BIOCAT-257 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-257 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: 1.0.0 > > > Make a completely reusable plugin out of the country_codes AND flag icons. > Use: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 -- This 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 Jun 9 10:37:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-259) Implement custom feed builder Message-ID: <23246746.1294.1307630226921.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-259?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-259: -------------------------------- Fix Version/s: Future > Implement custom feed builder > ----------------------------- > > Key: BIOCAT-259 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-259 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > Some people may want to subscribe to feeds for specific filters. > Build a very easy to use UI that allows people to specify the exact filters they require and then give them the URL to it. This can potentially all be done in JavaScript at client side. -- This 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 Jun 9 10:37:09 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:09 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-272) For Annotations plugin - update versioning module Message-ID: <4898383.1295.1307630229043.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-272?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-272. ------------------------------- > For Annotations plugin - update versioning module > ------------------------------------------------- > > Key: BIOCAT-272 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-272 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > > In main codebase we have applied this: http://github.com/jmckible/version_fu/commit/6621b379f96591c3299d69ae60d720b3214a9f16 > Look to using a newer version_fu in the Annotations plugin master GitHub master repo. -- This 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 Jun 9 10:37:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-272) For Annotations plugin - update versioning module Message-ID: <6204795.1296.1307630231127.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-272?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-272. --------------------------------- Resolution: No longer relevant > For Annotations plugin - update versioning module > ------------------------------------------------- > > Key: BIOCAT-272 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-272 > Project: BioCatalogue > Issue Type: Improvement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > > In main codebase we have applied this: http://github.com/jmckible/version_fu/commit/6621b379f96591c3299d69ae60d720b3214a9f16 > Look to using a newer version_fu in the Annotations plugin master GitHub master repo. -- This 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 Jun 9 10:37:13 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:13 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-2) ATOM feed for latest activity feed Message-ID: <23484887.1297.1307630233255.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-2?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-2. ----------------------------- > ATOM feed for latest activity feed > ---------------------------------- > > Key: BIOCAT-2 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-2 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Homepage > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > > Implement an ATOM feed for the latest activity -- This 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 Jun 9 10:37:15 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-2) ATOM feed for latest activity feed Message-ID: <29556895.1298.1307630235312.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-2?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-2. ------------------------------- Resolution: Implemented > ATOM feed for latest activity feed > ---------------------------------- > > Key: BIOCAT-2 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-2 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Homepage > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > > Implement an ATOM feed for the latest activity -- This 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 Jun 9 10:37:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-246) Use FeedBurner for the main ATOM feed Message-ID: <30237478.1292.1307630222309.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-246?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-246. --------------------------------- Resolution: No longer relevant > Use FeedBurner for the main ATOM feed > ------------------------------------- > > Key: BIOCAT-246 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-246 > Project: BioCatalogue > Issue Type: Task > Components: Activity Logging / Feeds / Notifications > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > > ... in order to track how many people are subscribed etc 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 Jun 9 10:37:18 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:37:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-157) Distinction between links within biocat and ouside biocat Message-ID: <21669570.1299.1307630238324.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-157?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-157: -------------------------------- Fix Version/s: Future > Distinction between links within biocat and ouside biocat > ---------------------------------------------------------- > > Key: BIOCAT-157 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-157 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > It's not clear from the beta site which links take users outside the catalogue. e.g the link of the endpoint takes you outside biocat but the provider name which looks like a url opens another page within biocat. A small icon to distinguish between those 2 things will be useful. -- This 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 Jun 9 10:25:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:25:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-140) Display common tags at top of search results Message-ID: <2439709.1267.1307629502995.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-140?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-140: -------------------------------- Fix Version/s: Future > Display common tags at top of search results > -------------------------------------------- > > Key: BIOCAT-140 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-140 > Project: BioCatalogue > Issue Type: New Feature > Components: Search / Filtering / Browsing, Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: Future > > > From Sam Schmidt - "In the search results, display the tags common to all results at the top ..." -- This 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 Jun 9 10:38:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:38:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-53) Add license header to annotations plugin Message-ID: <8551901.1300.1307630335349.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-53?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-53: ------------------------------- Fix Version/s: Future > Add license header to annotations plugin > ---------------------------------------- > > Key: BIOCAT-53 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-53 > Project: BioCatalogue > Issue Type: Refinement > Components: Annotations Plugin > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > Add the same license file + license headers to all 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 Jun 9 10:46:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:46:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-607) Refactor out annotation values as first class polymorphic objects Message-ID: <22920035.1301.1307630815347.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Fix For: 1.2.0 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 Jun 9 10:50:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-608) Improve the way display names for services are set Message-ID: <4320008.1302.1307631055357.JavaMail.jira@rosalind.cs.man.ac.uk> 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 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 Thu Jun 9 10:50:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:50:57 +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: <32699068.1303.1307631057584.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: -------------------------------- Fix Version/s: 1.1.0 > 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 > 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 Thu Jun 9 10:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 15:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-257) Move lib/country_codes.rb into a plugin Message-ID: <23254035.1304.1307631295359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-257?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-257: -------------------------------- Fix Version/s: Future (was: 1.0.0) Affects Version/s: 1.0.0 > Move lib/country_codes.rb into a plugin > --------------------------------------- > > Key: BIOCAT-257 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-257 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Trivial > Fix For: Future > > > Make a completely reusable plugin out of the country_codes AND flag icons. > Use: http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2 -- This 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 Jun 9 11:03:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:03:58 +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: <22427505.1306.1307631838258.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: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > 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: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.2 > > > 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 Thu Jun 9 11:04:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:04:00 +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: <33019447.1307.1307631840836.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.1) Priority: Major (was: Critical) > 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: 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 Jun 9 11:04:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:04:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-577) Rodrigo should be given access to google web master for BioCatalogue In-Reply-To: <29606112.704.1298039889389.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30487527.1308.1307631842970.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-577?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-577. --------------------------------- Resolution: Fixed Done > Rodrigo should be given access to google web master for BioCatalogue > -------------------------------------------------------------------- > > Key: BIOCAT-577 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-577 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 1 day > Remaining Estimate: 1 day > -- This 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 Jun 9 11:04:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:04:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-577) Rodrigo should be given access to google web master for BioCatalogue In-Reply-To: <29606112.704.1298039889389.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6165522.1309.1307631845249.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-577?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-577 stopped by Jiten Bhagat. > Rodrigo should be given access to google web master for BioCatalogue > -------------------------------------------------------------------- > > Key: BIOCAT-577 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-577 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 1 day > Remaining Estimate: 1 day > -- This 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 Jun 9 11:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-577) Rodrigo should be given access to google web master for BioCatalogue In-Reply-To: <29606112.704.1298039889389.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31782451.1305.1307631835405.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-577?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-577 started by Jiten Bhagat. > Rodrigo should be given access to google web master for BioCatalogue > -------------------------------------------------------------------- > > Key: BIOCAT-577 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-577 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 1 day > Remaining Estimate: 1 day > -- This 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 Jun 9 11:05:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-476) BioCat API needs a single call to get operations (methods) of a REST service In-Reply-To: <20858522.9801.1285581375410.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21763152.1310.1307631955369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-476: -------------------------------- Summary: BioCat API needs a single call to get operations (methods) of a REST service (was: BioCat API needs a single cal to get operations (methods) of a REST service) Assignee: Mannie Tagarira (was: Jiten Bhagat) Component/s: REST API > BioCat API needs a single call to get operations (methods) of a REST service > ---------------------------------------------------------------------------- > > Key: BIOCAT-476 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Alex Nenadic > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > BioCat API needs a single cal to get operations (methods) of a REST service. At the moment - 2 REST calls are needed to get this info and Sergejs did not want to use this in the BioCat plugin for Taverna as it was to heavy. -- This 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 Jun 9 11:30:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Jun 2011 16:30:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-476) BioCat API needs a single call to get operations (methods) of a REST service In-Reply-To: <20858522.9801.1285581375410.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4510011.1311.1307633455380.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-476. ------------------------------------ Resolution: Fixed The following endpoint was implemented /rest_methods (XML & JSON) > BioCat API needs a single call to get operations (methods) of a REST service > ---------------------------------------------------------------------------- > > Key: BIOCAT-476 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Alex Nenadic > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > BioCat API needs a single cal to get operations (methods) of a REST service. At the moment - 2 REST calls are needed to get this info and Sergejs did not want to use this in the BioCat plugin for Taverna as it was to heavy. -- This 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 Jun 9 11:32:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Jun 2011 16:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-353) Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs In-Reply-To: <31076462.1623.1274872997018.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15032704.1312.1307633575375.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-353. ------------------------------------ Resolution: Fixed Implemented in both JSON & XML > Remove/Implement endpoints: /soap_operation/{id}/inputs AND /soap_operation/{id}/outputs > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-353 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-353 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, SOAP Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > When making calls via the REST API those 2 endpoints are shown in the related section; they do not work. > Example: > Calling: http://www.biocatalogue.org/soap_operations/15369.xml returns some XML but the key lookout points are: > > ... > > > ... > > > > ... > > -- This 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 Jun 9 11:37:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Jun 2011 16:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-156) Remove beta from the biocat logo Message-ID: <18705563.1313.1307633875429.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-156: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Remove beta from the biocat logo > -------------------------------- > > Key: BIOCAT-156 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > Remove Beta from BioCatalogue logo on the main site. -- This 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 Jun 9 11:37:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Jun 2011 16:37:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-156) Remove beta from the biocat logo Message-ID: <7084517.1314.1307633877545.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-156 started by Mannie Tagarira. > Remove beta from the biocat logo > -------------------------------- > > Key: BIOCAT-156 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > Remove Beta from BioCatalogue logo on the main site. -- This 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 Jun 9 11:47:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Jun 2011 16:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-476) BioCat API needs a single call to get operations (methods) of a REST service In-Reply-To: <20858522.9801.1285581375410.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8075832.1315.1307634475377.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16816#comment-16816 ] Mannie Tagarira edited comment on BIOCAT-476 at 09/06/11 16:47: ---------------------------------------------------------------- The following endpoint was implemented /rest_services/{id}/methods (XML & JSON) was (Author: mannie): The following endpoint was implemented /rest_methods (XML & JSON) > BioCat API needs a single call to get operations (methods) of a REST service > ---------------------------------------------------------------------------- > > Key: BIOCAT-476 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-476 > Project: BioCatalogue > Issue Type: Improvement > Components: REST API > Reporter: Alex Nenadic > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > BioCat API needs a single cal to get operations (methods) of a REST service. At the moment - 2 REST calls are needed to get this info and Sergejs did not want to use this in the BioCat plugin for Taverna as it was to heavy. -- This 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 Jun 9 11:49:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 16:49:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-333) Paging does not work when a providers services are listed from service show page In-Reply-To: <7774406.91.1273726817082.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22541854.1316.1307634595371.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-333. --------------------------------- Resolution: Fixed This seems to be working fine. > Paging does not work when a providers services are listed from service show page > -------------------------------------------------------------------------------- > > Key: BIOCAT-333 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-333 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > When a provider link is clicked from a service show page, the provider profile is shown with all the providers services. If provider has several pages of services, then clicking next or page number take you back to provider profile. -- 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 Jun 9 12:01:47 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Jun 2011 12:01:47 -0400 (EDT) Subject: [BioCatalogue-developers] [2390] trunk: Removed the beta sign from the biocatalogue logo Message-ID: <20110609160147.961C03C8088@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jun 9 12:02:29 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Jun 2011 12:02:29 -0400 (EDT) Subject: [BioCatalogue-developers] [2391] trunk: [BIOCAT-319] Added /soap_services/wsdl_locations. xml to schema. Message-ID: <20110609160229.3E4423C8088@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 9 12:03:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 9 Jun 2011 17:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-156) Remove beta from the biocat logo Message-ID: <9151169.1317.1307635435351.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-156. ------------------------------------ Resolution: Fixed > Remove beta from the biocat logo > -------------------------------- > > Key: BIOCAT-156 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-156 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > Remove Beta from BioCatalogue logo on the main site. -- This 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 Jun 9 12:05:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 17:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-319) Add /soap_services/wsdl_locations to XML Schema for REST API In-Reply-To: <32175098.1.1273582037157.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19402861.1318.1307635555586.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-319. --------------------------------- Resolution: Fixed Done in revision 2391 > Add /soap_services/wsdl_locations to XML Schema for REST API > ------------------------------------------------------------ > > Key: BIOCAT-319 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jun 9 12:07:00 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Jun 2011 12:07:00 -0400 (EDT) Subject: [BioCatalogue-developers] [2392] trunk/script/biocatalogue/api/tests/xml_schema_validations.rb: [ BIOCAT-319] Added a test for the /soap_services/wsdl_locations XML endpoint . Message-ID: <20110609160700.A7D9618583A5@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 9 12:07:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 17:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-319) Add /soap_services/wsdl_locations to XML Schema for REST API In-Reply-To: <32175098.1.1273582037157.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16153411.1319.1307635675369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reopened BIOCAT-319: --------------------------------- Still need to run the full API tests first! > Add /soap_services/wsdl_locations to XML Schema for REST API > ------------------------------------------------------------ > > Key: BIOCAT-319 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 12:09:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 17:09:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-443) Update the REST API's XML schema to account for the REST services support endpoints In-Reply-To: <8259919.7505.1279535115302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21273764.1320.1307635795401.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16821#comment-16821 ] Jiten Bhagat commented on BIOCAT-443: ------------------------------------- This HAS been done. Now just need to run the full API test suite to make sure everything is okay. > Update the REST API's XML schema to account for the REST services support endpoints > ------------------------------------------------------------------------------------ > > Key: BIOCAT-443 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443 > Project: BioCatalogue > Issue Type: Task > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 12:16:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 17:16:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-320) Add /soap_services/wsdl_locations to REST API documentation In-Reply-To: <5755038.2.1273582277250.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5326355.1321.1307636215364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-320?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-320. --------------------------------- Resolution: Implemented Done > Add /soap_services/wsdl_locations to REST API documentation > ----------------------------------------------------------- > > Key: BIOCAT-320 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-320 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 12:18:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 17:18:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-575) Add system and API versions to JSON outputs In-Reply-To: <2265907.629.1297861689388.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23867675.1322.1307636335374.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-575?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-575: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Add system and API versions to JSON outputs > ------------------------------------------- > > Key: BIOCAT-575 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-575 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 9 12:21:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 9 Jun 2011 17:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-580) Error page returned when attempting to activate an account. The account is still activated anyway! In-Reply-To: <6669390.67.1298913567776.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <772686.1323.1307636515357.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-580?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-580. --------------------------------- Resolution: Cannot Reproduce This is likely to have been caused when it couldn't access Solr. > Error page returned when attempting to activate an account. The account is still activated anyway! > -------------------------------------------------------------------------------------------------- > > Key: BIOCAT-580 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-580 > Project: BioCatalogue > Issue Type: Task > Components: User Management > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Error page returned when attempting to activate a user account. The account is still activated anyway! -- 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 Jun 9 12:24:34 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Jun 2011 12:24:34 -0400 (EDT) Subject: [BioCatalogue-developers] [2393] trunk: Add .rvmrc file to repo Message-ID: <20110609162434.D7A423C8088@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 05:14:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 10:14:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-609) The email sent to BioCat admins about service providers with no services and/or hostnames does not always generate valid URLs Message-ID: <7440241.1324.1307697295474.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Affects Versions: 1.0.2 Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Minor 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 Fri Jun 10 05:48:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 10:48:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-610) Archived resources appear as having no annotations via the API even when they do have annotations Message-ID: <32100862.1325.1307699335367.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.2 /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 Fri Jun 10 05:50:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 10:50:56 +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: <17418513.1326.1307699456697.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 ] Mannie Tagarira updated BIOCAT-609: ----------------------------------- Fix Version/s: 1.0.2 Affects Version/s: (was: 1.0.2) > 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: 1.0.2 > > > 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 noreply at rubyforge.org Fri Jun 10 05:52:51 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Jun 2011 05:52:51 -0400 (EDT) Subject: [BioCatalogue-developers] [2394] trunk/lib/bio_catalogue/api/json.rb: Fix for JIRA task BIOCAT-575: Add system and API versions to JSON outputs Message-ID: <20110610095251.E2E89185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 05:56:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 10:56:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-575) Add system and API versions to JSON outputs In-Reply-To: <2265907.629.1297861689388.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13142489.1327.1307699815397.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-575?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-575. ------------------------------------ Resolution: Fixed { biocatalogue: { title: "The BioCatalogue", api_version: "1.2.0b", version: "1.0.0", resource_type: "BioCatalogue", collections: [], documentation: { ... } } } > Add system and API versions to JSON outputs > ------------------------------------------- > > Key: BIOCAT-575 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-575 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 10 05:56:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 10:56:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-611) Create a staging server VM image that matches the EBI's set up Message-ID: <26593137.1328.1307699817683.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.0.1 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 Fri Jun 10 06:02:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:02:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-612) Potentially add the system and API version numbers at the root of ALL API responses (XML and JSON) Message-ID: <14740.1329.1307700175359.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 -- 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 Fri Jun 10 06:02:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:02:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-613) Add the system and API version numbers to the footer of the website Message-ID: <24723716.1330.1307700177506.JavaMail.jira@rosalind.cs.man.ac.uk> Add the system and API version numbers to the footer of the website ------------------------------------------------------------------- Key: BIOCAT-613 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613 Project: BioCatalogue Issue Type: Task Components: Web Interface Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 10 06:04:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:04:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-614) Update the way the system version is picked up and placed in the API/footer etc. Message-ID: <31489667.1331.1307700295359.JavaMail.jira@rosalind.cs.man.ac.uk> Update the way the system version is picked up and placed in the API/footer etc. -------------------------------------------------------------------------------- Key: BIOCAT-614 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-614 Project: BioCatalogue Issue Type: Task Components: REST API, Web Interface Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.0.1 Currently, there is duplication in the places where the system version is stored and outputted. Consolidate this to use the new version_info system that is in place. -- This 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 Jun 10 06:04:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:04:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-615) Increment the version numbers (system and API) for release v1.0.1 accordingly Message-ID: <21078259.1332.1307700298661.JavaMail.jira@rosalind.cs.man.ac.uk> Increment the version numbers (system and API) for release v1.0.1 accordingly ----------------------------------------------------------------------------- Key: BIOCAT-615 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-615 Project: BioCatalogue Issue Type: Task Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker Fix For: 1.0.1 Note: system and API version numbers don't necessarily increment/change in tandem. The API version number ONLY changes if modifications to the API have been made. -- This 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 Jun 10 06:06:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:06:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-611) Create a staging server VM image that matches the EBI's set up In-Reply-To: <26593137.1328.1307699817683.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20082738.1333.1307700415350.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 updated BIOCAT-611: -------------------------------- Component/s: Server Management > 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 > > > 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 Fri Jun 10 06:08:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:08:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-614) Update the way the system version is picked up and placed in the API/footer etc. In-Reply-To: <31489667.1331.1307700295359.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3155332.1334.1307700535353.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-614?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-614. --------------------------------- Resolution: Not A Bug It already picks up this info from one centralised place - the biocat_main.rb file (although the system version is actually stored in the version_info.yml file in the root of the app). > Update the way the system version is picked up and placed in the API/footer etc. > -------------------------------------------------------------------------------- > > Key: BIOCAT-614 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-614 > Project: BioCatalogue > Issue Type: Task > Components: REST API, Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Currently, there is duplication in the places where the system version is stored and outputted. Consolidate this to use the new version_info system that is in place. -- This 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 Jun 10 06:14:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:14:55 +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: <22218888.1335.1307700895383.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: -------------------------------- Original Estimate: (was: 4 hours) Remaining Estimate: (was: 4 hours) Fix Version/s: 1.0.2 (was: 1.0.1) > Create a new VM for the BioCatalogue system > ------------------------------------------- > > Key: BIOCAT-499 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-499 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.2 > > > 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 Fri Jun 10 06:14:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:14:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-460) Document latest updates to the API In-Reply-To: <6899755.8166.1282752315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10544652.1336.1307700897883.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-460. --------------------------------- Resolution: Duplicate > Document latest updates to the API > ---------------------------------- > > Key: BIOCAT-460 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-460 > Project: BioCatalogue > Issue Type: Task > Components: REST API, Wiki > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 10 06:15:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:15:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-500) Document how to use and update the VM In-Reply-To: <16227861.9965.1286463195301.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25361282.1337.1307700900145.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-500: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > Document how to use and update the VM > ------------------------------------- > > Key: BIOCAT-500 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Document how to set up, use and update the BioCatalogue VM. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 10 06:25:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 11:25:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-329) Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI In-Reply-To: <18542635.64.1273667839433.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8694580.1338.1307701555384.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-329. ------------------------------------ Resolution: Fixed This has indeed been done: /soap_operations/428 > Need to deal with archived SoapOperation, SoapInput and SoapOutput items in the UI > ---------------------------------------------------------------------------------- > > Key: BIOCAT-329 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-329 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 5 hours > Time Spent: 4 hours > Remaining Estimate: 1 hour > -- 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 Jun 10 06:30:08 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Jun 2011 06:30:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2395] trunk/version_info.yml: [BIOCAT-615] Incremented the system version in preparation for the 1.0.1 release. Message-ID: <20110610103008.C3BA71858377@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 06:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-615) Increment the version numbers (system and API) for release v1.0.1 accordingly In-Reply-To: <21078259.1332.1307700298661.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10386152.1339.1307701915389.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-615?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16827#comment-16827 ] Jiten Bhagat commented on BIOCAT-615: ------------------------------------- Incremented the system version to 1.0.1. For the API version - it looks it has already been updated (to 1.2.0b) from the last release and doesn't need updating, since 1.2.0b hasn't been documented and announced yet. > Increment the version numbers (system and API) for release v1.0.1 accordingly > ----------------------------------------------------------------------------- > > Key: BIOCAT-615 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-615 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Note: system and API version numbers don't necessarily increment/change in tandem. The API version number ONLY changes if modifications to the API have been made. -- This 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 Jun 10 06:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 11:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-616) Need to deal with the deprecation/retiring of the Creative Commons Public Domain License Message-ID: <18000113.1340.1307703235352.JavaMail.jira@rosalind.cs.man.ac.uk> Need to deal with the deprecation/retiring of the Creative Commons Public Domain License ---------------------------------------------------------------------------------------- Key: BIOCAT-616 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-616 Project: BioCatalogue Issue Type: Task Components: Data Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.1.0 According to the [Terms of Use|http://www.biocatalogue.org/termsofuse], the content of the BioCatalogue is licensed under the [Creative Commons Public Domain License|http://creativecommons.org/licenses/publicdomain/]. However, this has been [_retired_ late in 2010|http://creativecommons.org/retiredlicenses]. Need to look into alternative licensing of content and prepare a transition process, which includes notifying everyone. -- This 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 Jun 10 07:07:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 12:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-569) Make the code and content licenses more prominent on the website + wiki In-Reply-To: <29578975.478.1297178529369.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9157714.1341.1307704075369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-569?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16828#comment-16828 ] Jiten Bhagat commented on BIOCAT-569: ------------------------------------- Updated on [wiki homepage|http://www.biocatalogue.org/wiki/doku.php?id=public] > Make the code and content licenses more prominent on the website + wiki > ----------------------------------------------------------------------- > > Key: BIOCAT-569 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-569 > Project: BioCatalogue > Issue Type: Task > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > We need to make it very clear, in as many places as possible, what the code and content licenses are for the BioCatalogue -- This 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 Jun 10 07:09:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 12:09:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-616) Need to deal with the deprecation/retiring of the Creative Commons Public Domain License In-Reply-To: <18000113.1340.1307703235352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22759555.1342.1307704195360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-616?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-616: -------------------------------- Description: According to the [Terms of Use|http://www.biocatalogue.org/termsofuse], the content of the BioCatalogue is licensed under the [Creative Commons Public Domain License|http://creativecommons.org/licenses/publicdomain/]. However, this has been [_retired_ late in 2010|http://creativecommons.org/retiredlicenses]. Need to look into alternative licensing of content and prepare a transition process, which includes notifying everyone. Possible alternative licenses (that are compatible): * [CC0 1.0 Universal (Public Domain License)|http://creativecommons.org/publicdomain/zero/1.0/] was: According to the [Terms of Use|http://www.biocatalogue.org/termsofuse], the content of the BioCatalogue is licensed under the [Creative Commons Public Domain License|http://creativecommons.org/licenses/publicdomain/]. However, this has been [_retired_ late in 2010|http://creativecommons.org/retiredlicenses]. Need to look into alternative licensing of content and prepare a transition process, which includes notifying everyone. > Need to deal with the deprecation/retiring of the Creative Commons Public Domain License > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-616 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-616 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > According to the [Terms of Use|http://www.biocatalogue.org/termsofuse], the content of the BioCatalogue is licensed under the [Creative Commons Public Domain License|http://creativecommons.org/licenses/publicdomain/]. However, this has been [_retired_ late in 2010|http://creativecommons.org/retiredlicenses]. > Need to look into alternative licensing of content and prepare a transition process, which includes notifying everyone. > Possible alternative licenses (that are compatible): > * [CC0 1.0 Universal (Public Domain License)|http://creativecommons.org/publicdomain/zero/1.0/] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Jun 10 07:32:20 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Jun 2011 07:32:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2396] trunk: Fix for JIRA tasks Message-ID: <20110610113221.313711858377@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 07:33:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 12:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-613) Add the system and API version numbers to the footer of the website In-Reply-To: <24723716.1330.1307700177506.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17087521.1343.1307705635365.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16829#comment-16829 ] Mannie Tagarira commented on BIOCAT-613: ---------------------------------------- Implemented but needs to be tested on Windows browsers. > Add the system and API version numbers to the footer of the website > ------------------------------------------------------------------- > > Key: BIOCAT-613 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 10 07:33:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 12:33:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-569) Make the code and content licenses more prominent on the website + wiki In-Reply-To: <29578975.478.1297178529369.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29177222.1344.1307705638270.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-569?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16830#comment-16830 ] Mannie Tagarira commented on BIOCAT-569: ---------------------------------------- Added a line in the footer of the website with links to this information. > Make the code and content licenses more prominent on the website + wiki > ----------------------------------------------------------------------- > > Key: BIOCAT-569 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-569 > Project: BioCatalogue > Issue Type: Task > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > We need to make it very clear, in as many places as possible, what the code and content licenses are for the BioCatalogue -- This 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 Jun 10 07:37:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 12:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-569) Make the code and content licenses more prominent on the website + wiki In-Reply-To: <29578975.478.1297178529369.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5442739.1345.1307705875358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-569?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-569. ------------------------------------ Resolution: Fixed > Make the code and content licenses more prominent on the website + wiki > ----------------------------------------------------------------------- > > Key: BIOCAT-569 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-569 > Project: BioCatalogue > Issue Type: Task > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > We need to make it very clear, in as many places as possible, what the code and content licenses are for the BioCatalogue -- This 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 Jun 10 07:53:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 12:53:55 +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: <21868232.1346.1307706835367.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 ] Mannie Tagarira updated BIOCAT-576: ----------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > 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 > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > 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 Fri Jun 10 07:55:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 12:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-617) Investigate the breakage related to the test harness Message-ID: <19384335.1347.1307706955354.JavaMail.jira@rosalind.cs.man.ac.uk> Investigate the breakage related to the test harness ---------------------------------------------------- Key: BIOCAT-617 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-617 Project: BioCatalogue Issue Type: Task Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.1 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 Fri Jun 10 07:59:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 12:59:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-618) Inspect the current state of OAuth and the possibility of using it to provide API keys to agens Message-ID: <18646049.1348.1307707195355.JavaMail.jira@rosalind.cs.man.ac.uk> Inspect the current state of OAuth and the possibility of using it to provide API keys to agens ----------------------------------------------------------------------------------------------- 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: 1.0.2 -- This 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 Jun 10 08:04:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 13:04:55 +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: <23099384.1349.1307707495360.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: -------------------------------- Summary: 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 (was: Inspect the current state of OAuth and the possibility of using it to provide API keys to agens) > 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: 1.0.2 > > -- 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 Jun 10 08:45:33 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Jun 2011 08:45:33 -0400 (EDT) Subject: [BioCatalogue-developers] [2397] trunk/app/views/services/_listing.html.erb: Fix for JIRA task Message-ID: <20110610124533.231A31858376@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 08:46:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 13:46:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-587) Archived services listings in "simple" view inconsistent with non-archived services listings In-Reply-To: <28179898.159.1302688135356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13315283.1350.1307710015381.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-587?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-587. ------------------------------------ Resolution: Fixed > Archived services listings in "simple" view inconsistent with non-archived services listings > -------------------------------------------------------------------------------------------- > > Key: BIOCAT-587 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-587 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: Bug - 20110413-1046.png > > > Archived service listing shows viewed and favourited counts (see attached screenshot) -- This 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 Jun 10 08:48:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 13:48:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-587) Archived services listings in "simple" view inconsistent with non-archived services listings In-Reply-To: <28179898.159.1302688135356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20919243.1351.1307710135358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-587?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-587: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Archived services listings in "simple" view inconsistent with non-archived services listings > -------------------------------------------------------------------------------------------- > > Key: BIOCAT-587 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-587 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > Attachments: Bug - 20110413-1046.png > > > Archived service listing shows viewed and favourited counts (see attached screenshot) -- 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 Jun 10 09:21:24 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Jun 2011 09:21:24 -0400 (EDT) Subject: [BioCatalogue-developers] [2398] trunk: Fix for JIRA task Message-ID: <20110610132124.C48101858377@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 09:21:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26805677.1352.1307712115353.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-586. ------------------------------------ Resolution: Fixed > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 10 09:37:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25064139.1353.1307713075358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-586: ----------------------------------- Attachment: screenshot-1.jpg > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: screenshot-1.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 10 09:39:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:39:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4027798.1354.1307713195364.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-586: ----------------------------------- Attachment: (was: screenshot-1.jpg) > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: TfscanService.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 10 09:39:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:39:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28420008.1355.1307713197750.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-586: ----------------------------------- Attachment: TfscanService.jpg > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: TfscanService.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 10 09:41:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-587) Archived services listings in "simple" view inconsistent with non-archived services listings In-Reply-To: <28179898.159.1302688135356.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21208882.1356.1307713315349.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-587?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-587: ----------------------------------- Attachment: TfscanService.jpg > Archived services listings in "simple" view inconsistent with non-archived services listings > -------------------------------------------------------------------------------------------- > > Key: BIOCAT-587 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-587 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > Attachments: Bug - 20110413-1046.png, TfscanService.jpg > > > Archived service listing shows viewed and favourited counts (see attached screenshot) -- This 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 Jun 10 09:50:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1520084.1357.1307713855387.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reopened BIOCAT-586: ------------------------------------ > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: TfscanService.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 10 09:52:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 14:52:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14021823.1358.1307713975360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-586: ----------------------------------- Attachment: bug .jpg Notice the 2 different shades of grey... The inner (darker) shade is currently hidden (and ignore) via the "grid_archived" CSS class > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: bug .jpg, TfscanService.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 10 11:05:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 16:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-619) Get Solr upgraded to 1.4.1 on the EBI servers Message-ID: <20785327.1359.1307718355434.JavaMail.jira@rosalind.cs.man.ac.uk> Get Solr upgraded to 1.4.1 on the EBI servers --------------------------------------------- Key: BIOCAT-619 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-619 Project: BioCatalogue Issue Type: Task Components: Search / Filtering / Browsing, Server Management Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.1.0 The servers at the EBI are currently running Solr 1.3 which isn't available for download any more and has been superseded by Solr 1.4.1. Look to upgrading Solr to 1.4.1. Ensure that this is all checked locally first (especially on the staging server VM image) and remember to do a full reindex and (possibly) upgrade the schema file. All steps will need to be recorded to ensure that full instructions are sent to the EBI. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 10 11:08:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 10 Jun 2011 16:08:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-590) Upgrade Solr to latest version In-Reply-To: <21006971.778.1305812875402.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21502949.1360.1307718535402.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-590?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-590. --------------------------------- Resolution: Duplicate > Upgrade Solr to latest version > ------------------------------ > > Key: BIOCAT-590 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-590 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Solr seems to misbehave regularly, so look to upgrading it to the latest version. -- 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 Jun 10 11:57:43 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 10 Jun 2011 11:57:43 -0400 (EDT) Subject: [BioCatalogue-developers] [2399] trunk/app/models/soap_service.rb: Fix for JIRA task Message-ID: <20110610155743.CAADB1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 10 11:58:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 10 Jun 2011 16:58:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-364) The service update checker should also update ServiceDeployment locations In-Reply-To: <5338610.1723.1275135377283.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2725313.1361.1307721535404.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16832#comment-16832 ] Mannie Tagarira commented on BIOCAT-364: ---------------------------------------- This has now been updated to account for endpoint updates as well as updates to the city & country. Please verify... > The service update checker should also update ServiceDeployment locations > ------------------------------------------------------------------------- > > Key: BIOCAT-364 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Currently, the service update checker process doesn't take into account updating of location info of service 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 Jun 13 09:16:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 14:16:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-364) The service update checker should also update ServiceDeployment locations In-Reply-To: <5338610.1723.1275135377283.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8826785.1371.1307971015441.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16835#comment-16835 ] Jiten Bhagat commented on BIOCAT-364: ------------------------------------- Could you check that this (lines 317-321 in app/models/soap_service.rb): {code} ServiceDeployment.create!(:service_id => self.service.id, :service_version_id => self.service_version.id, :endpoint => new_endpoint, :city => new_city, :country => new_country) {code} ... is working as expected? I believe it will cause an error because {{new_city}} and {{new_country}} don't exist at that stage. Please check this... > The service update checker should also update ServiceDeployment locations > ------------------------------------------------------------------------- > > Key: BIOCAT-364 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Currently, the service update checker process doesn't take into account updating of location info of service deployments. -- 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 Mon Jun 13 09:11:53 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 13 Jun 2011 14:11:53 +0100 Subject: [BioCatalogue-developers] [2399] trunk/app/models/soap_service.rb: Fix for JIRA task In-Reply-To: <20110610155743.CAADB1858361@rubyforge.org> References: <20110610155743.CAADB1858361@rubyforge.org> Message-ID: <4DF60C99.2030009@cs.man.ac.uk> Mannie, Could you check this please... Unless I'm missing something, this: > ServiceDeployment.create!(:service_id => self.service.id, > :service_version_id => self.service_version.id, > :endpoint => new_endpoint, > :city => new_city, > :country => new_country) ... will cause an error because 'new_city' and 'new_country' don't actually exist at that stage! Please could you verify this in the code. Thanks, Jits On 10/06/2011 16:57, noreply at rubyforge.org wrote: > > Revision > 2399 > Author > mannie > Date > 2011-06-10 11:57:43 -0400 (Fri, 10 Jun 2011) > > > Log Message > > Fix for JIRA task > > BIOCAT-364: The service update checker should also update ServiceDeployment locations > > > Modified Paths > > * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb> > > > Diff > > > Modified: trunk/app/models/soap_service.rb (2398 => 2399) > > > --- trunk/app/models/soap_service.rb 2011-06-10 13:21:24 UTC (rev 2398) > +++ trunk/app/models/soap_service.rb 2011-06-10 15:57:43 UTC (rev 2399) > @@ -311,15 +311,43 @@ > if self.service_deployments.length == 1 > s_d = self.service_deployments.first > changes.add_entry("The service's endpoint (base URL) has been updated from '#{s_d.endpoint}' to '#{new_endpoint}'") > - s_d.endpoint = new_endpoint > + s_d.endpoint = new_endpoint > s_d.save! > else > - ServiceDeployment.create!(:service_id => self.service.id, :service_version_id => self.service_version.id, :endpoint => new_endpoint) > + ServiceDeployment.create!(:service_id => self.service.id, > + :service_version_id => self.service_version.id, > + :endpoint => new_endpoint, > + :city => new_city, > + :country => new_country) > > changes.add_entry("The service's endpoint (base URL) has changed (to: '#{new_endpoint}') and a new service deployment has been added to this service.") > end > end > - > + > + # Update ServiceDeployment locations > + self.service_deployments.each { |s| > + wsdl_geoloc = BioCatalogue::Util.url_location_lookup(s.endpoint) > + new_city, new_country = BioCatalogue::Util.city_and_country_from_geoloc(wsdl_geoloc) > + > + existing_city = s.city || "" > + new_city ||= "" > + unless existing_city.downcase == new_city.downcase > + update_found = true > + s.city = new_city > + changes.add_entry("The service's city has been updated to '#{new_city}'") > + end > + > + existing_country = s.country || "" > + new_country ||= "" > + unless existing_country.downcase == new_country.downcase > + update_found = true > + s.country = new_country > + changes.add_entry("The service's country has been updated to '#{new_country}'") > + end > + > + s.save! > + } > + > # Now go through the Ports and Operations in the new service info > # and update/create as appropriate. Log which ones were found in the db, > # then go through the current ones in the db and delete any that were not > > > _______________________________________________ > 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 Mon Jun 13 10:22:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 15:22:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14065817.1373.1307974978040.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-586. --------------------------------- Resolution: Fixed > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: bug .jpg, TfscanService.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 13 10:23:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 15:23:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-586) Grid view does not take into account archived services In-Reply-To: <12748929.155.1302687835384.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17074953.1374.1307974980598.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16837#comment-16837 ] Jiten Bhagat commented on BIOCAT-586: ------------------------------------- We'll leave this as it is now (ie: without the two different shades of grey, just the default grey) as it looks okay. > Grid view does not take into account archived services > ------------------------------------------------------ > > Key: BIOCAT-586 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-586 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Attachments: bug .jpg, TfscanService.jpg > > > Currently, archived services in the grid view show exactly the same as non-archived services. This needs to be changed! -- This 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 Jun 13 10:32:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 15:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-620) Filtering options should only return those filter options that are available within the context Message-ID: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Filtering options should only return those filter options that are available within the context ----------------------------------------------------------------------------------------------- Key: BIOCAT-620 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 Project: BioCatalogue Issue Type: Bug Components: Search / Filtering / Browsing Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. For example, if you do: http://sandbox.biocatalogue.org/soap_operations.xml?q=blast ... and follow: http://sandbox.biocatalogue.org/soap_operations/filters?q=blast ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. This needs to be fixed both for the web interface AND API. -- 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 Jun 13 12:45:50 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 13 Jun 2011 12:45:50 -0400 (EDT) Subject: [BioCatalogue-developers] [2400] trunk: [BIOCAT-620] Partial solution for the issue with incorrect sets of filter options being returned when in a search /filter context (see the JIRA task for more info). Message-ID: <20110613164552.CD14D159802F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 13 12:46:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 17:46:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7521686.1382.1307983615486.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16841#comment-16841 ] Jiten Bhagat commented on BIOCAT-620: ------------------------------------- Partial fix in revision 2400: ONLY sorts out the issue for *soap_operations* and *rest_methods* AND only when a search query is provided. Combining of tags still has the original issue. This was specifically for the Taverna 2.3 release work (on the BioCat perspective). > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. -- This 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 Jun 13 12:46:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 17:46:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12046474.1383.1307983618402.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-620: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-13 17:46 Start Date: 2011-06-13 13:46 Worklog Time Spent: 3 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 3 hours Worklog Id: (was: 10505) > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. -- This 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 Jun 13 12:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 17:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20549128.1384.1307984035368.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-620: -------------------------------- Description: Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. For example, if you do: http://sandbox.biocatalogue.org/soap_operations.xml?q=blast ... and follow: http://sandbox.biocatalogue.org/soap_operations/filters?q=blast ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. This needs to be fixed both for the web interface AND API. *NOTE*: the counts need to be fixed too. was: Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. For example, if you do: http://sandbox.biocatalogue.org/soap_operations.xml?q=blast ... and follow: http://sandbox.biocatalogue.org/soap_operations/filters?q=blast ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. This needs to be fixed both for the web interface AND API. > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. > *NOTE*: the counts need to be fixed too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jun 13 12:54:19 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 13 Jun 2011 12:54:19 -0400 (EDT) Subject: [BioCatalogue-developers] [2401] trunk/lib/bio_catalogue/filtering: [BIOCAT-620] Fix the counts too! Message-ID: <20110613165419.959881678328@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 13 12:55:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 17:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15021907.1385.1307984155360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16842#comment-16842 ] Jiten Bhagat commented on BIOCAT-620: ------------------------------------- In revision 2401: also fixed the counts (for *soap_operations* and *rest_methods* only). > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. > *NOTE*: the counts need to be fixed too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 13 12:57:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 13 Jun 2011 17:57:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17220349.1386.1307984275355.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-620: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-13 17:57 Start Date: 2011-06-13 16:57 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Time Spent: 4 hours (was: 3 hours) Worklog Id: (was: 10506) > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. > *NOTE*: the counts need to be fixed too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 06:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 11:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21792104.1395.1308048295553.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16844#comment-16844 ] Jiten Bhagat commented on BIOCAT-620: ------------------------------------- Bumping this task to v1.1.0 release now as the main issue has been fixed for the Taverna 2.3 release. > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. > *NOTE*: the counts need to be fixed too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 06:44:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 11:44:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-620) Filtering options should only return those filter options that are available within the context In-Reply-To: <12682775.1380.1307975575355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17280559.1396.1308048298415.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-620: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.1) > Filtering options should only return those filter options that are available within the context > ----------------------------------------------------------------------------------------------- > > Key: BIOCAT-620 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-620 > Project: BioCatalogue > Issue Type: Bug > Components: Search / Filtering / Browsing > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > Time Spent: 4 hours > Remaining Estimate: 0 minutes > > Currently, whenever a set of filter options are returned, it will show ALL possible filter options on that resource rather than the just one's available within the current context. > For example, if you do: > http://sandbox.biocatalogue.org/soap_operations.xml?q=blast > ... and follow: > http://sandbox.biocatalogue.org/soap_operations/filters?q=blast > ... it **should** give you only the filter options that are available from there, not ALL filters on SOAP Operations. > This needs to be fixed both for the web interface AND API. > *NOTE*: the counts need to be fixed too. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Jun 14 07:02:25 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 14 Jun 2011 07:02:25 -0400 (EDT) Subject: [BioCatalogue-developers] [2402] trunk/public/2009/xml/rest: Use a local xml. xsd file as the one on W3C is not accessible most of the time. Message-ID: <20110614110226.08AB21598071@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jun 14 07:06:46 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 14 Jun 2011 07:06:46 -0400 (EDT) Subject: [BioCatalogue-developers] [2403] trunk/script/biocatalogue/api/tests/config.yml.pre: Minor config fix for API tests Message-ID: <20110614110646.376D2185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 14 07:07:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 12:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-443) Update the REST API's XML schema to account for the REST services support endpoints In-Reply-To: <8259919.7505.1279535115302.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28430248.1397.1308049675378.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-443. --------------------------------- Resolution: Fixed XML schema validations test suite passes > Update the REST API's XML schema to account for the REST services support endpoints > ------------------------------------------------------------------------------------ > > Key: BIOCAT-443 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-443 > Project: BioCatalogue > Issue Type: Task > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 07:09:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 12:09:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-319) Add /soap_services/wsdl_locations to XML Schema for REST API In-Reply-To: <32175098.1.1273582037157.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <827200.1398.1308049795371.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-319. --------------------------------- Resolution: Fixed XML schema validations test suite passes > Add /soap_services/wsdl_locations to XML Schema for REST API > ------------------------------------------------------------ > > Key: BIOCAT-319 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-319 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 07:12:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 12:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-621) Incorrect number of results being returned from filtering Message-ID: <12562916.1399.1308049975350.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.1 if you look at: http://sandbox.biocatalogue.org/soap_operations/filters.xml?q=fasta ... and take the filter: {code} {code} ... i.e. the filtered index: http://sandbox.biocatalogue.org/soap_operations.xml?q=fasta&tag_ops=%5Bblast%5D ... it returns 4 items instead of the reported 3. Investigate. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 07:27:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 12:27:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <5422119.1400.1308050875405.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=16847#comment-16847 ] Jiten Bhagat commented on BIOCAT-621: ------------------------------------- On closer investigation, the counts returned are wrong! > 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: 1.0.1 > > > if you look at: > http://sandbox.biocatalogue.org/soap_operations/filters.xml?q=fasta > ... and take the filter: > {code} > > {code} > ... i.e. the filtered index: > http://sandbox.biocatalogue.org/soap_operations.xml?q=fasta&tag_ops=%5Bblast%5D > ... it returns 4 items instead of the reported 3. > Investigate. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 07:34:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 12:34:55 +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: <25598307.1401.1308051295378.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=16847#comment-16847 ] Jiten Bhagat edited comment on BIOCAT-621 at 14/06/11 12:33: ------------------------------------------------------------- On closer investigation, the counts returned are wrong! ... and this is likely to do with the fact that there is a limit on the number of filters returned. was (Author: jbhagat): On closer investigation, the counts returned are wrong! > 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: 1.0.1 > > > if you look at: > http://sandbox.biocatalogue.org/soap_operations/filters.xml?q=fasta > ... and take the filter: > {code} > > {code} > ... i.e. the filtered index: > http://sandbox.biocatalogue.org/soap_operations.xml?q=fasta&tag_ops=%5Bblast%5D > ... it returns 4 items instead of the reported 3. > Investigate. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Jun 14 07:40:49 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 14 Jun 2011 07:40:49 -0400 (EDT) Subject: [BioCatalogue-developers] [2404] trunk/app/controllers/application_controller.rb: [BIOCAT-621] Temporary hack! Removed the default limit on the filter options generation (aside: it's a known issue that it doesn't work as expected!!) so that at least the correct counts are returned. Message-ID: <20110614114049.2753C185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 14 07:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 12:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <24703678.1402.1308051895358.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=16848#comment-16848 ] Jiten Bhagat commented on BIOCAT-621: ------------------------------------- As a temporary hack-fix, in revision2 404: the default limit is set to nil (ie: unlimited) so that at least the correct counts are generated. Maybe caching this will help? > 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: 1.0.1 > > > if you look at: > http://sandbox.biocatalogue.org/soap_operations/filters.xml?q=fasta > ... and take the filter: > {code} > > {code} > ... i.e. the filtered index: > http://sandbox.biocatalogue.org/soap_operations.xml?q=fasta&tag_ops=%5Bblast%5D > ... it returns 4 items instead of the reported 3. > Investigate. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 08:08:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 13:08:55 +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: <19620954.1403.1308053335367.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=16848#comment-16848 ] Jiten Bhagat edited comment on BIOCAT-621 at 14/06/11 13:08: ------------------------------------------------------------- As a temporary hack-fix, in revision 2404: the default limit is set to nil (ie: unlimited) so that at least the correct counts are generated. Maybe caching this will help? was (Author: jbhagat): As a temporary hack-fix, in revision2 404: the default limit is set to nil (ie: unlimited) so that at least the correct counts are generated. Maybe caching this will help? > 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: 1.0.1 > > > if you look at: > http://sandbox.biocatalogue.org/soap_operations/filters.xml?q=fasta > ... and take the filter: > {code} > > {code} > ... i.e. the filtered index: > http://sandbox.biocatalogue.org/soap_operations.xml?q=fasta&tag_ops=%5Bblast%5D > ... it returns 4 items instead of the reported 3. > Investigate. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 09:00:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 14:00:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-622) Return more info on the ancestors, in the REST API Message-ID: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Return more info on the ancestors, in the REST API -------------------------------------------------- Key: BIOCAT-622 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 Project: BioCatalogue Issue Type: Improvement Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLink}}s only. For example: {code} {code} This means that in order to find out more information about those ancestors an extra call to the API is necessary. To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. This wouldn't be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 14 09:06:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 14:06:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27856450.1405.1308056815372.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-622: -------------------------------- Description: Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: {code} {code} This means that in order to find out more information about those ancestors an extra call to the API is necessary. To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. This wouldn't be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. Note: this is specifically required by the Taverna 2.3 release. was: Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLink}}s only. For example: {code} {code} This means that in order to find out more information about those ancestors an extra call to the API is necessary. To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. This wouldn't be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. Note: this is specifically required by the Taverna 2.3 release. > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This wouldn't be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. > Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 14 09:18:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 14:18:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11393144.1407.1308057535356.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-622: -------------------------------- Description: Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: {code} {code} This means that in order to find out more information about those ancestors an extra call to the API is necessary. To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: - Mannie's iPad app - Taverna 2.3 (other parts of it) Note: this is specifically required by the Taverna 2.3 release. was: Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: {code} {code} This means that in order to find out more information about those ancestors an extra call to the API is necessary. To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. This wouldn't be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. Note: this is specifically required by the Taverna 2.3 release. > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: > - Mannie's iPad app > - Taverna 2.3 (other parts of it) > Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 14 09:37:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 14:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-623) Update API docs and changelog to mention this important (but not breaking) change to the API Message-ID: <10261285.1408.1308058675347.JavaMail.jira@rosalind.cs.man.ac.uk> Update API docs and changelog to mention this important (but not breaking) change to the API -------------------------------------------------------------------------------------------- Key: BIOCAT-623 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-623 Project: BioCatalogue Issue Type: Sub-task Components: Documentation Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 14 10:17:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 15:17:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-624) Add resourceName attribute to root node of all resource outputs in the API Message-ID: <1678160.1410.1308061075357.JavaMail.jira@rosalind.cs.man.ac.uk> Add resourceName attribute to root node of all resource outputs in the API -------------------------------------------------------------------------- Key: BIOCAT-624 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-624 Project: BioCatalogue Issue Type: Refinement Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.0.1 Due to the changes required in BIOCAT-622, some of the resource outputs now have {{resourceName}} set on root node. Make sure that ALL resource outputs that have a resource name have it set on the root node. -- 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 Jun 14 10:39:26 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 14 Jun 2011 10:39:26 -0400 (EDT) Subject: [BioCatalogue-developers] [2405] trunk: [BIOCAT-622] lists in API outputs now return inline resources rather than just ResourceLinks . Message-ID: <20110614143927.17CA71598071@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 14 10:40:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 15:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31852238.1411.1308062455413.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16850#comment-16850 ] Jiten Bhagat commented on BIOCAT-622: ------------------------------------- Initial work done in revision 2405. Need's full testing! > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: > - Mannie's iPad app > - Taverna 2.3 (other parts of it) > Note: this is specifically required by the Taverna 2.3 release. -- 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 Jun 14 11:05:38 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 14 Jun 2011 11:05:38 -0400 (EDT) Subject: [BioCatalogue-developers] [2406] trunk/lib/bio_catalogue/filtering/annotations.rb: Bugfix for the generation of filter options for annotations; it would fail whenever the annotatable object was missing ( which should never happen but for some reason has happened in the DB). Message-ID: <20110614150538.D0441185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 14 11:16:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 16:16:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-625) soap_operations index (in API) is not respecting the "include" parameter Message-ID: <7691718.1416.1308064615387.JavaMail.jira@rosalind.cs.man.ac.uk> soap_operations index (in API) is not respecting the "include" parameter ------------------------------------------------------------------------ Key: BIOCAT-625 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625 Project: BioCatalogue Issue Type: Bug Components: REST API Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker Fix For: 1.0.1 The soap_operations index is not respecting any {{include}} options in the URL, e.g.: http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. -- This 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 Jun 14 11:34:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 16:34:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27719161.1418.1308065697954.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-622: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-14 16:34 Start Date: 2011-06-14 13:34 Worklog Time Spent: 3 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 3 hours Worklog Id: (was: 10507) > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: > - Mannie's iPad app > - Taverna 2.3 (other parts of it) > Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 14 11:34:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 16:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-625) soap_services and rest_services indexes (in API) not respecting the "include" parameter In-Reply-To: <7691718.1416.1308064615387.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23732328.1417.1308065695503.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-625: -------------------------------- Summary: soap_services and rest_services indexes (in API) not respecting the "include" parameter (was: soap_operations index (in API) is not respecting the "include" parameter) Description: The soap_services and rest_services indexes are not respecting any {{include}} options in the URL, e.g.: http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. was: The soap_operations index is not respecting any {{include}} options in the URL, e.g.: http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. > soap_services and rest_services indexes (in API) not respecting the "include" parameter > --------------------------------------------------------------------------------------- > > Key: BIOCAT-625 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > The soap_services and rest_services indexes are not respecting any {{include}} options in the URL, e.g.: > http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors > This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. -- 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 Jun 14 11:35:25 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 14 Jun 2011 11:35:25 -0400 (EDT) Subject: [BioCatalogue-developers] [2407] trunk: [BIOCAT-625] soap_operations and rest_services indexes ( in API) were not respecting the "include" parameter. Message-ID: <20110614153525.5EB28185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 14 11:36:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 16:36:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-625) soap_services and rest_services indexes (in API) not respecting the "include" parameter In-Reply-To: <7691718.1416.1308064615387.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21251810.1419.1308065815382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16853#comment-16853 ] Jiten Bhagat commented on BIOCAT-625: ------------------------------------- Potentially fixed in revision 2407. > soap_services and rest_services indexes (in API) not respecting the "include" parameter > --------------------------------------------------------------------------------------- > > Key: BIOCAT-625 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > The soap_services and rest_services indexes are not respecting any {{include}} options in the URL, e.g.: > http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors > This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. -- This 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 Jun 14 11:42:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 16:42:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-625) soap_services and rest_services indexes (in API) not respecting the "include" parameter In-Reply-To: <7691718.1416.1308064615387.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3158417.1420.1308066175386.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-625: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-14 16:41 Start Date: 2011-06-14 16:00 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 1 hour Worklog Id: (was: 10508) > soap_services and rest_services indexes (in API) not respecting the "include" parameter > --------------------------------------------------------------------------------------- > > Key: BIOCAT-625 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > The soap_services and rest_services indexes are not respecting any {{include}} options in the URL, e.g.: > http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors > This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. -- This 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 Jun 14 11:42:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 14 Jun 2011 16:42:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-625) soap_services and rest_services indexes (in API) not respecting the "include" parameter In-Reply-To: <7691718.1416.1308064615387.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12765504.1421.1308066179138.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-625. --------------------------------- Resolution: Fixed > soap_services and rest_services indexes (in API) not respecting the "include" parameter > --------------------------------------------------------------------------------------- > > Key: BIOCAT-625 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-625 > Project: BioCatalogue > Issue Type: Bug > Components: REST API > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > Time Spent: 1 hour > Remaining Estimate: 0 minutes > > The soap_services and rest_services indexes are not respecting any {{include}} options in the URL, e.g.: > http://sandbox.biocatalogue.org/soap_services.xml?include=ancestors > This is because it's using the {{inline_item}} partial and not a {{result_item}} partial. -- 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 Jun 15 03:34:15 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Jun 2011 03:34:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2408] trunk/app/models/soap_service.rb: Fix for JIRA task Message-ID: <20110615073416.0840B159802F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 15 04:03:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 09:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-364) The service update checker should also update ServiceDeployment locations In-Reply-To: <5338610.1723.1275135377283.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5386187.1422.1308125035507.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-364. ------------------------------------ Resolution: Fixed line 317 has been reverted to: ServiceDeployment.create!(:service_id => self.service.id, :service_version_id => self.service_version.id, :endpoint => new_endpoint) > The service update checker should also update ServiceDeployment locations > ------------------------------------------------------------------------- > > Key: BIOCAT-364 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-364 > Project: BioCatalogue > Issue Type: New Feature > Components: Service Container > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Currently, the service update checker process doesn't take into account updating of location info of service deployments. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 04:21:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 09:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4976781.1423.1308126115398.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16855#comment-16855 ] Mannie Tagarira commented on BIOCAT-622: ---------------------------------------- This has no negative effect on the iOS app. > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: > - Mannie's iPad app > - Taverna 2.3 (other parts of it) > Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 15 05:52:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 10:52:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-626) Investigate the malformed content of the element in the REST API Message-ID: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Investigate the malformed content of the element in the REST API ---------------------------------------------------------------------- Key: BIOCAT-626 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 Project: BioCatalogue Issue Type: Task Components: REST API Affects Versions: 1.0.0 Reporter: Mannie Tagarira Assignee: Jiten Bhagat Fix For: 1.0.1 Resources: http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 http://sandbox.biocatalogue.org/services/2752.xml?include=all Search for: "http://www.ebi.ac.uk/ena/data/view/Taxon" -- 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 Jun 15 07:20:17 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Jun 2011 07:20:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2409] trunk/app: Updated the help text associated with the registration of rest endpoints. Message-ID: <20110615112019.2CD83159802F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 15 09:35:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 14:35:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-627) Identify reason for the service provider edit button not showing up... Message-ID: <23179520.1426.1308144955352.JavaMail.jira@rosalind.cs.man.ac.uk> Identify reason for the service provider edit button not showing up... ---------------------------------------------------------------------- Key: BIOCAT-627 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627 Project: BioCatalogue Issue Type: Task Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 09:54:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 14:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23247406.1427.1308146095384.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16856#comment-16856 ] Mannie Tagarira commented on BIOCAT-536: ---------------------------------------- Done. Please confirm... Was not sure what to do with the following attributes so I omitted them: - embrace_id for Service - SeekDa:availability for ServiceDeployment - version for ServiceVersion Also, it may be worth writing a script to sanitize "example of use" for SoapOperation so that "example_workflow" is used instead. Does the ServiceProvider resource really support display_name annotations? If not, this mapping needs to be removed. > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the API docs and wiki (http://www.biocatalogue.org/wiki/doku.php?id=development:annotation) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 09:59:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 14:59:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-627) Identify reason for the service provider edit button not showing up... In-Reply-To: <23179520.1426.1308144955352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32382945.1428.1308146395357.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16857#comment-16857 ] Mannie Tagarira commented on BIOCAT-627: ---------------------------------------- It seems that BioCatalogue::Auth.allow_user_to_curate_thing? is always returning false unless the logged in user is a curator. Consider changing this so that users that have submitted services for a provider can update the name too. > Identify reason for the service provider edit button not showing up... > ---------------------------------------------------------------------- > > Key: BIOCAT-627 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 10:06:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 15:06:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-627) Identify reason for the service provider edit button not showing up... In-Reply-To: <23179520.1426.1308144955352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17434957.1429.1308146815376.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-627 started by Mannie Tagarira. > Identify reason for the service provider edit button not showing up... > ---------------------------------------------------------------------- > > Key: BIOCAT-627 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 10:12:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 15:12:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-628) When an endpoint for a web service changes, the hostnames of the services providers are not updated Message-ID: <16633173.1430.1308147176953.JavaMail.jira@rosalind.cs.man.ac.uk> When an endpoint for a web service changes, the hostnames of the services providers are not updated --------------------------------------------------------------------------------------------------- Key: BIOCAT-628 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-628 Project: BioCatalogue Issue Type: Bug Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Jun 15 10:15:41 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Jun 2011 10:15:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2410] trunk/lib/bio_catalogue/auth.rb: Fix for JIRA task Message-ID: <20110615141541.6943118583A3@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 15 10:15:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 15:15:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-628) When an endpoint for a web service changes, the hostnames of the services providers are not updated In-Reply-To: <16633173.1430.1308147176953.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19383635.1432.1308147357793.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-628?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-628 started by Mannie Tagarira. > When an endpoint for a web service changes, the hostnames of the services providers are not updated > --------------------------------------------------------------------------------------------------- > > Key: BIOCAT-628 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-628 > Project: BioCatalogue > Issue Type: Bug > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 10:16:00 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 15:16:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-627) Identify reason for the service provider edit button not showing up... In-Reply-To: <23179520.1426.1308144955352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17626407.1433.1308147360292.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-627. ------------------------------------ Resolution: Fixed > Identify reason for the service provider edit button not showing up... > ---------------------------------------------------------------------- > > Key: BIOCAT-627 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 15 10:15:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 15 Jun 2011 15:15:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-627) Identify reason for the service provider edit button not showing up... In-Reply-To: <23179520.1426.1308144955352.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10752342.1431.1308147355376.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-627 stopped by Mannie Tagarira. > Identify reason for the service provider edit button not showing up... > ---------------------------------------------------------------------- > > Key: BIOCAT-627 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-627 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- 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 Jun 15 10:43:06 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 15 Jun 2011 15:43:06 +0100 Subject: [BioCatalogue-developers] [2410] trunk/lib/bio_catalogue/auth.rb: Fix for JIRA task In-Reply-To: <20110615141541.6943118583A3@rubyforge.org> References: <20110615141541.6943118583A3@rubyforge.org> Message-ID: <4DF8C4FA.9040508@cs.man.ac.uk> Good idea! Few things with this: > + when ServiceProvider > + thing.services.each { |s| > + is_submitter = s.submitter.id == user.id > + return true if is_submitter > + } 1) Cannot assume that submitter is User. Check s.submitter_type. 2) Instead of s.submitter.id consider using s.submitter_id so that the submitter object doesn't have to be loaded from the DB. 3) Consider checking the service_responsibles for the service rather than just the submitter. Jits On 15/06/2011 15:15, noreply at rubyforge.org wrote: > > Revision > 2410 > Author > mannie > Date > 2011-06-15 10:15:40 -0400 (Wed, 15 Jun 2011) > > > Log Message > > Fix for JIRA task > > BIOCAT-627: Identify reason for the service provider edit button not showing up... > > > Modified Paths > > * trunk/lib/bio_catalogue/auth.rb <#trunklibbio_catalogueauthrb> > > > Diff > > > Modified: trunk/lib/bio_catalogue/auth.rb (2409 => 2410) > > > --- trunk/lib/bio_catalogue/auth.rb 2011-06-15 11:20:03 UTC (rev 2409) > +++ trunk/lib/bio_catalogue/auth.rb 2011-06-15 14:15:40 UTC (rev 2410) > @@ -60,6 +60,11 @@ > return true if user.id == map.submitter_id&& thing.submitter_type == "User" > > return true if check_user_is_responsible_for_service_with_thing(user, map) > + when ServiceProvider > + thing.services.each { |s| > + is_submitter = s.submitter.id == user.id > + return true if is_submitter > + } > else > # Try to see if it belongs to a service and if so check that instead > if thing.is_a? ActiveRecord::Base > > > _______________________________________________ > 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 Jun 15 11:01:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 15 Jun 2011 16:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-615) Increment the version numbers (system and API) for release v1.0.1 accordingly In-Reply-To: <21078259.1332.1307700298661.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30108792.1441.1308150115360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-615?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-615. --------------------------------- Resolution: Fixed > Increment the version numbers (system and API) for release v1.0.1 accordingly > ----------------------------------------------------------------------------- > > Key: BIOCAT-615 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-615 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Fix For: 1.0.1 > > > Note: system and API version numbers don't necessarily increment/change in tandem. The API version number ONLY changes if modifications to the API have been made. -- This 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 Jun 15 11:15:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 15 Jun 2011 16:15:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-629) Upgrade to Solr 1.4.1 locally Message-ID: <32648861.1442.1308150955351.JavaMail.jira@rosalind.cs.man.ac.uk> Upgrade to Solr 1.4.1 locally ----------------------------- Key: BIOCAT-629 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-629 Project: BioCatalogue Issue Type: Sub-task Components: Search / Filtering / Browsing Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.1.0 Before upgrading Solr on the live servers (at the EBI), we need to first do this locally and on the staging environment and learn the lessons and document the steps first. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jun 16 04:28:40 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 04:28:40 -0400 (EDT) Subject: [BioCatalogue-developers] [2411] trunk/app/models: Fix for JIRA task Message-ID: <20110616082841.0335B1858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 04:30:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 09:30:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-628) When an endpoint for a web service changes, the hostnames of the services providers are not updated In-Reply-To: <16633173.1430.1308147176953.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6977856.1443.1308213055547.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-628?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-628. ------------------------------------ Resolution: Fixed An after_save validation to account for this was added (revision 2411) > When an endpoint for a web service changes, the hostnames of the services providers are not updated > --------------------------------------------------------------------------------------------------- > > Key: BIOCAT-628 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-628 > Project: BioCatalogue > Issue Type: Bug > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 04:57:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 09:57:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-626) Investigate the malformed content of the element in the REST API In-Reply-To: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2335261.1446.1308214675395.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16860#comment-16860 ] Mannie Tagarira commented on BIOCAT-626: ---------------------------------------- The URLs used by the URL monitors are example_endpoint annotations. >> Annotation.find(55073).value => "http://www.ebi.ac.uk/ena/data/view/FM177760\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000010-ERA000020\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000092\r\nhttp://www.ebi.ac.uk/ena/data/view/TI1941166100\r\nhttp://www.ebi.ac.uk/ena/data/view/Taxon:9606" Either the user was unaware that this would be used for monitoring OR they did and wanted to all the endpoints to be used... A decision needs to be made as to what to do about this. > Investigate the malformed content of the element in the REST API > ---------------------------------------------------------------------- > > Key: BIOCAT-626 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Resources: > http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 > http://sandbox.biocatalogue.org/services/2752.xml?include=all > Search for: > "http://www.ebi.ac.uk/ena/data/view/Taxon" -- This 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 Jun 16 04:59:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 09:59:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-626) Investigate the malformed content of the element in the REST API In-Reply-To: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28254323.1448.1308214797985.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16860#comment-16860 ] Mannie Tagarira edited comment on BIOCAT-626 at 16/06/11 09:59: ---------------------------------------------------------------- The URLs used by the URL monitors are example_endpoint annotations. {code:none} >> Annotation.find(55073).value => "http://www.ebi.ac.uk/ena/data/view/FM177760\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000010-ERA000020\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000092\r\nhttp://www.ebi.ac.uk/ena/data/view/TI1941166100\r\nhttp://www.ebi.ac.uk/ena/data/view/Taxon:9606" {code} Either the user was unaware that this would be used for monitoring OR they did and wanted to all the endpoints to be used... A decision needs to be made as to what to do about this. was (Author: mannie): The URLs used by the URL monitors are example_endpoint annotations. {code:ruby} >> Annotation.find(55073).value => "http://www.ebi.ac.uk/ena/data/view/FM177760\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000010-ERA000020\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000092\r\nhttp://www.ebi.ac.uk/ena/data/view/TI1941166100\r\nhttp://www.ebi.ac.uk/ena/data/view/Taxon:9606" {code} Either the user was unaware that this would be used for monitoring OR they did and wanted to all the endpoints to be used... A decision needs to be made as to what to do about this. > Investigate the malformed content of the element in the REST API > ---------------------------------------------------------------------- > > Key: BIOCAT-626 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Resources: > http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 > http://sandbox.biocatalogue.org/services/2752.xml?include=all > Search for: > "http://www.ebi.ac.uk/ena/data/view/Taxon" -- This 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 Jun 16 05:05:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (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: <26977122.1449.1308215155383.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 ] Work on BIOCAT-600 started by Mannie Tagarira. > 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: 1.0.2 > > > 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 Thu Jun 16 04:59:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 09:59:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-626) Investigate the malformed content of the element in the REST API In-Reply-To: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33533179.1447.1308214795598.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16860#comment-16860 ] Mannie Tagarira edited comment on BIOCAT-626 at 16/06/11 09:59: ---------------------------------------------------------------- The URLs used by the URL monitors are example_endpoint annotations. {code:ruby} >> Annotation.find(55073).value => "http://www.ebi.ac.uk/ena/data/view/FM177760\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000010-ERA000020\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000092\r\nhttp://www.ebi.ac.uk/ena/data/view/TI1941166100\r\nhttp://www.ebi.ac.uk/ena/data/view/Taxon:9606" {code} Either the user was unaware that this would be used for monitoring OR they did and wanted to all the endpoints to be used... A decision needs to be made as to what to do about this. was (Author: mannie): The URLs used by the URL monitors are example_endpoint annotations. >> Annotation.find(55073).value => "http://www.ebi.ac.uk/ena/data/view/FM177760\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000010-ERA000020\r\nhttp://www.ebi.ac.uk/ena/data/view/ERA000092\r\nhttp://www.ebi.ac.uk/ena/data/view/TI1941166100\r\nhttp://www.ebi.ac.uk/ena/data/view/Taxon:9606" Either the user was unaware that this would be used for monitoring OR they did and wanted to all the endpoints to be used... A decision needs to be made as to what to do about this. > Investigate the malformed content of the element in the REST API > ---------------------------------------------------------------------- > > Key: BIOCAT-626 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Resources: > http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 > http://sandbox.biocatalogue.org/services/2752.xml?include=all > Search for: > "http://www.ebi.ac.uk/ena/data/view/Taxon" -- 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 Jun 16 05:26:12 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 05:26:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2412] trunk/app/views/services/_monitoring_tab.html.erb: Fix for JIRA task Message-ID: <20110616092612.A2BF11858378@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 05:28:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:28:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-597) Investigate monitoring for archived services In-Reply-To: <16684682.944.1307435395526.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30246995.1450.1308216535385.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 ] Mannie Tagarira resolved BIOCAT-597. ------------------------------------ Resolution: Fixed Fixed in revision 2412. > 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: 1.0.2 > > > 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 Thu Jun 16 05:28:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:28:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <19699332.1451.1308216538582.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 ] Mannie Tagarira resolved BIOCAT-600. ------------------------------------ Resolution: Fixed Fixed in revision 2412. > 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: 1.0.2 > > > 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 Thu Jun 16 05:30:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:30:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-630) Add support for "include" 'methods' to the /rest_services/{id} XML endpoint Message-ID: <2402759.1453.1308216657693.JavaMail.jira@rosalind.cs.man.ac.uk> Add support for "include" 'methods' to the /rest_services/{id} XML endpoint --------------------------------------------------------------------------- Key: BIOCAT-630 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630 Project: BioCatalogue Issue Type: Bug Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jun 16 05:31:23 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 05:31:23 -0400 (EDT) Subject: [BioCatalogue-developers] [2413] trunk/app/controllers/tags_controller.rb: Minor cleanup Message-ID: <20110616093123.857B618583A4@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 05:32:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-631) Add link to /rest_services/{id}/methods in the "related" section of the XML api Message-ID: <4859443.1454.1308216775364.JavaMail.jira@rosalind.cs.man.ac.uk> Add link to /rest_services/{id}/methods in the "related" section of the XML api ------------------------------------------------------------------------------- Key: BIOCAT-631 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631 Project: BioCatalogue Issue Type: Bug Components: REST API, REST Services Support Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 05:32:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:32:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-631) Add link to /rest_services/{id}/methods in the "related" section of the XML api In-Reply-To: <4859443.1454.1308216775364.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12647153.1455.1308216777703.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-631 started by Mannie Tagarira. > Add link to /rest_services/{id}/methods in the "related" section of the XML api > ------------------------------------------------------------------------------- > > Key: BIOCAT-631 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 05:33:04 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:33:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-630) Add support for "include" 'methods' to the /rest_services/{id} XML endpoint In-Reply-To: <2402759.1453.1308216657693.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11240809.1457.1308216784311.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-630: ----------------------------------- Component/s: REST API REST Services Support > Add support for "include" 'methods' to the /rest_services/{id} XML endpoint > --------------------------------------------------------------------------- > > Key: BIOCAT-630 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jun 16 05:36:19 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 05:36:19 -0400 (EDT) Subject: [BioCatalogue-developers] [2414] trunk/app/views/rest_services/api/_related_links.xml.builder: Fix for JIRA task Message-ID: <20110616093619.E582E18583A6@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 05:36:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:36:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-630) Add support for "include" 'methods' to the /rest_services/{id} XML endpoint In-Reply-To: <2402759.1453.1308216657693.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30396689.1459.1308217017777.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-630 stopped by Mannie Tagarira. > Add support for "include" 'methods' to the /rest_services/{id} XML endpoint > --------------------------------------------------------------------------- > > Key: BIOCAT-630 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 05:36:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:36:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-630) Add support for "include" 'methods' to the /rest_services/{id} XML endpoint In-Reply-To: <2402759.1453.1308216657693.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6484891.1458.1308217015382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-630 started by Mannie Tagarira. > Add support for "include" 'methods' to the /rest_services/{id} XML endpoint > --------------------------------------------------------------------------- > > Key: BIOCAT-630 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 05:38:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:38:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-631) Add link to /rest_services/{id}/methods in the "related" section of the XML api In-Reply-To: <4859443.1454.1308216775364.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23485989.1460.1308217135366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-631. ------------------------------------ Resolution: Fixed Fixed in rev. 2414 > Add link to /rest_services/{id}/methods in the "related" section of the XML api > ------------------------------------------------------------------------------- > > Key: BIOCAT-631 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 05:38:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 10:38:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-630) Add support for "include" 'methods' to the /rest_services/{id} XML endpoint In-Reply-To: <2402759.1453.1308216657693.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18341379.1461.1308217137833.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-630 started by Mannie Tagarira. > Add support for "include" 'methods' to the /rest_services/{id} XML endpoint > --------------------------------------------------------------------------- > > Key: BIOCAT-630 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 06:12:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <14937725.1466.1308219175835.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-612?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16868#comment-16868 ] Jiten Bhagat commented on BIOCAT-612: ------------------------------------- One option is to add these to the {{ResourceLink}} type, but this may conflate it. Another option is to add these to each top level resource (but this makes it a bit more fragile since we have to remember to add them in for any new resources, though XML schema validation test should complain here). > 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: 1.1.0 > > -- 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 Jun 16 06:27:00 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 06:27:00 -0400 (EDT) Subject: [BioCatalogue-developers] [2415] trunk/app/views/rest_services/show.xml.builder: Fix for JIRA task Message-ID: <20110616102700.C41ED18583A5@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 06:28:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 11:28:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-630) Add support for "include" 'methods' to the /rest_services/{id} XML endpoint In-Reply-To: <2402759.1453.1308216657693.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7210915.1467.1308220135598.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-630. ------------------------------------ Resolution: Fixed Fixed in rev. 2415 /rest_services/{id}.xml?include=methods /rest_services/{id}.xml?include=all > Add support for "include" 'methods' to the /rest_services/{id} XML endpoint > --------------------------------------------------------------------------- > > Key: BIOCAT-630 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-630 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 06:32:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:32:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30501346.1468.1308220375361.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16870#comment-16870 ] Jiten Bhagat commented on BIOCAT-622: ------------------------------------- All API tests pass and this seems to be working as expected. The only thing is that performance has now been affected. A new JIRA task to improve on that will be created. > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: > - Mannie's iPad app > - Taverna 2.3 (other parts of it) > Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 16 06:32:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:32:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-622) Return more info on the ancestors, in the REST API In-Reply-To: <5946486.1404.1308056455400.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30851043.1469.1308220378602.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-622. --------------------------------- Resolution: Fixed > Return more info on the ancestors, in the REST API > -------------------------------------------------- > > Key: BIOCAT-622 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-622 > Project: BioCatalogue > Issue Type: Improvement > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > Time Spent: 3 hours > Remaining Estimate: 0 minutes > > Currently, wherever {{}} are shown in API outputs, it gives a list of {{ResourceLinks}} only. For example: > {code} > > > > > {code} > This means that in order to find out more information about those ancestors an extra call to the API is necessary. > To avoid this, we can just return the core info for that resource. So make the change across all outputs that have {{}} to give back this info. > This *shouldn't* be a breaking change to the API because all the objects being returned are just specialisations of {{ResourceLink}} in the API anyways. BUT check this with current consumers of the API: > - Mannie's iPad app > - Taverna 2.3 (other parts of it) > Note: this is specifically required by the Taverna 2.3 release. -- This 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 Jun 16 06:36:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:36:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-632) Improve the performance of API calls now that return more details Message-ID: <31372983.1470.1308220615376.JavaMail.jira@rosalind.cs.man.ac.uk> Improve the performance of API calls now that return more details ----------------------------------------------------------------------------- Key: BIOCAT-632 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-632 Project: BioCatalogue Issue Type: Improvement Components: Performance / Optimisations, REST API Affects Versions: 1.0.1 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.2 Due to the changes introduced in http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662, the performance of API calls to resources has slowed down considerably. This is largely to do with the large amount of partial rendering. Improve this! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 06:36:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:36:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-621) Incorrect number of results being returned from filtering In-Reply-To: <12562916.1399.1308049975350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15898723.1471.1308220617545.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-621?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-621: -------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > 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: 1.0.2 > > > 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 Thu Jun 16 06:37:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:37:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-621) Incorrect number of results being returned from filtering In-Reply-To: <12562916.1399.1308049975350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10503877.1472.1308220620144.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-621?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-621: -------------------------------- 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: 1.0.2 > > > 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 Thu Jun 16 06:42:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 16 Jun 2011 11:42:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-626) Investigate the malformed content of the element in the REST API In-Reply-To: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23282147.1473.1308220975389.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira reassigned BIOCAT-626: -------------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Investigate the malformed content of the element in the REST API > ---------------------------------------------------------------------- > > Key: BIOCAT-626 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > Resources: > http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 > http://sandbox.biocatalogue.org/services/2752.xml?include=all > Search for: > "http://www.ebi.ac.uk/ena/data/view/Taxon" -- 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 Jun 16 06:46:55 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 06:46:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2416] trunk/public/2009/xml/rest/schema-v1.xsd: [BIOCAT-631] Added the new element to the schema. Message-ID: <20110616104655.25AA018583A3@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 06:47:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 11:47:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-631) Add link to /rest_services/{id}/methods in the "related" section of the XML api In-Reply-To: <4859443.1454.1308216775364.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31418328.1474.1308221276865.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16872#comment-16872 ] Jiten Bhagat commented on BIOCAT-631: ------------------------------------- In revision 2416 - added to XML schema. > Add link to /rest_services/{id}/methods in the "related" section of the XML api > ------------------------------------------------------------------------------- > > Key: BIOCAT-631 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-631 > Project: BioCatalogue > Issue Type: Bug > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jun 16 08:42:41 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 08:42:41 -0400 (EDT) Subject: [BioCatalogue-developers] [2417] trunk/lib/bio_catalogue/filtering: Fix counts on the filter options when no search query is provided Message-ID: <20110616124241.8653218583A9@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 08:47:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 13:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-532) Inform Alan or Alex how they should update the BioCat plugin for Taverna to take into account archived things In-Reply-To: <32074650.559.1289921549163.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32310181.1514.1308228475370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-532?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-532. --------------------------------- Resolution: Fixed Done. Alan is checking for all cases of something being archived. E.g. for SOAP operations check for: - the SOAP operation itself being marked as archived - the SOAP operation's ancestor Service being marked as archived > Inform Alan or Alex how they should update the BioCat plugin for Taverna to take into account archived things > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-532 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-532 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > The inclusion of archived status in the API should be used by the BioCatalogue plugin for Taverna. > Meet with Alan or Alex to discuss how this could be done. -- This 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 Jun 16 09:00:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:00:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <489608.1515.1308229255372.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-612?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16878#comment-16878 ] Jiten Bhagat commented on BIOCAT-612: ------------------------------------- On second thought - really need to rethink this. Adding "version" could severely confuse the outputs as people may think its the version of that resource. Maybe only add "apiVersion" in there for now? > 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: 1.1.0 > > -- 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 Jun 16 09:02:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:02:55 +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: <18287753.1516.1308229375393.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: 1.0.2 (was: 1.1.0) Bumping to v1.0.2 release so that we do this only when the new changes to the API have been stabilised and documented. > 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: 1.0.2 > > -- This 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 Jun 16 09:02:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:02:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-624) Add resourceName attribute to root node of all resource outputs in the API In-Reply-To: <1678160.1410.1308061075357.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11795666.1517.1308229378237.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-624?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-624 started by Jiten Bhagat. > Add resourceName attribute to root node of all resource outputs in the API > -------------------------------------------------------------------------- > > Key: BIOCAT-624 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-624 > Project: BioCatalogue > Issue Type: Refinement > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Due to the changes required in BIOCAT-622, some of the resource outputs now have {{resourceName}} set on root node. Make sure that ALL resource outputs that have a resource name have it set on the root node. -- This 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 Jun 16 09:12:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-633) Add "scope" parameter to /tags index so you can get a subset of tags Message-ID: <24019167.1523.1308229975349.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 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 noreply at rubyforge.org Thu Jun 16 09:35:15 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 16 Jun 2011 09:35:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2418] trunk/app/views: [BIOCAT-624] "resourceName" added to the root of all relevant XML API outputs Message-ID: <20110616133516.0080C159802F@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jun 16 09:36:12 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:36:12 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-624) Add resourceName attribute to root node of all resource outputs in the API In-Reply-To: <1678160.1410.1308061075357.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <27578019.1524.1308231372014.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-624?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-624. --------------------------------- Resolution: Fixed Done, in revision 2418. > Add resourceName attribute to root node of all resource outputs in the API > -------------------------------------------------------------------------- > > Key: BIOCAT-624 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-624 > Project: BioCatalogue > Issue Type: Refinement > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Due to the changes required in BIOCAT-622, some of the resource outputs now have {{resourceName}} set on root node. Make sure that ALL resource outputs that have a resource name have it set on the root node. -- This 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 Jun 16 09:37:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-613) Add the system and API version numbers to the footer of the website In-Reply-To: <24723716.1330.1307700177506.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21435063.1525.1308231475366.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-613. --------------------------------- Resolution: Fixed Looks good! > Add the system and API version numbers to the footer of the website > ------------------------------------------------------------------- > > Key: BIOCAT-613 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 16 09:37:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 16 Jun 2011 14:37:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-613) Add the system and API version numbers to the footer of the website In-Reply-To: <24723716.1330.1307700177506.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28066786.1526.1308231477787.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-613. ------------------------------- > Add the system and API version numbers to the footer of the website > ------------------------------------------------------------------- > > Key: BIOCAT-613 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-613 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Jun 17 05:01:06 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 05:01:06 -0400 (EDT) Subject: [BioCatalogue-developers] [2419] trunk/public/: Ignore the links checker report Message-ID: <20110617090106.B6C691858361@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Jun 17 06:12:00 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 06:12:00 -0400 (EDT) Subject: [BioCatalogue-developers] [2420] trunk/lib/bio_catalogue/monitoring.rb: Updated the monitoring process to ignore URL monitors which do not contain pingable URLs . Message-ID: <20110617101200.EA0A81678356@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 17 06:29:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 11:29:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-634) Figure out how to properly record monitoring information for REST endpoints tested using example_endpoint annotations Message-ID: <9393676.1563.1308306595396.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Service Monitoring Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.2 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 Fri Jun 17 08:43:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 13:43:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-635) Add element to UrlMonitor in XML API Message-ID: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Add element to UrlMonitor in XML API ------------------------------------------------ Key: BIOCAT-635 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 An element is required just below the element of the XML representation of UrlMonitor. -- This 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 Jun 17 08:45:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 13:45:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-626) Investigate the malformed content of the element in the REST API In-Reply-To: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15832391.1568.1308314755410.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-626. ------------------------------------ Resolution: Fixed The first valid URI has been used. > Investigate the malformed content of the element in the REST API > ---------------------------------------------------------------------- > > Key: BIOCAT-626 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > Resources: > http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 > http://sandbox.biocatalogue.org/services/2752.xml?include=all > Search for: > "http://www.ebi.ac.uk/ena/data/view/Taxon" -- This 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 Jun 17 08:45:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 13:45:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-626) Investigate the malformed content of the element in the REST API In-Reply-To: <25822528.1424.1308131575393.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4273469.1569.1308314757640.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16894#comment-16894 ] Mannie Tagarira edited comment on BIOCAT-626 at 17/06/11 13:45: ---------------------------------------------------------------- The first valid URI has been used (in the web UI as well as via the REST API) was (Author: mannie): The first valid URI has been used. > Investigate the malformed content of the element in the REST API > ---------------------------------------------------------------------- > > Key: BIOCAT-626 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-626 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > > Resources: > http://sandbox.biocatalogue.org/rest_methods.xml?include=all&per_page=1 > http://sandbox.biocatalogue.org/services/2752.xml?include=all > Search for: > "http://www.ebi.ac.uk/ena/data/view/Taxon" -- 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 Jun 17 08:51:05 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 08:51:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2421] trunk: - Updated the ServiceTestsController so that service tests can be viewed via the API without the need to login . Message-ID: <20110617125105.322A41858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 17 09:19:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:19:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-636) Add an "activated" element to the UrlMonitor API representation Message-ID: <24178350.1570.1308316795379.JavaMail.jira@rosalind.cs.man.ac.uk> Add an "activated" element to the UrlMonitor API representation --------------------------------------------------------------- Key: BIOCAT-636 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636 Project: BioCatalogue Issue Type: Task Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 17 09:19:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:19:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-636) Add an "activated" element to the UrlMonitor API representation In-Reply-To: <24178350.1570.1308316795379.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9760428.1571.1308316798471.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-636 started by Mannie Tagarira. > Add an "activated" element to the UrlMonitor API representation > --------------------------------------------------------------- > > Key: BIOCAT-636 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > Original Estimate: 30 minutes > Remaining Estimate: 30 minutes > -- This 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 Jun 17 09:26:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:26:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-635) Add element to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29664242.1572.1308317215379.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16895#comment-16895 ] Mannie Tagarira commented on BIOCAT-635: ---------------------------------------- {code:xml} 2010-12-08T05:00:24Z false ... {code} > Add element to UrlMonitor in XML API > ------------------------------------------------ > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > An element is required just below the element of the XML representation of UrlMonitor. -- This 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 Jun 17 09:28:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:28:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-635) Add element to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25270761.1573.1308317335399.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16895#comment-16895 ] Mannie Tagarira edited comment on BIOCAT-635 at 17/06/11 14:27: ---------------------------------------------------------------- {code:xml} ... false ... {code} was (Author: mannie): {code:xml} 2010-12-08T05:00:24Z false ... {code} > Add element to UrlMonitor in XML API > ------------------------------------------------ > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > An element is required just below the element of the XML representation of UrlMonitor. -- This 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 Jun 17 09:28:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:28:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-635) Add and elements to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1506202.1574.1308317337618.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-635: ----------------------------------- Comment: was deleted (was: {code:xml} ... false ... {code}) > Add and elements to UrlMonitor in XML API > ------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of UrlMonitor. > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 17 09:29:01 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:29:01 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-635) Add and elements to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10190839.1575.1308317341487.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-635: ----------------------------------- Description: and elements are required just below the element of the XML representation of UrlMonitor. {code:xml} ... false ... {code} was: and elements are required just below the element of the XML representation of UrlMonitor. > Add and elements to UrlMonitor in XML API > ------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of UrlMonitor. > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 17 09:29:03 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:29:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-635) Add and elements to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19743474.1576.1308317343794.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-635: ----------------------------------- Summary: Add and elements to UrlMonitor in XML API (was: Add element to UrlMonitor in XML API) Description: and elements are required just below the element of the XML representation of UrlMonitor. (was: An element is required just below the element of the XML representation of UrlMonitor.) > Add and elements to UrlMonitor in XML API > ------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of UrlMonitor. -- 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 Jun 17 09:34:38 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 09:34:38 -0400 (EDT) Subject: [BioCatalogue-developers] [2422] trunk/app: Fix for Jira task BIOCAT-636: Add an "activated" element to the UrlMonitor API representation Message-ID: <20110617133438.560421858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 17 09:38:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:38:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-636) Add an "activated" element to the UrlMonitor API representation In-Reply-To: <24178350.1570.1308316795379.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12253289.1577.1308317935359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-636. ------------------------------------ Resolution: Fixed Fixed in rev. 2422 > Add an "activated" element to the UrlMonitor API representation > --------------------------------------------------------------- > > Key: BIOCAT-636 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > Original Estimate: 30 minutes > Remaining Estimate: 30 minutes > -- This 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 Jun 17 09:50:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 14:50:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (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: <22675848.1579.1308318655373.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 ] Work on BIOCAT-610 started by Mannie Tagarira. > 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: 1.0.2 > > > /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 Fri Jun 17 10:37:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 15:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (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: <21159338.1582.1308321475393.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 ] Work on BIOCAT-610 stopped by Mannie Tagarira. > 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: 1.0.2 > > > /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 noreply at rubyforge.org Fri Jun 17 10:41:32 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 10:41:32 -0400 (EDT) Subject: [BioCatalogue-developers] [2423] trunk: Various fixes Message-ID: <20110617144132.87DCA1858346@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 17 10:41:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 15:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <16285386.1583.1308321715352.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 ] Mannie Tagarira resolved BIOCAT-610. ------------------------------------ Resolution: Fixed This is not really an issue. Filtering the annotations index will not show the tags "associated" with an object; it will show the tag annotations "on" the actual object. The JSON tests cases have therefore been updated accordingly. > 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: 1.0.2 > > > /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 Fri Jun 17 10:43:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 17 Jun 2011 15:43:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-635) Add and elements to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17228755.1584.1308321835358.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-635: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Add and elements to UrlMonitor in XML API > ------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of UrlMonitor. > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Fri Jun 17 10:45:48 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 10:45:48 -0400 (EDT) Subject: [BioCatalogue-developers] [2424] trunk/script/biocatalogue/api/tests/json_tests.rb: Updated test cases in response to Jira task BIOCAT-610: Archived resources appear as having no annotations via the API even when they do have annotations Message-ID: <20110617144548.8E5911858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Jun 17 10:45:55 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 10:45:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2425] trunk/app/models/service.rb: Removed superfluous logging Message-ID: <20110617144555.A80A71858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Jun 17 10:46:29 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 10:46:29 -0400 (EDT) Subject: [BioCatalogue-developers] [2426] trunk/app/models/service_test.rb: Minor fix to logging Message-ID: <20110617144630.119331858346@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 17 11:25:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 16:25:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (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: <21149176.1596.1308324355352.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 ] Work on BIOCAT-609 started by Mannie Tagarira. > 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: 1.0.2 > > > 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 noreply at rubyforge.org Fri Jun 17 11:46:18 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Jun 2011 11:46:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2427] trunk/app: Fix for JIRA task BIOCAT-609: The email sent to BioCat admins about service providers with no services and /or hostnames does not always generate valid URLs Message-ID: <20110617154618.742301598071@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 17 11:47:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 17 Jun 2011 16:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (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: <15808601.1602.1308325675360.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 ] Mannie Tagarira resolved BIOCAT-609. ------------------------------------ Resolution: Fixed Fixed in rev. 2427 > 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: 1.0.2 > > > 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 Mon Jun 20 04:12:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 09:12:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-637) Update XML Schema to account for and elements in UrlMonitor Message-ID: <31258569.1616.1308557575489.JavaMail.jira@rosalind.cs.man.ac.uk> Update XML Schema to account for and elements in UrlMonitor ------------------------------------------------------------------------------------- Key: BIOCAT-637 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637 Project: BioCatalogue Issue Type: Task Reporter: Mannie Tagarira Assignee: Jiten Bhagat Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 04:40:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 09:40:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-635) Add and elements to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4541096.1617.1308559256154.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-635: ----------------------------------- Description: and elements are required just below the element of the XML representation of UrlMonitor. was: and elements are required just below the element of the XML representation of UrlMonitor. {code:xml} ... false ... {code} > Add and elements to UrlMonitor in XML API > ------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of UrlMonitor. -- This 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 Jun 20 04:41:02 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 09:41:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-635) Add and elements to UrlMonitor in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4408935.1619.1308559262425.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-635. ------------------------------------ Resolution: Fixed > Add and elements to UrlMonitor in XML API > ------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of UrlMonitor. -- This 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 Jun 20 04:41:00 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 09:41:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-637) Update XML Schema to account for and elements in UrlMonitor In-Reply-To: <31258569.1616.1308557575489.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14643930.1618.1308559260124.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-637: ----------------------------------- Description: {code:xml} ... false ... {code} > Update XML Schema to account for and elements in UrlMonitor > ------------------------------------------------------------------------------------- > > Key: BIOCAT-637 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 06:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 20 Jun 2011 11:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-637) Update XML Schema to account for and elements in UrlMonitor In-Reply-To: <31258569.1616.1308557575489.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17675017.1620.1308566035490.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-637 started by Jiten Bhagat. > Update XML Schema to account for and elements in UrlMonitor > ------------------------------------------------------------------------------------- > > Key: BIOCAT-637 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 06:40:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 11:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-637) Update XML Schema to account for and elements in ServiceTest In-Reply-To: <31258569.1616.1308557575489.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <31760560.1621.1308566455391.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-637: ----------------------------------- Summary: Update XML Schema to account for and elements in ServiceTest (was: Update XML Schema to account for and elements in UrlMonitor) > Update XML Schema to account for and elements in ServiceTest > -------------------------------------------------------------------------------------- > > Key: BIOCAT-637 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 06:44:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 11:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-636) Add an "activated" element to the ServiceTest API representation In-Reply-To: <24178350.1570.1308316795379.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14256419.1622.1308566695382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-636: ----------------------------------- Summary: Add an "activated" element to the ServiceTest API representation (was: Add an "activated" element to the UrlMonitor API representation) > Add an "activated" element to the ServiceTest API representation > ---------------------------------------------------------------- > > Key: BIOCAT-636 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-636 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.1 > > Original Estimate: 30 minutes > Remaining Estimate: 30 minutes > -- This 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 Jun 20 06:44:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 11:44:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-635) Add and elements to ServiceTest in XML API In-Reply-To: <25554177.1567.1308314635351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9940615.1623.1308566697682.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-635: ----------------------------------- Summary: Add and elements to ServiceTest in XML API (was: Add and elements to UrlMonitor in XML API) Description: and elements are required just below the element of the XML representation of ServiceTest. was: and elements are required just below the element of the XML representation of UrlMonitor. > Add and elements to ServiceTest in XML API > -------------------------------------------------------------------- > > Key: BIOCAT-635 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-635 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > > and elements are required just below the element of the XML representation of ServiceTest. -- 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 Jun 20 08:28:37 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Jun 2011 08:28:37 -0400 (EDT) Subject: [BioCatalogue-developers] [2428] trunk/app/controllers/application_controller.rb: Small bugfix for the logging of search queries done on the services index Message-ID: <20110620122837.A15CC1858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 20 08:29:55 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Jun 2011 08:29:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2429] trunk/app/controllers/application_controller.rb: Don' t log search here, since it's already logged in the index log Message-ID: <20110620122955.C96BB1858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 20 08:48:15 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Jun 2011 08:48:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2430] trunk/public/2009/xml/rest/schema-v1.xsd: [BIOCAT-637] Updated XML schema for new fields in ServiceTest Message-ID: <20110620124815.689581858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 20 08:58:21 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Jun 2011 08:58:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2431] trunk/lib/bio_catalogue: Refactored out the search results class into a separate module Message-ID: <20110620125822.06F031598071@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jun 20 09:08:10 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Jun 2011 09:08:10 -0400 (EDT) Subject: [BioCatalogue-developers] [2432] trunk: - Updated the ServiceTestController so that when a ServiceTest is enabled/ disabled the user is stays on the same page as opposed to being redirected to /services/{id}#testscripts Message-ID: <20110620130810.AF1991858372@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jun 20 09:24:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 14:24:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (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) Message-ID: <27341174.1627.1308576295454.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.2 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 Jun 20 09:30:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 14:30:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <17448542.1628.1308576655428.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=16910#comment-16910 ] Mannie Tagarira commented on BIOCAT-638: ---------------------------------------- Consider adding a button in the web UI to allow users to select which example_endpoint annotations to use for monitoring. This button will only be shown on example_endpoint annotations only. The specified annotation will be hidden from public view if it has been selected for monitoring use. What should be done about existing example_endpoint annotations that are in use (since some were specifically added for monitoring whereas other were not)? > 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: 1.0.2 > > > 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 Jun 20 09:42:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 20 Jun 2011 14:42:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-637) Update XML Schema to account for and elements in ServiceTest In-Reply-To: <31258569.1616.1308557575489.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13251284.1629.1308577375372.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-637 stopped by Jiten Bhagat. > Update XML Schema to account for and elements in ServiceTest > -------------------------------------------------------------------------------------- > > Key: BIOCAT-637 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 09:44:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 20 Jun 2011 14:44:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-637) Update XML Schema to account for and elements in ServiceTest In-Reply-To: <31258569.1616.1308557575489.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2965245.1630.1308577495384.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-637. --------------------------------- Resolution: Fixed > Update XML Schema to account for and elements in ServiceTest > -------------------------------------------------------------------------------------- > > Key: BIOCAT-637 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-637 > Project: BioCatalogue > Issue Type: Task > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > {code:xml} > ... > false > > ... > {code} -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 11:16:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 16:16:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-639) Some RestMethods have description annotations but the REST API shows nothing Message-ID: <18058490.1631.1308583015448.JavaMail.jira@rosalind.cs.man.ac.uk> Some RestMethods have description annotations but the REST API shows nothing ---------------------------------------------------------------------------- Key: BIOCAT-639 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-639 Project: BioCatalogue Issue Type: Bug Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Critical Fix For: 1.0.1 -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jun 20 11:16:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 20 Jun 2011 16:16:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-639) Some RestMethods have description annotations but the REST API shows nothing In-Reply-To: <18058490.1631.1308583015448.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17365417.1632.1308583018598.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-639?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-639 started by Mannie Tagarira. > Some RestMethods have description annotations but the REST API shows nothing > ---------------------------------------------------------------------------- > > Key: BIOCAT-639 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-639 > Project: BioCatalogue > Issue Type: Bug > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Jun 21 03:51:36 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Jun 2011 03:51:36 -0400 (EDT) Subject: [BioCatalogue-developers] [2433] trunk/app: [BIOCAT-639] Message-ID: <20110621075136.ADD591598071@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 21 03:56:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 08:56:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-640) Look into the differentiating between "provider descriptions" and "preferred descriptions" in the REST API for entities such as RestMethods, SoapOperations, etc Message-ID: <18747788.1637.1308643015517.JavaMail.jira@rosalind.cs.man.ac.uk> Look into the differentiating between "provider descriptions" and "preferred descriptions" in the REST API for entities such as RestMethods, SoapOperations, etc ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-640 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-640 Project: BioCatalogue Issue Type: Improvement Components: REST API Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.2.0 At the moment, the preferred_description method on service components returns the description provided by the service provider. If this description does not exist, the first description annotation is used instead. In future, the notion of a preferred description may be change to take into account descriptions which have been "approved" by curators. A way of differentiating between these two types of descriptions may therefore be needed. -- This 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 Jun 21 04:00:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 09:00:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-639) Some RestMethods have description annotations but the REST API shows nothing In-Reply-To: <18058490.1631.1308583015448.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8557761.1638.1308643255392.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-639?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-639. ------------------------------------ Resolution: Fixed Fixed in revision 2433 > Some RestMethods have description annotations but the REST API shows nothing > ---------------------------------------------------------------------------- > > Key: BIOCAT-639 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-639 > Project: BioCatalogue > Issue Type: Bug > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.0.1 > > -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 05:21:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 10:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-423) Fix Service Provider name autocomplete to show escaped names In-Reply-To: <29360194.6732.1277733735420.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13400544.1641.1308648115388.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-423: ----------------------------------- Component/s: Service Provider Management (was: Misc Codebase) > Fix Service Provider name autocomplete to show escaped names > ------------------------------------------------------------ > > Key: BIOCAT-423 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423 > Project: BioCatalogue > Issue Type: Bug > Components: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.0.2 > > > When a Service Provider has a name like "my provider ", it is shown as "my provider" in the autocomplete. When it has been selected, it will fill in the text box with "my provider alert("warning...");". > The autocomplete should show the name as is... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 05:21:58 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 10:21:58 +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: <17505482.1642.1308648118574.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: ----------------------------------- Component/s: REST Services Support > 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 > Fix For: 1.0.2 > > > 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 Jun 21 05:30:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 10:30:55 +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: <32529138.1645.1308648655367.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: ----------------------------------- Summary: Investigate the breakage related to the service monitoring framework (was: Investigate the breakage related to the test harness) Component/s: Service Monitoring Test scripts ARE being executed on a daily basis; they are, however, all failing... > 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 > Fix For: 1.0.1 > > > 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 Tue Jun 21 05:33:56 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 10:33:56 +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: <1833816.1646.1308648836773.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=16915#comment-16915 ] Mannie Tagarira edited comment on BIOCAT-617 at 21/06/11 10:33: ---------------------------------------------------------------- Test scripts ARE being executed on a daily basis; they are, however, all failing... (a good candidate for this case are the INB services). The last test script (noticed) that passed passed on the 31st of May 2011; /service_tests/2398 was (Author: mannie): Test scripts ARE being executed on a daily basis; they are, however, all failing... > 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 > Fix For: 1.0.1 > > > 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 Tue Jun 21 05:36:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 10:36:55 +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: <31140726.1647.1308649015358.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=16915#comment-16915 ] Mannie Tagarira edited comment on BIOCAT-617 at 21/06/11 10:36: ---------------------------------------------------------------- Test scripts ARE being executed on a daily basis; they are, however, all failing... (a good candidate for this case are the INB services). The last test script (noticed) that passed passed on the 31st of May 2011; /service_tests/2398 It is also the case that test scripts that USED TO pass and then failed havent been monitored for months as well. was (Author: mannie): Test scripts ARE being executed on a daily basis; they are, however, all failing... (a good candidate for this case are the INB services). The last test script (noticed) that passed passed on the 31st of May 2011; /service_tests/2398 > 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 > Fix For: 1.0.1 > > > 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 Tue Jun 21 05:58:04 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 10:58:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-641) Find a better way to differentiate (at a glace) between services or soap operations with the same name Message-ID: <14314667.1654.1308650284956.JavaMail.jira@rosalind.cs.man.ac.uk> Find a better way to differentiate (at a glace) 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 Reporter: Mannie Tagarira Assignee: Mannie Tagarira Fix For: 1.1.0 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. -- This 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 Jun 21 06:00:03 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 11:00:03 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-641) Find a better way to differentiate (at a glace) between services or soap operations with the same name In-Reply-To: <14314667.1654.1308650284956.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6327417.1658.1308650403561.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: ----------------------------------- Description: 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. was: 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. Component/s: SOAP Services Support > Find a better way to differentiate (at a glace) 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 > > > 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 Tue Jun 21 06:03:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 11:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-641) Find a better way to differentiate (at a glace) between services or soap operations with the same name In-Reply-To: <14314667.1654.1308650284956.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19263512.1661.1308650635358.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: ----------------------------------- Fix Version/s: 1.0.2 (was: 1.1.0) > Find a better way to differentiate (at a glace) 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: 1.0.2 > > > 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 Tue Jun 21 06:05:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 11:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-641) Find a better way to differentiate (at a glace) between services or soap operations with the same name In-Reply-To: <14314667.1654.1308650284956.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11891949.1662.1308650755349.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: -service_providers-240#services.jpg > Find a better way to differentiate (at a glace) 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: 1.0.2 > > 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 issues at mygrid.org.uk Tue Jun 21 07:01:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 12:01:55 +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: <14177537.1666.1308654115357.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=16915#comment-16915 ] Mannie Tagarira edited comment on BIOCAT-617 at 21/06/11 12:01: ---------------------------------------------------------------- Test scripts ARE being executed on a daily basis; they are, however, all failing... (a good candidate for this case are the INB services). The last test script (noticed) that passed passed on the 31st of May 2011; /service_tests/2398 It may be worth noting that all EMBOSS test scripts are passing. It is also the case that test scripts that USED TO pass and then failed havent been monitored for months as well. was (Author: mannie): Test scripts ARE being executed on a daily basis; they are, however, all failing... (a good candidate for this case are the INB services). The last test script (noticed) that passed passed on the 31st of May 2011; /service_tests/2398 It is also the case that test scripts that USED TO pass and then failed havent been monitored for months as well. > 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 > Fix For: 1.0.1 > > > 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 Tue Jun 21 09:04:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 21 Jun 2011 14:04:55 +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: <32360718.1671.1308661495358.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: ----------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) Priority: Blocker (was: Major) > 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: 1.0.2 > > > 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 Tue Jun 21 09:24:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 14:24:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (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: <15658603.1673.1308662695384.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-611?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-611: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-21 14:24 Start Date: 2011-05-12 14:24 Worklog Time Spent: 2 weeks Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 2 weeks Worklog Id: (was: 10510) > 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 Jun 21 09:26:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 14:26:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7647893.1674.1308662815395.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-536: -------------------------------- Description: Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] (was: Update the annotation field mappings both in the API docs and wiki (http://www.biocatalogue.org/wiki/doku.php?id=development:annotation)) > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 09:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 14:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10830164.1675.1308663115378.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16919#comment-16919 ] Jiten Bhagat commented on BIOCAT-536: ------------------------------------- >Does the ServiceProvider resource really support display_name annotations? If not, this mapping needs to be removed. Good point. Removed. > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 09:31:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 14:31:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20830147.1676.1308663118265.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16919#comment-16919 ] Jiten Bhagat edited comment on BIOCAT-536 at 21/06/11 14:31: ------------------------------------------------------------- bq. Does the ServiceProvider resource really support display_name annotations? If not, this mapping needs to be removed. Good point. Removed. was (Author: jbhagat): >Does the ServiceProvider resource really support display_name annotations? If not, this mapping needs to be removed. Good point. Removed. > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 09:32:00 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 14:32:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14780669.1677.1308663120613.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16920#comment-16920 ] Jiten Bhagat commented on BIOCAT-536: ------------------------------------- The [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] still needs to be updated (we'll do that after the release and as part of the docs process). > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 09:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 14:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-536) Update the annotation field mappings both in the API docs and wiki In-Reply-To: <7210831.567.1289922389159.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <8021507.1678.1308663235349.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-536: -------------------------------- Parent: BIOCAT-535 Issue Type: Sub-task (was: Task) > Update the annotation field mappings both in the API docs and wiki > ------------------------------------------------------------------ > > Key: BIOCAT-536 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-536 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Update the annotation field mappings both in the [API docs|http://www.biocatalogue.org/wiki/doku.php?id=public:api#annotation_fields_breakdown] and the [Annotations wiki page|http://www.biocatalogue.org/wiki/doku.php?id=development:annotation] -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Jun 21 09:49:12 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Jun 2011 09:49:12 -0400 (EDT) Subject: [BioCatalogue-developers] [2434] trunk: Fixes to the stats generation for search. Message-ID: <20110621134912.2C65F185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jun 21 10:15:30 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Jun 2011 10:15:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2435] trunk/script/biocatalogue/similar_searches_report.rb: Redirect output of script to a file Message-ID: <20110621141530.F163B185836C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 21 10:21:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 15:21:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-642) Failing to parse WSDL: http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl Message-ID: <22897105.1684.1308666115355.JavaMail.jira@rosalind.cs.man.ac.uk> Failing to parse WSDL: http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl -------------------------------------------------------------------------- Key: BIOCAT-642 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-642 Project: BioCatalogue Issue Type: Bug Components: SOAP Services Support Affects Versions: 1.0.1 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.2 The following WSDL: {code} http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl {code} ... fails when trying to parse it. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 21 10:24:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 15:24:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-584) Stop monitoring of the test site In-Reply-To: <18223488.107.1300357107911.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4158991.1685.1308666296791.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16759#comment-16759 ] Jiten Bhagat edited comment on BIOCAT-584 at 21/06/11 15:24: ------------------------------------------------------------- Looks like the monitoring has been switched off on the test site already. When doing releases we need this to be switched back on (even if just temporarily or manually running it) so that we can check that the monitoring system is working. was (Author: jbhagat): Looks like the monitoring has been switched on the test site already. When doing releases we need this to be switched back on (even if just temporarily or manually running it) so that we can check that the monitoring system is working. > Stop monitoring of the test site > -------------------------------- > > Key: BIOCAT-584 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > Stop monitoring of the test site as no one is really checking these and they are redundant given the live site monitoring -- This 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 Jun 21 10:24:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 15:24:59 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-584) Stop monitoring of the test site In-Reply-To: <18223488.107.1300357107911.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12605909.1686.1308666299453.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-584. --------------------------------- Resolution: Fixed > Stop monitoring of the test site > -------------------------------- > > Key: BIOCAT-584 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-584 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.0.1 > > Original Estimate: 1 hour > Remaining Estimate: 1 hour > > Stop monitoring of the test site as no one is really checking these and they are redundant given the live site monitoring -- This 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 Jun 21 10:26:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 21 Jun 2011 15:26:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-643) Test out v1.0.1 on the test site Message-ID: <863672.1687.1308666415346.JavaMail.jira@rosalind.cs.man.ac.uk> 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 Thu Jun 23 06:40:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 23 Jun 2011 11:40:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-644) Failing to create new REST endpoints Message-ID: <5731097.1711.1308825655356.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.1 To replicate: # 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 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 Jun 23 06:42:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 23 Jun 2011 11:42:55 +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: <9768624.1712.1308825775366.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 ] Jiten Bhagat updated BIOCAT-644: -------------------------------- Description: To replicate: # 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://http//sift.bii.a-star.edu.sg/www/SIFT_dbSNP.html?id={value}") 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!* was: To replicate: # 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 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!* > 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: 1.0.1 > > > To replicate: > # 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://http//sift.bii.a-star.edu.sg/www/SIFT_dbSNP.html?id={value}") 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 Jun 23 06:42:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 23 Jun 2011 11:42:57 +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: <4731907.1713.1308825777665.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 ] Jiten Bhagat updated BIOCAT-644: -------------------------------- Description: 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://http//sift.bii.a-star.edu.sg/www/SIFT_dbSNP.html?id={value}") 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!* was: To replicate: # 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://http//sift.bii.a-star.edu.sg/www/SIFT_dbSNP.html?id={value}") 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!* > 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: 1.0.1 > > > To duplicate the issue: > # Log in > # Register a new REST service or go to an existing one > # Click on the "REST Endpoints" tab > # Click on "Add New Endpoints" > # Put in a valid new REST endpoint in the text box (e.g. "http://http//sift.bii.a-star.edu.sg/www/SIFT_dbSNP.html?id={value}") 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 Jun 23 06:46:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 23 Jun 2011 11:46:55 +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: <307234.1714.1308826015361.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 ] Jiten Bhagat updated BIOCAT-644: -------------------------------- Description: 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!* was: 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://http//sift.bii.a-star.edu.sg/www/SIFT_dbSNP.html?id={value}") 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!* > 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: 1.0.1 > > > To duplicate the issue: > # Log in > # Register a new REST service or go to an existing one > # Click on the "REST Endpoints" tab > # Click on "Add New Endpoints" > # Put in a valid new REST endpoint in the text box (e.g. "http://example.org/test/{id}") and submit > You will get the following error message in the web interface: > {code} > The following endpoints could not be added: > ... > {code} > Looking at the logs and db, it looks like a {{RestResource}} is being created (but an incorrect one) but a corresponding {{RestMethod}} is not being created. > Also, possibly not relevant, I keep seeing this in the logs multiple times: > {code} > ERROROAuth::Signature::UnknownSignatureMethod > {code} > *This needs some thorough investigation!* -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jun 23 06:48:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 23 Jun 2011 11:48:55 +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: <31294863.1715.1308826135405.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=16929#comment-16929 ] Jiten Bhagat commented on BIOCAT-644: ------------------------------------- On further testing, this looks to be happening intermittently. Needs some thorough testing. > 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: 1.0.1 > > > To duplicate the issue: > # Log in > # Register a new REST service or go to an existing one > # Click on the "REST Endpoints" tab > # Click on "Add New Endpoints" > # Put in a valid new REST endpoint in the text box (e.g. "http://example.org/test/{id}") and submit > You will get the following error message in the web interface: > {code} > The following endpoints could not be added: > ... > {code} > Looking at the logs and db, it looks like a {{RestResource}} is being created (but an incorrect one) but a corresponding {{RestMethod}} is not being created. > Also, possibly not relevant, I keep seeing this in the logs multiple times: > {code} > ERROROAuth::Signature::UnknownSignatureMethod > {code} > *This needs some thorough investigation!* -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Jun 24 06:37:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 24 Jun 2011 11:37:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-645) Increase timeouts in Solr config Message-ID: <28716187.1820.1308911875468.JavaMail.jira@rosalind.cs.man.ac.uk> Increase timeouts in Solr config -------------------------------- Key: BIOCAT-645 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-645 Project: BioCatalogue Issue Type: Improvement Components: Search / Filtering / Browsing, Server Management Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 In the Solr config file (vendor/plugins/acts_as_solr/solr/solr/conf/solrconfig.xml) the timeouts are currently set at: {code} 5000 10000 {code} Increase these as timeouts are being hit as a result. Note that making them too high could cause some serious lock waiting situations, so proceed with caution! -- 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 Jun 24 06:40:01 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 24 Jun 2011 06:40:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2436] trunk/vendor/plugins/acts_as_solr/solr/solr/conf/solrconfig.xml: [ BIOCAT-645] Increased the timeouts in the Solr config. Message-ID: <20110624104001.77D161858363@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Fri Jun 24 06:41:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 24 Jun 2011 11:41:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-645) Increase timeouts in Solr config In-Reply-To: <28716187.1820.1308911875468.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3889966.1821.1308912115389.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-645?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16971#comment-16971 ] Jiten Bhagat commented on BIOCAT-645: ------------------------------------- In revision 2436, increased to: {code} 10000 15000 {code} > Increase timeouts in Solr config > -------------------------------- > > Key: BIOCAT-645 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-645 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > In the Solr config file (vendor/plugins/acts_as_solr/solr/solr/conf/solrconfig.xml) the timeouts are currently set at: > {code} > 5000 > 10000 > {code} > Increase these as timeouts are being hit as a result. > Note that making them too high could cause some serious lock waiting situations, so proceed with 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 Fri Jun 24 06:53:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 24 Jun 2011 11:53:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-646) Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) Message-ID: <16600212.1822.1308912835346.JavaMail.jira@rosalind.cs.man.ac.uk> Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) ------------------------------------------------------------------------------------------------------------- Key: BIOCAT-646 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646 Project: BioCatalogue Issue Type: Task Components: Search / Filtering / Browsing, Server Management Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 As mentioned here: http://wiki.apache.org/solr/SolrPerformanceFactors#OutOfMemoryErrors, out of memory errors could be the reason for lock timeouts and other issues in Solr. Check what the memory allocation is for Tomcat on the EBI servers and also play with this on the staging server VM to see if an optimal memory setting can be found. -- This 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 Jun 24 07:18:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 24 Jun 2011 12:18:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-646) Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) In-Reply-To: <16600212.1822.1308912835346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17944078.1823.1308914335355.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16972#comment-16972 ] Jiten Bhagat commented on BIOCAT-646: ------------------------------------- In the file (TOMCAT_HOME}/bin/catalina.sh I added: {code} JAVA_OPTS="-Xms512m -Xmx1024m" {code} ... and this seemed to help. Suggest to the EBI admins to change their settings to this as well. > Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-646 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > As mentioned here: http://wiki.apache.org/solr/SolrPerformanceFactors#OutOfMemoryErrors, out of memory errors could be the reason for lock timeouts and other issues in Solr. > Check what the memory allocation is for Tomcat on the EBI servers and also play with this on the staging server VM to see if an optimal memory setting can be found. -- This 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 Jun 24 07:20:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 24 Jun 2011 12:20:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-645) Increase timeouts in Solr config In-Reply-To: <28716187.1820.1308911875468.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28862285.1824.1308914455408.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-645?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-645. --------------------------------- Resolution: Implemented This timeout change seems to have helped. Closing this issue for now. > Increase timeouts in Solr config > -------------------------------- > > Key: BIOCAT-645 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-645 > Project: BioCatalogue > Issue Type: Improvement > Components: Search / Filtering / Browsing, Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > In the Solr config file (vendor/plugins/acts_as_solr/solr/solr/conf/solrconfig.xml) the timeouts are currently set at: > {code} > 5000 > 10000 > {code} > Increase these as timeouts are being hit as a result. > Note that making them too high could cause some serious lock waiting situations, so proceed with 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 Fri Jun 24 07:20:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 24 Jun 2011 12:20:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Issue Comment Edited: (BIOCAT-646) Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) In-Reply-To: <16600212.1822.1308912835346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23538654.1825.1308914457861.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16972#comment-16972 ] Jiten Bhagat edited comment on BIOCAT-646 at 24/06/11 12:19: ------------------------------------------------------------- In the file {TOMCAT_HOME}/bin/catalina.sh I added: {code} JAVA_OPTS="-Xms512m -Xmx1024m" {code} ... and this seemed to help. Suggest to the EBI admins to change their settings to this as well. was (Author: jbhagat): In the file (TOMCAT_HOME}/bin/catalina.sh I added: {code} JAVA_OPTS="-Xms512m -Xmx1024m" {code} ... and this seemed to help. Suggest to the EBI admins to change their settings to this as well. > Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-646 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > As mentioned here: http://wiki.apache.org/solr/SolrPerformanceFactors#OutOfMemoryErrors, out of memory errors could be the reason for lock timeouts and other issues in Solr. > Check what the memory allocation is for Tomcat on the EBI servers and also play with this on the staging server VM to see if an optimal memory setting can be found. -- This 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 Jun 24 08:42:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 24 Jun 2011 13:42:55 +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: <2486907.1826.1308919375384.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: ----------------------------------- Fix Version/s: 1.0.2 (was: 1.0.1) > 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: 1.0.2 > > > 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 Fri Jun 24 08:47:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 24 Jun 2011 13:47:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-647) If a service has a query parameter AND a template parameter of the same name, one of them is ignored Message-ID: <17763498.1827.1308919675350.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.2 Registering the endpoint "POST http://example.org/iphiphpih/{id}?id={value}" doesn't generate the correct URL template 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 Fri Jun 24 08:49:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 24 Jun 2011 13:49:55 +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: <223395.1828.1308919795369.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: ----------------------------------- Description: Registering the following endpoint doesn't generate the correct URL template {code:none} POST http://example.org/iphiphpih/{id}?id={value} {code} the template becomes "http://example.org/iphiphpih/{id}" it misses out the "id" query parameter was: Registering the endpoint "POST http://example.org/iphiphpih/{id}?id={value}" doesn't generate the correct URL template the template becomes "http://example.org/iphiphpih/{id}" it misses out the "id" query parameter > 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: 1.0.2 > > > Registering the following endpoint doesn't generate the correct URL template > {code:none} > POST http://example.org/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 Fri Jun 24 08:49:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Fri, 24 Jun 2011 13:49:57 +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: <19426211.1829.1308919797743.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: ----------------------------------- Description: 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 was: Registering the following endpoint doesn't generate the correct URL template {code:none} POST http://example.org/iphiphpih/{id}?id={value} {code} the template becomes "http://example.org/iphiphpih/{id}" it misses out the "id" query parameter > 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: 1.0.2 > > > 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 Mon Jun 27 11:49:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 27 Jun 2011 16:49:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-475) Rendering problem in safari when rendering search results In-Reply-To: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10421375.2081.1309189795441.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17082#comment-17082 ] Mannie Tagarira commented on BIOCAT-475: ---------------------------------------- THIS particular issue seems to have dissolved over the releases. There is however an issue regarding how the BioCatalogue is framed within WebKit powered browsers. I have noticed this on ALL Apple devices and a couple of other mobile platforms. > Rendering problem in safari when rendering search results > --------------------------------------------------------- > > Key: BIOCAT-475 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.0.2 > > Attachments: screenshot-1.jpg > > > buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 04:23:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 09:23:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-648) Disabled status of service tests not shown in monitoring tab on service profile page Message-ID: <31783970.2125.1309249435437.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Fix For: 1.0.2 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 Jun 28 04:25:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 09:25:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-649) Investigate whether those responsible for a service can see disabled service tests Message-ID: <3163840.2126.1309249555347.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Priority: Critical Fix For: 1.0.2 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 Jun 28 04:27:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 09:27:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-650) Docs don't indicate what test scripts should return Message-ID: <25235642.2127.1309249675351.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.2 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 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 Tue Jun 28 04:35:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 09:35:55 +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: <25510891.2128.1309250155369.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 ] Jiten Bhagat updated BIOCAT-650: -------------------------------- Description: 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. was: 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 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. > 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: 1.0.2 > > > 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 jits at cs.man.ac.uk Tue Jun 28 04:36:15 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Jun 2011 09:36:15 +0100 Subject: [BioCatalogue-developers] [Biocatalogue-support] BioCatalogue feedback from Rob Finn (finnr@janelia.hhmi.org) In-Reply-To: <4e08bc67c38d0_2741b9bb1341f1@ves-hx-2f.ebi.ac.uk.tmail> References: <4e08bc67c38d0_2741b9bb1341f1@ves-hx-2f.ebi.ac.uk.tmail> Message-ID: <4E09927F.10903@cs.man.ac.uk> Hi Rob, I believe the scripts need to return an integer code where 0 means everything went okay and anything apart from that indicates an error code. You may have come across the documentation page for test scripts - - but major apologies that we haven't made the return code requirement clearer and provided more guidance for test script writers. I've flagged this on our task list [1]. In the meantime, I have disabled your test so that it doesn't produce any more failing results. When you get the chance, please could you update the test script and then you can submit it as a new one to your service and delete the old one with it's failing history (or feel free to request us to do so). Let me know if I can assist in any other way. Kind regards, Jiten Bhagat [1] http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-650 On 27/06/2011 18:22, contact at biocatalogue.org wrote: > > BioCatalogue feedback from: Rob Finn (finnr at janelia.hhmi.org) > > Subject: phmmer test failing > > Message: > Hi, > > I recently uploaded a test script for one of the services that I am responsible for: http://www.biocatalogue.org/services/2783#test-scripts > > However, it keeps failing the tests. Maybe I missed something on the site, but is there an expected response from test script? At the moment it just spits out the response. From the interface, I can not currently see why it is failing. Could you point me in the right direction so that I can fix it please? > > Thanks, > > Rob > _______________________________________________ > Biocatalogue-support mailing list > Biocatalogue-support at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-support From jits at cs.man.ac.uk Tue Jun 28 04:39:41 2011 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Jun 2011 09:39:41 +0100 Subject: [BioCatalogue-developers] Potential Jira Tasks for 1.1 In-Reply-To: <3BFAFEE9-CBA6-429F-8D60-9200F68C3BCD@gmail.com> References: <3BFAFEE9-CBA6-429F-8D60-9200F68C3BCD@gmail.com> Message-ID: <4E09934D.2070508@cs.man.ac.uk> Excellent! Thanks Mannie. I think we should go ahead and just merge v1.0.2 into v1.1 and aim for a v1.1 release in 3-4 weeks time. Then from v1.1 we can fork to the "CatalogueX" new codebase. How does that sound to you? If we agree, then I'll bulk update the tasks to change the version number. In the meantime, please could you start work on some of the existing tasks for the v1.0.1 release? (especially the updating of the API docs). Jits On 28/06/2011 09:10, Mannie Tagarira wrote: > Hi Jits, > > As requested I have filtered the 1.0.2 task list down; whether or not > these are doable over a 2 day period is a different topic... > [#BIOCAT-644] Failing to create new REST endpoints - myGrid > > [#BIOCAT-632] Improve the performance of API calls now that > return more details - myGrid > > [#BIOCAT-548] Investigate why there is a huge number of search entries > in the activity logs with empty search terms - myGrid > > [#BIOCAT-542] After deleting an annotation from the service overview, > it is not deterministic which of the tabs is shown to the user - > myGrid > [#BIOCAT-634] Figure out how to properly record monitoring information > for REST endpoints tested using example_endpoint annotations - myGrid > > [#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) - myGrid > > [#BIOCAT-447] Test SSL on the BioCatalogue main site - myGrid > > [#BIOCAT-243] Make ALL routes/pages HTTPS - myGrid > > [#BIOCAT-568] Double rendering problem when ssl is switched on! - > myGrid > [#BIOCAT-509] Document the user roles and privileges used in the > system - myGrid > [#BIOCAT-500] Document how to use and update the VM - myGrid > > [#BIOCAT-561] Update the public facing BioCatalogue Roadmap - myGrid > > > Regards, > Mannie > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jun 28 05:31:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:31:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-231) Enable tag filter not persisting Message-ID: <28748692.2135.1309253515389.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-231: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Enable tag filter not persisting > -------------------------------- > > Key: BIOCAT-231 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-231 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > the 'enable tag filter' doesn't stay. i have to keep on clicking on it anytime i want to browse for new services...very frustrating. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:03 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:03 +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: <6766477.2138.1309253523166.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: 1.1.0 (was: 1.0.2) > Create a new VM for the BioCatalogue system > ------------------------------------------- > > Key: BIOCAT-499 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-499 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > There is an old Fedora 11 VM that was used previously to allow people to easily set up their own BioCatalogue instance. This is now badly out of date. > So create a new VM (preferably Ubuntu based) with all the latest stuff. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:06 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:06 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-632) Improve the performance of API calls now that return more details In-Reply-To: <31372983.1470.1308220615376.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5376621.2139.1309253526112.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-632?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-632: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Improve the performance of API calls now that return more details > ----------------------------------------------------------------------------- > > Key: BIOCAT-632 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-632 > Project: BioCatalogue > Issue Type: Improvement > Components: Performance / Optimisations, REST API > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > Due to the changes introduced in http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-662, the performance of API calls to resources has slowed down considerably. This is largely to do with the large amount of partial rendering. > Improve this! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:08 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:08 +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: <15468068.2140.1309253528591.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > 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 Jun 28 05:32:11 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:11 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-591) Investigate running multiple delayed_job workers on the live EBI setup In-Reply-To: <14672693.779.1305818395351.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19659097.2141.1309253531392.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-591?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-591: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Investigate running multiple delayed_job workers on the live EBI setup > ---------------------------------------------------------------------- > > Key: BIOCAT-591 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-591 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Having only one delayed_job worker running means that if it get's clogged up or freezes then all jobs stop getting processed. > Look into having multiple (at least 2 delayed_job workers) running. Possibly one per node. > This needs to be done in a careful manner so as not to break the current set up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:16 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-423) Fix Service Provider name autocomplete to show escaped names In-Reply-To: <29360194.6732.1277733735420.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1564159.2143.1309253536666.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-423: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Fix Service Provider name autocomplete to show escaped names > ------------------------------------------------------------ > > Key: BIOCAT-423 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-423 > Project: BioCatalogue > Issue Type: Bug > Components: Service Provider Management > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Fix For: 1.1.0 > > > When a Service Provider has a name like "my provider ", it is shown as "my provider" in the autocomplete. When it has been selected, it will fill in the text box with "my provider alert("warning...");". > The autocomplete should show the name as is... -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:19 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-548) Investigate why there is a huge number of search entries in the activity logs with empty search terms In-Reply-To: <9364871.312.1291218472813.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28922613.2144.1309253539498.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-548: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Investigate why there is a huge number of search entries in the activity logs with empty search terms > ----------------------------------------------------------------------------------------------------- > > Key: BIOCAT-548 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-548 > Project: BioCatalogue > Issue Type: Task > Components: Data > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > It appears that the activity logs indicate a high number of searches. However, the majority of these search are not associated with any search term. This needs to be investigated. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:14 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:14 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-500) Document how to use and update the VM In-Reply-To: <16227861.9965.1286463195301.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11073354.2142.1309253534035.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-500: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Document how to use and update the VM > ------------------------------------- > > Key: BIOCAT-500 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > Original Estimate: 3 hours > Remaining Estimate: 3 hours > > Document how to set up, use and update the BioCatalogue VM. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:24 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:24 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-542) After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user In-Reply-To: <20071148.102.1290181372807.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21204367.2146.1309253544954.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-542: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > After deleting an annotation from the service overview, it is not deterministic which of the tabs is shown to the user > ---------------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-542 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-542 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > -- 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 Jun 28 05:32:27 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:27 +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: <31721697.2147.1309253547553.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 > 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 Jun 28 05:32:30 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:30 +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: <20895148.2148.1309253550119.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > > /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 Jun 28 05:32:33 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:33 +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: <13670946.2149.1309253553096.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: Jiten Bhagat > 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 Jun 28 05:32:35 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:35 +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: <16913008.2150.1309253555602.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: 1.1.0 (was: 1.0.2) > 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 > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > 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 Jun 28 05:32:38 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:38 +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: <7433128.2151.1309253558647.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > > 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 Jun 28 05:32:41 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:41 +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: <9781418.2152.1309253561302.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > -- 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 Jun 28 05:32:46 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:46 +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: <16609556.2154.1309253566185.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > > 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 Jun 28 05:32:49 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:49 +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: <13290695.2155.1309253569131.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: 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. -- This 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 Jun 28 05:32:51 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:51 +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: <28369752.2156.1309253571651.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > > 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 Jun 28 05:32:54 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:54 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-249) error_to_home and other such should return appropriate HTTP codes Message-ID: <2008015.2157.1309253574208.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-249: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > error_to_home and other such should return appropriate HTTP codes > ----------------------------------------------------------------- > > Key: BIOCAT-249 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-249 > Project: BioCatalogue > Issue Type: Improvement > Components: Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Methods like error_to_home etc should return appropriate HTTP status codes. Right now there's just a redirect, and no way of telling that a genuine error has occurred. > Need to rethink this whole thing. Maybe beef up the 404 etc error pages and have those served up. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:56 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-475) Rendering problem in safari when rendering search results In-Reply-To: <32851103.9736.1285188315321.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <1381427.2158.1309253576552.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-475: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Rendering problem in safari when rendering search results > --------------------------------------------------------- > > Key: BIOCAT-475 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-475 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > Attachments: screenshot-1.jpg > > > buttons and listing are misaligned in safari when search results are returned. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:32:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:59 +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: <15793072.2159.1309253579269.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 ] Jiten Bhagat updated BIOCAT-644: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Tue Jun 28 05:33:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:02 +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: <12968370.2160.1309253582018.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 > 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 Jun 28 05:33:05 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:05 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-289) Filters disappear when I switch between different views Message-ID: <24696864.2161.1309253585133.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-289?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-289: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Filters disappear when I switch between different views > ------------------------------------------------------- > > Key: BIOCAT-289 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-289 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > When I filter services (e.g by provider, location etc.) and switch to simple view for example, it clears off all the selected filters. > Need to remember the filters selected when switching views. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:33:07 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:07 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-362) Add archive/unarchive events to the ActivityLogs and then the activity feed(s) In-Reply-To: <27841565.1720.1275053057051.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16857278.2162.1309253587818.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-362?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-362: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Add archive/unarchive events to the ActivityLogs and then the activity feed(s) > ------------------------------------------------------------------------------ > > Key: BIOCAT-362 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-362 > Project: BioCatalogue > Issue Type: New Feature > Components: Activity Logging / Feeds / Notifications, Web Interface > Environment: RoR > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > Original Estimate: 5 hours > Remaining Estimate: 5 hours > > Currently, no ActivityLog events are being made when archive/unarchive services occur. Need to log these events and then show them 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 Tue Jun 28 05:33:10 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:10 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-642) Failing to parse WSDL: http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl In-Reply-To: <22897105.1684.1308666115355.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7950050.2163.1309253590549.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-642?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-642: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Failing to parse WSDL: http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl > -------------------------------------------------------------------------- > > Key: BIOCAT-642 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-642 > Project: BioCatalogue > Issue Type: Bug > Components: SOAP Services Support > Affects Versions: 1.0.1 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > The following WSDL: > {code} > http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_2_ws0.wsdl > {code} > ... fails when trying to parse it. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:33:13 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:13 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-22) Broken links in the feta imports Message-ID: <31702182.2164.1309253593202.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-22?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-22: ------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Broken links in the feta imports > -------------------------------- > > Key: BIOCAT-22 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-22 > Project: BioCatalogue > Issue Type: Bug > Components: Content Acquisition, Data > Reporter: Franck Tanoh > Assignee: Jiten Bhagat > Fix For: 1.1.0 > > > Revisit links from the feta import. Some (example workflows listed in the other annotation in biocat) don't work anymore: > http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/extractPosition_workflow.xml (blast should be capital BLAST) > http://www.mygrid.org.uk/feta/mygrid/example_workflow/DDBJ/blast/getSupportDatabaseList_workflow.xml (doesn't exist) -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:33:15 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:15 +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: <5929421.2165.1309253595614.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: Jiten Bhagat > 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 Jun 28 05:33:18 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:18 +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: <7416209.2166.1309253598698.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: Jiten Bhagat > 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 Jun 28 05:33:21 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <17633864.2167.1309253601435.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 ] Jiten Bhagat updated BIOCAT-413: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Tue Jun 28 05:33:23 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:23 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-260) Tooltip hover issues Message-ID: <22569343.2168.1309253603954.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-260?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-260: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Tooltip hover issues > -------------------- > > Key: BIOCAT-260 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-260 > Project: BioCatalogue > Issue Type: Bug > Reporter: Sergejs Aleksejevs > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.0 > > > As reported by Sergey: > "I've just noticed that the tooltips over 'Latest Services Feed' and > the 'Follow me on Twitter' icons in the action bar appear under these > icons themselves (this doesn't normally happen with other tooltips - at > least not that I've seen)." > Occurs in FF and IE apparently. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:33:26 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:26 +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: <22917659.2169.1309253606334.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > -- 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 Jun 28 05:33:28 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:28 +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: <30507721.2170.1309253608918.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 ] Jiten Bhagat updated BIOCAT-650: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Tue Jun 28 05:33:32 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:32 +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: <27344508.2171.1309253612680.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: 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 -- This 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 Jun 28 05:33:35 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:35 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-487) Exception generated by linked_data handler In-Reply-To: <18811203.9902.1285777575311.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32944356.2172.1309253615287.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-487: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Exception generated by linked_data handler > ------------------------------------------ > > Key: BIOCAT-487 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-487 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Affects Versions: 1.0.0 > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Minor > Fix For: 1.1.0 > > > LinkedDataHandler metal app... > Intial URL: /services/10 > undefined method `to_sym' for nil:NilClass > /rails/biocatalogue/app/metal/linked_data_handler.rb:86:in `call' > rails/biocatalogue/app/metal/linked_data_handler.rb:43:in `call' > lib/ruby/1.8/benchmark.rb:293:in `measure' -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:33:38 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:38 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-561) Update the public facing BioCatalogue Roadmap In-Reply-To: <5092817.172.1296128110712.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22222516.2173.1309253618186.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-561: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Update the public facing BioCatalogue Roadmap > --------------------------------------------- > > Key: BIOCAT-561 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-561 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Reporter: Eric Nzuobontane > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > The BioCatalogue Roadmap needs to be updated with the 2011 plans. Current roadmap is for 2010! -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 05:33:40 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:40 +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: <30023548.2174.1309253620686.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: 1.1.0 (was: 1.0.2) > 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: 1.1.0 > > -- 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 Jun 28 05:33:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-243) Make ALL routes/pages HTTPS Message-ID: <30979985.2175.1309253623526.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Make ALL routes/pages HTTPS > --------------------------- > > 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 Jun 28 05:33:45 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:45 +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: <30404135.2176.1309253625941.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 ] Jiten Bhagat updated BIOCAT-647: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Tue Jun 28 05:33:48 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:48 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-318) Improve styling of "Part of Service..." Message-ID: <7620232.2177.1309253628551.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: Jiten Bhagat > Fix For: 1.1.0 > > 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 Jun 28 05:33:51 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:51 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-621) Incorrect number of results being returned from filtering In-Reply-To: <12562916.1399.1308049975350.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10001388.2178.1309253631083.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-621?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-621: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Jun 28 05:33:54 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:54 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-641) Find a better way to differentiate (at a glace) between services or soap operations with the same name In-Reply-To: <14314667.1654.1308650284956.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10744817.2179.1309253634345.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 ] Jiten Bhagat updated BIOCAT-641: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Find a better way to differentiate (at a glace) 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 issues at mygrid.org.uk Tue Jun 28 05:33:56 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:56 +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: <2732952.2180.1309253636908.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Jun 28 05:33:59 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:33:59 +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: <18641961.2181.1309253639501.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 ] Jiten Bhagat updated BIOCAT-617: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Tue Jun 28 05:34:02 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:34:02 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-295) Investigate double render error with "error_to_back_or_home" helper Message-ID: <13588501.2182.1309253642089.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: Jiten Bhagat > 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 Jun 28 05:34:04 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:34:04 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <530162.2183.1309253644735.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 updated BIOCAT-551: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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 Tue Jun 28 05:32:43 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:43 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-447) Test SSL on the BioCatalogue main site In-Reply-To: <337413.7600.1280153355313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30352383.2153.1309253563769.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-447?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-447: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > Test SSL on the BioCatalogue main site > -------------------------------------- > > Key: BIOCAT-447 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-447 > Project: BioCatalogue > Issue Type: Sub-task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Critical > Fix For: 1.1.0 > > -- 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 Jun 28 05:32:22 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 10:32:22 +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: <23326527.2145.1309253542476.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: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.2) > 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: 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 Tue Jun 28 12:11:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 17:11:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-651) Reorder service providers index by number of services Message-ID: <9184075.2280.1309277515392.JavaMail.jira@rosalind.cs.man.ac.uk> Reorder service providers index by number of services ----------------------------------------------------- Key: BIOCAT-651 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651 Project: BioCatalogue Issue Type: Improvement Components: Web Interface Affects Versions: 1.0.0 Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical Fix For: 1.0.1 Currently, service providers are sorted by latest, but this shows lots of new ones that have the default names based on the hostname, which doesn't look very good at all. Change the default search order to order by number of services by a provider. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jun 28 12:13:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 17:13:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-652) INB services have test scripts that were never passing (!) Message-ID: <3954854.2281.1309277635375.JavaMail.jira@rosalind.cs.man.ac.uk> 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: Jiten Bhagat Priority: Critical Fix For: 1.1.0 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 Tue Jun 28 12:13:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 17:13:57 +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: <14434988.2282.1309277637815.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 ] Jiten Bhagat updated BIOCAT-652: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Priority: Blocker (was: Critical) > 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 > > > 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 Tue Jun 28 12:17:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 28 Jun 2011 17:17:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-653) New curation feature: delete empty service provider in the web UI Message-ID: <6424713.2283.1309277875346.JavaMail.jira@rosalind.cs.man.ac.uk> New curation feature: 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 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 Wed Jun 29 04:11:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 29 Jun 2011 09:11:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-535) After release, update API docs and data model diagram In-Reply-To: <24641103.566.1289922271996.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19553692.2288.1309335115479.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-535?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17144#comment-17144 ] Mannie Tagarira commented on BIOCAT-535: ---------------------------------------- Updated: - http://www.biocatalogue.org/wiki/doku.php?id=public:api - http://www.biocatalogue.org/wiki/doku.php?id=public:api:endpoints - http://www.biocatalogue.org/wiki/doku.php?id=development:rought_notes_on_write_api TODO: - Add changes made to the system between 01 Sept 2010 and 29 June 2011 - Update the changelog (both the summary and the detailed) > After release, update API docs and data model diagram > ----------------------------------------------------- > > Key: BIOCAT-535 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-535 > Project: BioCatalogue > Issue Type: Task > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > After the release has been carried out and before announcing, update the API docs and data model diagram using the material provided by Mannie (as a starting point). -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 29 04:55:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 09:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (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: <16997580.2289.1309337755398.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 started 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 Wed Jun 29 05:01:58 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:01:58 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-646) Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) In-Reply-To: <16600212.1822.1308912835346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5775741.2291.1309338118979.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-646. --------------------------------- Resolution: Fixed > Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-646 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > As mentioned here: http://wiki.apache.org/solr/SolrPerformanceFactors#OutOfMemoryErrors, out of memory errors could be the reason for lock timeouts and other issues in Solr. > Check what the memory allocation is for Tomcat on the EBI servers and also play with this on the staging server VM to see if an optimal memory setting can be found. -- This 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 Jun 29 05:01:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:01:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-646) Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) In-Reply-To: <16600212.1822.1308912835346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4403628.2290.1309338115398.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17145#comment-17145 ] Jiten Bhagat commented on BIOCAT-646: ------------------------------------- Settings on the EBI servers are: {quote} test instance -Xms256m -Xmx512m prod istance -Xms1024m -Xmx1024m {quote} > Investigate the memory allocation to Tomcat on the EBI servers (as a potential cause of Solr timeouts/issues) > ------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-646 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-646 > Project: BioCatalogue > Issue Type: Task > Components: Search / Filtering / Browsing, Server Management > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > As mentioned here: http://wiki.apache.org/solr/SolrPerformanceFactors#OutOfMemoryErrors, out of memory errors could be the reason for lock timeouts and other issues in Solr. > Check what the memory allocation is for Tomcat on the EBI servers and also play with this on the staging server VM to see if an optimal memory setting can be found. -- This 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 Jun 29 05:03:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:03:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-653) New curation feature: delete empty service provider in the web UI In-Reply-To: <6424713.2283.1309277875346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30993925.2292.1309338235381.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 updated BIOCAT-653: -------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > New curation feature: 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: Mannie Tagarira > Priority: Blocker > Fix For: 1.0.1 > > > 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 Wed Jun 29 05:05:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:05:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-654) Make Carole a Curator on the live site Message-ID: <7163612.2293.1309338355454.JavaMail.jira@rosalind.cs.man.ac.uk> 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. -- This 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 Jun 29 05:07:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:07:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-655) Show curator and admin badges in the UI Message-ID: <24162756.2294.1309338475347.JavaMail.jira@rosalind.cs.man.ac.uk> 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 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 Wed Jun 29 05:09:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:09:55 +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: <29612317.2295.1309338595363.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=17146#comment-17146 ] Jiten Bhagat commented on BIOCAT-611: ------------------------------------- This is now mostly done. Just need to update it with the final v1.0.1 release code when that is ready. > 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 Wed Jun 29 05:11:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:11:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-656) Change styling of all dropdown menus / buttons on the various show pages so that they are more prominent as actions Message-ID: <69462.2296.1309338715350.JavaMail.jira@rosalind.cs.man.ac.uk> Change styling of all dropdown menus / buttons on the various show pages so that they are more prominent as actions ------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-656 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-656 Project: BioCatalogue Issue Type: Improvement Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.1.0 Currently, the action buttons on pages like the services profile page are just not prominent enough. Make this very obvious by turning it into a toolbar like thing. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 29 05:58:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 10:58:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-657) Investigate why certain test scripts are failing! Message-ID: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.0.1 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 Wed Jun 29 06:00:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:00:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-658) Ability to test out test scripts via the interface to check if they work with the test harness Message-ID: <1216271.2306.1309341655352.JavaMail.jira@rosalind.cs.man.ac.uk> 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: 1.1.0 Request from a user: {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} -- This 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 Jun 29 06:02:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:02:55 +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: <18384965.2307.1309341775369.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: -------------------------------- Description: 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} was: Request from a user: {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} > 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: 1.1.0 > > > 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} -- 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 Jun 29 06:06:55 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 06:06:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2437] trunk/script/biocatalogue: Soaplab servers report script Message-ID: <20110629100655.2D1681858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 29 06:06:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:06:55 +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: <1728880.2311.1309342015360.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: -------------------------------- Description: 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. was: 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} > 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: 1.1.0 > > > 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 Wed Jun 29 06:23:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:23:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-659) New curation feature: deactivate users Message-ID: <6729550.2318.1309343035349.JavaMail.jira@rosalind.cs.man.ac.uk> 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 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 Wed Jun 29 06:25:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:25:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-653) New curation feature: delete empty service provider in the web UI In-Reply-To: <6424713.2283.1309277875346.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23970148.2319.1309343155354.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 updated BIOCAT-653: -------------------------------- Assignee: Jiten Bhagat (was: Mannie Tagarira) > New curation feature: 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 > > > 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 Wed Jun 29 06:34:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 29 Jun 2011 11:34:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33128371.2322.1309343695385.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 ] Work on BIOCAT-657 started by Mannie Tagarira. > 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: 1.0.1 > > > 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 Wed Jun 29 06:54:55 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 06:54:55 -0400 (EDT) Subject: [BioCatalogue-developers] [2438] trunk: [BIOCAT-653] New curation feature: ability to delete empty service provider in the web UI. Message-ID: <20110629105455.1E4E01858367@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 29 06:54:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:54:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (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: <8522789.2331.1309344895351.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 updated BIOCAT-653: -------------------------------- Summary: New curation feature: ability to delete empty service provider in the web UI (was: New curation feature: delete empty service provider in the web UI) > 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 > > > 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 Wed Jun 29 06:56:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:56:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (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: <32016430.2332.1309345015425.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-653?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-653: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-29 11:55 Start Date: 2011-06-29 09:55 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 2 hours Worklog Id: (was: 10511) > 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 Wed Jun 29 06:56:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 11:56:57 +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: <22335755.2333.1309345017755.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=17158#comment-17158 ] Jiten Bhagat commented on BIOCAT-653: ------------------------------------- Initial implementation done in revision 2438. Needs further testing. > 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 noreply at rubyforge.org Wed Jun 29 08:33:24 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 08:33:24 -0400 (EDT) Subject: [BioCatalogue-developers] [2439] trunk: [BIOCAT-659] New curation feature: deactivate users. Message-ID: <20110629123332.1725A19783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 29 08:33:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 13:33:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (BIOCAT-659) New curation feature: deactivate users In-Reply-To: <6729550.2318.1309343035349.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28664240.2346.1309350835382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-659?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-659: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-29 13:33 Start Date: 2011-06-29 23:33 Worklog Time Spent: 2 hours Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 2 hours Worklog Id: (was: 10512) > 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 Wed Jun 29 08:33:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 13:33:57 +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: <26720062.2347.1309350837774.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=17161#comment-17161 ] Jiten Bhagat commented on BIOCAT-659: ------------------------------------- Initial work carried out in revision 2439. Needs further testing. > 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 Wed Jun 29 08:38:09 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 08:38:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2440] trunk/app/helpers/activity_feeds_helper.rb: Squashed a bug where users that had been deactivated were still showing up in the activity feeds . Message-ID: <20110629123811.28E081858367@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 29 08:45:37 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 08:45:37 -0400 (EDT) Subject: [BioCatalogue-developers] [2441] trunk/app/controllers/users_controller.rb: Make some activity logs + cleanup Message-ID: <20110629124537.D62ED19783C0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 29 09:55:18 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 09:55:18 -0400 (EDT) Subject: [BioCatalogue-developers] [2442] trunk: [BIOCAT-655] Show curator and admin badges in the UI Message-ID: <20110629135518.36230185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 29 09:55:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 14:55:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work logged: (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: <19837966.2356.1309355755437.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-655?page=com.atlassian.jira.plugin.system.issuetabpanels:worklog-tabpanel\#worklog-{worklog.getId()} ] Jiten Bhagat logged work on BIOCAT-655: --------------------------------------- Author: Jiten Bhagat Created on: 2011-06-29 14:55 Start Date: 2011-06-29 13:55 Worklog Time Spent: 1 hour Issue Time Tracking ------------------- Remaining Estimate: 0 minutes Time Spent: 1 hour Worklog Id: (was: 10513) > 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 Wed Jun 29 09:55:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 14:55:57 +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: <17098787.2357.1309355757671.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=17167#comment-17167 ] Jiten Bhagat commented on BIOCAT-655: ------------------------------------- Initial work done in revision 2442. Needs further testing. > 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 noreply at rubyforge.org Wed Jun 29 10:16:15 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 10:16:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2443] trunk: Style tweaks Message-ID: <20110629141615.CC59E185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jun 29 10:48:30 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 10:48:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2444] trunk/app: Add sorting to the Service Providers index and set default sort to name ( A-Z) Message-ID: <20110629144830.70D5C1678337@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 29 10:49:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 15:49:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-651) Reorder service providers index by number of services In-Reply-To: <9184075.2280.1309277515392.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28976008.2364.1309358995391.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17171#comment-17171 ] Jiten Bhagat commented on BIOCAT-651: ------------------------------------- For now I've set the default sort order to "Name (A-Z)" > Reorder service providers index by number of services > ----------------------------------------------------- > > Key: BIOCAT-651 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.0.1 > > > Currently, service providers are sorted by latest, but this shows lots of new ones that have the default names based on the hostname, which doesn't look very good at all. > Change the default search order to order by number of services by a provider. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 29 10:51:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 15:51:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-651) Reorder service providers index by number of services In-Reply-To: <9184075.2280.1309277515392.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21489749.2365.1309359115380.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-651: -------------------------------- Fix Version/s: 1.1.0 (was: 1.0.1) > Reorder service providers index by number of services > ----------------------------------------------------- > > Key: BIOCAT-651 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-651 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Affects Versions: 1.0.0 > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > Fix For: 1.1.0 > > > Currently, service providers are sorted by latest, but this shows lots of new ones that have the default names based on the hostname, which doesn't look very good at all. > Change the default search order to order by number of services by a provider. -- This message is automatically generated by JIRA. - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jun 29 10:51:57 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 15:51:57 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-660) Add more info to the service provider listings Message-ID: <24596760.2366.1309359117588.JavaMail.jira@rosalind.cs.man.ac.uk> Add more info to the service provider listings ---------------------------------------------- Key: BIOCAT-660 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-660 Project: BioCatalogue Issue Type: Improvement Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat Fix For: 1.0.1 Add more info, like the number of services, to the service provider listings. -- 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 Jun 29 11:00:49 2011 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Jun 2011 11:00:49 -0400 (EDT) Subject: [BioCatalogue-developers] [2445] trunk/app/views/service_providers/_listing.html.erb: [BIOCAT-660] Add more info to the service provider listings. Message-ID: <20110629150049.E07BE185834E@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jun 29 11:02:55 2011 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 29 Jun 2011 16:02:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-660) Add more info to the service provider listings In-Reply-To: <24596760.2366.1309359117588.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <19285239.2367.1309359775376.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-660?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-660. --------------------------------- Resolution: Implemented In revision 2445 > Add more info to the service provider listings > ---------------------------------------------- > > Key: BIOCAT-660 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-660 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Fix For: 1.0.1 > > > Add more info, like the number of services, to the service provider listings. -- This 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 Jun 30 07:44:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 30 Jun 2011 12:44:55 +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: <18291407.2458.1309434295381.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=17227#comment-17227 ] Mannie Tagarira commented on BIOCAT-657: ---------------------------------------- It turns out the test scripts are running; only that the harness was ALWAYS throwing an exception and thus returning inappropriate status codes. This needs further investigation. > 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: 1.0.1 > > > 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 Jun 30 12:58:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 30 Jun 2011 17:58:55 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-657) Investigate why certain test scripts are failing! In-Reply-To: <30607250.2305.1309341535354.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <13219586.2497.1309453135382.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 ] Work on BIOCAT-657 stopped by Mannie Tagarira. > 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: 1.0.1 > > > 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 Jun 30 13:12:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 30 Jun 2011 18:12:55 +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: <8340329.2498.1309453975370.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=17247#comment-17247 ] Mannie Tagarira commented on BIOCAT-657: ---------------------------------------- - Running Python v2.6.1 I managed to get a few more services passing after: - installing the libs identified @ http://www.biocatalogue.org/wiki/doku.php?id=development:testscripts_in_biocatalogue - making a few changes as identified by the attached diff Notes: - INB services scripts **all** returned status code 1 - http://www.biocatalogue.org/service_tests/4876 returned error code 127 which was very odd given that the test script returns either a 1 or a 0. Having repurposed the script so that all it does is exit with a status code other than 0, 1, and 127 (e.g 33) I kept getting back a 127. This would suggest that some scripts are executing properly if at all **Important**: - Better exception handling is required (refer to the diff). Test results are still posted to the biocatalogue even when an exception (which may not even be resulting from the test script's execution) occurs. This is incorrect > 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: 1.0.1 > > > 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 Jun 30 13:14:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 30 Jun 2011 18:14:55 +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: <17553526.2499.1309454095377.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: ----------------------------------- Attachment: diff.jpg this is a diff of the changes mentioned in the comments. the original version is on the left whilst the updated version is on the right. as of Thursday 30 June 2011 these changes have **not** been checked into source control > 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: 1.0.1 > > 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 Jun 30 13:16:55 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 30 Jun 2011 18:16:55 +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: <18570099.2500.1309454215381.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=17248#comment-17248 ] Mannie Tagarira edited comment on BIOCAT-657 at 30/06/11 18:15: ---------------------------------------------------------------- the attached image is a diff of the changes mentioned in the comment above. the original version is on the left whilst the updated version is on the right. as of Thursday 30 June 2011 these changes have **not** been checked into source control was (Author: mannie): this is a diff of the changes mentioned in the comments. the original version is on the left whilst the updated version is on the right. as of Thursday 30 June 2011 these changes have **not** been checked into source control > 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: 1.0.1 > > 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 Jun 30 13:16:57 2011 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 30 Jun 2011 18:16:57 +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: <2024821.2501.1309454217556.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=17248#comment-17248 ] Mannie Tagarira edited comment on BIOCAT-657 at 30/06/11 18:16: ---------------------------------------------------------------- the attached image is a diff of the changes mentioned in the comment above. the original version of the file is on the left whilst the updated version is on the right. the file in question is testscript_runner.py as of Thursday 30 June 2011 these changes have **not** been checked into source control was (Author: mannie): the attached image is a diff of the changes mentioned in the comment above. the original version is on the left whilst the updated version is on the right. as of Thursday 30 June 2011 these changes have **not** been checked into source control > Investigate why certain test scripts are failing! > ------------------------------------------------- > >