From issues at mygrid.org.uk Thu Jul 1 05:51:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 1 Jul 2010 10:51:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-429) Update the protocol for updating the BioCatalogue website on EBI wiki Message-ID: <28477819.6994.1277977875320.JavaMail.jira@rosalind.cs.man.ac.uk> 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. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Jul 1 16:13:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 01 Jul 2010 21:13:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'JACOP/FuncNet' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'JACOP/FuncNet' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/219 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 2 02:45:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 07:45:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/784 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Jul 2 08:00:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 2 Jul 2010 08:00:08 -0400 (EDT) Subject: [BioCatalogue-developers] [2122] trunk/app/views/rest_methods/_listing.html.erb: bug fix for url template in RestMethod listing, it was showing the same resource path for all the different endpoints... Message-ID: <20100702120009.5E2C61858373@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Jul 2 08:07:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 13:07:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS supermatcher' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS supermatcher' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/723 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 2 08:10:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 13:10:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS supermatcher' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS supermatcher' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/723 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Jul 2 08:25:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 2 Jul 2010 08:25:14 -0400 (EDT) Subject: [BioCatalogue-developers] [2123] trunk/app/views/rest_services/_show_service_tabs.html.erb: cleanup for calls made to render the listing partial for RestMethod Message-ID: <20100702122514.66A971858357@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Jul 2 08:59:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 13:59:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runNCut' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runNCut' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/970 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 2 10:40:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 15:40:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/989 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 2 10:47:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 15:47:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromGenericSequenceCollectionToFASTA' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromGenericSequenceCollectionToFASTA' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/773 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 2 12:21:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 02 Jul 2010 17:21:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMultiPairwiseMetaAlignment' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMultiPairwiseMetaAlignment' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/782 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Sat Jul 3 02:44:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Sat, 3 Jul 2010 07:44:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-372) Documentation URL not being picked up by the WSDL parser In-Reply-To: <22066438.2608.1275930437035.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33035824.7079.1278139455460.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-372 stopped by Eric Nzuobontane. > Documentation URL not being picked up by the WSDL parser > -------------------------------------------------------- > > Key: BIOCAT-372 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-372 > Project: BioCatalogue > Issue Type: Bug > Components: Service Submission > Reporter: Jiten Bhagat > Assignee: Eric Nzuobontane > Priority: Critical > > As reported by Olivier Sallou: > bq. I just submitted a new service (wsdl interproscan) but we have some errors: at submission, documentation tag is not recognized, and as a consequence is not filled automatically (though used to do so). I manually added it. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Sat Jul 3 02:50:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Sat, 3 Jul 2010 07:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-430) Re-factor the service monitoring view to bring in line with the improved view of the soap operations Message-ID: <31922042.7080.1278139815362.JavaMail.jira@rosalind.cs.man.ac.uk> Re-factor the service monitoring view to bring in line with the improved view of the soap operations ----------------------------------------------------------------------------------------------------- Key: BIOCAT-430 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-430 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane The monitoring view needs to be refactored in order to make it more user friendly. Similar to the soap operations tab, the monitoring view should list the service test with just some important data exposed with the possibility of drilling down to individual operations. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Sat Jul 3 11:16:04 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 03 Jul 2010 16:16:04 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'blastProDom' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'blastProDom' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/137 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 4 00:57:50 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Jul 2010 05:57:50 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parsePropertySequenceFromFSOLVText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parsePropertySequenceFromFSOLVText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/992 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 4 08:21:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 04 Jul 2010 13:21:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMultiPairwiseMetaAlignment' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMultiPairwiseMetaAlignment' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/782 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Jul 6 03:50:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 08:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-431) Update copyright date in footer to 2008-2010 Message-ID: <31361560.7125.1278402615439.JavaMail.jira@rosalind.cs.man.ac.uk> Update copyright date in footer to 2008-2010 -------------------------------------------- Key: BIOCAT-431 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-431 Project: BioCatalogue Issue Type: Task Components: Web Interface Reporter: Jiten Bhagat Assignee: Jiten Bhagat -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:04:19 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:04:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-405) Create 2 wiki pages for curation app: one to serve as a "front page" and the other for developers In-Reply-To: <17552405.6320.1276853835309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16730915.7129.1278407059941.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-405?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-405. ------------------------------------ Resolution: Fixed > Create 2 wiki pages for curation app: one to serve as a "front page" and the other for developers > ------------------------------------------------------------------------------------------------- > > Key: BIOCAT-405 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-405 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition, Wiki > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:04:23 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:04:23 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-405) Create 2 wiki pages for curation app: one to serve as a "front page" and the other for developers In-Reply-To: <17552405.6320.1276853835309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9392213.7130.1278407063207.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-405?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-405. ---------------------------------- > Create 2 wiki pages for curation app: one to serve as a "front page" and the other for developers > ------------------------------------------------------------------------------------------------- > > Key: BIOCAT-405 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-405 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition, Wiki > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:06:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-406) Test app in other OSs apart from Mac OS X 10.5 In-Reply-To: <31264361.6361.1277118856217.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14696708.7131.1278407175360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-406?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15501#action_15501 ] Mannie Tagarira commented on BIOCAT-406: ---------------------------------------- App runs in ubuntu linux, but does not run on Windows Vista... More investigation needed > Test app in other OSs apart from Mac OS X 10.5 > ---------------------------------------------- > > Key: BIOCAT-406 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-406 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > > The app was developed on Mac OS X 10.5, and the main user (the same user who was testing the app) uses the same operating system. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:06:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:06:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-401) Start a wiki page to document REST Services In-Reply-To: <25813643.6315.1276853295310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <528549.7132.1278407176665.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-401?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-401. ------------------------------------ Resolution: Fixed > Start a wiki page to document REST Services > ------------------------------------------- > > Key: BIOCAT-401 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-401 > Project: BioCatalogue > Issue Type: New Feature > Components: Wiki > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:08:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:08:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-401) Start a wiki page to document REST Services In-Reply-To: <25813643.6315.1276853295310.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21359650.7133.1278407295337.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-401?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-401. ---------------------------------- > Start a wiki page to document REST Services > ------------------------------------------- > > Key: BIOCAT-401 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-401 > Project: BioCatalogue > Issue Type: New Feature > Components: Wiki > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:04:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:04:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-426) In the exported spreadsheet, make sure the description annotations do not overlap the cell's boundaries In-Reply-To: <16654055.6743.1277820915428.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7100175.7126.1278407055475.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-426?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-426. ------------------------------------ Resolution: Fixed > In the exported spreadsheet, make sure the description annotations do not overlap the cell's boundaries > ------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-426 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-426 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:04:18 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:04:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-409) Implement a cache for all performed searches In-Reply-To: <7774214.6508.1277221095333.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28057971.7128.1278407058748.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-409?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-409: ----------------------------------- Summary: Implement a cache for all performed searches (was: Implement cache for all performed searched) > Implement a cache for all performed searches > -------------------------------------------- > > Key: BIOCAT-409 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-409 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Minor > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:04:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:04:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-426) In the exported spreadsheet, make sure the description annotations do not overlap the cell's boundaries In-Reply-To: <16654055.6743.1277820915428.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11606669.7127.1278407057321.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-426?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-426. ---------------------------------- > In the exported spreadsheet, make sure the description annotations do not overlap the cell's boundaries > ------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-426 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-426 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:58:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:58:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-420) Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page In-Reply-To: <32402712.6706.1277483415408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <17483813.7141.1278410297405.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-420 started by Mannie Tagarira. > Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page > ----------------------------------------------------------------------------- > > Key: BIOCAT-420 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > > The current styling of the 'edit' and 'delete' buttons on the REST method page is not consistent with the regular styling provided by the 'button_slim' class. Fix these to be consistent with all other buttons and get rid of all the convoluted styling for them! > In terms of icons within these buttons, don't show them as background images. Instead put them on the left as part of the rendered HTML. See other places around the UI for example of how to do this. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 05:58:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 10:58:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (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: <31923397.7140.1278410295373.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 ] Work on BIOCAT-413 started by Mannie Tagarira. > 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). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 06:07:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 11:07:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-420) Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page In-Reply-To: <32402712.6706.1277483415408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5828856.7142.1278410835415.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-420 stopped by Mannie Tagarira. > Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page > ----------------------------------------------------------------------------- > > Key: BIOCAT-420 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > > The current styling of the 'edit' and 'delete' buttons on the REST method page is not consistent with the regular styling provided by the 'button_slim' class. Fix these to be consistent with all other buttons and get rid of all the convoluted styling for them! > In terms of icons within these buttons, don't show them as background images. Instead put them on the left as part of the rendered HTML. See other places around the UI for example of how to do this. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Tue Jul 6 06:07:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 06 Jul 2010 11:07:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:www.cnb.uam.es:getStatisticalLog' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:www.cnb.uam.es:getStatisticalLog' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1027 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Jul 6 06:16:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 11:16:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-420) Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page In-Reply-To: <32402712.6706.1277483415408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26722711.7143.1278411375398.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-420 started by Mannie Tagarira. > Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page > ----------------------------------------------------------------------------- > > Key: BIOCAT-420 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > > The current styling of the 'edit' and 'delete' buttons on the REST method page is not consistent with the regular styling provided by the 'button_slim' class. Fix these to be consistent with all other buttons and get rid of all the convoluted styling for them! > In terms of icons within these buttons, don't show them as background images. Instead put them on the left as part of the rendered HTML. See other places around the UI for example of how to do this. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 08:38:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 13:38:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-432) In Safari, the action buttons for annotations are misaligned In-Reply-To: <29503507.7146.1278418575502.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32533990.7147.1278419895547.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-432?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-432. ---------------------------------- Resolution: Fixed Fixed. > In Safari, the action buttons for annotations are misaligned > ------------------------------------------------------------ > > Key: BIOCAT-432 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-432 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Mannie Tagarira > Assignee: Jiten Bhagat > > The "edit" button appears to be placed slightly higher than the "delete" button -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 08:16:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 13:16:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-432) In Safari, the action buttons for annotations are misaligned Message-ID: <29503507.7146.1278418575502.JavaMail.jira@rosalind.cs.man.ac.uk> In Safari, the action buttons for annotations are misaligned ------------------------------------------------------------ Key: BIOCAT-432 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-432 Project: BioCatalogue Issue Type: Bug Components: Web Interface Reporter: Mannie Tagarira Assignee: Jiten Bhagat The "edit" button appears to be placed slightly higher than the "delete" button -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Jul 6 08:48:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 6 Jul 2010 08:48:31 -0400 (EDT) Subject: [BioCatalogue-developers] [2124] trunk: - fixed css bug for the annotation' s actions button being misaligned Message-ID: <20100706124832.ABEBD1858386@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 6 08:50:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 13:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-420) Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page In-Reply-To: <32402712.6706.1277483415408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15180441.7148.1278420615452.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-420. ------------------------------------ Resolution: Fixed > Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page > ----------------------------------------------------------------------------- > > Key: BIOCAT-420 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > > The current styling of the 'edit' and 'delete' buttons on the REST method page is not consistent with the regular styling provided by the 'button_slim' class. Fix these to be consistent with all other buttons and get rid of all the convoluted styling for them! > In terms of icons within these buttons, don't show them as background images. Instead put them on the left as part of the rendered HTML. See other places around the UI for example of how to do this. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 08:50:17 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 13:50:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-420) Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page In-Reply-To: <32402712.6706.1277483415408.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22241666.7149.1278420617536.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-420. ---------------------------------- > Fix CSS styling of the "edit" and "delete" buttons on /rest_methods/{id} page > ----------------------------------------------------------------------------- > > Key: BIOCAT-420 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-420 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > > The current styling of the 'edit' and 'delete' buttons on the REST method page is not consistent with the regular styling provided by the 'button_slim' class. Fix these to be consistent with all other buttons and get rid of all the convoluted styling for them! > In terms of icons within these buttons, don't show them as background images. Instead put them on the left as part of the rendered HTML. See other places around the UI for example of how to do this. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Tue Jul 6 09:58:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 6 Jul 2010 09:58:49 -0400 (EDT) Subject: [BioCatalogue-developers] [2125] branches/soaplab-and-monitoring/app: re-factor monitoring views and add % success gauge graph for service tests Message-ID: <20100706135849.A9EC01858389@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 6 10:28:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 15:28:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (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: <13418716.7159.1278426495416.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 ] Work on BIOCAT-413 stopped by Mannie Tagarira. > 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). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 10:30:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 6 Jul 2010 15:30:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (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: <29680451.7160.1278426615347.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-413?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15509#action_15509 ] Mannie Tagarira commented on BIOCAT-413: ---------------------------------------- Just to confirm, the issue is caused by the last fix to the auto_link method. I am looking into this... > 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). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Tue Jul 6 10:58:05 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 06 Jul 2010 15:58:05 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runTargetPDAS' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runTargetPDAS' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1093 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Tue Jul 6 15:40:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 6 Jul 2010 20:40:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-433) Provide a live db snapshot for the ISMB demo Message-ID: <1078597.7189.1278445215374.JavaMail.jira@rosalind.cs.man.ac.uk> Provide a live db snapshot for the ISMB demo -------------------------------------------- Key: BIOCAT-433 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-433 Project: BioCatalogue Issue Type: Task Components: Data Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 16:01:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 21:01:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32551484.7191.1278446475325.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reassigned BIOCAT-425: ----------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 16:01:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 21:01:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-417) Implement endpoint groupings for REST services In-Reply-To: <7121431.6643.1277395995304.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26177120.7192.1278446477382.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-417?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reassigned BIOCAT-417: ----------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) Initial work carried out by Jits. Feature released to website. Mannie to polish up. > Implement endpoint groupings for REST services > ---------------------------------------------- > > Key: BIOCAT-417 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-417 > Project: BioCatalogue > Issue Type: New Feature > Components: REST Services Support, Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > Original Estimate: 4 hours > Time Spent: 5 hours, 30 minutes > Remaining Estimate: 2 hours, 30 minutes > > This is mainly required by Trish Whetzel, for the BioPortal services. She needs something like: > NCBO Services > .. Hierarchy Services > .... Endpoint 1 > .... Endpoint 2 > .. Search Services > .... > So we need to implement something very basic, literally just adding a "group_name" field to the RestMethod model. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 16:03:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 21:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-306) Implement service update checker Message-ID: <30432403.7193.1278446595418.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-306?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat resolved BIOCAT-306. --------------------------------- Resolution: Implemented Work carried out and feature released to live site. Further tasks should be added as new tasks. > Implement service update checker > -------------------------------- > > Key: BIOCAT-306 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-306 > Project: BioCatalogue > Issue Type: New Feature > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > We need the ability to check when the WSDL for a SOAP service has been updated, so that we can update the records/annotations in BioCatalogue and store a changelog of the exact changes. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 16:03:16 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 21:03:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-306) Implement service update checker Message-ID: <27952237.7194.1278446596572.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-306?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat closed BIOCAT-306. ------------------------------- > Implement service update checker > -------------------------------- > > Key: BIOCAT-306 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-306 > Project: BioCatalogue > Issue Type: New Feature > Components: SOAP Services Support > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > We need the ability to check when the WSDL for a SOAP service has been updated, so that we can update the records/annotations in BioCatalogue and store a changelog of the exact changes. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 16:03:17 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 21:03:17 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <4010268.7195.1278446597939.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reassigned BIOCAT-286: ----------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 15:59:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 20:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-243) Make important pages HTTPS Message-ID: <33554019.7190.1278446355382.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 reassigned BIOCAT-243: ----------------------------------- Assignee: Mannie Tagarira (was: Jiten Bhagat) > Make important pages HTTPS > -------------------------- > > Key: BIOCAT-243 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > > ... like log in, register etc etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Jul 6 16:19:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 6 Jul 2010 21:19:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-107) Implement descriptions pages for annotation attributes Message-ID: <13917097.7196.1278447555338.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: Mannie Tagarira (was: Jiten Bhagat) Description: 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. was: So things like: http://biocatalogue.org/attribute/description ... have a page and are not just empty URLs. > 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 > Priority: Critical > > 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. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Tue Jul 6 17:08:31 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 06 Jul 2010 22:08:31 +0100 Subject: [BioCatalogue-developers] Mannie's work Message-ID: <4C339B4F.7080401@cs.man.ac.uk> Hi Mannie, I wanted to outline some tasks for you for now until the end of next week (whilst I'm away) and onwards for the rest of your placement (though don't treat this as an exclusive list!) To start with, I suggest that for this week you go through all the 'Blocker' and 'Critical' tasks that are assigned to you on JIRA and try to get them all done. Then from next week and onwards I would like you to start tackling the following (probably in this order): 1) Familiarise yourself with how the REST API is currently built. 2) Build JSON outputs for the current REST API endpoints (you can see how it's currently done for Annotations). 3) Read this page [1] and implement a similar kind of activity limits system for the BioCatalogue (especially for REST API calls, but also for things like adding annotations, etc). Feel free to reuse Sergey's code from myExperiment. 4) Start planning work on REST API endpoints for REST services (which Sergey will need soon). But don't necessarily start implementing anything just yet. 5) Work on some ideas/prototyping on how we can build better communities of curators (including taking the ideas from [2] and [3]). 6) More work on the curation dashboard (see JIRA tasks for what reports are required). Please use branches whenever you think something will end up being a big piece of work, as we need to keep trunk "clean" for bugfixes etc. Please add tasks to JIRA to cover all these things (if they don't exist already). Feel free to assign longer term ones to me or Eric. Please coordinate with myself, Franck and Eric as you go along. Let discuss this some more tomorrow if you need. Jits [1] http://wiki.myexperiment.org/index.php/Developer:Activity_Limits [2] http://www.biocatalogue.org/wiki/doku.php?id=development:curators_incentives [3] Franck and I have discussed an idea revolving around Curator "stamps" or badges. The idea being that someone like Franck can give (unlimited) badges to others to make them "curators" (if they accept), and then those people can then give 1 or 2 "invites" to others to become curators too. Thereby increasing the network of curators. This could tie in with some kind of point system - people can earn more points for more contributions to the site. One thing to consider is whether this second level of curators (one below Franck) gets full rights on services, like Franck does (the answer is probably: No!) From ericnzuo at ebi.ac.uk Wed Jul 7 04:30:50 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 07 Jul 2010 09:30:50 +0100 Subject: [BioCatalogue-developers] monitoring views Message-ID: <4C343B3A.9040400@ebi.ac.uk> Hi, Following the discussion like week, I have done some work on the monitoring tab and would like some feedback. So now in a similar pattern to soap operations, you have a listing of all the service tests from which you can drill down to the individual test. See the attached screen shots. Please let me know what you think. Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 4.png Type: image/png Size: 413250 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 3.png Type: image/png Size: 422576 bytes Desc: not available URL: From ericnzuo at ebi.ac.uk Wed Jul 7 04:57:13 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 07 Jul 2010 09:57:13 +0100 Subject: [BioCatalogue-developers] [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" In-Reply-To: <4c34100710ff9_764a15a9e3b02fc81f9@pweb-3b.ebi.ac.uk.tmail> References: <4c34100710ff9_764a15a9e3b02fc81f9@pweb-3b.ebi.ac.uk.tmail> Message-ID: <4C344169.6000705@ebi.ac.uk> Looks like someone has been trying to attack the contact form! Eric BioCatalogue Errors wrote: > A ActionController::InvalidAuthenticityToken occurred in contact#create: > > ActionController::InvalidAuthenticityToken > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/request_forgery_protection.rb:79:in `verify_authenticity_token' > > ------------------------------- > Request: > ------------------------------- > > * URL : http://www.biocatalogue.org/contact > * Method : POST > * IP address: 202.108.50.71 > * Parameters: {"commit"=>"Submit", "from"=>"aMSbsdmliHteePXQg", "action"=>"create", "authenticity_token"=>"2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU=", "subject"=>"vvQxglEjUPJtpSBzRl", "controller"=>"contact", "content"=>"OmFKmD http://fj6hNsFfkfp92kf9v8dbs4NUias.com", "length_check"=>"yNvZFrSDLPojAprNkaP", "email"=>"samanta22 at hotmail.com"} > * Rails root: /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue > > ------------------------------- > Session: > ------------------------------- > > * session id: nil > * data: nil > > ------------------------------- > Environment: > ------------------------------- > > * CONTENT_LENGTH : 252 > * CONTENT_TYPE : application/x-www-form-urlencoded > * DOCUMENT_ROOT : /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue/public > * HTTP_ACCEPT : text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 > * HTTP_CACHE_CONTROL : max-age=86400 > * HTTP_CONTENT_TYPE : application/x-www-form-urlencoded > * HTTP_COOKIE : _session_id=053b8419e79931dc7c8fa1e80d4cf0a6 > * HTTP_COOKIE2 : $Version="1" > * HTTP_HOST : www.biocatalogue.org > * HTTP_REFERER : http://www.biocatalogue.org/contact > * HTTP_USER_AGENT : Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.1; SV1) > * HTTP_X_CLUSTER_CLIENT_IP : 202.108.50.71 > * PATH_INFO : /contact > * QUERY_STRING : > * REMOTE_ADDR : 202.108.50.71 > * REMOTE_PORT : 39316 > * REQUEST_METHOD : POST > * REQUEST_URI : /contact > * SCRIPT_NAME : > * SERVER_ADDR : 172.18.1.108 > * SERVER_ADMIN : root at localhost > * SERVER_NAME : www.biocatalogue.org > * SERVER_PORT : 80 > * SERVER_PROTOCOL : HTTP/1.1 > * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) > * _ : _ > * action_controller.request.query_parameters : > * action_controller.request.request_parameters: commitSubmitfromaMSbsdmliHteePXQgauthenticity_token2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU=subjectvvQxglEjUPJtpSBzRlcontentOmFKmD http://fj6hNsFfkfp92kf9v8dbs4NUias.comlength_checkyNvZFrSDLPojAprNkaPemailsamanta22 at hotmail.com > * action_controller.rescue.request : # > * action_controller.rescue.response : # > * rack.errors : # > * rack.input : # > * rack.multiprocess : true > * rack.multithread : false > * rack.request : # > * rack.request.cookie_hash : _session_id053b8419e79931dc7c8fa1e80d4cf0a6 > * rack.request.cookie_string : _session_id=053b8419e79931dc7c8fa1e80d4cf0a6 > * rack.request.form_hash : commitSubmitfromaMSbsdmliHteePXQgauthenticity_token2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU=subjectvvQxglEjUPJtpSBzRlcontentOmFKmD http://fj6hNsFfkfp92kf9v8dbs4NUias.comlength_checkyNvZFrSDLPojAprNkaPemailsamanta22 at hotmail.com > * rack.request.form_input : # > * rack.request.form_vars : authenticity_token=2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU%3D&from=aMSbsdmliHteePXQg&email=samanta22%40hotmail.com&subject=vvQxglEjUPJtpSBzRl&content=OmFKmD+http%3A%2F%2Ffj6hNsFfkfp92kf9v8dbs4NUias.com&length_check=yNvZFrSDLPojAprNkaP&commit=Submit > * rack.request.query_hash : > * rack.request.query_string : > * rack.routing_args : actioncreatecontrollercontact > * rack.run_once : false > * rack.session : use_tab_cookiefalse_csrf_tokenua2pnImsV1/j4uhivQYkBeOVtHN93EQFB7MjqILRz+c=previous_url/contactflash > * rack.session.options : securefalseexpire_afterkey_session_idid053b8419e79931dc7c8fa1e80d4cf0a6httponlytruedomaincookie_onlytruepath/ > * rack.session.record : # > * rack.url_scheme : http > * rack.version : 10 > > * Process: 30282 > * Server : pweb-3b > > * request.format: text/html > > ------------------------------- > Backtrace: > ------------------------------- > > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/request_forgery_protection.rb:79:in `verify_authenticity_token' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `send' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in `evaluate_method' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:225:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:629:in `run_before_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:615:in `call_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in `perform_action_without_benchmark' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in `realtime' > [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in `ms' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in `perform_action_without_rescue' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in `perform_action_without_flash' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in `perform_action' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `send' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in `process_without_filters' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in `process' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in `dispatch' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in `_call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in `initialize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in `call' > [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in `cache' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in `call' > [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `synchronize' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in `call' > [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in `call' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in `process_request' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in `start_request_handler' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in `safe_fork' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in `start' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in `lookup_or_add' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in `synchronize' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in `spawn_rails_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in `spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in `handle_spawn_application' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `__send__' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in `main_loop' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in `start_synchronously' > /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Wed Jul 7 05:02:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 7 Jul 2010 10:02:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-433) Provide a live db snapshot for the ISMB demo In-Reply-To: <1078597.7189.1278445215374.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33350315.7198.1278493335818.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-433?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-433. ------------------------------------- Resolution: Responded > Provide a live db snapshot for the ISMB demo > -------------------------------------------- > > Key: BIOCAT-433 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-433 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 hour > Remaining Estimate: 1 hour > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Wed Jul 7 05:07:03 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 07 Jul 2010 10:07:03 +0100 Subject: [BioCatalogue-developers] [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" In-Reply-To: <4C344169.6000705@ebi.ac.uk> References: <4c34100710ff9_764a15a9e3b02fc81f9@pweb-3b.ebi.ac.uk.tmail> <4C344169.6000705@ebi.ac.uk> Message-ID: <4C3443B7.4070906@cs.man.ac.uk> Yeah, common spam attacks. Hence why having a captcha type system (even basic) helps so much. Rails' ActionController::InvalidAuthenticityToken also helps here. Jits Eric Nzuobontane wrote: > Looks like someone has been trying to attack the contact form! > > Eric > > > > BioCatalogue Errors wrote: >> A ActionController::InvalidAuthenticityToken occurred in contact#create: >> >> ActionController::InvalidAuthenticityToken >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/request_forgery_protection.rb:79:in >> `verify_authenticity_token' >> >> ------------------------------- >> Request: >> ------------------------------- >> >> * URL : http://www.biocatalogue.org/contact >> * Method : POST >> * IP address: 202.108.50.71 >> * Parameters: {"commit"=>"Submit", "from"=>"aMSbsdmliHteePXQg", >> "action"=>"create", >> "authenticity_token"=>"2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU=", >> "subject"=>"vvQxglEjUPJtpSBzRl", "controller"=>"contact", >> "content"=>"OmFKmD http://fj6hNsFfkfp92kf9v8dbs4NUias.com", >> "length_check"=>"yNvZFrSDLPojAprNkaP", "email"=>"samanta22 at hotmail.com"} >> * Rails root: >> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue >> >> ------------------------------- >> Session: >> ------------------------------- >> >> * session id: nil >> * data: nil >> >> ------------------------------- >> Environment: >> ------------------------------- >> >> * CONTENT_LENGTH : 252 >> * CONTENT_TYPE : >> application/x-www-form-urlencoded >> * DOCUMENT_ROOT : >> /net/nas11a/vol1/alien-www/html/biocatalogue/rails/biocatalogue/public >> * HTTP_ACCEPT : >> text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 >> * HTTP_CACHE_CONTROL : max-age=86400 >> * HTTP_CONTENT_TYPE : >> application/x-www-form-urlencoded >> * HTTP_COOKIE : >> _session_id=053b8419e79931dc7c8fa1e80d4cf0a6 >> * HTTP_COOKIE2 : $Version="1" >> * HTTP_HOST : www.biocatalogue.org >> * HTTP_REFERER : >> http://www.biocatalogue.org/contact >> * HTTP_USER_AGENT : Mozilla/4.0 >> (compatible; MSIE 6.0; Windows NT 5.1; SV1) >> * HTTP_X_CLUSTER_CLIENT_IP : 202.108.50.71 >> * PATH_INFO : /contact >> * QUERY_STRING : * >> REMOTE_ADDR : 202.108.50.71 >> * REMOTE_PORT : 39316 >> * REQUEST_METHOD : POST >> * REQUEST_URI : /contact >> * SCRIPT_NAME : * >> SERVER_ADDR : 172.18.1.108 >> * SERVER_ADMIN : root at localhost >> * SERVER_NAME : www.biocatalogue.org >> * SERVER_PORT : 80 >> * SERVER_PROTOCOL : HTTP/1.1 >> * SERVER_SOFTWARE : Apache/2.2.3 (CentOS) >> * _ : _ >> * action_controller.request.query_parameters : * >> action_controller.request.request_parameters: >> commitSubmitfromaMSbsdmliHteePXQgauthenticity_token2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU=subjectvvQxglEjUPJtpSBzRlcontentOmFKmD >> http://fj6hNsFfkfp92kf9v8dbs4NUias.comlength_checkyNvZFrSDLPojAprNkaPemailsamanta22 at hotmail.com >> >> * action_controller.rescue.request : >> # >> * action_controller.rescue.response : >> # >> * rack.errors : # >> * rack.input : >> # >> * rack.multiprocess : true >> * rack.multithread : false >> * rack.request : >> # >> * rack.request.cookie_hash : >> _session_id053b8419e79931dc7c8fa1e80d4cf0a6 >> * rack.request.cookie_string : >> _session_id=053b8419e79931dc7c8fa1e80d4cf0a6 >> * rack.request.form_hash : >> commitSubmitfromaMSbsdmliHteePXQgauthenticity_token2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU=subjectvvQxglEjUPJtpSBzRlcontentOmFKmD >> http://fj6hNsFfkfp92kf9v8dbs4NUias.comlength_checkyNvZFrSDLPojAprNkaPemailsamanta22 at hotmail.com >> >> * rack.request.form_input : >> # >> * rack.request.form_vars : >> authenticity_token=2yNYRyCPwqRPMxrNy2FVowAh1irDGzhR3e3yr8G2ncU%3D&from=aMSbsdmliHteePXQg&email=samanta22%40hotmail.com&subject=vvQxglEjUPJtpSBzRl&content=OmFKmD+http%3A%2F%2Ffj6hNsFfkfp92kf9v8dbs4NUias.com&length_check=yNvZFrSDLPojAprNkaP&commit=Submit >> >> * rack.request.query_hash : * >> rack.request.query_string : * >> rack.routing_args : >> actioncreatecontrollercontact >> * rack.run_once : false >> * rack.session : >> use_tab_cookiefalse_csrf_tokenua2pnImsV1/j4uhivQYkBeOVtHN93EQFB7MjqILRz+c=previous_url/contactflash >> >> * rack.session.options : >> securefalseexpire_afterkey_session_idid053b8419e79931dc7c8fa1e80d4cf0a6httponlytruedomaincookie_onlytruepath/ >> >> * rack.session.record : >> # >> * rack.url_scheme : http >> * rack.version : 10 >> * Process: 30282 >> * Server : pweb-3b >> * request.format: text/html >> >> ------------------------------- >> Backtrace: >> ------------------------------- >> >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/request_forgery_protection.rb:79:in >> `verify_authenticity_token' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:178:in >> `evaluate_method' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/callbacks.rb:166:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:225:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:629:in >> `run_before_filters' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:615:in >> `call_filters' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:610:in >> `perform_action_without_benchmark' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:10:in >> `realtime' >> >> [RAILS_ROOT]/vendor/rails/activesupport/lib/active_support/core_ext/benchmark.rb:17:in >> `ms' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/benchmarking.rb:68:in >> `perform_action_without_rescue' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rescue.rb:160:in >> `perform_action_without_flash' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/flash.rb:141:in >> `perform_action' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `send' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:523:in >> `process_without_filters' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/filters.rb:606:in >> `process' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:391:in >> `process' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/base.rb:386:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/routing/route_set.rb:433:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:88:in >> `dispatch' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:111:in >> `_call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:82:in >> `initialize' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/head.rb:9:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/methodoverride.rb:24:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/params_parser.rb:15:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/rewindable_input.rb:25:in >> `call' >> [RAILS_ROOT]/vendor/rails/railties/lib/rails/rack/metal.rb:47:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/session/abstract_store.rb:122:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:29:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/query_cache.rb:34:in >> `cache' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:9:in >> `cache' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/query_cache.rb:28:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_pool.rb:361:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/failsafe.rb:11:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `synchronize' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/vendor/rack-1.0/rack/lock.rb:11:in >> `call' >> >> [RAILS_ROOT]/vendor/rails/actionpack/lib/action_controller/dispatcher.rb:106:in >> `call' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/rack/request_handler.rb:91:in >> `process_request' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_request_handler.rb:206:in >> `main_loop' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:376:in >> `start_request_handler' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:334:in >> `handle_spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/utils.rb:182:in >> `safe_fork' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:332:in >> `handle_spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:162:in >> `start' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/railz/application_spawner.rb:213:in >> `start' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:261:in >> `spawn_rails_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:126:in >> `lookup_or_add' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:255:in >> `spawn_rails_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:80:in >> `synchronize' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server_collection.rb:79:in >> `synchronize' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:254:in >> `spawn_rails_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:153:in >> `spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/spawn_manager.rb:286:in >> `handle_spawn_application' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `__send__' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:351:in >> `main_loop' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/lib/phusion_passenger/abstract_server.rb:195:in >> `start_synchronously' >> >> /ebi/www/plive/ruby/gems/gems/passenger-2.2.4/bin/passenger-spawn-server:61 >> >> >> > > From issues at mygrid.org.uk Wed Jul 7 05:01:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 7 Jul 2010 10:01:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-433) Provide a live db snapshot for the ISMB demo In-Reply-To: <1078597.7189.1278445215374.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29108598.7197.1278493275522.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-433?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15513#action_15513 ] Eric Nzuobontane commented on BIOCAT-433: ----------------------------------------- Data now available in dropbox > Provide a live db snapshot for the ISMB demo > -------------------------------------------- > > Key: BIOCAT-433 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-433 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 hour > Remaining Estimate: 1 hour > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Wed Jul 7 05:29:27 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 07 Jul 2010 10:29:27 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C344581.8090407@cs.man.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C344581.8090407@cs.man.ac.uk> Message-ID: <4C3448F7.3040902@ebi.ac.uk> Hi Sergev, Thanks for the feedback. > > > In "Picture 4": > > - "About test scripts" folding section appears inside the details for > one of the tests. I think that should be above the area with the tabs. yes, I think that makes sense. > - Also, it would help if the tabs with test titles also contained > icons for those tests' statuses. OK, I will add the status icons. On the right of the picture is a guage graph showing the % success of the test. Did you notice that? cheers, Eric > > Thank you, > Sergey > > > On 07/07/2010 09:30, Eric Nzuobontane wrote: >> Hi, >> >> Following the discussion like week, I have done some work on the >> monitoring tab and would like some feedback. So now in a similar >> pattern to soap operations, you have a listing of all the service >> tests from which you can drill down to the individual test. See the >> attached screen shots. >> >> Please let me know what you think. >> >> Eric >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed Jul 7 05:33:55 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 07 Jul 2010 10:33:55 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C343B3A.9040400@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> Message-ID: <4C344A03.3030601@cs.man.ac.uk> Looks good Eric! One immediate thing I noticed is the lack of classification of the kinds of services tests (do users care?) Ie: simple availability check versus test scripts. Maybe you could have groupings like how the REST endpoints groupings are shown in the UI? I'll have a closer look later. Jits Eric Nzuobontane wrote: > Hi, > > Following the discussion like week, I have done some work on the > monitoring tab and would like some feedback. So now in a similar > pattern to soap operations, you have a listing of all the service > tests from which you can drill down to the individual test. See the > attached screen shots. > > Please let me know what you think. > > Eric > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From alekses6 at cs.man.ac.uk Wed Jul 7 05:35:16 2010 From: alekses6 at cs.man.ac.uk (Sergejs Aleksejevs) Date: Wed, 07 Jul 2010 10:35:16 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C3448F7.3040902@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C344581.8090407@cs.man.ac.uk> <4C3448F7.3040902@ebi.ac.uk> Message-ID: <4C344A54.8090601@cs.man.ac.uk> Hi Eric, I did notice the gauge with the percentage - I thought it looked nice, but I wasn't sure how exactly is it possible to measure the percentage. I thought of the tests as being pass/fail binary gates. Or is this gauge showing the historical average percentage of passing/failing that test? (Either way, it would probably help if there was some explanation text / tooltip - it may be there already, but I've managed to delete your original email already, so can't check that). Thank you, Sergey On 07/07/2010 10:29, Eric Nzuobontane wrote: > Hi Sergev, > > Thanks for the feedback. >> >> >> In "Picture 4": >> >> - "About test scripts" folding section appears inside the details for >> one of the tests. I think that should be above the area with the tabs. > yes, I think that makes sense. >> - Also, it would help if the tabs with test titles also contained >> icons for those tests' statuses. > OK, I will add the status icons. On the right of the picture is a > guage graph showing the % success of the test. Did you notice that? > > cheers, > > Eric > > > >> >> Thank you, >> Sergey >> >> >> On 07/07/2010 09:30, Eric Nzuobontane wrote: >>> Hi, >>> >>> Following the discussion like week, I have done some work on the >>> monitoring tab and would like some feedback. So now in a similar >>> pattern to soap operations, you have a listing of all the service >>> tests from which you can drill down to the individual test. See the >>> attached screen shots. >>> >>> Please let me know what you think. >>> >>> Eric >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From issues at mygrid.org.uk Wed Jul 7 05:36:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 7 Jul 2010 10:36:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-434) Add status icons to the tabs on the details of service tests Message-ID: <3981993.7201.1278495375309.JavaMail.jira@rosalind.cs.man.ac.uk> Add status icons to the tabs on the details of service tests ------------------------------------------------------------ Key: BIOCAT-434 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-434 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Eric Nzuobontane Assignee: Jiten Bhagat It will be helpful to add the status icons of the services tests in the details tabs for service tests. That will enable users to quickly target tests of interest depending on their status -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jul 7 05:38:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 7 Jul 2010 10:38:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-434) Add status icons to the tabs on the details of service tests In-Reply-To: <3981993.7201.1278495375309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <15617786.7202.1278495495331.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-434?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-434: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Add status icons to the tabs on the details of service tests > ------------------------------------------------------------ > > Key: BIOCAT-434 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-434 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > It will be helpful to add the status icons of the services tests in the details tabs for service tests. That will enable users to quickly target tests of interest depending on their status -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Wed Jul 7 05:39:31 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 07 Jul 2010 10:39:31 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C344A03.3030601@cs.man.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C344A03.3030601@cs.man.ac.uk> Message-ID: <4C344B53.7050107@cs.man.ac.uk> The HTML layout in Picture 3 is broken. Looks like a possibly broken
tag to me.. Also, the Quick Browse box isnt showing as expected. Jits Jiten Bhagat wrote: > Looks good Eric! > > One immediate thing I noticed is the lack of classification of the kinds > of services tests (do users care?) Ie: simple availability check versus > test scripts. Maybe you could have groupings like how the REST endpoints > groupings are shown in the UI? > > I'll have a closer look later. > > Jits > > > Eric Nzuobontane wrote: > >> Hi, >> >> Following the discussion like week, I have done some work on the >> monitoring tab and would like some feedback. So now in a similar >> pattern to soap operations, you have a listing of all the service >> tests from which you can drill down to the individual test. See the >> attached screen shots. >> >> Please let me know what you think. >> >> Eric >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From alekses6 at cs.man.ac.uk Wed Jul 7 05:14:41 2010 From: alekses6 at cs.man.ac.uk (Sergejs Aleksejevs) Date: Wed, 07 Jul 2010 10:14:41 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C343B3A.9040400@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> Message-ID: <4C344581.8090407@cs.man.ac.uk> Hello, In "Picture 4": - "About test scripts" folding section appears inside the details for one of the tests. I think that should be above the area with the tabs. - Also, it would help if the tabs with test titles also contained icons for those tests' statuses. Thank you, Sergey On 07/07/2010 09:30, Eric Nzuobontane wrote: > Hi, > > Following the discussion like week, I have done some work on the > monitoring tab and would like some feedback. So now in a similar > pattern to soap operations, you have a listing of all the service > tests from which you can drill down to the individual test. See the > attached screen shots. > > Please let me know what you think. > > Eric > > > _______________________________________________ > 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 ericnzuo at ebi.ac.uk Wed Jul 7 06:42:50 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 07 Jul 2010 11:42:50 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C344A03.3030601@cs.man.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C344A03.3030601@cs.man.ac.uk> Message-ID: <4C345A2A.8070305@ebi.ac.uk> Jiten Bhagat wrote: > Looks good Eric! > > One immediate thing I noticed is the lack of classification of the kinds > of services tests (do users care?) I was thinking about this as well. I do not know whether users really care. Somewhere at the back of my mind was thinking that people really just want to know if a service is ok or not. And usually will look further into the things which are not ok. > Ie: simple availability check versus > test scripts. Maybe you could have groupings like how the REST endpoints > groupings are shown in the UI? > If that helps, then why not. > Eric Nzuobontane wrote: > >> Hi, >> >> Following the discussion like week, I have done some work on the >> monitoring tab and would like some feedback. So now in a similar >> pattern to soap operations, you have a listing of all the service >> tests from which you can drill down to the individual test. See the >> attached screen shots. >> >> Please let me know what you think. >> >> Eric >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Wed Jul 7 06:45:14 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 07 Jul 2010 11:45:14 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C344A54.8090601@cs.man.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C344581.8090407@cs.man.ac.uk> <4C3448F7.3040902@ebi.ac.uk> <4C344A54.8090601@cs.man.ac.uk> Message-ID: <4C345ABA.4090706@ebi.ac.uk> Sergejs Aleksejevs wrote: > Hi Eric, > > I did notice the gauge with the percentage - I thought it looked nice, > but I wasn't sure how exactly is it possible to measure the > percentage. I thought of the tests as being pass/fail binary gates. Or > is this gauge showing the historical average percentage of > passing/failing that test? yes, this is historical % percentage > (Either way, it would probably help if there was some explanation text > / tooltip - it may be there already, but I've managed to delete your > original email already, so can't check that). That is on my list. Thanks, Eric > > > On 07/07/2010 10:29, Eric Nzuobontane wrote: >> Hi Sergev, >> >> Thanks for the feedback. >>> >>> >>> In "Picture 4": >>> >>> - "About test scripts" folding section appears inside the details >>> for one of the tests. I think that should be above the area with the >>> tabs. >> yes, I think that makes sense. >>> - Also, it would help if the tabs with test titles also contained >>> icons for those tests' statuses. >> OK, I will add the status icons. On the right of the picture is a >> guage graph showing the % success of the test. Did you notice that? >> >> cheers, >> >> Eric >> >> >> >>> >>> Thank you, >>> Sergey >>> >>> >>> On 07/07/2010 09:30, Eric Nzuobontane wrote: >>>> Hi, >>>> >>>> Following the discussion like week, I have done some work on the >>>> monitoring tab and would like some feedback. So now in a similar >>>> pattern to soap operations, you have a listing of all the service >>>> tests from which you can drill down to the individual test. See >>>> the attached screen shots. >>>> >>>> Please let me know what you think. >>>> >>>> Eric >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed Jul 7 06:50:34 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 07 Jul 2010 11:50:34 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C345A2A.8070305@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C344A03.3030601@cs.man.ac.uk> <4C345A2A.8070305@ebi.ac.uk> Message-ID: <4C345BFA.8010202@cs.man.ac.uk> I think they might care once they want to understand the *relevance* of that particular status of that test. Eg: if 2 tests failed and 1 passed, which are more relevant? I think grouping, plus some explanation of the relevance of each group is essential. Jits Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> Looks good Eric! >> >> One immediate thing I noticed is the lack of classification of the kinds >> of services tests (do users care?) > I was thinking about this as well. I do not know whether users really > care. Somewhere at the back of my mind was thinking that people really > just want to know if a service is ok or not. And usually will look > further into the things which are not ok. > >> Ie: simple availability check versus >> test scripts. Maybe you could have groupings like how the REST endpoints >> groupings are shown in the UI? >> > If that helps, then why not. >> Eric Nzuobontane wrote: >> >>> Hi, >>> >>> Following the discussion like week, I have done some work on the >>> monitoring tab and would like some feedback. So now in a similar >>> pattern to soap operations, you have a listing of all the service >>> tests from which you can drill down to the individual test. See the >>> attached screen shots. >>> >>> Please let me know what you think. >>> >>> Eric >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > > From noreply at rubyforge.org Wed Jul 7 07:43:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Jul 2010 07:43:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2126] trunk/app/controllers: - added support for SSL on pages that contain forms asking for user details Message-ID: <20100707114301.9B0AB1858348@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 7 07:46:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 7 Jul 2010 12:46:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-435) Test SSL on the BioCatalogue test site Message-ID: <21116395.7204.1278503175449.JavaMail.jira@rosalind.cs.man.ac.uk> Test SSL on the BioCatalogue test site -------------------------------------- Key: BIOCAT-435 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435 Project: BioCatalogue Issue Type: Task Components: Misc Codebase, User Management Reporter: Mannie Tagarira Assignee: Eric Nzuobontane Priority: Blocker -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jul 7 07:46:18 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 7 Jul 2010 12:46:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-435) Update the BioCatalogue test site to try out SSL support In-Reply-To: <21116395.7204.1278503175449.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4792095.7205.1278503178528.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira updated BIOCAT-435: ----------------------------------- Summary: Update the BioCatalogue test site to try out SSL support (was: Test SSL on the BioCatalogue test site) > Update the BioCatalogue test site to try out SSL support > -------------------------------------------------------- > > Key: BIOCAT-435 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, User Management > Reporter: Mannie Tagarira > Assignee: Eric Nzuobontane > Priority: Blocker > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jul 7 09:21:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 7 Jul 2010 14:21:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-435) Update the BioCatalogue test site to try out SSL support In-Reply-To: <21116395.7204.1278503175449.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <32041480.7206.1278508875418.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-435 started by Eric Nzuobontane. > Update the BioCatalogue test site to try out SSL support > -------------------------------------------------------- > > Key: BIOCAT-435 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, User Management > Reporter: Mannie Tagarira > Assignee: Eric Nzuobontane > Priority: Blocker > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Wed Jul 7 09:50:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 7 Jul 2010 09:50:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2127] trunk/vendor/plugins: - froze the ssl_requirement plugin to the codebase Message-ID: <20100707135009.950CC1858321@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Wed Jul 7 09:58:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 7 Jul 2010 14:58:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <30978096.7207.1278511095403.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-286 started by Mannie Tagarira. > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Jul 7 10:04:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 7 Jul 2010 15:04:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-243) Make important pages HTTPS Message-ID: <23182514.7208.1278511455386.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-243 started by Mannie Tagarira. > Make important pages HTTPS > -------------------------- > > Key: BIOCAT-243 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > > ... like log in, register etc etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Wed Jul 7 23:10:05 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 08 Jul 2010 04:10:05 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignment' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignment' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/778 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Thu Jul 8 05:55:22 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 10:55:22 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-243) Make important pages HTTPS Message-ID: <28680021.7210.1278582922326.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-243 stopped by Mannie Tagarira. > Make important pages HTTPS > -------------------------- > > Key: BIOCAT-243 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-243 > Project: BioCatalogue > Issue Type: Improvement > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Blocker > > ... like log in, register etc etc -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 05:55:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 10:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-436) Create a self signed SSL certificate for the test site Message-ID: <9701620.7209.1278582915429.JavaMail.jira@rosalind.cs.man.ac.uk> Create a self signed SSL certificate for the test site ------------------------------------------------------ Key: BIOCAT-436 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-436 Project: BioCatalogue Issue Type: Task Components: Misc Codebase Reporter: Mannie Tagarira Assignee: Eric Nzuobontane The BioCatalogue SSL certificate is for "www.biocatalogue.org". This does not account for BioCatalogue subdomains. A self signed certificate for "test.biocatalogue.org" is needed to test out SSL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 06:59:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 8 Jul 2010 11:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-437) Add some explanation to the historical success rate graph for service tests. Message-ID: <19368424.7211.1278586755457.JavaMail.jira@rosalind.cs.man.ac.uk> Add some explanation to the historical success rate graph for service tests. ---------------------------------------------------------------------------- Key: BIOCAT-437 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-437 Project: BioCatalogue Issue Type: Sub-task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat Use the tooltip mechanism to add some information to/by the graph of the historical success rates for service tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 06:59:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 8 Jul 2010 11:59:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-437) Add some explanation to the historical success rate graph for service tests. In-Reply-To: <19368424.7211.1278586755457.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <225127.7212.1278586758375.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-437?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-437: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Add some explanation to the historical success rate graph for service tests. > ---------------------------------------------------------------------------- > > Key: BIOCAT-437 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-437 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Use the tooltip mechanism to add some information to/by the graph of the historical success rates for service tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 8 08:34:15 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 8 Jul 2010 08:34:15 -0400 (EDT) Subject: [BioCatalogue-developers] [2128] trunk/lib: - added files that were omitted in the last commit Message-ID: <20100708123415.D873D1858388@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 8 08:38:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 13:38:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <14567523.7216.1278592695381.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-286. ------------------------------------ Resolution: Fixed Added a whitelist helper extension, where extra tags can be specified for inclusion or omission. > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 08:38:20 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 13:38:20 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <15041475.7217.1278592700694.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-286. ---------------------------------- > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 08:52:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 13:52:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22125881.7218.1278593535325.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-425 started by Mannie Tagarira. > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 09:01:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 14:01:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25793078.7219.1278594075481.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-425. ------------------------------------ Resolution: Fixed The group names have been titleized; so "my groUP name" => "My Group Name" > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 8 09:02:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 8 Jul 2010 09:02:05 -0400 (EDT) Subject: [BioCatalogue-developers] [2129] trunk/app/models/rest_method.rb: - titleized the group names to make group name case insensitive Message-ID: <20100708130205.75B47185837C@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 8 09:03:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 14:03:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12023480.7220.1278594195353.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-425. ---------------------------------- > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 09:11:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 8 Jul 2010 14:11:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-438) Group service tests into classes( simple url checks, test scripts...) Message-ID: <16510953.7221.1278594675338.JavaMail.jira@rosalind.cs.man.ac.uk> Group service tests into classes( simple url checks, test scripts...) --------------------------------------------------------------------- Key: BIOCAT-438 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-438 Project: BioCatalogue Issue Type: Sub-task Components: Web Interface Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Grouping service test according their classes would give clarity on what types of tests are available. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 11:43:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 16:43:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-439) Build JSON outputs for the current REST API endpoints Message-ID: <4922873.7231.1278603795325.JavaMail.jira@rosalind.cs.man.ac.uk> Build JSON outputs for the current REST API endpoints ----------------------------------------------------- Key: BIOCAT-439 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-439 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 11:44:00 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 16:44:00 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-439) Build JSON outputs for the current REST API endpoints In-Reply-To: <4922873.7231.1278603795325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <6291450.7232.1278603840951.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-439?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-439 started by Mannie Tagarira. > Build JSON outputs for the current REST API endpoints > ----------------------------------------------------- > > Key: BIOCAT-439 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-439 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 11:44:14 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 16:44:14 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-440) Implement activity limits for REST API calls Message-ID: <483658.7233.1278603854488.JavaMail.jira@rosalind.cs.man.ac.uk> Implement activity limits 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: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 11:44:26 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 8 Jul 2010 16:44:26 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-441) Implement REST API endpoints for REST services Message-ID: <25950329.7234.1278603866463.JavaMail.jira@rosalind.cs.man.ac.uk> Implement REST API endpoints for REST services ---------------------------------------------- Key: BIOCAT-441 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441 Project: BioCatalogue Issue Type: New Feature Components: REST API, REST Services Support Reporter: Mannie Tagarira Assignee: Mannie Tagarira -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 8 13:47:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 8 Jul 2010 18:47:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-436) Create a self signed SSL certificate for the test site In-Reply-To: <9701620.7209.1278582915429.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12767547.7235.1278611235369.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-436?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15518#action_15518 ] Eric Nzuobontane commented on BIOCAT-436: ----------------------------------------- The certificate is now available on test.biocatalogue.org. This needs to be verified. > Create a self signed SSL certificate for the test site > ------------------------------------------------------ > > Key: BIOCAT-436 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-436 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Eric Nzuobontane > > The BioCatalogue SSL certificate is for "www.biocatalogue.org". This does not account for BioCatalogue subdomains. A self signed certificate for "test.biocatalogue.org" is needed to test out SSL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Jul 8 16:58:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 08 Jul 2010 21:58:59 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'PcProf predict physico-chemical profiles of proteins (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'PcProf predict physico-chemical profiles of proteins (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/275 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Jul 9 08:34:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 9 Jul 2010 08:34:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2130] trunk: - bug fix for annotations that were not displaying properly Message-ID: <20100709123408.00D54185837A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Jul 9 12:50:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 9 Jul 2010 12:50:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2131] trunk: - updated all the REST API GET /{resource}/ {id} endpoints to output JSON Message-ID: <20100709165020.2DB6C1678315@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Jul 9 19:40:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 00:40:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromEMBL' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromEMBL' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/791 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 9 20:13:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 01:13:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:solvateStructureFromGROMACS_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:solvateStructureFromGROMACS_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1181 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 9 21:02:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 02:02:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getNAMD_MD_StructureFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getNAMD_MD_StructureFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1144 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 10 07:46:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 12:46:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'blastProDom' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'blastProDom' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/137 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 10 11:34:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 16:34:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runGeneIDGFF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runGeneIDGFF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/769 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 10 13:27:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 18:27:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPHDFromFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPHDFromFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/999 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 10 18:42:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 10 Jul 2010 23:42:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStatisticalLog' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStatisticalLog' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1111 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 10 23:14:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Jul 2010 04:14:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getProtProtInterfaceFromPDBId' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getProtProtInterfaceFromPDBId' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1105 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 11 06:18:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Jul 2010 11:18:11 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:unzipTrajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:unzipTrajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1172 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 11 08:33:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Jul 2010 13:33:31 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:searchPdbForPattern' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:searchPdbForPattern' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1115 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 11 10:39:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 11 Jul 2010 15:39:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseMultipleAlignFromBLASTText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/989 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 11 20:47:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Jul 2010 01:47:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getSnapshotFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getSnapshotFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1135 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 11 20:49:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Jul 2010 01:49:14 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:loadPersistentFile' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:loadPersistentFile' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1114 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 11 21:38:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Jul 2010 02:38:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolDefinitions' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolDefinitions' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1086 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Jul 12 02:14:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Jul 2010 07:14:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runOFunCUT' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runOFunCUT' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/973 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Jul 12 14:30:46 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 12 Jul 2010 19:30:46 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getLigandIdFromPDBId' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getLigandIdFromPDBId' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1106 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Mon Jul 12 15:08:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 12 Jul 2010 20:08:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <14414448.7330.1278961695316.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15537#action_15537 ] Jiten Bhagat commented on BIOCAT-425: ------------------------------------- Just to check - are you explicitly changing the group name value the user provides? If so, how does it handle group names such as "KEGG Search" etc. My suggestion would be to not change anything at all, but change the grouping to handle the names in a case insensitive way. > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jul 12 15:57:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 12 Jul 2010 20:57:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <9294846.7331.1278964635324.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15538#action_15538 ] Jiten Bhagat commented on BIOCAT-286: ------------------------------------- 2 things: 1. We already use the following lines somewhere in the system (I think it's in config/initializers/biocat_main.rb) so no need to add the white_list_helper: WhiteListHelper.tags.merge ... WhiteListHelper.attributes.merge ... 2. The solution you've committed only fixes the particular example below (ie: the attribute 'xmlns:efet'. We need a broader and more longer term solution to handle other cases (if such a solution even actually exists!). Maybe certain attributes like example_data shouldn't be white listed, but just fully html escaped? > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jul 12 15:59:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 12 Jul 2010 20:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <2532374.7332.1278964755319.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reopened BIOCAT-286: --------------------------------- See comments > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jul 12 16:06:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 12 Jul 2010 21:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29261242.7333.1278965175309.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat reopened BIOCAT-425: --------------------------------- See comments > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Mon Jul 12 20:51:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 01:51:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPropertySequenceFromFeatureAASequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPropertySequenceFromFeatureAASequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1167 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Jul 13 06:45:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Jul 2010 06:45:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2132] branches/soaplab-and-monitoring/app: further work on monitoring UI Message-ID: <20100713104556.912A2185837D@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jul 13 07:13:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 12:13:03 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromGenericSequenceToFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromGenericSequenceToFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/772 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Jul 13 07:30:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Jul 2010 07:30:22 -0400 (EDT) Subject: [BioCatalogue-developers] [2133] branches/rest-api-updates/: branch for REST API JSONification and REST services support Message-ID: <20100713113022.335A2185837E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Jul 13 08:03:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Jul 2010 08:03:45 -0400 (EDT) Subject: [BioCatalogue-developers] [2134] branches/rest-api-updates: - implemented JSON for collections endpoints e.g. Message-ID: <20100713120345.88BF31678317@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jul 13 08:34:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 13:34:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getAMBER_MD_StructureFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getAMBER_MD_StructureFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1145 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Jul 13 09:18:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Jul 2010 09:18:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2135] branches/soaplab-and-monitoring/app/views/service_tests: tooltip icon for historical success rate of test scripts Message-ID: <20100713131856.845171858386@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jul 13 09:42:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 14:42:59 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolInfo' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolInfo' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1084 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Jul 13 11:21:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Jul 2010 11:21:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2136] branches/rest-api-updates: - added JSON outputs for the following endpoints Message-ID: <20100713152127.CF4081858381@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jul 13 11:28:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 16:28:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1128 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 11:33:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 16:33:34 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runMDFromMD_TrajectoryDCD' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runMDFromMD_TrajectoryDCD' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1139 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Tue Jul 13 11:36:22 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 13 Jul 2010 16:36:22 +0100 Subject: [BioCatalogue-developers] [Fwd: [2136] branches/rest-api-updates: - added JSON outputs for the following endpoints] Message-ID: <4C3C87F6.3020108@cs.man.ac.uk> Mannie, Please could you move: lib/bio_catalogue/json.rb ... to: lib/bio_catalogue/api/json.rb And thus change its full scoped reference to: BioCatalogue::Api::Json (notice the capitalisation I use to keep with the Rails autoloading conventions for any files in lib/) Jits -------- Original Message -------- Subject: [BioCatalogue-developers] [2136] branches/rest-api-updates: - added JSON outputs for the following endpoints Date: Tue, 13 Jul 2010 11:21:27 -0400 (EDT) From: noreply at rubyforge.org To: biocatalogue-developers at rubyforge.org Revision 2136 Author mannie Date 2010-07-13 11:21:27 -0400 (Tue, 13 Jul 2010) Log Message - added JSON outputs for the following endpoints /annotations/filters /services/filters /soap_operations/filters Modified Paths * branches/rest-api-updates/app/controllers/annotations_controller.rb <#branchesrestapiupdatesappcontrollersannotations_controllerrb> * branches/rest-api-updates/app/controllers/services_controller.rb <#branchesrestapiupdatesappcontrollersservices_controllerrb> * branches/rest-api-updates/app/controllers/soap_operations_controller.rb <#branchesrestapiupdatesappcontrollerssoap_operations_controllerrb> * branches/rest-api-updates/lib/bio_catalogue/json.rb <#branchesrestapiupdateslibbio_cataloguejsonrb> Diff -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Attached Message Part URL: From noreply at rubyforge.org Tue Jul 13 12:12:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 13 Jul 2010 12:12:52 -0400 (EDT) Subject: [BioCatalogue-developers] [2137] branches/rest-api-updates: - changed the module namespace for BioCatalogue::JSON to BioCatalogue::Api ::Json Message-ID: <20100713161253.1AA921858386@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Jul 13 17:23:19 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 22:23:19 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPersistentFile' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPersistentFile' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1113 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 17:39:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 22:39:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:parseAccessibilityFromPHDText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:parseAccessibilityFromPHDText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1110 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 18:29:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 13 Jul 2010 23:29:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromPrankToSLR' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromPrankToSLR' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1094 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 19:10:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 00:10:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:addDisulphideBondsFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:addDisulphideBondsFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1141 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 19:43:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 00:43:11 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getEigenvaluesFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getEigenvaluesFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1157 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 20:01:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 01:01:56 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:displayAlignmentFromTreeDetAnnotation' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:displayAlignmentFromTreeDetAnnotation' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1091 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 20:04:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 01:04:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getAverageStructureFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getAverageStructureFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1131 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 20:28:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 01:28:58 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runMDFromGROMACS_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runMDFromGROMACS_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1149 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 13 21:36:07 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 02:36:07 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToDNASequenceCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/786 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Wed Jul 14 05:49:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Wed, 14 Jul 2010 10:49:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-439) Build JSON outputs for the current REST API endpoints In-Reply-To: <4922873.7231.1278603795325.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5798294.7400.1279100955338.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-439?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-439. ------------------------------------ Resolution: Fixed > Build JSON outputs for the current REST API endpoints > ----------------------------------------------------- > > Key: BIOCAT-439 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-439 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Wed Jul 14 07:27:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 12:27:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runS3det' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runS3det' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1100 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Jul 14 07:32:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 12:32:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'SIMPA protein secondary structure prediction (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'SIMPA protein secondary structure prediction (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/272 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Jul 14 10:23:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 14 Jul 2010 10:23:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2138] trunk/app/models: archive services on delete of a soaplab_server instance Message-ID: <20100714142301.E1F56185839F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 14 10:24:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 14 Jul 2010 10:24:43 -0400 (EDT) Subject: [BioCatalogue-developers] [2139] trunk/lib/bio_catalogue: background job to update soap service descriptions from soaplab Message-ID: <20100714142443.4BB8719782DC@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Jul 14 11:33:29 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 14 Jul 2010 16:33:29 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C343B3A.9040400@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> Message-ID: Hi Eric, Well done for the effort. I find the gauge difficult to understand. Besides we're hiding info such as behavior of the service in a given month, year etc. I still think that graphs are better than gauge in our case. e.g a 2D graph showing the behavior of a service in a month/years etc. I also agree with jits point: That's the first thing users will look for when something goes 'red'. Franck On 7 July 2010 09:30, Eric Nzuobontane wrote: > Hi, > > Following the discussion like week, I have done some work on the monitoring > tab and would like some feedback. So now in a similar pattern to soap > operations, you have a listing of all the service tests from which you can > drill down to the individual test. ?See the attached screen shots. > > Please let me know what you think. > > Eric > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > -- ?"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Wed Jul 14 12:30:12 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 14 Jul 2010 17:30:12 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: References: <4C343B3A.9040400@ebi.ac.uk> Message-ID: <4C3DE614.7090605@ebi.ac.uk> ok, following initial comments from Jits and Sergey, these are the current views. While I see the point that a historical graph will add the notion of time over which a test passed or failed, I fail to see how useful it is for people to know that a test failed last year. For me, these thing are only indicators to help user make a decision as to whether to use a service or not. Eric Franck Tanoh wrote: > Hi Eric, > > Well done for the effort. > I find the gauge difficult to understand. Besides we're hiding info > such as behavior of the service in a given month, year etc. > I still think that graphs are better than gauge in our case. e.g a 2D > graph showing the behavior of a service in a month/years etc. > > I also agree with jits point: of the relevance of each group is essential> > That's the first thing users will look for when something goes 'red'. > > Franck > > > On 7 July 2010 09:30, Eric Nzuobontane wrote: > >> Hi, >> >> Following the discussion like week, I have done some work on the monitoring >> tab and would like some feedback. So now in a similar pattern to soap >> operations, you have a listing of all the service tests from which you can >> drill down to the individual test. See the attached screen shots. >> >> Please let me know what you think. >> >> Eric >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 5.png Type: image/png Size: 85498 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 6.png Type: image/png Size: 121551 bytes Desc: not available URL: From utopia at cs.man.ac.uk Wed Jul 14 15:31:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 14 Jul 2010 20:31:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runNCut' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runNCut' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/970 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Jul 14 20:31:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Jul 2010 01:31:49 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runTTSFinder' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runTTSFinder' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1104 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Jul 14 22:14:35 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Jul 2010 03:14:35 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMemeText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMemeText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/774 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Jul 14 22:44:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Jul 2010 03:44:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runLeapFromAMBER_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runLeapFromAMBER_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1182 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Jul 15 05:30:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Jul 2010 05:30:30 -0400 (EDT) Subject: [BioCatalogue-developers] [2140] trunk/app/helpers/rest_services_helper.rb: - bug fix for REST template generator Message-ID: <20100715093031.27ADE1858373@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Jul 15 05:38:00 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 15 Jul 2010 10:38:00 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C3DE614.7090605@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C3DE614.7090605@ebi.ac.uk> Message-ID: >While I see the point that a historical graph will add the notion of > time over which a test passed or failed, I fail to see how useful it is for > people to know that a test failed last year. I admit that graph may not be appropriate for the type of test we do (fail or pass) but the notion of time may give users an indication when not to use a service. It is therefore useful to keep a record of when a service fails. This can reveal for example when service providers have their service/server maintenance or when a service is updated. Franck On 14 July 2010 17:30, Eric Nzuobontane wrote: > ok, following initial comments from Jits and Sergey, these are the current > views. ?While I see the point that a historical graph will add the notion of > time over ?which a test passed or failed, I fail to see how useful it is for > people to know that a test failed last year. For me, these thing are only > indicators to help user make a decision as to whether to use a service or > not. > > Eric > > > Franck Tanoh wrote: >> >> Hi Eric, >> >> Well done for the effort. >> I find the gauge difficult to understand. Besides we're hiding info >> such as behavior of the service in a given month, year etc. >> I still think that graphs are better than gauge in our case. e.g a 2D >> graph showing the behavior of a service in a month/years ?etc. >> >> I also agree with jits point: > of the relevance of each group is essential> >> That's the first thing users will look for when something goes 'red'. >> >> Franck >> >> >> On 7 July 2010 09:30, Eric Nzuobontane wrote: >> >>> >>> Hi, >>> >>> Following the discussion like week, I have done some work on the >>> monitoring >>> tab and would like some feedback. So now in a similar pattern to soap >>> operations, you have a listing of all the service tests from which you >>> can >>> drill down to the individual test. ?See the attached screen shots. >>> >>> Please let me know what you think. >>> >>> Eric >>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel ? : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >>> >> >> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- ?"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Thu Jul 15 05:47:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Jul 2010 05:47:20 -0400 (EDT) Subject: [BioCatalogue-developers] [2141] branches/rest-api-updates: - bug fix for REST template generator Message-ID: <20100715094721.0D9CE19783C6@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 15 05:52:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 15 Jul 2010 10:52:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-441) Implement REST API endpoints for REST services In-Reply-To: <25950329.7234.1278603866463.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28570256.7465.1279187535315.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-441 started by Mannie Tagarira. > Implement REST API endpoints for REST services > ---------------------------------------------- > > Key: BIOCAT-441 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 15 06:00:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Jul 2010 06:00:52 -0400 (EDT) Subject: [BioCatalogue-developers] [2142] branches/rest-api-updates/app/models/rest_parameter.rb: - bug fix for RestParameter#to_json; the "constrained_values" of the returned JSON was returning a list with a single element ( a string containing all the constrained_values) Message-ID: <20100715100052.54C2A185838A@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Jul 15 11:16:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 15 Jul 2010 16:16:48 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromFASTA_NA_multiToNucleotideSeqCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromFASTA_NA_multiToNucleotideSeqCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1076 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Jul 15 12:20:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 15 Jul 2010 12:20:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2143] branches/rest-api-updates: - implemented endpoints (JSON + XML): Message-ID: <20100715162001.3735E1678318@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Jul 15 21:21:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 02:21:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromiHOPtoMOBY' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromiHOPtoMOBY' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1079 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jul 15 21:40:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 02:40:01 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:cnio.es:runFASSFromMSF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:cnio.es:runFASSFromMSF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/978 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 16 02:21:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 07:21:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2810 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 16 05:13:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 10:13:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:www.bioinfo.uma.es:getAminoAcidSequenceCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:www.bioinfo.uma.es:getAminoAcidSequenceCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/961 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 16 05:21:12 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 10:21:12 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getNAMD_ConfFromNAMD_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getNAMD_ConfFromNAMD_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1137 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Fri Jul 16 05:42:09 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 16 Jul 2010 10:42:09 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C3DE614.7090605@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C3DE614.7090605@ebi.ac.uk> Message-ID: <4C402971.2080809@cs.man.ac.uk> Eric, The groupings look much better. But can you please have a look at how it's done on the REST endpoints tab and also the RestMethod show page and do it exactly like that (ie: use the same UI styles). I agree with Franck that the gauge on it's own is confusing. If possible, and if not too perf-intensive, I would suggest having two graphs: - one showing availability over time, but where the x axis is weekly and the y axis is the average success rate per week. This will hopefully give more of an indicative and historical curve rather than just a binary state graph. - one showing the overall percentage of success, like you have now, but showing a different style from the gauge (which I think looks a little too complex). Maybe something like a vertical thermometer. I can do some UI touch up on this before this is released. Jits Eric Nzuobontane wrote: > ok, following initial comments from Jits and Sergey, these are the > current views. While I see the point that a historical graph will add > the notion of time over which a test passed or failed, I fail to see > how useful it is for people to know that a test failed last year. For > me, these thing are only indicators to help user make a decision as to > whether to use a service or not. > > Eric > > > Franck Tanoh wrote: >> Hi Eric, >> >> Well done for the effort. >> I find the gauge difficult to understand. Besides we're hiding info >> such as behavior of the service in a given month, year etc. >> I still think that graphs are better than gauge in our case. e.g a 2D >> graph showing the behavior of a service in a month/years etc. >> >> I also agree with jits point: > of the relevance of each group is essential> >> That's the first thing users will look for when something goes 'red'. >> >> Franck >> >> >> On 7 July 2010 09:30, Eric Nzuobontane wrote: >> >>> Hi, >>> >>> Following the discussion like week, I have done some work on the >>> monitoring >>> tab and would like some feedback. So now in a similar pattern to soap >>> operations, you have a listing of all the service tests from which >>> you can >>> drill down to the individual test. See the attached screen shots. >>> >>> Please let me know what you think. >>> >>> Eric >>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >>> >> >> >> >> > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Fri Jul 16 05:59:30 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 16 Jul 2010 10:59:30 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C402971.2080809@cs.man.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C3DE614.7090605@ebi.ac.uk> <4C402971.2080809@cs.man.ac.uk> Message-ID: <4C402D82.6060206@ebi.ac.uk> Jiten Bhagat wrote: > Eric, > > The groupings look much better. But can you please have a look at how > it's done on the REST endpoints tab and also the RestMethod show page > and do it exactly like that (ie: use the same UI styles). > I will have a look at these. > I agree with Franck that the gauge on it's own is confusing. If > possible, and if not too perf-intensive, I would suggest having two graphs: > - one showing availability over time, but where the x axis is weekly and > the y axis is the average success rate per week. This will hopefully > give more of an indicative and historical curve rather than just a > binary state graph. > for performance reasons, we could decide to limit the range over which the graphs are shown. Say the last half year and possibly pre-calculate > - one showing the overall percentage of success, like you have now, but > showing a different style from the gauge (which I think looks a little > too complex). Maybe something like a vertical thermometer. > From the 4 graphs styles that the seer gem which I am using can represent, the gauge seem more appropriate to show level. But I could remove the different color ranges which may be adding to perception of complexity. If it looks complex to you, I wonder if anyone would bother looking at it or trying to understand it. Does it really help? If it does not, maybe just a number would do. Just something like X% sucess rate. > I can do some UI touch up on this before this is released. > > Jits > > > Eric Nzuobontane wrote: > >> ok, following initial comments from Jits and Sergey, these are the >> current views. While I see the point that a historical graph will add >> the notion of time over which a test passed or failed, I fail to see >> how useful it is for people to know that a test failed last year. For >> me, these thing are only indicators to help user make a decision as to >> whether to use a service or not. >> >> Eric >> >> >> Franck Tanoh wrote: >> >>> Hi Eric, >>> >>> Well done for the effort. >>> I find the gauge difficult to understand. Besides we're hiding info >>> such as behavior of the service in a given month, year etc. >>> I still think that graphs are better than gauge in our case. e.g a 2D >>> graph showing the behavior of a service in a month/years etc. >>> >>> I also agree with jits point: >> of the relevance of each group is essential> >>> That's the first thing users will look for when something goes 'red'. >>> >>> Franck >>> >>> >>> On 7 July 2010 09:30, Eric Nzuobontane wrote: >>> >>> >>>> Hi, >>>> >>>> Following the discussion like week, I have done some work on the >>>> monitoring >>>> tab and would like some feedback. So now in a similar pattern to soap >>>> operations, you have a listing of all the service tests from which >>>> you can >>>> drill down to the individual test. See the attached screen shots. >>>> >>>> Please let me know what you think. >>>> >>>> Eric >>>> >>>> -- >>>> Eric Nzuobontane >>>> ================================== >>>> European Bioinformatics Institute >>>> Wellcome Trust Genome Campus >>>> Hinxton, Cambridge >>>> CB10 1SD >>>> United Kingdom >>>> >>>> Tel : +44 1223 492654 >>>> email : ericnzuo at ebi.ac.uk >>>> ================================== >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >>>> >>>> >>> >>> >>> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Fri Jul 16 06:02:43 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 16 Jul 2010 11:02:43 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C402D82.6060206@ebi.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C3DE614.7090605@ebi.ac.uk> <4C402971.2080809@cs.man.ac.uk> <4C402D82.6060206@ebi.ac.uk> Message-ID: <4C402E43.7000107@cs.man.ac.uk> > From the 4 graphs styles that the seer gem which I am using can > represent, the gauge seem more appropriate to show level. But I could > remove the different color ranges which may be adding to perception of > complexity. If it looks complex to you, I wonder if anyone would > bother looking at it or trying to understand it. Does it really help? > If it does not, maybe just a number would do. Just something like X% > sucess rate. I was thinking this too :-) A big "x%" would be more easily understandable. Jits Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> Eric, >> >> The groupings look much better. But can you please have a look at how >> it's done on the REST endpoints tab and also the RestMethod show page >> and do it exactly like that (ie: use the same UI styles). >> > I will have a look at these. >> I agree with Franck that the gauge on it's own is confusing. If >> possible, and if not too perf-intensive, I would suggest having two >> graphs: >> - one showing availability over time, but where the x axis is weekly and >> the y axis is the average success rate per week. This will hopefully >> give more of an indicative and historical curve rather than just a >> binary state graph. >> > for performance reasons, we could decide to limit the range over which > the graphs are shown. Say the last half year and possibly pre-calculate >> - one showing the overall percentage of success, like you have now, but >> showing a different style from the gauge (which I think looks a little >> too complex). Maybe something like a vertical thermometer. >> > From the 4 graphs styles that the seer gem which I am using can > represent, the gauge seem more appropriate to show level. But I could > remove the different color ranges which may be adding to perception of > complexity. If it looks complex to you, I wonder if anyone would > bother looking at it or trying to understand it. Does it really help? > If it does not, maybe just a number would do. Just something like X% > sucess rate. >> I can do some UI touch up on this before this is released. >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> ok, following initial comments from Jits and Sergey, these are the >>> current views. While I see the point that a historical graph will add >>> the notion of time over which a test passed or failed, I fail to see >>> how useful it is for people to know that a test failed last year. For >>> me, these thing are only indicators to help user make a decision as to >>> whether to use a service or not. >>> >>> Eric >>> >>> >>> Franck Tanoh wrote: >>> >>>> Hi Eric, >>>> >>>> Well done for the effort. >>>> I find the gauge difficult to understand. Besides we're hiding info >>>> such as behavior of the service in a given month, year etc. >>>> I still think that graphs are better than gauge in our case. e.g a 2D >>>> graph showing the behavior of a service in a month/years etc. >>>> >>>> I also agree with jits point: >>> of the relevance of each group is essential> >>>> That's the first thing users will look for when something goes 'red'. >>>> >>>> Franck >>>> >>>> >>>> On 7 July 2010 09:30, Eric Nzuobontane wrote: >>>> >>>> >>>>> Hi, >>>>> >>>>> Following the discussion like week, I have done some work on the >>>>> monitoring >>>>> tab and would like some feedback. So now in a similar pattern to soap >>>>> operations, you have a listing of all the service tests from which >>>>> you can >>>>> drill down to the individual test. See the attached screen shots. >>>>> >>>>> Please let me know what you think. >>>>> >>>>> Eric >>>>> >>>>> -- >>>>> Eric Nzuobontane >>>>> ================================== >>>>> European Bioinformatics Institute >>>>> Wellcome Trust Genome Campus >>>>> Hinxton, Cambridge >>>>> CB10 1SD >>>>> United Kingdom >>>>> >>>>> Tel : +44 1223 492654 >>>>> email : ericnzuo at ebi.ac.uk >>>>> ================================== >>>>> >>>>> >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>> >>>>> >>>>> >>>> >>>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > > From utopia at cs.man.ac.uk Fri Jul 16 08:38:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 13:38:47 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2810 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 16 08:44:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 16 Jul 2010 13:44:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getChainedCorrelationsFromCorrelationMatrix' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getChainedCorrelationsFromCorrelationMatrix' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1153 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Fri Jul 16 11:56:24 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 16 Jul 2010 16:56:24 +0100 Subject: [BioCatalogue-developers] monitoring views In-Reply-To: <4C402E43.7000107@cs.man.ac.uk> References: <4C343B3A.9040400@ebi.ac.uk> <4C3DE614.7090605@ebi.ac.uk> <4C402971.2080809@cs.man.ac.uk> <4C402D82.6060206@ebi.ac.uk> <4C402E43.7000107@cs.man.ac.uk> Message-ID: <4C408128.4050207@ebi.ac.uk> Would this be more understandable? With some expected styling improvements of course! Eric Jiten Bhagat wrote: >> From the 4 graphs styles that the seer gem which I am using can >> represent, the gauge seem more appropriate to show level. But I could >> remove the different color ranges which may be adding to perception of >> complexity. If it looks complex to you, I wonder if anyone would >> bother looking at it or trying to understand it. Does it really help? >> If it does not, maybe just a number would do. Just something like X% >> sucess rate. >> > > I was thinking this too :-) A big "x%" would be more easily understandable. > > Jits > > > > Eric Nzuobontane wrote: > >> Jiten Bhagat wrote: >> >>> Eric, >>> >>> The groupings look much better. But can you please have a look at how >>> it's done on the REST endpoints tab and also the RestMethod show page >>> and do it exactly like that (ie: use the same UI styles). >>> >>> >> I will have a look at these. >> >>> I agree with Franck that the gauge on it's own is confusing. If >>> possible, and if not too perf-intensive, I would suggest having two >>> graphs: >>> - one showing availability over time, but where the x axis is weekly and >>> the y axis is the average success rate per week. This will hopefully >>> give more of an indicative and historical curve rather than just a >>> binary state graph. >>> >>> >> for performance reasons, we could decide to limit the range over which >> the graphs are shown. Say the last half year and possibly pre-calculate >> >>> - one showing the overall percentage of success, like you have now, but >>> showing a different style from the gauge (which I think looks a little >>> too complex). Maybe something like a vertical thermometer. >>> >>> >> From the 4 graphs styles that the seer gem which I am using can >> represent, the gauge seem more appropriate to show level. But I could >> remove the different color ranges which may be adding to perception of >> complexity. If it looks complex to you, I wonder if anyone would >> bother looking at it or trying to understand it. Does it really help? >> If it does not, maybe just a number would do. Just something like X% >> sucess rate. >> >>> I can do some UI touch up on this before this is released. >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> ok, following initial comments from Jits and Sergey, these are the >>>> current views. While I see the point that a historical graph will add >>>> the notion of time over which a test passed or failed, I fail to see >>>> how useful it is for people to know that a test failed last year. For >>>> me, these thing are only indicators to help user make a decision as to >>>> whether to use a service or not. >>>> >>>> Eric >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>> >>>>> Hi Eric, >>>>> >>>>> Well done for the effort. >>>>> I find the gauge difficult to understand. Besides we're hiding info >>>>> such as behavior of the service in a given month, year etc. >>>>> I still think that graphs are better than gauge in our case. e.g a 2D >>>>> graph showing the behavior of a service in a month/years etc. >>>>> >>>>> I also agree with jits point: >>>> of the relevance of each group is essential> >>>>> That's the first thing users will look for when something goes 'red'. >>>>> >>>>> Franck >>>>> >>>>> >>>>> On 7 July 2010 09:30, Eric Nzuobontane wrote: >>>>> >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> Following the discussion like week, I have done some work on the >>>>>> monitoring >>>>>> tab and would like some feedback. So now in a similar pattern to soap >>>>>> operations, you have a listing of all the service tests from which >>>>>> you can >>>>>> drill down to the individual test. See the attached screen shots. >>>>>> >>>>>> Please let me know what you think. >>>>>> >>>>>> Eric >>>>>> >>>>>> -- >>>>>> Eric Nzuobontane >>>>>> ================================== >>>>>> European Bioinformatics Institute >>>>>> Wellcome Trust Genome Campus >>>>>> Hinxton, Cambridge >>>>>> CB10 1SD >>>>>> United Kingdom >>>>>> >>>>>> Tel : +44 1223 492654 >>>>>> email : ericnzuo at ebi.ac.uk >>>>>> ================================== >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> BioCatalogue-developers mailing list >>>>>> BioCatalogue-developers at rubyforge.org >>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 7.png Type: image/png Size: 125479 bytes Desc: not available URL: From utopia at cs.man.ac.uk Sat Jul 17 15:36:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 17 Jul 2010 20:36:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:getStructureFromPDB' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:getStructureFromPDB' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/986 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Sun Jul 18 12:01:01 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 18 Jul 2010 17:01:01 +0100 Subject: [BioCatalogue-developers] [Fwd: [2138] trunk/app/models: archive services on delete of a soaplab_server instance] Message-ID: <4C43253D.6020704@cs.man.ac.uk> Hi Eric, There seems to be a number of things going on in this commit, which unfortunately the commit message doesn't describe :-( Seems like monitoring changes (connect to SOAP operation), refactorings and bugfixes on top of what the commit message says. W.r.t. to archiving services when a soaplab_server instance is deleted - is it possible to delete soaplab server instances in the UI? If so, I'm not sure if archiving the associated services is the right thing to do. I would think that if a provider wanted to *delete* the soaplab server instance they would want to delete the associated services. We need to check this with Franck. Maybe archiving of soaplab server is better? Jits -------- Original Message -------- Subject: [BioCatalogue-developers] [2138] trunk/app/models: archive services on delete of a soaplab_server instance Date: Wed, 14 Jul 2010 10:23:01 -0400 (EDT) From: noreply at rubyforge.org To: biocatalogue-developers at rubyforge.org Revision 2138 Author ebontane Date 2010-07-14 10:23:01 -0400 (Wed, 14 Jul 2010) Log Message archive services on delete of a soaplab_server instance Modified Paths * trunk/app/models/service_test.rb <#trunkappmodelsservice_testrb> * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb> * trunk/app/models/soaplab_server.rb <#trunkappmodelssoaplab_serverrb> Diff Modified: trunk/app/models/service_test.rb (2137 => 2138) --- trunk/app/models/service_test.rb 2010-07-13 16:12:52 UTC (rev 2137) +++ trunk/app/models/service_test.rb 2010-07-14 14:23:01 UTC (rev 2138) @@ -123,9 +123,9 @@ last_success = TestResult.find(:first, :conditions => ["service_test_id=? AND result=0 ", self.id], :order => 'created_at DESC') unless last_success.nil? - return TestResult.find(:all, :conditions => ["service_test_id=? AND result=1 AND created_at > ? ", + return TestResult.find(:first, :conditions => ["service_test_id=? AND result=1 AND created_at > ? ", self.id, last_success.created_at], - :order => 'created_at ASC').first.created_at + :order => 'created_at ASC').created_at end return self.test_results.first.created_at end Modified: trunk/app/models/soap_service.rb (2137 => 2138) --- trunk/app/models/soap_service.rb 2010-07-13 16:12:52 UTC (rev 2137) +++ trunk/app/models/soap_service.rb 2010-07-14 14:23:01 UTC (rev 2138) @@ -616,9 +616,10 @@ def update_description_from_soaplab!(is_soaplab=false) if self.soaplab_service? || is_soaplab - desc = nil + desc = nil + proxy = nil begin - SystemTimer.timeout(60.seconds) do + SystemTimer.timeout(30.seconds) do proxy = SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver end if !proxy.respond_to?('describe') @@ -657,10 +658,21 @@ def connect? begin - SystemTimer.timeout(60.seconds) do + SystemTimer.timeout(30.seconds) do proxy = SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver operations = proxy.methods(false) - return true if !operations.empty? + if !operations.empty? + begin + puts operations.first + proxy.send(operations.first) + return true + rescue ArgumentError => ex + puts ex.class.name + puts ex + return true + end + end + return false end rescue Exception => ex logger.warn("Failed to connect to service") Modified: trunk/app/models/soaplab_server.rb (2137 => 2138) --- trunk/app/models/soaplab_server.rb 2010-07-13 16:12:52 UTC (rev 2137) +++ trunk/app/models/soaplab_server.rb 2010-07-14 14:23:01 UTC (rev 2138) @@ -9,6 +9,10 @@ require 'ftools' class SoaplabServer < ActiveRecord::Base + + after_create :update_relationships + before_destroy :archive_services + if ENABLE_CACHE_MONEY is_cached :repository => $cache index :location @@ -22,7 +26,9 @@ validates_uniqueness_of :location, :message => " for this server seems to exist in BioCatalogue" validates_url_format_of :location, :allow_nil => false + + if ENABLE_SEARCH acts_as_solr(:fields => [ :location ]) end @@ -43,6 +49,9 @@ dup = SoapService.check_duplicate(url, data["endpoint"]) if success and dup != nil existing_services << dup + unless dup.latest_version.service_versionified.description_from_soaplab + dup.latest_version.service_versionified.update_description_from_soaplab!(true) + end logger.info("This service exists in the database") else transaction do @@ -51,6 +60,7 @@ c_success = soap_service.submit_service( data["endpoint"], current_user, {} ) if c_success new_wsdls << url + soap_service.update_description_from_soaplab!(true) if soap_service logger.info("Registered service - #{url}. SUCCESS:") else error_urls << url @@ -68,6 +78,7 @@ end create_relationships(new_wsdls) create_tags(find_services_in_catalogue(new_wsdls), current_user) + self.update_descriptions_from_soaplab! return [new_wsdls, existing_services, error_urls] end @@ -85,7 +96,7 @@ proxy.wiredump_dev = STDERR categories.each{|cat| data[cat] = proxy.getAvailableAnalysesInCategory(cat) - proxy.wiredump_dev = STDERR + #proxy.wiredump_dev = STDERR data[cat].collect! {|a| analysis = {} analysis['name'] = a @@ -139,7 +150,7 @@ # find all the services in catalogue for this server # given the list of wsdls def find_services_in_catalogue(wsdls =[]) - return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| ss.service } + return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| ss.service }.compact end # the relationship table maps services to a soaplab instance @@ -215,5 +226,18 @@ Delayed::Job.enqueue(BioCatalogue::Jobs::UpdateSoaplabServiceDescription.new(service.id)) end end + + def update_relationships + registered_wsdls = self.services.collect{|s| s.latest_version.service_versionified.wsdl_location }.compact + data = services_factory().values.flatten + all_wsdls = data.collect{|d| d['location']}.compact + create_relationships(all_wsdls - registered_wsdls) + end + + def archive_services + self.services.each do |service| + service.archive! + end + end end -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Attached Message Part URL: From ericnzuo at ebi.ac.uk Sun Jul 18 18:12:35 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Sun, 18 Jul 2010 23:12:35 +0100 (BST) Subject: [BioCatalogue-developers] [Fwd: [2138] trunk/app/models: archive services on delete of a soaplab_server instance] In-Reply-To: <4C43253D.6020704@cs.man.ac.uk> References: <4C43253D.6020704@cs.man.ac.uk> Message-ID: <49076.213.106.89.217.1279491155.squirrel@webmail.ebi.ac.uk> > Hi Eric, > > There seems to be a number of things going on in this commit, which > unfortunately the commit message doesn't describe :-( Seems like > monitoring changes (connect to SOAP operation), refactorings and > bugfixes on top of what the commit message says. yes, there are additional fixes in that commit and maybe should "various soaplab and monitoring fixes" to indicate that it was not just the archiving that was happening. But it was the main thing that was additionl > > W.r.t. to archiving services when a soaplab_server instance is deleted - > is it possible to delete soaplab server instances in the UI? NO If so, I'm > not sure if archiving the associated services is the right thing to do. > I would think that if a provider wanted to *delete* the soaplab server > instance they would want to delete the associated services. Well, that may be their intention. However, given that soaplab services are just soap services, the original services may have been registered by someone else not through the soaplab mechanism. It that case, it would be undesirable to allow that soaplab instance to remove those services. We need to > check this with Franck. Maybe archiving of soaplab server is better? Certainly. Franck what do you think? Eric > > -------- Original Message -------- > Subject: [BioCatalogue-developers] [2138] trunk/app/models: archive > services on delete of a soaplab_server instance > Date: Wed, 14 Jul 2010 10:23:01 -0400 (EDT) > From: noreply at rubyforge.org > To: biocatalogue-developers at rubyforge.org > > > > Revision > 2138 > Author > ebontane > Date > 2010-07-14 10:23:01 -0400 (Wed, 14 Jul 2010) > > > Log Message > > archive services on delete of a soaplab_server instance > > > Modified Paths > > * trunk/app/models/service_test.rb <#trunkappmodelsservice_testrb> > * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb> > * trunk/app/models/soaplab_server.rb <#trunkappmodelssoaplab_serverrb> > > > Diff > > > Modified: trunk/app/models/service_test.rb (2137 => 2138) > > > --- trunk/app/models/service_test.rb 2010-07-13 16:12:52 UTC (rev 2137) > +++ trunk/app/models/service_test.rb 2010-07-14 14:23:01 UTC (rev 2138) > @@ -123,9 +123,9 @@ > last_success = TestResult.find(:first, :conditions => > ["service_test_id=? AND result=0 ", self.id], > :order => 'created_at > DESC') > unless last_success.nil? > - return TestResult.find(:all, :conditions => ["service_test_id=? > AND result=1 AND created_at > ? ", > + return TestResult.find(:first, :conditions => ["service_test_id=? > AND result=1 AND created_at > ? ", > self.id, > last_success.created_at], > - :order => > 'created_at ASC').first.created_at > + :order => > 'created_at ASC').created_at > end > return self.test_results.first.created_at > end > > > Modified: trunk/app/models/soap_service.rb (2137 => 2138) > > > --- trunk/app/models/soap_service.rb 2010-07-13 16:12:52 UTC (rev 2137) > +++ trunk/app/models/soap_service.rb 2010-07-14 14:23:01 UTC (rev 2138) > @@ -616,9 +616,10 @@ > > def update_description_from_soaplab!(is_soaplab=false) > if self.soaplab_service? || is_soaplab > - desc = nil > + desc = nil > + proxy = nil > begin > - SystemTimer.timeout(60.seconds) do > + SystemTimer.timeout(30.seconds) do > proxy = > SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver > end > if !proxy.respond_to?('describe') > @@ -657,10 +658,21 @@ > > def connect? > begin > - SystemTimer.timeout(60.seconds) do > + SystemTimer.timeout(30.seconds) do > proxy = > SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver > operations = proxy.methods(false) > - return true if !operations.empty? > + if !operations.empty? > + begin > + puts operations.first > + proxy.send(operations.first) > + return true > + rescue ArgumentError => ex > + puts ex.class.name > + puts ex > + return true > + end > + end > + return false > end > rescue Exception => ex > logger.warn("Failed to connect to service") > > > Modified: trunk/app/models/soaplab_server.rb (2137 => 2138) > > > --- trunk/app/models/soaplab_server.rb 2010-07-13 16:12:52 UTC (rev 2137) > +++ trunk/app/models/soaplab_server.rb 2010-07-14 14:23:01 UTC (rev 2138) > @@ -9,6 +9,10 @@ > require 'ftools' > > class SoaplabServer < ActiveRecord::Base > + > + after_create :update_relationships > + before_destroy :archive_services > + > if ENABLE_CACHE_MONEY > is_cached :repository => $cache > index :location > @@ -22,7 +26,9 @@ > validates_uniqueness_of :location, :message => " for this server seems > to exist in BioCatalogue" > validates_url_format_of :location, > :allow_nil => false > + > > + > if ENABLE_SEARCH > acts_as_solr(:fields => [ :location ]) > end > @@ -43,6 +49,9 @@ > dup = SoapService.check_duplicate(url, data["endpoint"]) > if success and dup != nil > existing_services << dup > + unless > dup.latest_version.service_versionified.description_from_soaplab > + > dup.latest_version.service_versionified.update_description_from_soaplab!(true) > + end > logger.info("This service exists in the database") > else > transaction do > @@ -51,6 +60,7 @@ > c_success = soap_service.submit_service( data["endpoint"], > current_user, {} ) > if c_success > new_wsdls << url > + soap_service.update_description_from_soaplab!(true) if > soap_service > logger.info("Registered service - #{url}. SUCCESS:") > else > error_urls << url > @@ -68,6 +78,7 @@ > end > create_relationships(new_wsdls) > create_tags(find_services_in_catalogue(new_wsdls), current_user) > + self.update_descriptions_from_soaplab! > return [new_wsdls, existing_services, error_urls] > end > > @@ -85,7 +96,7 @@ > proxy.wiredump_dev = STDERR > categories.each{|cat| > data[cat] = proxy.getAvailableAnalysesInCategory(cat) > - proxy.wiredump_dev = STDERR > + #proxy.wiredump_dev = STDERR > data[cat].collect! {|a| > analysis = {} > analysis['name'] = a > @@ -139,7 +150,7 @@ > # find all the services in catalogue for this server > # given the list of wsdls > def find_services_in_catalogue(wsdls =[]) > - return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| > ss.service } > + return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| > ss.service }.compact > end > > # the relationship table maps services to a soaplab instance > @@ -215,5 +226,18 @@ > Delayed::Job.enqueue(BioCatalogue::Jobs::UpdateSoaplabServiceDescription.new(service.id)) > end > end > + > + def update_relationships > + registered_wsdls = self.services.collect{|s| > s.latest_version.service_versionified.wsdl_location }.compact > + data = services_factory().values.flatten > + all_wsdls = data.collect{|d| d['location']}.compact > + create_relationships(all_wsdls - registered_wsdls) > + end > + > + def archive_services > + self.services.each do |service| > + service.archive! > + end > + end > > end > > From issues at mygrid.org.uk Mon Jul 19 06:23:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 19 Jul 2010 11:23:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-442) Improve search algorithm (eliminate use of BioCatalogue::Mapper.compound_ids_to_model_objects) Message-ID: <23853784.7504.1279534995408.JavaMail.jira@rosalind.cs.man.ac.uk> Improve search algorithm (eliminate use of BioCatalogue::Mapper.compound_ids_to_model_objects) ---------------------------------------------------------------------------------------------- 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 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jul 19 06:25:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 19 Jul 2010 11:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-443) Update the REST API's XML schema to account for the REST services support endpoints Message-ID: <8259919.7505.1279535115302.JavaMail.jira@rosalind.cs.man.ac.uk> 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 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jul 19 06:34:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 19 Jul 2010 06:34:10 -0400 (EDT) Subject: [BioCatalogue-developers] [2144] branches/rest-api-updates/app: - implemented endoints (JSON + XML): Message-ID: <20100719103411.1B5141858378@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 19 09:00:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 19 Jul 2010 14:00:15 +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: <7490548.7508.1279544415408.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 ] Mannie Tagarira updated BIOCAT-442: ----------------------------------- Summary: Optimize BioCatalogue::Mapper.compound_ids_to_model_objects for better performance (was: Improve search algorithm (eliminate use of BioCatalogue::Mapper.compound_ids_to_model_objects)) Description: 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. > 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 > > 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. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jul 19 09:10:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 19 Jul 2010 09:10:43 -0400 (EDT) Subject: [BioCatalogue-developers] [2145] branches/rest-api-updates: - implemented enpoints Message-ID: <20100719131043.32CFC1678317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 19 09:32:13 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 19 Jul 2010 09:32:13 -0400 (EDT) Subject: [BioCatalogue-developers] [2146] branches/rest-api-updates/app: - implemented endpoints (JSON + XML) Message-ID: <20100719133213.4991A167831A@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Jul 19 12:30:38 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 19 Jul 2010 17:30:38 +0100 Subject: [BioCatalogue-developers] [Fwd: [2138] trunk/app/models: archive services on delete of a soaplab_server instance] In-Reply-To: <49076.213.106.89.217.1279491155.squirrel@webmail.ebi.ac.uk> References: <4C43253D.6020704@cs.man.ac.uk> <49076.213.106.89.217.1279491155.squirrel@webmail.ebi.ac.uk> Message-ID: > Well, that may be their intention. However, given that soaplab services > are just soap services, the original services may have been registered by > someone else not through the soaplab mechanism. It that case, it would be > undesirable to allow that soaplab instance to remove those services. I don't think we can link soaplab services from a given server to other soaplab services from the same server but submitted using the soap mechanism. So deleting one will not affect the other. If a provider wants to delete a soaplab server instance, he probably want to delete all soaplab service associated to it. But I think since we have the 'archived service' functionality we should push more archiving than deleting. >> check this with Franck. Maybe archiving of soaplab server is better? Certainly. Archiving is better. deleting should be the last last option. For example when the service has no relevance to life science or some political reasons ... Franck On 18 July 2010 23:12, wrote: >> Hi Eric, >> >> There seems to be a number of things going on in this commit, which >> unfortunately the commit message doesn't describe :-( Seems like >> monitoring changes (connect to SOAP operation), refactorings and >> bugfixes on top of what the commit message says. > > yes, there are additional fixes in that commit and maybe should "various > soaplab ?and monitoring fixes" to indicate that it was not just the > archiving that was happening. But it was the main thing that was additionl >> >> W.r.t. to archiving services when a soaplab_server instance is deleted - >> is it possible to delete soaplab server instances in the UI? > NO > > ?If so, I'm >> not sure if archiving the associated services is the right thing to do. >> I would think that if a provider wanted to *delete* the soaplab server >> instance they would want to delete the associated services. > > Well, that may be their intention. However, given that soaplab services > are just soap services, the original services may have been registered by > someone else not through the soaplab mechanism. It that case, it would be > undesirable to allow that soaplab instance to remove those services. > > We need to >> check this with Franck. Maybe archiving of soaplab server is better? > > Certainly. Franck what do you think? > > Eric > > > >> >> -------- Original Message -------- >> Subject: ? ? ?[BioCatalogue-developers] [2138] trunk/app/models: archive >> services on delete of a soaplab_server instance >> Date: ? ? ? ? Wed, 14 Jul 2010 10:23:01 -0400 (EDT) >> From: ? ? ? ? noreply at rubyforge.org >> To: ? biocatalogue-developers at rubyforge.org >> >> >> >> Revision >> ? ? 2138 >> Author >> ? ? ebontane >> Date >> ? ? 2010-07-14 10:23:01 -0400 (Wed, 14 Jul 2010) >> >> >> ? ? ? Log Message >> >> archive services on delete of a soaplab_server instance >> >> >> ? ? ? Modified Paths >> >> ? ? * trunk/app/models/service_test.rb <#trunkappmodelsservice_testrb> >> ? ? * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb> >> ? ? * trunk/app/models/soaplab_server.rb <#trunkappmodelssoaplab_serverrb> >> >> >> ? ? ? Diff >> >> >> ? ? ? ? Modified: trunk/app/models/service_test.rb (2137 => 2138) >> >> >> --- trunk/app/models/service_test.rb ?2010-07-13 16:12:52 UTC (rev 2137) >> +++ trunk/app/models/service_test.rb ?2010-07-14 14:23:01 UTC (rev 2138) >> @@ -123,9 +123,9 @@ >> ? ? ? ?last_success = TestResult.find(:first, :conditions => >> ["service_test_id=? AND result=0 ", self.id], >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?:order => 'created_at >> DESC') >> ? ? ? ?unless last_success.nil? >> - ? ? ? ?return TestResult.find(:all, :conditions => ["service_test_id=? >> AND result=1 AND created_at > ? ", >> + ? ? ? ?return TestResult.find(:first, :conditions => ["service_test_id=? >> AND result=1 AND created_at > ? ", >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?self.id, >> last_success.created_at], >> - ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?:order => >> 'created_at ASC').first.created_at >> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?:order => >> 'created_at ASC').created_at >> ? ? ? ?end >> ? ? ? ?return self.test_results.first.created_at >> ? ? ?end >> >> >> ? ? ? ? Modified: trunk/app/models/soap_service.rb (2137 => 2138) >> >> >> --- trunk/app/models/soap_service.rb ?2010-07-13 16:12:52 UTC (rev 2137) >> +++ trunk/app/models/soap_service.rb ?2010-07-14 14:23:01 UTC (rev 2138) >> @@ -616,9 +616,10 @@ >> >> ? ?def update_description_from_soaplab!(is_soaplab=false) >> ? ? ?if self.soaplab_service? || is_soaplab >> - ? ? ?desc = nil >> + ? ? ?desc ?= nil >> + ? ? ?proxy = nil >> ? ? ? ?begin >> - ? ? ? ?SystemTimer.timeout(60.seconds) do >> + ? ? ? ?SystemTimer.timeout(30.seconds) do >> ? ? ? ? ? ?proxy = >> SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver >> ? ? ? ? ?end >> ? ? ? ? ?if !proxy.respond_to?('describe') >> @@ -657,10 +658,21 @@ >> >> ? ?def connect? >> ? ? ?begin >> - ? ? ?SystemTimer.timeout(60.seconds) do >> + ? ? ?SystemTimer.timeout(30.seconds) do >> ? ? ? ? ?proxy = >> SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver >> ? ? ? ? ?operations = proxy.methods(false) >> - ? ? ? ?return true if !operations.empty? >> + ? ? ? ?if !operations.empty? >> + ? ? ? ? ?begin >> + ? ? ? ? ? ?puts operations.first >> + ? ? ? ? ? ?proxy.send(operations.first) >> + ? ? ? ? ? ?return true >> + ? ? ? ? ?rescue ArgumentError => ex >> + ? ? ? ? ? ?puts ex.class.name >> + ? ? ? ? ? ?puts ex >> + ? ? ? ? ? ?return true >> + ? ? ? ? ?end >> + ? ? ? ?end >> + ? ? ? ?return false >> ? ? ? ?end >> ? ? ?rescue Exception => ex >> ? ? ? ?logger.warn("Failed to connect to service") >> >> >> ? ? ? ? Modified: trunk/app/models/soaplab_server.rb (2137 => 2138) >> >> >> --- trunk/app/models/soaplab_server.rb ? ? ? ?2010-07-13 16:12:52 UTC (rev 2137) >> +++ trunk/app/models/soaplab_server.rb ? ? ? ?2010-07-14 14:23:01 UTC (rev 2138) >> @@ -9,6 +9,10 @@ >> ?require 'ftools' >> >> ?class SoaplabServer < ActiveRecord::Base >> + >> + ?after_create :update_relationships >> + ?before_destroy :archive_services >> + >> ? ?if ENABLE_CACHE_MONEY >> ? ? ?is_cached :repository => $cache >> ? ? ?index :location >> @@ -22,7 +26,9 @@ >> ? ?validates_uniqueness_of :location, :message => " for this server seems >> to exist in BioCatalogue" >> ? ?validates_url_format_of :location, >> ? ? ? ? ? ? ? ? ? ? ? ? ? ?:allow_nil => false >> + >> >> + >> ? ?if ENABLE_SEARCH >> ? ? ?acts_as_solr(:fields => [ :location ]) >> ? ?end >> @@ -43,6 +49,9 @@ >> ? ? ? ? ? dup = SoapService.check_duplicate(url, data["endpoint"]) >> ? ? ? ?if success and dup != nil >> ? ? ? ? ? existing_services << dup >> + ? ? ? ? unless >> dup.latest_version.service_versionified.description_from_soaplab >> + >> dup.latest_version.service_versionified.update_description_from_soaplab!(true) >> + ? ? ? ? end >> ? ? ? ? ? logger.info("This service exists in the database") >> ? ? ? ?else >> ? ? ? ? ?transaction do >> @@ -51,6 +60,7 @@ >> ? ? ? ? ? ? ? ?c_success = soap_service.submit_service( data["endpoint"], >> current_user, {} ) >> ? ? ? ? ? ? ? ?if c_success >> ? ? ? ? ? ? ? ? ?new_wsdls << url >> + ? ? ? ? ? ? ? ?soap_service.update_description_from_soaplab!(true) if >> soap_service >> ? ? ? ? ? ? ? ? ?logger.info("Registered service - #{url}. SUCCESS:") >> ? ? ? ? ? ? ? ?else >> ? ? ? ? ? ? ? ? ?error_urls << url >> @@ -68,6 +78,7 @@ >> ? ? ?end >> ? ? ?create_relationships(new_wsdls) >> ? ? ?create_tags(find_services_in_catalogue(new_wsdls), current_user) >> + ? ?self.update_descriptions_from_soaplab! >> ? ? ?return [new_wsdls, existing_services, error_urls] >> ? ?end >> >> @@ -85,7 +96,7 @@ >> ? ? ? ?proxy.wiredump_dev = STDERR >> ? ? ? ?categories.each{|cat| >> ? ? ? ? ?data[cat] = proxy.getAvailableAnalysesInCategory(cat) >> - ? ? ? ?proxy.wiredump_dev = STDERR >> + ? ? ? ?#proxy.wiredump_dev = STDERR >> ? ? ? ? ?data[cat].collect! {|a| >> ? ? ? ? ? ?analysis ? ? ? ? ? ? = {} >> ? ? ? ? ? ?analysis['name'] ? ? = a >> @@ -139,7 +150,7 @@ >> ? ?# find all the services in catalogue for this server >> ? ?# given the list of wsdls >> ? ?def find_services_in_catalogue(wsdls =[]) >> - ? ?return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| >> ss.service } >> + ? ?return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| >> ss.service }.compact >> ? ?end >> >> ? ?# the relationship table maps services to a soaplab instance >> @@ -215,5 +226,18 @@ >> ? ? ? ?Delayed::Job.enqueue(BioCatalogue::Jobs::UpdateSoaplabServiceDescription.new(service.id)) >> ? ? ?end >> ? ?end >> + >> + ?def update_relationships >> + ? ?registered_wsdls = self.services.collect{|s| >> s.latest_version.service_versionified.wsdl_location }.compact >> + ? ?data ?= services_factory().values.flatten >> + ? ?all_wsdls = data.collect{|d| d['location']}.compact >> + ? ?create_relationships(all_wsdls - registered_wsdls) >> + ?end >> + >> + ?def archive_services >> + ? ?self.services.each do |service| >> + ? ? ?service.archive! >> + ? ?end >> + ?end >> >> ?end >> >> > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- ?"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Mon Jul 19 13:31:56 2010 From: ericnzuo at ebi.ac.uk (ericnzuo at ebi.ac.uk) Date: Mon, 19 Jul 2010 18:31:56 +0100 (BST) Subject: [BioCatalogue-developers] [Fwd: [2138] trunk/app/models: archive services on delete of a soaplab_server instance] In-Reply-To: References: <4C43253D.6020704@cs.man.ac.uk> <49076.213.106.89.217.1279491155.squirrel@webmail.ebi.ac.uk> Message-ID: <40161.213.106.89.217.1279560716.squirrel@webmail.ebi.ac.uk> >> Well, that may be their intention. However, given that soaplab services >> are just soap services, the original services may have been registered >> by >> someone else not through the soaplab mechanism. It that case, it would >> be >> undesirable to allow that soaplab instance to remove those services. > I don't think we can link soaplab services from a given server to > other soaplab services from the same server but submitted using the > soap mechanism. So deleting one will not affect the other. Franck, that is exactly what we do. Otherwise you will have to allow duplicate entries or you will have to delete any soaplab service submitted via soap whenever the soaplab server is submitted. I am not sure you want to do either > If a provider wants to delete a soaplab server instance, he probably > want to delete all soaplab service associated to it. But I think since > we have the 'archived service' functionality we should push more > archiving than deleting. > >>> check this with Franck. Maybe archiving of soaplab server is better? > Certainly. Archiving is better. deleting should be the last last > option. For example when the service has no relevance to life science > or some political reasons ... That has been my thinking as well. > > Franck > > On 18 July 2010 23:12, wrote: >>> Hi Eric, >>> >>> There seems to be a number of things going on in this commit, which >>> unfortunately the commit message doesn't describe :-( Seems like >>> monitoring changes (connect to SOAP operation), refactorings and >>> bugfixes on top of what the commit message says. >> >> yes, there are additional fixes in that commit and maybe should "various >> soaplab ?and monitoring fixes" to indicate that it was not just the >> archiving that was happening. But it was the main thing that was >> additionl >>> >>> W.r.t. to archiving services when a soaplab_server instance is deleted >>> - >>> is it possible to delete soaplab server instances in the UI? >> NO >> >> ?If so, I'm >>> not sure if archiving the associated services is the right thing to do. >>> I would think that if a provider wanted to *delete* the soaplab server >>> instance they would want to delete the associated services. >> >> Well, that may be their intention. However, given that soaplab services >> are just soap services, the original services may have been registered >> by >> someone else not through the soaplab mechanism. It that case, it would >> be >> undesirable to allow that soaplab instance to remove those services. >> >> We need to >>> check this with Franck. Maybe archiving of soaplab server is better? >> >> Certainly. Franck what do you think? >> >> Eric >> >> >> >>> >>> -------- Original Message -------- >>> Subject: ? ? ?[BioCatalogue-developers] [2138] trunk/app/models: >>> archive >>> services on delete of a soaplab_server instance >>> Date: ? ? ? ? Wed, 14 Jul 2010 10:23:01 -0400 (EDT) >>> From: ? ? ? ? noreply at rubyforge.org >>> To: ? biocatalogue-developers at rubyforge.org >>> >>> >>> >>> Revision >>> ? ? 2138 >>> Author >>> ? ? ebontane >>> Date >>> ? ? 2010-07-14 10:23:01 -0400 (Wed, 14 Jul 2010) >>> >>> >>> ? ? ? Log Message >>> >>> archive services on delete of a soaplab_server instance >>> >>> >>> ? ? ? Modified Paths >>> >>> ? ? * trunk/app/models/service_test.rb <#trunkappmodelsservice_testrb> >>> ? ? * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb> >>> ? ? * trunk/app/models/soaplab_server.rb >>> <#trunkappmodelssoaplab_serverrb> >>> >>> >>> ? ? ? Diff >>> >>> >>> ? ? ? ? Modified: trunk/app/models/service_test.rb (2137 => 2138) >>> >>> >>> --- trunk/app/models/service_test.rb ?2010-07-13 16:12:52 UTC (rev >>> 2137) >>> +++ trunk/app/models/service_test.rb ?2010-07-14 14:23:01 UTC (rev >>> 2138) >>> @@ -123,9 +123,9 @@ >>> ? ? ? ?last_success = TestResult.find(:first, :conditions => >>> ["service_test_id=? AND result=0 ", self.id], >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?:order => 'created_at >>> DESC') >>> ? ? ? ?unless last_success.nil? >>> - ? ? ? ?return TestResult.find(:all, :conditions => >>> ["service_test_id=? >>> AND result=1 AND created_at > ? ", >>> + ? ? ? ?return TestResult.find(:first, :conditions => >>> ["service_test_id=? >>> AND result=1 AND created_at > ? ", >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? >>> ? ?self.id, >>> last_success.created_at], >>> - ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?:order => >>> 'created_at ASC').first.created_at >>> + ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?:order => >>> 'created_at ASC').created_at >>> ? ? ? ?end >>> ? ? ? ?return self.test_results.first.created_at >>> ? ? ?end >>> >>> >>> ? ? ? ? Modified: trunk/app/models/soap_service.rb (2137 => 2138) >>> >>> >>> --- trunk/app/models/soap_service.rb ?2010-07-13 16:12:52 UTC (rev >>> 2137) >>> +++ trunk/app/models/soap_service.rb ?2010-07-14 14:23:01 UTC (rev >>> 2138) >>> @@ -616,9 +616,10 @@ >>> >>> ? ?def update_description_from_soaplab!(is_soaplab=false) >>> ? ? ?if self.soaplab_service? || is_soaplab >>> - ? ? ?desc = nil >>> + ? ? ?desc ?= nil >>> + ? ? ?proxy = nil >>> ? ? ? ?begin >>> - ? ? ? ?SystemTimer.timeout(60.seconds) do >>> + ? ? ? ?SystemTimer.timeout(30.seconds) do >>> ? ? ? ? ? ?proxy = >>> SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver >>> ? ? ? ? ?end >>> ? ? ? ? ?if !proxy.respond_to?('describe') >>> @@ -657,10 +658,21 @@ >>> >>> ? ?def connect? >>> ? ? ?begin >>> - ? ? ?SystemTimer.timeout(60.seconds) do >>> + ? ? ?SystemTimer.timeout(30.seconds) do >>> ? ? ? ? ?proxy = >>> SOAP::WSDLDriverFactory.new(self.wsdl_location).create_rpc_driver >>> ? ? ? ? ?operations = proxy.methods(false) >>> - ? ? ? ?return true if !operations.empty? >>> + ? ? ? ?if !operations.empty? >>> + ? ? ? ? ?begin >>> + ? ? ? ? ? ?puts operations.first >>> + ? ? ? ? ? ?proxy.send(operations.first) >>> + ? ? ? ? ? ?return true >>> + ? ? ? ? ?rescue ArgumentError => ex >>> + ? ? ? ? ? ?puts ex.class.name >>> + ? ? ? ? ? ?puts ex >>> + ? ? ? ? ? ?return true >>> + ? ? ? ? ?end >>> + ? ? ? ?end >>> + ? ? ? ?return false >>> ? ? ? ?end >>> ? ? ?rescue Exception => ex >>> ? ? ? ?logger.warn("Failed to connect to service") >>> >>> >>> ? ? ? ? Modified: trunk/app/models/soaplab_server.rb (2137 => 2138) >>> >>> >>> --- trunk/app/models/soaplab_server.rb ? ? ? ?2010-07-13 16:12:52 UTC >>> (rev 2137) >>> +++ trunk/app/models/soaplab_server.rb ? ? ? ?2010-07-14 14:23:01 UTC >>> (rev 2138) >>> @@ -9,6 +9,10 @@ >>> ?require 'ftools' >>> >>> ?class SoaplabServer < ActiveRecord::Base >>> + >>> + ?after_create :update_relationships >>> + ?before_destroy :archive_services >>> + >>> ? ?if ENABLE_CACHE_MONEY >>> ? ? ?is_cached :repository => $cache >>> ? ? ?index :location >>> @@ -22,7 +26,9 @@ >>> ? ?validates_uniqueness_of :location, :message => " for this server >>> seems >>> to exist in BioCatalogue" >>> ? ?validates_url_format_of :location, >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ?:allow_nil => false >>> + >>> >>> + >>> ? ?if ENABLE_SEARCH >>> ? ? ?acts_as_solr(:fields => [ :location ]) >>> ? ?end >>> @@ -43,6 +49,9 @@ >>> ? ? ? ? ? dup = SoapService.check_duplicate(url, data["endpoint"]) >>> ? ? ? ?if success and dup != nil >>> ? ? ? ? ? existing_services << dup >>> + ? ? ? ? unless >>> dup.latest_version.service_versionified.description_from_soaplab >>> + >>> dup.latest_version.service_versionified.update_description_from_soaplab!(true) >>> + ? ? ? ? end >>> ? ? ? ? ? logger.info("This service exists in the database") >>> ? ? ? ?else >>> ? ? ? ? ?transaction do >>> @@ -51,6 +60,7 @@ >>> ? ? ? ? ? ? ? ?c_success = soap_service.submit_service( >>> data["endpoint"], >>> current_user, {} ) >>> ? ? ? ? ? ? ? ?if c_success >>> ? ? ? ? ? ? ? ? ?new_wsdls << url >>> + ? ? ? ? ? ? ? ?soap_service.update_description_from_soaplab!(true) if >>> soap_service >>> ? ? ? ? ? ? ? ? ?logger.info("Registered service - #{url}. SUCCESS:") >>> ? ? ? ? ? ? ? ?else >>> ? ? ? ? ? ? ? ? ?error_urls << url >>> @@ -68,6 +78,7 @@ >>> ? ? ?end >>> ? ? ?create_relationships(new_wsdls) >>> ? ? ?create_tags(find_services_in_catalogue(new_wsdls), current_user) >>> + ? ?self.update_descriptions_from_soaplab! >>> ? ? ?return [new_wsdls, existing_services, error_urls] >>> ? ?end >>> >>> @@ -85,7 +96,7 @@ >>> ? ? ? ?proxy.wiredump_dev = STDERR >>> ? ? ? ?categories.each{|cat| >>> ? ? ? ? ?data[cat] = proxy.getAvailableAnalysesInCategory(cat) >>> - ? ? ? ?proxy.wiredump_dev = STDERR >>> + ? ? ? ?#proxy.wiredump_dev = STDERR >>> ? ? ? ? ?data[cat].collect! {|a| >>> ? ? ? ? ? ?analysis ? ? ? ? ? ? = {} >>> ? ? ? ? ? ?analysis['name'] ? ? = a >>> @@ -139,7 +150,7 @@ >>> ? ?# find all the services in catalogue for this server >>> ? ?# given the list of wsdls >>> ? ?def find_services_in_catalogue(wsdls =[]) >>> - ? ?return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| >>> ss.service } >>> + ? ?return SoapService.find_all_by_wsdl_location(wsdls).collect{ |ss| >>> ss.service }.compact >>> ? ?end >>> >>> ? ?# the relationship table maps services to a soaplab instance >>> @@ -215,5 +226,18 @@ >>> ? ? ? >>> ?Delayed::Job.enqueue(BioCatalogue::Jobs::UpdateSoaplabServiceDescription.new(service.id)) >>> ? ? ?end >>> ? ?end >>> + >>> + ?def update_relationships >>> + ? ?registered_wsdls = self.services.collect{|s| >>> s.latest_version.service_versionified.wsdl_location }.compact >>> + ? ?data ?= services_factory().values.flatten >>> + ? ?all_wsdls = data.collect{|d| d['location']}.compact >>> + ? ?create_relationships(all_wsdls - registered_wsdls) >>> + ?end >>> + >>> + ?def archive_services >>> + ? ?self.services.each do |service| >>> + ? ? ?service.archive! >>> + ? ?end >>> + ?end >>> >>> ?end >>> >>> >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > > > -- > ?"Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > From utopia at cs.man.ac.uk Tue Jul 20 01:23:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Jul 2010 06:23:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getMaskTrajectoryFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getMaskTrajectoryFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1148 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 20 06:57:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Jul 2010 11:57:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:optimizeStructureFromAMBER_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:optimizeStructureFromAMBER_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1175 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Jul 20 08:21:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 20 Jul 2010 08:21:24 -0400 (EDT) Subject: [BioCatalogue-developers] [2147] branches/rest-api-updates: - implemented endpoints (JSON + XML) Message-ID: <20100720122124.B1EF31858361@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Jul 20 08:26:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Tue, 20 Jul 2010 13:26:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-444) Optimize the code to retrieve display name annotations in BioCatalogue::Filtering::Annotations.get_filters_for_annotatables Message-ID: <754586.7519.1279628775436.JavaMail.jira@rosalind.cs.man.ac.uk> 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 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Tue Jul 20 09:39:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Jul 2010 14:39:56 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPrincipalComponentFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPrincipalComponentFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1161 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 20 11:08:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Jul 2010 16:08:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryNetCDF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryNetCDF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1133 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 20 14:57:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 20 Jul 2010 19:57:23 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:cleanStructureFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:cleanStructureFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1142 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 20 19:44:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 21 Jul 2010 00:44:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolInteractions' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolInteractions' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1088 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Jul 21 06:32:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 21 Jul 2010 11:32:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:computeDistancesFromPDB' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:computeDistancesFromPDB' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1152 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Wed Jul 21 07:49:31 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 21 Jul 2010 12:49:31 +0100 Subject: [BioCatalogue-developers] can't login the test site Message-ID: hi Guys, When i try to login to the test site it redirects me to ' https://test.biocatalogue.org/session' then displayed that something has gone wrong. Looks like the whole test site is HTTPS. Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Wed Jul 21 08:52:14 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 21 Jul 2010 13:52:14 +0100 Subject: [BioCatalogue-developers] can't login the test site In-Reply-To: References: Message-ID: <4C46ED7E.8090608@ebi.ac.uk> Mannie requested an update to the test site which included code to enable connections over ssl. Unfortunately, this has not been working yet and I have contacted Mannie to follow up this but he has not gotten around to resolving these issues. I think these need to be resolved rather soon as they would be a blocker on trunk. Eric Franck Tanoh wrote: > hi Guys, > > When i try to login to the test site it redirects me to > 'https://test.biocatalogue.org/session' then displayed that something > has gone wrong. > Looks like the whole test site is HTTPS. > > Cheers, > Franck > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From mannie.tags at googlemail.com Wed Jul 21 09:02:30 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Wed, 21 Jul 2010 14:02:30 +0100 Subject: [BioCatalogue-developers] can't login the test site In-Reply-To: <4C46ED7E.8090608@ebi.ac.uk> References: <4C46ED7E.8090608@ebi.ac.uk> Message-ID: Eric, I will remove the ssl_required statements from the controllers, effectively reverting to the original state of the catalogue prior to this work. I will do some proper work on the SSL stuff after the REST API... Regards, Mannie On 21 Jul 2010, at 13:52, Eric Nzuobontane wrote: > Mannie requested an update to the test site which included code to > enable connections over ssl. Unfortunately, this has not been > working yet and I have contacted Mannie to follow up this but he has > not gotten around to resolving these issues. I think these need to > be resolved rather soon as they would be a blocker on trunk. > > Eric > > > > Franck Tanoh wrote: >> hi Guys, >> >> When i try to login to the test site it redirects me to 'https://test.biocatalogue.org/session' >> then displayed that something has gone wrong. >> Looks like the whole test site is HTTPS. >> >> Cheers, >> Franck >> >> -- >> "Science knows no country, because knowledge belongs to humanity, >> and is the torch which illuminates the world." - Louis Pasteur >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Wed Jul 21 10:32:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Jul 2010 10:32:42 -0400 (EDT) Subject: [BioCatalogue-developers] [2148] branches/rest-api-updates: - updated API tests for JSON endpoints Message-ID: <20100721143242.6E1AF185836F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 21 11:32:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 21 Jul 2010 11:32:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2149] branches/soaplab-and-monitoring: -addition of model field to store pre-calculated success rate for services tests . Message-ID: <20100721153201.9E8AE1858378@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 22 05:11:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 10:11:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-435) Update the BioCatalogue test site to try out SSL support In-Reply-To: <21116395.7204.1278503175449.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <2687628.7553.1279789875523.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-435. ------------------------------------- Resolution: Fixed > Update the BioCatalogue test site to try out SSL support > -------------------------------------------------------- > > Key: BIOCAT-435 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-435 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase, User Management > Reporter: Mannie Tagarira > Assignee: Eric Nzuobontane > Priority: Blocker > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 22 05:16:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Jul 2010 05:16:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2150] branches/rest-api-updates/script/biocatalogue/api/tests: - updated the test for /search.json Message-ID: <20100722091609.C81741858371@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 22 05:58:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 10:58:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-403) In the exported spreadsheet, differentiate between existing annotations and new annotations In-Reply-To: <32711689.6318.1276853595313.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <18273957.7554.1279792695372.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-403 stopped by Mannie Tagarira. > In the exported spreadsheet, differentiate between existing annotations and new annotations > ------------------------------------------------------------------------------------------- > > Key: BIOCAT-403 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-403 > Project: BioCatalogue > Issue Type: Sub-task > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 06:00:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 11:00:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-378) Develop app for mass curation via spreadsheets In-Reply-To: <21283392.5166.1276592415369.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7106874.7555.1279792815335.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-378?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-378 stopped by Mannie Tagarira. > Develop app for mass curation via spreadsheets > ---------------------------------------------- > > Key: BIOCAT-378 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-378 > Project: BioCatalogue > Issue Type: New Feature > Components: Content Acquisition > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Original Estimate: 3 weeks > Remaining Estimate: 3 weeks > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Jul 22 06:14:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 22 Jul 2010 11:14:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathwayinference' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'pathwayinference' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2812 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Thu Jul 22 06:16:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 11:16:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <25478564.7557.1279793775370.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-425 started by Mannie Tagarira. > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 06:25:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 11:25:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <17512506.7558.1279794315416.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-286 started by Mannie Tagarira. > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 06:59:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 11:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-445) Upgrade main packages/libraries use by BioCatalogue Message-ID: <3176667.7559.1279796355366.JavaMail.jira@rosalind.cs.man.ac.uk> 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 mainly performance 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. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 07:01:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 12:01:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-445) Upgrade main packages/libraries use by BioCatalogue In-Reply-To: <3176667.7559.1279796355366.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21483653.7561.1279796476469.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 ] Eric Nzuobontane updated BIOCAT-445: ------------------------------------ Description: 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 was: It is desirable for mainly performance 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 > 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. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 08:00:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 13:00:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-427) Create a listing(index) page for all soaplab servers In-Reply-To: <22444182.6857.1277885355466.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21615363.7564.1279800015450.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-427?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-427. ------------------------------------- Resolution: Implemented > Create a listing(index) page for all soaplab servers > ---------------------------------------------------- > > Key: BIOCAT-427 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-427 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > In a similar way to the listing of the services, a listing for soaplab servers should be created -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 08:00:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 13:00:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-434) Add status icons to the tabs on the details of service tests In-Reply-To: <3981993.7201.1278495375309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <29844426.7565.1279800016823.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-434?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-434. ------------------------------------- Resolution: Implemented > Add status icons to the tabs on the details of service tests > ------------------------------------------------------------ > > Key: BIOCAT-434 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-434 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 4 hours > Remaining Estimate: 4 hours > > It will be helpful to add the status icons of the services tests in the details tabs for service tests. That will enable users to quickly target tests of interest depending on their status -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 08:00:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 13:00:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-437) Add some explanation to the historical success rate graph for service tests. In-Reply-To: <19368424.7211.1278586755457.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9590526.7566.1279800018231.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-437?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-437. ------------------------------------- Resolution: Implemented > Add some explanation to the historical success rate graph for service tests. > ---------------------------------------------------------------------------- > > Key: BIOCAT-437 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-437 > Project: BioCatalogue > Issue Type: Sub-task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Use the tooltip mechanism to add some information to/by the graph of the historical success rates for service tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 08:02:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 22 Jul 2010 13:02:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-428) Re-use the alternative name mechanism for Services on Soaplab server instances. In-Reply-To: <26015125.6865.1277892015347.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <573252.7567.1279800135312.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-428?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-428. ------------------------------------- Resolution: Implemented > Re-use the alternative name mechanism for Services on Soaplab server instances. > ------------------------------------------------------------------------------- > > Key: BIOCAT-428 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-428 > Project: BioCatalogue > Issue Type: Sub-task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Allow users to set alternative names(display names) for soaplab server instances. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 08:18:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 13:18:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <27324915.7568.1279801095426.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15612#action_15612 ] Mannie Tagarira commented on BIOCAT-286: ---------------------------------------- The previously added white_list_helper has now been removed. AnnotationsHelper#annotation_prepare_description now takes in an extra argument, do_white_list, which defaults to true. If false is passed in, the annotation does not get processed by white_list, an html_escape is done instead. > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 22 08:18:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 13:18:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-286) xmlns attributes are stripped from my example input Message-ID: <29214891.7569.1279801096570.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-286. ------------------------------------ Resolution: Fixed > xmlns attributes are stripped from my example input > --------------------------------------------------- > > Key: BIOCAT-286 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-286 > Project: BioCatalogue > Issue Type: Bug > Components: Web Interface > Reporter: Jiten Bhagat > Assignee: Mannie Tagarira > Priority: Critical > > <Pieter>I'm trying to add a piece of XML as example input to a service. When I click edit I see the original XML fragment as I added it, but when I click close the xmlns attributes are stripped from my example input. As result you you see a fragment with elements that have a namespace abbreviation, but the corresponding namespace is missing. If a user would try to copy paste this example input to test the corresponding service this may result in rather cryptic "generic server error" messages, which are most likely the result of a crashing XML parser that tripped over the missing namespace declaration. Take for example a look at the example input I added for the eFetchPubmedService: > This tag: > <efet:eFetchRequest xmlns:efet="http://www.ncbi.nlm.nih.gov/soap/eutils/efetch_pubmed"> > Is listed as: > <efet:eFetchRequest> > operation here: http://www.biocatalogue.org/services/30-efetchpubmedservice_314266#operations -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 22 08:21:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Jul 2010 08:21:17 -0400 (EDT) Subject: [BioCatalogue-developers] [2151] trunk: - updated AnnotationsHelper#annotation_prepare_description to process the annotation using either white_list or html_escape Message-ID: <20100722122117.4A877185838E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jul 22 08:49:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Jul 2010 08:49:32 -0400 (EDT) Subject: [BioCatalogue-developers] [2152] trunk/app/models/rest_method.rb: - updated RestMethod. group_rest_methods to group using case insensitive group names Message-ID: <20100722124932.4BE241858346@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 22 08:51:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 22 Jul 2010 13:51:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-425) Make REST group name capital insensitive In-Reply-To: <460355.6742.1277817855342.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <740080.7570.1279803075359.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-425. ------------------------------------ Resolution: Fixed > Make REST group name capital insensitive > ----------------------------------------- > > Key: BIOCAT-425 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-425 > Project: BioCatalogue > Issue Type: Sub-task > Components: REST Services Support > Reporter: Franck Tanoh > Assignee: Mannie Tagarira > > Check out the different group name here: http://test.biocatalogue.org/rest_methods/91 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 22 10:56:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 22 Jul 2010 10:56:49 -0400 (EDT) Subject: [BioCatalogue-developers] [2153] branches/rest-api-updates: - updated /api (JSON + XML) Message-ID: <20100722145649.298B81858361@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Jul 22 11:34:34 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 22 Jul 2010 16:34:34 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable Message-ID: Hi Eric, i keep on disabling the test script for this ddbj blast service: http://www.biocatalogue.org/services/8 But it all the time enable again whenever the test script monitor is run. We agreed last time (after the last F2F) that this test script has a lot of dependency from utopia we're unable to bring into biocat so should be disabled. Are all the disable test scripts enable again anytime the script are tested? Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Jul 22 11:51:51 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 22 Jul 2010 16:51:51 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: References: Message-ID: <4C486917.3060102@ebi.ac.uk> Franck Tanoh wrote: > Hi Eric, > > i keep on disabling the test script for this ddbj blast service: > http://www.biocatalogue.org/services/8 > But it all the time enable again whenever the test script monitor is run. > > We agreed last time (after the last F2F) that this test script has a > lot of dependency from utopia we're unable to bring into biocat so > should be disabled. > Are all the disable test scripts enable again anytime the script are > tested? Yes unfortunately, for all services that are not archived. But I have already committed a fix for that. It is a very simple one line fix. I noticed it myself and I find it annoying. Eric > > Cheers, > Franck > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu Jul 22 12:36:40 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 22 Jul 2010 17:36:40 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C486917.3060102@ebi.ac.uk> References: <4C486917.3060102@ebi.ac.uk> Message-ID: <4C487398.2000209@cs.man.ac.uk> What happens when a service is archived and then unarchived after the tests have been automagically disabled? Jits Eric Nzuobontane wrote: > Franck Tanoh wrote: >> Hi Eric, >> >> i keep on disabling the test script for this ddbj blast service: >> http://www.biocatalogue.org/services/8 But it all the time enable >> again whenever the test script monitor is run. >> >> We agreed last time (after the last F2F) that this test script has a >> lot of dependency from utopia we're unable to bring into biocat so >> should be disabled. >> Are all the disable test scripts enable again anytime the script are >> tested? > Yes unfortunately, for all services that are not archived. But I have > already committed a fix for that. It is a very simple one line fix. I > noticed it myself and I find it annoying. > > Eric > >> >> Cheers, >> Franck >> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, >> and is the torch which illuminates the world." - Louis Pasteur >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From utopia at cs.man.ac.uk Thu Jul 22 22:45:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Jul 2010 03:45:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS pepwheel' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS pepwheel' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/458 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 23 01:14:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Jul 2010 06:14:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS syco' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS syco' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1652 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 23 03:25:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Jul 2010 08:25:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS vrnaduplex' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS vrnaduplex' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1728 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 23 04:55:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Jul 2010 09:55:02 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'The ELM Resource Structure Filter' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'The ELM Resource Structure Filter' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1620 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 23 05:02:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Jul 2010 10:02:18 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS syco' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS syco' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1652 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Fri Jul 23 05:05:09 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 23 Jul 2010 10:05:09 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C487398.2000209@cs.man.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> Message-ID: <4C495B45.3030604@ebi.ac.uk> I think nothing should happen. The tests should remain disabled and user should manually enable them if necessary. Jiten Bhagat wrote: > What happens when a service is archived and then unarchived after the > tests have been automagically disabled? > > Jits > > > Eric Nzuobontane wrote: > >> Franck Tanoh wrote: >> >>> Hi Eric, >>> >>> i keep on disabling the test script for this ddbj blast service: >>> http://www.biocatalogue.org/services/8 But it all the time enable >>> again whenever the test script monitor is run. >>> >>> We agreed last time (after the last F2F) that this test script has a >>> lot of dependency from utopia we're unable to bring into biocat so >>> should be disabled. >>> Are all the disable test scripts enable again anytime the script are >>> tested? >>> >> Yes unfortunately, for all services that are not archived. But I have >> already committed a fix for that. It is a very simple one line fix. I >> noticed it myself and I find it annoying. >> >> Eric >> >> >>> Cheers, >>> Franck >>> >>> >>> -- >>> "Science knows no country, because knowledge belongs to humanity, >>> and is the torch which illuminates the world." - Louis Pasteur >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Fri Jul 23 05:21:05 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 23 Jul 2010 10:21:05 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C495B45.3030604@ebi.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> Message-ID: <4C495F01.5020502@cs.man.ac.uk> I'm not certain that's the "right" behaviour. Franck, what do you think? Jits Eric Nzuobontane wrote: > I think nothing should happen. The tests should remain disabled and > user should manually enable them if necessary. > > > Jiten Bhagat wrote: >> What happens when a service is archived and then unarchived after the >> tests have been automagically disabled? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> Franck Tanoh wrote: >>> >>>> Hi Eric, >>>> >>>> i keep on disabling the test script for this ddbj blast service: >>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>> again whenever the test script monitor is run. >>>> >>>> We agreed last time (after the last F2F) that this test script has a >>>> lot of dependency from utopia we're unable to bring into biocat so >>>> should be disabled. >>>> Are all the disable test scripts enable again anytime the script are >>>> tested? >>>> >>> Yes unfortunately, for all services that are not archived. But I have >>> already committed a fix for that. It is a very simple one line fix. I >>> noticed it myself and I find it annoying. >>> >>> Eric >>> >>> >>>> Cheers, >>>> Franck >>>> >>>> >>>> -- >>>> "Science knows no country, because knowledge belongs to humanity, >>>> and is the torch which illuminates the world." - Louis Pasteur >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>> > > From ericnzuo at ebi.ac.uk Fri Jul 23 05:38:06 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 23 Jul 2010 10:38:06 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C495F01.5020502@cs.man.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> <4C495F01.5020502@cs.man.ac.uk> Message-ID: <4C4962FE.6020506@ebi.ac.uk> Jiten Bhagat wrote: > I'm not certain that's the "right" behaviour. Franck, what do you think? > I do not believe that there is a 'right' behavior. I believe that there is a 'desirable' behavior . You could ask the monitoring framework to re-activate the test for enabled services. Maybe you can go further to say which tests should be enabled and which should not. But do you need that level of complexity? If you have to automatically enable tests, which is what I though initially should happen for all activated services, you would need to have additional configurations to specify when a curator/developer actually wants a test disabled even though the service is active. > Jits > > > Eric Nzuobontane wrote: > >> I think nothing should happen. The tests should remain disabled and >> user should manually enable them if necessary. >> >> >> Jiten Bhagat wrote: >> >>> What happens when a service is archived and then unarchived after the >>> tests have been automagically disabled? >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> Franck Tanoh wrote: >>>> >>>> >>>>> Hi Eric, >>>>> >>>>> i keep on disabling the test script for this ddbj blast service: >>>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>>> again whenever the test script monitor is run. >>>>> >>>>> We agreed last time (after the last F2F) that this test script has a >>>>> lot of dependency from utopia we're unable to bring into biocat so >>>>> should be disabled. >>>>> Are all the disable test scripts enable again anytime the script are >>>>> tested? >>>>> >>>>> >>>> Yes unfortunately, for all services that are not archived. But I have >>>> already committed a fix for that. It is a very simple one line fix. I >>>> noticed it myself and I find it annoying. >>>> >>>> Eric >>>> >>>> >>>> >>>>> Cheers, >>>>> Franck >>>>> >>>>> >>>>> -- >>>>> "Science knows no country, because knowledge belongs to humanity, >>>>> and is the torch which illuminates the world." - Louis Pasteur >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>> >>>>> >>>> >>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Fri Jul 23 05:52:10 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 23 Jul 2010 10:52:10 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C4962FE.6020506@ebi.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> <4C495F01.5020502@cs.man.ac.uk> <4C4962FE.6020506@ebi.ac.uk> Message-ID: <4C49664A.3000206@cs.man.ac.uk> Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> I'm not certain that's the "right" behaviour. Franck, what do you think? >> > I do not believe that there is a 'right' behavior. I believe that > there is a 'desirable' behavior . You could ask the monitoring > framework to re-activate the test for enabled services. Maybe you can > go further to say which tests should be enabled and which should not. > But do you need that level of complexity? If you have to automatically > enable tests, which is what I though initially should happen for all > activated services, you would need to have additional configurations > to specify when a curator/developer actually wants a test disabled > even though the service is active. Let's separate out the technical complexity of this from the desired behaviour for users. Right now... - user submits a service - user decides to archive the service - system disables all services tests for the service - user decides to unarchive the service - monitoring is now not happening for the service - user is confused as to what to do because no prior information/help has been given about this To me this is not an acceptable situation. Now, I understand that this is a bit of an edge case, but nevertheless an issue exists, and we need to acknowledge it and do something about it. Now we need to determine the most cost effective solution. Could be we just need some help text when unarchiving to inform the user that the service tests are disabled and that they should be manually enabled the tests they want. We need *something* to solve this issue. (Can submitters/responsibles of a service enable/disable service tests?) Jits > > > >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> I think nothing should happen. The tests should remain disabled and >>> user should manually enable them if necessary. >>> >>> >>> Jiten Bhagat wrote: >>> >>>> What happens when a service is archived and then unarchived after the >>>> tests have been automagically disabled? >>>> >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>>> Franck Tanoh wrote: >>>>> >>>>>> Hi Eric, >>>>>> >>>>>> i keep on disabling the test script for this ddbj blast service: >>>>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>>>> again whenever the test script monitor is run. >>>>>> >>>>>> We agreed last time (after the last F2F) that this test script has a >>>>>> lot of dependency from utopia we're unable to bring into biocat so >>>>>> should be disabled. >>>>>> Are all the disable test scripts enable again anytime the script are >>>>>> tested? >>>>>> >>>>> Yes unfortunately, for all services that are not archived. But I have >>>>> already committed a fix for that. It is a very simple one line fix. I >>>>> noticed it myself and I find it annoying. >>>>> >>>>> Eric >>>>> >>>>> >>>>>> Cheers, >>>>>> Franck >>>>>> >>>>>> >>>>>> -- >>>>>> "Science knows no country, because knowledge belongs to humanity, >>>>>> and is the torch which illuminates the world." - Louis Pasteur >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> BioCatalogue-developers mailing list >>>>>> BioCatalogue-developers at rubyforge.org >>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>> >>>>> >>> > > From jits at cs.man.ac.uk Fri Jul 23 06:16:32 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 23 Jul 2010 11:16:32 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C49664A.3000206@cs.man.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> <4C495F01.5020502@cs.man.ac.uk> <4C4962FE.6020506@ebi.ac.uk> <4C49664A.3000206@cs.man.ac.uk> Message-ID: <4C496C00.30506@cs.man.ac.uk> Looks like only admins can see and enable/disable service tests? So the user would have had no chance to even enable the disabled tests! Jits Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> Jiten Bhagat wrote: >> >>> I'm not certain that's the "right" behaviour. Franck, what do you think? >>> >>> >> I do not believe that there is a 'right' behavior. I believe that >> there is a 'desirable' behavior . You could ask the monitoring >> framework to re-activate the test for enabled services. Maybe you can >> go further to say which tests should be enabled and which should not. >> But do you need that level of complexity? If you have to automatically >> enable tests, which is what I though initially should happen for all >> activated services, you would need to have additional configurations >> to specify when a curator/developer actually wants a test disabled >> even though the service is active. >> > > Let's separate out the technical complexity of this from the desired > behaviour for users. > > Right now... > - user submits a service > - user decides to archive the service > - system disables all services tests for the service > - user decides to unarchive the service > - monitoring is now not happening for the service > - user is confused as to what to do because no prior information/help > has been given about this > > To me this is not an acceptable situation. > > Now, I understand that this is a bit of an edge case, but nevertheless > an issue exists, and we need to acknowledge it and do something about > it. Now we need to determine the most cost effective solution. Could be > we just need some help text when unarchiving to inform the user that the > service tests are disabled and that they should be manually enabled the > tests they want. We need *something* to solve this issue. (Can > submitters/responsibles of a service enable/disable service tests?) > > Jits > > > >> >> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> I think nothing should happen. The tests should remain disabled and >>>> user should manually enable them if necessary. >>>> >>>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>>> What happens when a service is archived and then unarchived after the >>>>> tests have been automagically disabled? >>>>> >>>>> Jits >>>>> >>>>> >>>>> Eric Nzuobontane wrote: >>>>> >>>>> >>>>> >>>>>> Franck Tanoh wrote: >>>>>> >>>>>> >>>>>>> Hi Eric, >>>>>>> >>>>>>> i keep on disabling the test script for this ddbj blast service: >>>>>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>>>>> again whenever the test script monitor is run. >>>>>>> >>>>>>> We agreed last time (after the last F2F) that this test script has a >>>>>>> lot of dependency from utopia we're unable to bring into biocat so >>>>>>> should be disabled. >>>>>>> Are all the disable test scripts enable again anytime the script are >>>>>>> tested? >>>>>>> >>>>>>> >>>>>> Yes unfortunately, for all services that are not archived. But I have >>>>>> already committed a fix for that. It is a very simple one line fix. I >>>>>> noticed it myself and I find it annoying. >>>>>> >>>>>> Eric >>>>>> >>>>>> >>>>>> >>>>>>> Cheers, >>>>>>> Franck >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> "Science knows no country, because knowledge belongs to humanity, >>>>>>> and is the torch which illuminates the world." - Louis Pasteur >>>>>>> ------------------------------------------------------------------------ >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioCatalogue-developers mailing list >>>>>>> BioCatalogue-developers at rubyforge.org >>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>>> >>>>>>> >>>>>> >>>>>> >>>> >>>> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Fri Jul 23 06:17:31 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 23 Jul 2010 11:17:31 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C49664A.3000206@cs.man.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> <4C495F01.5020502@cs.man.ac.uk> <4C4962FE.6020506@ebi.ac.uk> <4C49664A.3000206@cs.man.ac.uk> Message-ID: <4C496C3B.50106@ebi.ac.uk> Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> Jiten Bhagat wrote: >> >>> I'm not certain that's the "right" behaviour. Franck, what do you think? >>> >>> >> I do not believe that there is a 'right' behavior. I believe that >> there is a 'desirable' behavior . You could ask the monitoring >> framework to re-activate the test for enabled services. Maybe you can >> go further to say which tests should be enabled and which should not. >> But do you need that level of complexity? If you have to automatically >> enable tests, which is what I though initially should happen for all >> activated services, you would need to have additional configurations >> to specify when a curator/developer actually wants a test disabled >> even though the service is active. >> > > Let's separate out the technical complexity of this from the desired > behaviour for users. > > Right now... > - user submits a service > - user decides to archive the service > - system disables all services tests for the service > - user decides to unarchive the service > - monitoring is now not happening for the service > - user is confused as to what to do because no prior information/help > has been given about this > With the current codebase in production, the tests will be re-enabled when service is unarchived. But that means it is enabling every test for active services, hence the comment from Franck. However, with the intended change, the above scenario would happen. > To me this is not an acceptable situation. > > Now, I understand that this is a bit of an edge case, but nevertheless > an issue exists, and we need to acknowledge it and do something about > it. Now we need to determine the most cost effective solution. Could be > we just need some help text when unarchiving to inform the user that the > service tests are disabled and that they should be manually enabled the > tests they want. We need *something* to solve this issue. (Can > submitters/responsibles of a service enable/disable service tests?) > Yes we need to do something. I was just not sure what that something should be. At the moment, only admins can enable/disable tests. > Jits > > > >> >> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> I think nothing should happen. The tests should remain disabled and >>>> user should manually enable them if necessary. >>>> >>>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>>> What happens when a service is archived and then unarchived after the >>>>> tests have been automagically disabled? >>>>> >>>>> Jits >>>>> >>>>> >>>>> Eric Nzuobontane wrote: >>>>> >>>>> >>>>> >>>>>> Franck Tanoh wrote: >>>>>> >>>>>> >>>>>>> Hi Eric, >>>>>>> >>>>>>> i keep on disabling the test script for this ddbj blast service: >>>>>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>>>>> again whenever the test script monitor is run. >>>>>>> >>>>>>> We agreed last time (after the last F2F) that this test script has a >>>>>>> lot of dependency from utopia we're unable to bring into biocat so >>>>>>> should be disabled. >>>>>>> Are all the disable test scripts enable again anytime the script are >>>>>>> tested? >>>>>>> >>>>>>> >>>>>> Yes unfortunately, for all services that are not archived. But I have >>>>>> already committed a fix for that. It is a very simple one line fix. I >>>>>> noticed it myself and I find it annoying. >>>>>> >>>>>> Eric >>>>>> >>>>>> >>>>>> >>>>>>> Cheers, >>>>>>> Franck >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> "Science knows no country, because knowledge belongs to humanity, >>>>>>> and is the torch which illuminates the world." - Louis Pasteur >>>>>>> ------------------------------------------------------------------------ >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioCatalogue-developers mailing list >>>>>>> BioCatalogue-developers at rubyforge.org >>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>>> >>>>>>> >>>>>> >>>>>> >>>> >>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Fri Jul 23 06:32:21 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 23 Jul 2010 11:32:21 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-446) Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service Message-ID: <16685674.7582.1279881141133.JavaMail.jira@rosalind.cs.man.ac.uk> Anyone responsible for a service( this includes : submitter, other responsibles, curators and admins) should be able to enable/disable tests on the service ----------------------------------------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-446 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-446 Project: BioCatalogue Issue Type: Task Components: Service Monitoring Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane At the moment, only admins are able to enable/disable tests. This should be extended to anyone responsible for the service -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ytanoh at cs.man.ac.uk Fri Jul 23 07:07:31 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 23 Jul 2010 12:07:31 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: <4C496C3B.50106@ebi.ac.uk> References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> <4C495F01.5020502@cs.man.ac.uk> <4C4962FE.6020506@ebi.ac.uk> <4C49664A.3000206@cs.man.ac.uk> <4C496C3B.50106@ebi.ac.uk> Message-ID: Hi guys, >Yes we need to do something. I was just not sure what that something should be. At the moment, only admins can enable/disable tests. no good. At least the submitter or the maintainer of the service should be able to enable/disable the test script. When a member or maintainer of a service unarchived it, my view is that we should prompt him to check or updates few things about the service: - for example ask him to confirm that the test script (if the service has one) is still valid for the service, if so enable it. - prompt him to check for existing annotation as well. - etc. So, I think it's fine to let members manually enable test script after they unarchived a service but we need to prompt them to do it. Automating the process may create a lot of test failure because if a service is unarchived, it probably means something has changed, which the old test script might not be able to pick up. therefore, the priority as far as i'm concerned should be to allow submitters to enable/disable their test script. once that possible, we can simply warm them to enable it again if they unarchive a service. Cheers, Franck On 23 July 2010 11:17, Eric Nzuobontane wrote: > Jiten Bhagat wrote: > >> Eric Nzuobontane wrote: >> >> >>> Jiten Bhagat wrote: >>> >>> >>>> I'm not certain that's the "right" behaviour. Franck, what do you think? >>>> >>>> >>> I do not believe that there is a 'right' behavior. I believe that >>> there is a 'desirable' behavior . You could ask the monitoring >>> framework to re-activate the test for enabled services. Maybe you can >>> go further to say which tests should be enabled and which should not. >>> But do you need that level of complexity? If you have to automatically >>> enable tests, which is what I though initially should happen for all >>> activated services, you would need to have additional configurations >>> to specify when a curator/developer actually wants a test disabled even >>> though the service is active. >>> >>> >> >> Let's separate out the technical complexity of this from the desired >> behaviour for users. >> >> Right now... >> - user submits a service >> - user decides to archive the service >> - system disables all services tests for the service >> - user decides to unarchive the service >> - monitoring is now not happening for the service >> - user is confused as to what to do because no prior information/help >> has been given about this >> >> > With the current codebase in production, the tests will be re-enabled when > service is unarchived. But that means it is enabling every test for active > services, hence the comment from Franck. However, with the intended change, > the above scenario would happen. > > To me this is not an acceptable situation. >> >> Now, I understand that this is a bit of an edge case, but nevertheless >> an issue exists, and we need to acknowledge it and do something about >> it. Now we need to determine the most cost effective solution. Could be >> we just need some help text when unarchiving to inform the user that the >> service tests are disabled and that they should be manually enabled the >> tests they want. We need *something* to solve this issue. (Can >> submitters/responsibles of a service enable/disable service tests?) >> >> > Yes we need to do something. I was just not sure what that something should > be. At the moment, only admins can enable/disable tests. > > Jits >> >> >> >> >>> >>> >>> >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>>> I think nothing should happen. The tests should remain disabled and >>>>> user should manually enable them if necessary. >>>>> >>>>> >>>>> Jiten Bhagat wrote: >>>>> >>>>> >>>>>> What happens when a service is archived and then unarchived after the >>>>>> tests have been automagically disabled? >>>>>> >>>>>> Jits >>>>>> >>>>>> >>>>>> Eric Nzuobontane wrote: >>>>>> >>>>>> >>>>>>> Franck Tanoh wrote: >>>>>>> >>>>>>> >>>>>>>> Hi Eric, >>>>>>>> >>>>>>>> i keep on disabling the test script for this ddbj blast service: >>>>>>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>>>>>> again whenever the test script monitor is run. >>>>>>>> >>>>>>>> We agreed last time (after the last F2F) that this test script has a >>>>>>>> lot of dependency from utopia we're unable to bring into biocat so >>>>>>>> should be disabled. >>>>>>>> Are all the disable test scripts enable again anytime the script are >>>>>>>> tested? >>>>>>>> >>>>>>>> >>>>>>> Yes unfortunately, for all services that are not archived. But I have >>>>>>> already committed a fix for that. It is a very simple one line fix. I >>>>>>> noticed it myself and I find it annoying. >>>>>>> >>>>>>> Eric >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Cheers, >>>>>>>> Franck >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> "Science knows no country, because knowledge belongs to humanity, >>>>>>>> and is the torch which illuminates the world." - Louis Pasteur >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> BioCatalogue-developers mailing list >>>>>>>> BioCatalogue-developers at rubyforge.org >>>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Fri Jul 23 09:07:37 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 23 Jul 2010 14:07:37 +0100 Subject: [BioCatalogue-developers] ddbj blast test script enable In-Reply-To: References: <4C486917.3060102@ebi.ac.uk> <4C487398.2000209@cs.man.ac.uk> <4C495B45.3030604@ebi.ac.uk> <4C495F01.5020502@cs.man.ac.uk> <4C4962FE.6020506@ebi.ac.uk> <4C49664A.3000206@cs.man.ac.uk> <4C496C3B.50106@ebi.ac.uk> Message-ID: <4C499419.9010204@cs.man.ac.uk> Sounds good to me, Franck. Jits Franck Tanoh wrote: > Hi guys, > > >> Yes we need to do something. I was just not sure what that something should >> > be. At the moment, only admins can enable/disable tests. > no good. At least the submitter or the maintainer of the service should be > able to enable/disable the test script. > > When a member or maintainer of a service unarchived it, my view is that we > should prompt him to check or updates few things about the service: > - for example ask him to confirm that the test script (if the service has > one) is still valid for the service, if so enable it. > - prompt him to check for existing annotation as well. > - etc. > So, I think it's fine to let members manually enable test script after they > unarchived a service but we need to prompt them to do it. > Automating the process may create a lot of test failure because if a service > is unarchived, it probably means something has changed, which the old test > script might not be able to pick up. therefore, the priority as far as i'm > concerned should be to allow submitters to enable/disable their test script. > once that possible, we can simply warm them to enable it again if they > unarchive a service. > > Cheers, > Franck > > On 23 July 2010 11:17, Eric Nzuobontane wrote: > > >> Jiten Bhagat wrote: >> >> >>> Eric Nzuobontane wrote: >>> >>> >>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>> >>>>> I'm not certain that's the "right" behaviour. Franck, what do you think? >>>>> >>>>> >>>>> >>>> I do not believe that there is a 'right' behavior. I believe that >>>> there is a 'desirable' behavior . You could ask the monitoring >>>> framework to re-activate the test for enabled services. Maybe you can >>>> go further to say which tests should be enabled and which should not. >>>> But do you need that level of complexity? If you have to automatically >>>> enable tests, which is what I though initially should happen for all >>>> activated services, you would need to have additional configurations >>>> to specify when a curator/developer actually wants a test disabled even >>>> though the service is active. >>>> >>>> >>>> >>> Let's separate out the technical complexity of this from the desired >>> behaviour for users. >>> >>> Right now... >>> - user submits a service >>> - user decides to archive the service >>> - system disables all services tests for the service >>> - user decides to unarchive the service >>> - monitoring is now not happening for the service >>> - user is confused as to what to do because no prior information/help >>> has been given about this >>> >>> >>> >> With the current codebase in production, the tests will be re-enabled when >> service is unarchived. But that means it is enabling every test for active >> services, hence the comment from Franck. However, with the intended change, >> the above scenario would happen. >> >> To me this is not an acceptable situation. >> >>> Now, I understand that this is a bit of an edge case, but nevertheless >>> an issue exists, and we need to acknowledge it and do something about >>> it. Now we need to determine the most cost effective solution. Could be >>> we just need some help text when unarchiving to inform the user that the >>> service tests are disabled and that they should be manually enabled the >>> tests they want. We need *something* to solve this issue. (Can >>> submitters/responsibles of a service enable/disable service tests?) >>> >>> >>> >> Yes we need to do something. I was just not sure what that something should >> be. At the moment, only admins can enable/disable tests. >> >> Jits >> >>> >>> >>> >>>> >>>> >>>>> Jits >>>>> >>>>> >>>>> Eric Nzuobontane wrote: >>>>> >>>>> >>>>> >>>>>> I think nothing should happen. The tests should remain disabled and >>>>>> user should manually enable them if necessary. >>>>>> >>>>>> >>>>>> Jiten Bhagat wrote: >>>>>> >>>>>> >>>>>> >>>>>>> What happens when a service is archived and then unarchived after the >>>>>>> tests have been automagically disabled? >>>>>>> >>>>>>> Jits >>>>>>> >>>>>>> >>>>>>> Eric Nzuobontane wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Franck Tanoh wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Hi Eric, >>>>>>>>> >>>>>>>>> i keep on disabling the test script for this ddbj blast service: >>>>>>>>> http://www.biocatalogue.org/services/8 But it all the time enable >>>>>>>>> again whenever the test script monitor is run. >>>>>>>>> >>>>>>>>> We agreed last time (after the last F2F) that this test script has a >>>>>>>>> lot of dependency from utopia we're unable to bring into biocat so >>>>>>>>> should be disabled. >>>>>>>>> Are all the disable test scripts enable again anytime the script are >>>>>>>>> tested? >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> Yes unfortunately, for all services that are not archived. But I have >>>>>>>> already committed a fix for that. It is a very simple one line fix. I >>>>>>>> noticed it myself and I find it annoying. >>>>>>>> >>>>>>>> Eric >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> Franck >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> "Science knows no country, because knowledge belongs to humanity, >>>>>>>>> and is the torch which illuminates the world." - Louis Pasteur >>>>>>>>> >>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> BioCatalogue-developers mailing list >>>>>>>>> BioCatalogue-developers at rubyforge.org >>>>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > > From ytanoh at cs.man.ac.uk Fri Jul 23 10:34:32 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 23 Jul 2010 15:34:32 +0100 Subject: [BioCatalogue-developers] latest data Message-ID: Hi Eric, Could you send Jits the latest data from the live site (from now if possible) so that he can produce the annotation stats, pls? Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Jul 23 10:43:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 23 Jul 2010 10:43:04 -0400 (EDT) Subject: [BioCatalogue-developers] [2154] branches/rest-api-updates: - implemented write capability to endpoints /rest_resources and / soap_services (returns: JSON for the top level service if successful) Message-ID: <20100723144304.71EB019782D4@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Jul 23 18:49:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 23 Jul 2010 23:49:11 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathwayinference' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'pathwayinference' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2812 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 24 07:29:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 24 Jul 2010 12:29:14 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathwayinference' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathwayinference' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2812 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Jul 24 12:48:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 24 Jul 2010 17:48:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS vrnaduplex' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS vrnaduplex' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1728 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 25 23:11:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 26 Jul 2010 04:11:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS pepwheel' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS pepwheel' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/458 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Jul 25 21:45:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 26 Jul 2010 02:45:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getDimensionalityFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getDimensionalityFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1156 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Mon Jul 26 04:48:19 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 26 Jul 2010 09:48:19 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-441) Implement REST API endpoints for REST services In-Reply-To: <25950329.7234.1278603866463.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4164358.7591.1280134099521.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira resolved BIOCAT-441. ------------------------------------ Resolution: Implemented > Implement REST API endpoints for REST services > ---------------------------------------------- > > Key: BIOCAT-441 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jul 26 04:48:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 26 Jul 2010 09:48:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work stopped: (BIOCAT-441) Implement REST API endpoints for REST services In-Reply-To: <25950329.7234.1278603866463.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <20435424.7590.1280134095470.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-441 stopped by Mannie Tagarira. > Implement REST API endpoints for REST services > ---------------------------------------------- > > Key: BIOCAT-441 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-441 > Project: BioCatalogue > Issue Type: New Feature > Components: REST API, REST Services Support > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Jul 26 05:19:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Jul 2010 05:19:40 -0400 (EDT) Subject: [BioCatalogue-developers] [2155] branches/soaplab-and-monitoring/app: - Give permission to all people responsible for a service to enable/ disable it Message-ID: <20100726091940.C2C1B1678316@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Jul 26 06:17:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 26 Jul 2010 11:17:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'The ELM Resource Structure Filter' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'The ELM Resource Structure Filter' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1620 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Jul 26 06:17:44 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 26 Jul 2010 11:17:44 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'The ELM Resource Structure Filter' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'The ELM Resource Structure Filter' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1620 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Jul 26 06:55:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Jul 2010 06:55:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2156] branches/rest-api-updates/app/controllers: - changed the content of the JSON response following successful service registration ; the response now contains the status of the request (201 or 202), and a link to the created service Message-ID: <20100726105553.A39AB1858346@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 26 07:12:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Jul 2010 07:12:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2157] trunk: - removed the ensure_proper_protocol override Message-ID: <20100726111256.3F5D71858351@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 26 07:34:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Jul 2010 07:34:43 -0400 (EDT) Subject: [BioCatalogue-developers] [2158] trunk/app/controllers: - changed ssl_allowed to ssl_required for pages that capture user information Message-ID: <20100726113443.AD6021858356@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 26 07:59:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Jul 2010 07:59:02 -0400 (EDT) Subject: [BioCatalogue-developers] [2159] trunk/app/controllers/responsibility_requests_controller.rb: - added ssl_required to responsibility_requests_controller.rb Message-ID: <20100726115902.1A8821858356@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Jul 26 09:38:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 26 Jul 2010 09:38:26 -0400 (EDT) Subject: [BioCatalogue-developers] [2160] trunk: -merging the "soaplab-and-monitoring" branch into trunk. Message-ID: <20100726133826.590FC1858366@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Jul 26 10:07:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 26 Jul 2010 15:07:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Closed: (BIOCAT-436) Create a self signed SSL certificate for the test site In-Reply-To: <9701620.7209.1278582915429.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5847852.7599.1280153235349.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-436?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Mannie Tagarira closed BIOCAT-436. ---------------------------------- Resolution: Responded > Create a self signed SSL certificate for the test site > ------------------------------------------------------ > > Key: BIOCAT-436 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-436 > Project: BioCatalogue > Issue Type: Task > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Eric Nzuobontane > > The BioCatalogue SSL certificate is for "www.biocatalogue.org". This does not account for BioCatalogue subdomains. A self signed certificate for "test.biocatalogue.org" is needed to test out SSL. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Jul 26 10:09:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Mon, 26 Jul 2010 15:09:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-447) Test SSL on the BioCatalogue main site Message-ID: <337413.7600.1280153355313.JavaMail.jira@rosalind.cs.man.ac.uk> 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 -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Mon Jul 26 23:39:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 27 Jul 2010 04:39:58 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:loadPersistentFile' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:loadPersistentFile' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1114 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Jul 27 02:07:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 27 Jul 2010 07:07:32 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getAMBER_MD_StructureFromPDBText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getAMBER_MD_StructureFromPDBText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1145 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Jul 28 11:56:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 28 Jul 2010 11:56:21 -0400 (EDT) Subject: [BioCatalogue-developers] [2161] branches/rest-api-updates: - added the oauth-plugin plugin and oauth-0.4.1 gem Message-ID: <20100728155622.6B85C197828C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Jul 28 11:58:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 28 Jul 2010 11:58:56 -0400 (EDT) Subject: [BioCatalogue-developers] [2162] branches/rest-api-updates/vendor/gems/oauth-0.3.4/: - removed the oauth-0.3.4 gem as my svn client was refusing to remove it Message-ID: <20100728155856.CFD3F1858374@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Jul 29 05:38:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 29 Jul 2010 05:38:32 -0400 (EDT) Subject: [BioCatalogue-developers] [2163] branches/rest-api-updates/app/controllers: - added oauth support to write endpoints Message-ID: <20100729093832.BD5A71858377@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Thu Jul 29 06:13:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 29 Jul 2010 11:13:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-448) Integrate OAuth into the application Message-ID: <4348614.7764.1280398395360.JavaMail.jira@rosalind.cs.man.ac.uk> Integrate OAuth into the application ------------------------------------ Key: BIOCAT-448 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-448 Project: BioCatalogue Issue Type: New Feature Components: Misc Codebase Reporter: Mannie Tagarira Assignee: Mannie Tagarira Priority: Blocker -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 29 06:13:16 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 29 Jul 2010 11:13:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-448) Integrate OAuth into the application In-Reply-To: <4348614.7764.1280398395360.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7063090.7765.1280398396539.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-448?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-448 started by Mannie Tagarira. > Integrate OAuth into the application > ------------------------------------ > > Key: BIOCAT-448 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-448 > Project: BioCatalogue > Issue Type: New Feature > Components: Misc Codebase > Reporter: Mannie Tagarira > Assignee: Mannie Tagarira > Priority: Blocker > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Jul 29 06:15:15 2010 From: issues at mygrid.org.uk (Mannie Tagarira (JIRA)) Date: Thu, 29 Jul 2010 11:15:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-449) Expose other BioCatalogue functionality through the REST API Message-ID: <14800995.7766.1280398515300.JavaMail.jira@rosalind.cs.man.ac.uk> Expose other BioCatalogue functionality through the REST API ------------------------------------------------------------ Key: BIOCAT-449 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-449 Project: BioCatalogue Issue Type: Improvement Components: REST API Reporter: Mannie Tagarira Assignee: Jiten Bhagat This includes stuff such as user "favourites" and so on -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Jul 29 06:35:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 29 Jul 2010 06:35:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2164] branches/rest-api-updates/app/controllers: - updated : login_required before filters to :login_or_oauth_required Message-ID: <20100729103502.00FE71858389@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Jul 29 08:22:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 29 Jul 2010 13:22:36 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromPrankToSLR' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromPrankToSLR' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1094 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jul 29 11:13:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 29 Jul 2010 16:13:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getProtProtInterfaceFromPDBId' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getProtProtInterfaceFromPDBId' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1105 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Jul 29 05:51:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 29 Jul 2010 10:51:11 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'EMBOSS topo' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'EMBOSS topo' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1820 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Jul 30 12:50:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 30 Jul 2010 12:50:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2165] branches/rest-api-updates: - misc. Message-ID: <20100730165053.4302B1858370@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Jul 30 15:55:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 30 Jul 2010 20:55:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getSnapshotFromMD_Trajectory' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getSnapshotFromMD_Trajectory' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1135 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 30 15:58:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 30 Jul 2010 20:58:57 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getStatisticalLog' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getStatisticalLog' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1062 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Jul 30 18:31:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 30 Jul 2010 23:31:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runCExonic' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runCExonic' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1098 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team