From noreply at rubyforge.org Wed Apr 1 05:46:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Apr 2009 05:46:45 -0400 (EDT) Subject: [BioCatalogue-developers] [546] trunk/wget_deployment_endpoints.rb: updated comments Message-ID: <20090401094647.CA03B1858118@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 1 08:50:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Apr 2009 08:50:30 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2581] Annontations plugin: prevent duplicate values Message-ID: <20090401125030.4C286185811E@rubyforge.org> Task #2581 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annontations plugin: prevent duplicate values Complete: 95% Status: Open Description: Basically, right now it is possible to add the same value for the same attribute (and even by the same user)... this is not ideal and by default it should probably not allow duplicate annotations (ie: same value on same attribute). Also add a config setting to override this for specific attributes (eg: we might want to allow multiple tags to be added, to indicate popularity). Follow-Ups: ------------------------------------------------------- Date: 2009-04-01 12:50 By: jits Comment: Done, tested, but not fully verified. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2581&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Apr 1 12:25:44 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Apr 2009 12:25:44 -0400 (EDT) Subject: [BioCatalogue-developers] [547] trunk: [UNSTABLE] Latest Feta Import work: Message-ID: <20090401162544.89454197857F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 1 16:07:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 1 Apr 2009 16:07:58 -0400 (EDT) Subject: [BioCatalogue-developers] [548] trunk/feta_import.rb: Latest work on Feta import script Message-ID: <20090401200758.17FFA1858188@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 2 10:51:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 2 Apr 2009 10:51:29 -0400 (EDT) Subject: [BioCatalogue-developers] [549] trunk/feta_import.rb: Initial completion of the Feta import script Message-ID: <20090402145129.49A0718580F9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 2 12:52:18 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 2 Apr 2009 12:52:18 -0400 (EDT) Subject: [BioCatalogue-developers] [550] trunk/feta_import.rb: Bugfixes for Feta import script. Message-ID: <20090402165218.795D818580F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 3 07:26:50 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 07:26:50 -0400 (EDT) Subject: [BioCatalogue-developers] [551] trunk: Better error handling and logging for WSDL parser. Message-ID: <20090403112650.A1E451858116@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 3 09:15:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 09:15:30 -0400 (EDT) Subject: [BioCatalogue-developers] [552] trunk/feta_import.rb: Stable version of the Feta import script. Message-ID: <20090403131530.86B40185811F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 3 09:18:52 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 09:18:52 -0400 (EDT) Subject: [BioCatalogue-developers] [553] trunk/feta_import.rb: Fixes for soaplab Message-ID: <20090403131852.971A41858112@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Fri Apr 3 09:36:54 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 03 Apr 2009 14:36:54 +0100 Subject: [BioCatalogue-developers] Beta site update on Monday Message-ID: <49D610F6.9040303@cs.man.ac.uk> Hi guys, Are we okay to do an update to the beta site on Monday? I would like to do the feta import then and this requires a full update. Cheers, Jits From noreply at rubyforge.org Fri Apr 3 09:38:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 09:38:31 -0400 (EDT) Subject: [BioCatalogue-developers] [554] trunk: Added Agents scaffold so that UI doesn' t break after Feta import. Message-ID: <20090403133831.6522D1858112@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 3 09:51:32 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 09:51:32 -0400 (EDT) Subject: [BioCatalogue-developers] [555] trunk/app/models/annotation.rb: Removed the white_list operation on annotation values before save ( ie sanitising the content). Message-ID: <20090403135132.5F9AB18580FA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 3 10:51:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 10:51:58 -0400 (EDT) Subject: [BioCatalogue-developers] [556] trunk: Style updates for tag clouds and tag lists Message-ID: <20090403145158.D551A18580F7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Apr 3 12:15:44 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 3 Apr 2009 12:15:44 -0400 (EDT) Subject: [BioCatalogue-developers] [557] trunk: UI work for name aliases. Message-ID: <20090403161544.D9DD01978571@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 6 13:00:32 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 6 Apr 2009 13:00:32 -0400 (EDT) Subject: [BioCatalogue-developers] [558] trunk: Major refactoring for the tag cloud generation, in preparation for special rendering of ontological term URIs. Message-ID: <20090406170032.8A1261858108@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 6 13:43:34 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 6 Apr 2009 13:43:34 -0400 (EDT) Subject: [BioCatalogue-developers] [559] trunk: initial work on the upload of test scripts. Message-ID: <20090406174334.A16F318580F7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Apr 6 15:08:59 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 6 Apr 2009 15:08:59 -0400 (EDT) Subject: [BioCatalogue-developers] [560] trunk/app/helpers/tags_helper.rb: Bugfix for broken commit. Message-ID: <20090406190859.738B1185810A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 08:54:04 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 08:54:04 -0400 (EDT) Subject: [BioCatalogue-developers] [561] trunk/config/initializers/biocat_main.rb: Important configuration for "Tag" annotations - now the values are not downcased when saved, since Ontology term URIs can have terms that are mixed case. Message-ID: <20090407125404.F4025185818B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 09:06:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 09:06:28 -0400 (EDT) Subject: [BioCatalogue-developers] [562] trunk/wget_deployment_endpoints.rb: catch timeout exceptions Message-ID: <20090407130628.D1AD7197858F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 10:10:21 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 10:10:21 -0400 (EDT) Subject: [BioCatalogue-developers] [563] trunk/wget_deployment_endpoints.rb: fix for exception handling Message-ID: <20090407141021.D8A5F18580FA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 10:15:20 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 10:15:20 -0400 (EDT) Subject: [BioCatalogue-developers] [564] trunk: Initial attempt at showing ontological term URI tags differently. Message-ID: <20090407141520.9CBC41779926@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 12:22:56 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 12:22:56 -0400 (EDT) Subject: [BioCatalogue-developers] [565] trunk: Improved tag cloud by adding rounded corners. Message-ID: <20090407162256.A32361858137@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 13:00:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 13:00:58 -0400 (EDT) Subject: [BioCatalogue-developers] [566] trunk: - Fix for small tag clouds. Message-ID: <20090407170058.EB37F1978571@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Apr 7 13:28:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 7 Apr 2009 13:28:11 -0400 (EDT) Subject: [BioCatalogue-developers] [567] trunk/app/controllers/tags_controller.rb: Tag search results now take into account the ontology term URIs. Message-ID: <20090407172811.6C057185819F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 8 06:05:16 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Apr 2009 06:05:16 -0400 (EDT) Subject: [BioCatalogue-developers] [568] trunk/app/views/services/index.html.erb: Made the tag cloud ( on service index page) width dynamic so it can cater for browser resizes. Message-ID: <20090408100517.70501185811B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 8 07:12:00 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Apr 2009 07:12:00 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2611] Annotations: add creditation mechanism Message-ID: <20090408111200.5983E1858134@rubyforge.org> Task #2611 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annotations: add creditation mechanism Complete: 0% Status: Open Description: Annotations may have a specific "source" but sometimes "credit" needs to be given to other people/entities for that annotation. So implement a creditation mechanism in the plugin. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2611&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Apr 8 10:12:23 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Apr 2009 10:12:23 -0400 (EDT) Subject: [BioCatalogue-developers] [569] trunk: Reworking of source of import data: Message-ID: <20090408141223.D55B01779921@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 8 12:03:25 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Apr 2009 12:03:25 -0400 (EDT) Subject: [BioCatalogue-developers] [570] trunk: Implemeted a much better way of showing the numbers of annotations. Message-ID: <20090408160325.946DB18580F7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 8 12:15:49 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Apr 2009 12:15:49 -0400 (EDT) Subject: [BioCatalogue-developers] [571] trunk: Style changes for annotation count boxes. Message-ID: <20090408161549.E797D1858119@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 8 12:45:20 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 8 Apr 2009 12:45:20 -0400 (EDT) Subject: [BioCatalogue-developers] [572] trunk: Style fixes for bloody IE! Message-ID: <20090408164520.E5BD11779921@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 9 06:50:36 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Apr 2009 06:50:36 -0400 (EDT) Subject: [BioCatalogue-developers] [573] trunk: Some refactorings and updates for tags and tag clouds. Message-ID: <20090409105036.2052518580E2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 9 06:57:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Apr 2009 06:57:29 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2612] Annotations: any finder should be able to take a list of options Message-ID: <20090409105729.CC2FD185810E@rubyforge.org> Task #2612 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annotations: any finder should be able to take a list of options Complete: 0% Status: Open Description: For any finder method in the annotations plugin, it should be possible to provide a list of options as well as a single option. E.g.: should be able to get a set of annotations for multiple attributes in one query. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2612&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Apr 9 09:36:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Apr 2009 09:36:39 -0400 (EDT) Subject: [BioCatalogue-developers] [574] trunk/app: Tag cloud renderer now does "weighted" or "flat". Message-ID: <20090409133639.5D4311978589@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Apr 9 10:11:48 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 9 Apr 2009 10:11:48 -0400 (EDT) Subject: [BioCatalogue-developers] [575] trunk/app: Simple show page for Registries. Message-ID: <20090409141148.AB8831858182@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Apr 15 06:47:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Apr 2009 06:47:38 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2613] Ability to add/delete "documentation url" Message-ID: <20090415104738.DB9281779921@rubyforge.org> Task #2613 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Ability to add/delete "documentation url" Complete: 0% Status: Open Description: Add/delete "documentation url" annotations. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2613&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Apr 15 10:00:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Apr 2009 10:00:31 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2614] All annotation add icons/texts should only show on hover Message-ID: <20090415140031.E84FD1858137@rubyforge.org> Task #2614 has been updated. Project: BioCatalogue Subproject: Pilot Summary: All annotation add icons/texts should only show on hover Complete: 0% Status: Open Description: Right now it looks very ugly where there is "log in to add..." or "add description". Make this only show on hover. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2614&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Apr 15 14:06:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Apr 2009 14:06:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2614] All annotation add icons/texts should only show on hover Message-ID: <20090415180614.560CC185835C@rubyforge.org> Task #2614 has been updated. Project: BioCatalogue Subproject: Pilot Summary: All annotation add icons/texts should only show on hover Complete: 95% Status: Open Description: Right now it looks very ugly where there is "log in to add..." or "add description". Make this only show on hover. Follow-Ups: ------------------------------------------------------- Date: 2009-04-15 18:06 By: jits Comment: Done. Needs full testing. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2614&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Apr 15 14:07:21 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 15 Apr 2009 14:07:21 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2615] Issue with popups on IE (when on operations tab) Message-ID: <20090415180721.760CB1858361@rubyforge.org> Task #2615 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Issue with popups on IE (when on operations tab) Complete: 0% Status: Open Description: When using IE and when opening the popup on the operations tab of soap services, the background becomes fully grey, which is not good! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2615&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Fri Apr 17 10:34:52 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 17 Apr 2009 15:34:52 +0100 Subject: [BioCatalogue-developers] SOAP/WSDL in Ruby Message-ID: <49E8938C.3090209@cs.man.ac.uk> Possibly look into this: http://wso2.org/projects/wsf/ruby From noreply at rubyforge.org Fri Apr 17 11:18:20 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Apr 2009 11:18:20 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2616] Fix WSDL parsing for certain WSDLs Message-ID: <20090417151820.9DFF218580F9@rubyforge.org> Task #2616 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fix WSDL parsing for certain WSDLs Complete: 0% Status: Open Description: E.g.: trying to parse: http://www.webservicex.com/globalweather.asmx?WSDL ... breaks... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2616&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Apr 17 11:20:16 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 17 Apr 2009 11:20:16 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2617] Fix WSDL parsing - not picking up all descriptions Message-ID: <20090417152017.06CF918580F9@rubyforge.org> Task #2617 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fix WSDL parsing - not picking up all descriptions Complete: 0% Status: Open Description: E.g.: http://edoc3.bibliothek.uni-halle.de:8080/axis/vascoda.wsdl has some descriptions about the operation etc BUT the WSDL parsing isn't picking this up... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2617&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Apr 19 10:44:15 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 19 Apr 2009 10:44:15 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2618] Allow adding of example *sets* of inputs for operations Message-ID: <20090419144415.9D468197857C@rubyforge.org> Task #2618 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Allow adding of example *sets* of inputs for operations Complete: 0% Status: Open Description: From Jerzy: "4. Is it possible to create an example set of inputs. Some inputs go only together. " ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2618&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Apr 19 13:37:27 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 19 Apr 2009 13:37:27 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2619] Investigate: no values for min_occurs and max_occurs Message-ID: <20090419173727.EFBB81D78602@rubyforge.org> Task #2619 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Investigate: no values for min_occurs and max_occurs Complete: 0% Status: Open Description: min_occurs and max_occurs for soap_inputs and soap_outputs currently have no values whatsoever, and this needs investigating. It could be due to WSDL parsing or it could just be that we don't need those fields in the DB (in which case we should remove them) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2619&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 20 08:27:49 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Apr 2009 08:27:49 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2612] Annotations: any finder should be able to take a list of options Message-ID: <20090420122749.82C0D18580E2@rubyforge.org> Task #2612 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annotations: any finder should be able to take a list of options Complete: 75% Status: Open Description: For any finder method in the annotations plugin, it should be possible to provide a list of options as well as a single option. E.g.: should be able to get a set of annotations for multiple attributes in one query. Follow-Ups: ------------------------------------------------------- Date: 2009-04-20 12:27 By: jits Comment: Implemented some of these. There may be more required, so keeping this open. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2612&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 20 08:28:12 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 20 Apr 2009 08:28:12 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2614] All annotation add icons/texts should only show on hover Message-ID: <20090420122812.D663818581DE@rubyforge.org> Task #2614 has been updated. Project: BioCatalogue Subproject: Pilot Summary: All annotation add icons/texts should only show on hover Complete: 100% Status: Closed Description: Right now it looks very ugly where there is "log in to add..." or "add description". Make this only show on hover. Follow-Ups: ------------------------------------------------------- Date: 2009-04-20 12:28 By: jits Comment: Done ------------------------------------------------------- Date: 2009-04-15 18:06 By: jits Comment: Done. Needs full testing. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2614&group_id=6901&group_project_id=12540 From support at seekda.com Mon Apr 20 13:04:42 2009 From: support at seekda.com (seekda Support) Date: Mon, 20 Apr 2009 19:04:42 +0200 Subject: [BioCatalogue-developers] Complete Your seekda Registration Message-ID: <17382958.121240247082007.JavaMail.tomcat@localhost> Dear biocatalogue-developers at rubyforge.org, Thank you for wanting to join seekda! In order to confirm your registration and use extra features of seekda search engine you need to activate your account by accessing the following URL or pasting it directly into browser: https://seekda.com/new_account?action=verify&token=BS4820AVmWFOr4cEmBTh (Note: If clicking the link does not open a browser window, copy the URL and paste it into a browser location bar.) Feel free to contact seekda at support at seekda.com anytime. Your seekda team, ~seekda ___________________________ seekda Web Services seekda.com From noreply at rubyforge.org Tue Apr 21 12:46:27 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Apr 2009 12:46:27 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2620] unable to search word like 'go term' Message-ID: <20090421164628.02B1F18581DD@rubyforge.org> Task #2620 has been updated. Project: BioCatalogue Subproject: Pilot Summary: unable to search word like 'go term' Complete: 0% Status: Open Description: search with 'go term' does not return a hit. however when i search with 'go_term' i have a hit. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2620&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Apr 21 12:51:08 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Apr 2009 12:51:08 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2621] comments on biocat not visable Message-ID: <20090421165108.615E318581DD@rubyforge.org> Task #2621 has been updated. Project: BioCatalogue Subproject: Pilot Summary: comments on biocat not visable Complete: 0% Status: Open Description: the comment thread is a the bottom of the page, making it impossible to view.... my suggestion is to have a kind of tab or link somewhere at the top of the page to point users to the comments at the bottom. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2621&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Apr 21 12:53:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 21 Apr 2009 12:53:17 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2622] operations have unique url? Message-ID: <20090421165317.490C518581DD@rubyforge.org> Task #2622 has been updated. Project: BioCatalogue Subproject: Pilot Summary: operations have unique url? Complete: 0% Status: Open Description: Operations in biocat don't seem to have a unique URL. I mean i can't point someone to an operation using the URL ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2622&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Wed Apr 22 05:20:58 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 22 Apr 2009 10:20:58 +0100 Subject: [BioCatalogue-developers] SOAP/WSDL in Ruby In-Reply-To: <49EED58F.6030503@ebi.ac.uk> References: <49E8938C.3090209@cs.man.ac.uk> <49EED58F.6030503@ebi.ac.uk> Message-ID: <49EEE17A.9040702@cs.man.ac.uk> Exactly my thoughts :-) Cheers Eric. Jits Eric Nzuobontane wrote: > Thanks Jits, > I will have a look at this. It looks quite interesting and maybe give > us a route to replacing our current wsdl parser. > > Eric > > > Jiten Bhagat wrote: >> Possibly look into this: >> http://wso2.org/projects/wsf/ruby > From jits at cs.man.ac.uk Wed Apr 22 10:37:12 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 22 Apr 2009 15:37:12 +0100 Subject: [BioCatalogue-developers] Duplicate services Message-ID: <49EF2B98.5080705@cs.man.ac.uk> http://beta.biocatalogue.org/search?query=fproml&commit= returns duplicate services From ericnzuo at ebi.ac.uk Wed Apr 22 10:58:57 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 22 Apr 2009 15:58:57 +0100 Subject: [BioCatalogue-developers] Duplicate services In-Reply-To: <49EF2B98.5080705@cs.man.ac.uk> References: <49EF2B98.5080705@cs.man.ac.uk> Message-ID: <49EF30B1.30707@ebi.ac.uk> We probably need a cleanup but this what I suspect happened: When there was this long delay during service submission, request to the application might have be resent due to the application not responding in time. That by-passes our duplicate check because of the interval within which the requests are received by the application. I believe that problem is cured now with the improved response time but it can potentially happen again. Eric Jiten Bhagat wrote: > http://beta.biocatalogue.org/search?query=fproml&commit= returns > duplicate services > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Wed Apr 22 11:00:59 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 22 Apr 2009 16:00:59 +0100 Subject: [BioCatalogue-developers] Duplicate services In-Reply-To: <49EF30B1.30707@ebi.ac.uk> References: <49EF2B98.5080705@cs.man.ac.uk> <49EF30B1.30707@ebi.ac.uk> Message-ID: <49EF312B.70205@cs.man.ac.uk> Ahh, so you mean the soaplab server was submitted twice within a short period of time? Jits Eric Nzuobontane wrote: > We probably need a cleanup but this what I suspect happened: When > there was this long delay during service submission, request to the > application might have be resent due to the application not responding > in time. That by-passes our duplicate check because of the interval > within which the requests are received by the application. I believe > that problem is cured now with the improved response time but it can > potentially happen again. > > Eric > > > Jiten Bhagat wrote: >> http://beta.biocatalogue.org/search?query=fproml&commit= returns >> duplicate services >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From jits at cs.man.ac.uk Wed Apr 22 11:10:55 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 22 Apr 2009 16:10:55 +0100 Subject: [BioCatalogue-developers] Duplicate services In-Reply-To: <49EF3292.50905@ebi.ac.uk> References: <49EF2B98.5080705@cs.man.ac.uk> <49EF30B1.30707@ebi.ac.uk> <49EF312B.70205@cs.man.ac.uk> <49EF3292.50905@ebi.ac.uk> Message-ID: <49EF337F.8010609@cs.man.ac.uk> Eric Nzuobontane wrote: > >> Ahh, so you mean the soaplab server was submitted twice within a >> short period of time? > no, the soap service. I know this because there was a duplicate from > myself and I think from Rodrigo & Franck Okay, I know that specific service is submitted as a SOAP service, but what I mean is that it is part of a soaplab server, so it must have been that the soaplab server was submitted twice within a short period of time, by the same person (uludag). I think we should investigate this and making the sure the process isn't happening twice, in two different transactions (or even one transaction)... Jits > >> >> Jits >> >> >> Eric Nzuobontane wrote: >>> We probably need a cleanup but this what I suspect happened: When >>> there was this long delay during service submission, request to the >>> application might have be resent due to the application not >>> responding in time. That by-passes our duplicate check because of >>> the interval within which the requests are received by the >>> application. I believe that problem is cured now with the improved >>> response time but it can potentially happen again. >>> >>> Eric >>> >>> >>> Jiten Bhagat wrote: >>>> http://beta.biocatalogue.org/search?query=fproml&commit= returns >>>> duplicate services >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > From noreply at rubyforge.org Wed Apr 22 12:04:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 22 Apr 2009 12:04:30 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2623] Add forgot your password link to main login page Message-ID: <20090422160430.7FEF21858137@rubyforge.org> Task #2623 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add forgot your password link to main login page Complete: 0% Status: Open Description: The "forgot your password" link should also be on main log in page. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2623&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Apr 22 12:15:32 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 22 Apr 2009 12:15:32 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2624] Collapse filtering options box Message-ID: <20090422161532.8B9F318581E2@rubyforge.org> Task #2624 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Collapse filtering options box Complete: 0% Status: Open Description: Collapse the filtering options box at the top of the browse page. Maybe only show the top 10, with "more..." option ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2624&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Thu Apr 23 12:25:16 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 23 Apr 2009 17:25:16 +0100 Subject: [BioCatalogue-developers] [Fwd: [BIOCATALOGUE-FRIENDS] BioCatalogue beta latest updates!!!] Message-ID: <49F0966C.60702@cs.man.ac.uk> Well done guys! :-) Jits -------- Original Message -------- Subject: [BIOCATALOGUE-FRIENDS] BioCatalogue beta latest updates!!! Date: Thu, 23 Apr 2009 17:23:36 +0100 From: Franck Tanoh Reply-To: Friends of the BioCatalogue project To: BIOCATALOGUE-FRIENDS at listserv.manchester.ac.uk Hi all, We have updated the BioCatalogue beta site with the following new features: 1- Ability to register REST services. 2-Commenting and discussions (powered by Disqus) 3-Ability for users to provide many more types of annotations (like examples, name aliases and so on) 4-At-a-glance counts of annotations on services (grouped by provider, user and other registries). 5-Better browsing of services (including filtering by service type(s) and service provider(s), and sorting of results). 6-Ability to change your password 7-Lots of UI enhancements and tweaks Also most of the metadata from Feta (http://www.mygrid.org.uk/feta/mygrid/descriptions/ ) has been imported and we are working on bringing in services from SeekDa (http://seekda.com/), Embrace (http://www.embraceregistry.net/) and BioMoby (http://www.biomoby.org/). The beta site: http://beta.biocatalogue.org/ Note that the beta site is not password protected anymore. For support or bugs reports please email: biocatalogue-support at rubyforge.org Feedback, suggestions and comments welcome. We look forward to working with you in developing the BioCatalogue Regards, The BioCatalogue Team -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur The BIOCATALOGUE-FRIENDS list is archived at: http://listserv.manchester.ac.uk/cgi-bin/wa?A0=BIOCATALOGUE-FRIENDS From ytanoh at cs.man.ac.uk Thu Apr 23 12:30:24 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 23 Apr 2009 17:30:24 +0100 Subject: [BioCatalogue-developers] [Fwd: [BIOCATALOGUE-FRIENDS] BioCataloguebeta latest updates!!!] In-Reply-To: <49F0966C.60702@cs.man.ac.uk> Message-ID: Well done to you as well and big HAPPY BIRTHDAY!!! Franck -----Original Message----- From: biocatalogue-developers-bounces at rubyforge.org [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Jiten Bhagat Sent: 23 April 2009 17:25 To: biocatalogue-developers at rubyforge.org Subject: [BioCatalogue-developers] [Fwd: [BIOCATALOGUE-FRIENDS] BioCataloguebeta latest updates!!!] Well done guys! :-) Jits -------- Original Message -------- Subject: [BIOCATALOGUE-FRIENDS] BioCatalogue beta latest updates!!! Date: Thu, 23 Apr 2009 17:23:36 +0100 From: Franck Tanoh Reply-To: Friends of the BioCatalogue project To: BIOCATALOGUE-FRIENDS at listserv.manchester.ac.uk Hi all, We have updated the BioCatalogue beta site with the following new features: 1- Ability to register REST services. 2-Commenting and discussions (powered by Disqus) 3-Ability for users to provide many more types of annotations (like examples, name aliases and so on) 4-At-a-glance counts of annotations on services (grouped by provider, user and other registries). 5-Better browsing of services (including filtering by service type(s) and service provider(s), and sorting of results). 6-Ability to change your password 7-Lots of UI enhancements and tweaks Also most of the metadata from Feta (http://www.mygrid.org.uk/feta/mygrid/descriptions/ ) has been imported and we are working on bringing in services from SeekDa (http://seekda.com/), Embrace (http://www.embraceregistry.net/) and BioMoby (http://www.biomoby.org/). The beta site: http://beta.biocatalogue.org/ Note that the beta site is not password protected anymore. For support or bugs reports please email: biocatalogue-support at rubyforge.org Feedback, suggestions and comments welcome. We look forward to working with you in developing the BioCatalogue Regards, The BioCatalogue Team -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur The BIOCATALOGUE-FRIENDS list is archived at: http://listserv.manchester.ac.uk/cgi-bin/wa?A0=BIOCATALOGUE-FRIENDS _______________________________________________ BioCatalogue-developers mailing list BioCatalogue-developers at rubyforge.org http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Fri Apr 24 09:33:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 24 Apr 2009 09:33:39 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2627] Move normalisation of URLs to the specific models Message-ID: <20090424133339.B2CFF18580F6@rubyforge.org> Task #2627 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Move normalisation of URLs to the specific models Complete: 0% Status: Open Description: Currently, the normalisation of URLs (ie: using: Addressable::URI.parse(..).normalise.to_s) is done in various places like the controllers and in import scripts (feta, seekda etc). Instead, they should be done in the models, in places like the check_duplicate method and when setting URL based fields. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2627&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Apr 24 10:02:04 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 24 Apr 2009 10:02:04 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2621] comments on biocat not visable Message-ID: <20090424140204.2292818580EA@rubyforge.org> Task #2621 has been updated. Project: BioCatalogue Subproject: Pilot Summary: comments on biocat not visable Complete: 0% Status: Closed Description: the comment thread is a the bottom of the page, making it impossible to view.... my suggestion is to have a kind of tab or link somewhere at the top of the page to point users to the comments at the bottom. Follow-Ups: ------------------------------------------------------- Date: 2009-04-24 14:02 By: jits Comment: Done (added link to top right) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2621&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Apr 24 11:26:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 24 Apr 2009 11:26:28 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2628] Write stats page Message-ID: <20090424152628.36E181598030@rubyforge.org> Task #2628 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Write stats page Complete: 0% Status: Open Description: Write a specific stats page for useful statistics about the BioCatalogue (such as the avg no of annotations per service, the min and max no of annotation and so on), so that Carole (or anyone else) can get useful stats about the BioCatalogue. Note: this will be performance intensive so maybe it should be password protected or something? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2628&group_id=6901&group_project_id=12540 From ericnzuo at ebi.ac.uk Mon Apr 27 05:16:29 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 27 Apr 2009 10:16:29 +0100 Subject: [BioCatalogue-developers] I tried beta.biocatalogue.org and it failed In-Reply-To: <49F576A7.6090403@cs.man.ac.uk> References: <49F4F5E5.1020908@manchester.ac.uk> <49F50062.8030902@ebi.ac.uk> <49F568B6.8080608@ebi.ac.uk> <49F576A7.6090403@cs.man.ac.uk> Message-ID: <49F577ED.9050304@ebi.ac.uk> The beta site should be up now. Please report any issues. We are working towards restoring the test site as well. That should be back up soon Cheers, Eric Jiten Bhagat wrote: > Thanks Eric. > > As soon as the test site is back up please could you update it and let > me know. > > Cheers, > Jits > > > Eric Nzuobontane wrote: >> Dear all, >> As a consequence of the power outage yesterday, >> http://beta.biocatalogue.org is currently not available. We are working >> towards restoring the service as soon as possible. >> >> Eric >> >> >> Rodrigo Lopez wrote: >>> Hi, >>> >>> There was a serious electricity outage at the Sanger Centre's data >>> centre on Sunday. Almost all EBI equipment was powercycled as a result >>> and services started coming back during the late afternoon. Services >>> will resume normal operation early on Monday morning. Technicians >>> are on >>> site at the moment sorting out matters. >>> >>> R:. >>> >>> Carole Goble wrote: >>>> and it failed at the EBI >>>> >>>> ERROR 500 The request cannot be carried out by the server >>>> >>>> this is not encouraging. I speak to this in public on Tuesday. >>>> >>>> we are supposed to be 24/7....... >>>> >>>> Carole From ericnzuo at ebi.ac.uk Mon Apr 27 05:57:29 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 27 Apr 2009 10:57:29 +0100 Subject: [BioCatalogue-developers] service availability on seekda/service finder In-Reply-To: <49F57736.8070600@seekda.com> References: <49F571BA.2040604@ebi.ac.uk> <49F57736.8070600@seekda.com> Message-ID: <49F58189.8020708@ebi.ac.uk> Hi Holger, > Hi Eric, > > you are asking in the context of SOA4ALL? > No, I was asking in the context of the http://beta.biocatalogue.org > Have you read > http://seekda.com/blog/monitoring-the-availability-of-web-services/? > yes, I have. The post did tell me what you do and I think providing more than just online/offline status information is quite interesting, though like it is said it the post, these are representative measures rather than definite ones. Because I want to integrate such metric in biocatalogue, I am interested in how you achieve this as well. > And yes we are willing, depending on the license you intend to go for we > could think about a joint development. > I believe this is a definite possibility and a welcomed one as well. I would discuss with my team and we will try to find a way to collaborate. > What are your plans on going beyond what we have right now? > Some ideas have been tried in the context of the embrace registry[http://www.embraceregistry.net] which we are also willing to adopt. One of them is allowing a certain class of users, (hopefully service providers ) to provide some tests that can be used to verify the functionality of the service. We hope these could also go beyond just calling an operation of the service but actually provide some functional client of the service which can serve as a basis for other client development and/or integration into other applications. regards, Eric > best > Holger > > > Eric Nzuobontane wrote: > >> Hi Holger, >> >> I am in the process of putting some functionality in place to monitor >> services. In the first instance, we would like to have the service >> availability in a similar way to to seekda. We think that information >> is very useful and the graphical display can show quickly if there >> have been issues with the service in the past. I was just wondering if >> you will be willing to share with us the way you get the availability >> metrics in seekda? >> >> I would be most grateful for your help. >> >> Eric >> >> > > > From noreply at rubyforge.org Mon Apr 27 06:07:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 27 Apr 2009 06:07:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2631] Display common tags at top of search results Message-ID: <20090427100707.4E4A418581DF@rubyforge.org> Task #2631 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Display common tags at top of search results Complete: 0% Status: Open Description: From Sam Schmidt - "In the search results, display the tags common to all results at the top ..." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2631&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 27 06:09:05 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 27 Apr 2009 06:09:05 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2632] Possibly move aka next to title Message-ID: <20090427100905.1F5D11858137@rubyforge.org> Task #2632 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Possibly move aka next to title Complete: 0% Status: Open Description: From Sam Schmidt. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2632&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 27 06:22:15 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 27 Apr 2009 06:22:15 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2633] Search needs to handle pluralisations Message-ID: <20090427102215.BAEBE177993D@rubyforge.org> Task #2633 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Search needs to handle pluralisations Complete: 0% Status: Open Description: From Sam Schmidt - "The other thing was; there doesn't appear to be LIKE searching? Searching for "Phylogenetics" returns 0 results, where "Phylogenetic" returns 5." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2633&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 27 06:22:49 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 27 Apr 2009 06:22:49 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2634] Work on synonyms for search Message-ID: <20090427102250.0E1D01858110@rubyforge.org> Task #2634 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Work on synonyms for search Complete: 0% Status: Open Description: Work on synonyms for search ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2634&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Apr 27 07:23:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 27 Apr 2009 07:23:24 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2635] Make stats calculations run as a background task Message-ID: <20090427112324.D3AB618580F5@rubyforge.org> Task #2635 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Make stats calculations run as a background task Complete: 0% Status: Open Description: Right now the stats run within a request. which is baaad. Make this run as an asynchronous background task instead. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2635&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Mon Apr 27 06:37:18 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Apr 2009 11:37:18 +0100 Subject: [BioCatalogue-developers] Biocat. In-Reply-To: <78b31dca0904242032w47b5f321k95c079412ed3862f@mail.gmail.com> References: <78b31dca0904242032w47b5f321k95c079412ed3862f@mail.gmail.com> Message-ID: <49F58ADE.8060002@cs.man.ac.uk> Hello Sam. Sam Schmidt wrote: > G'day Jiten, > > I just logged into Biocat and had a very quick look, great work. Thanks :-) > > To constructively offer some pedantic criticism ! When I viewed the > search results page, at first glance I thought "whats what"... > (thought looking again now I think this was due to metadata being > displayed in service description)... I wonder if the following > suggestions may be useful without being restrictive? Yeah, I do know what you mean about the amount of metadata being shown. We had this issue with myExperiment as well, but ultimately users wanted lots of metadata so that they could scan the results quickly. One possibility we have been mulling over is two different views on listings - "quick" and "detailed", which users can switch between. > > - In the search results, display the tags common to all results at the > top - as opposed to on individual records. Great idea, thanks. It will be very tricky to implement (since we employ paging of results to improve on performance) but I will add this to our task list. > - Display aka after title. Initially I thought the service names would be too long, so having the aka after the title would make it looked too cramped. Also, there can be any number of name aliases on a service (the "aka"'s) so overflow might be an issue. I'll look into this though, thanks. > - Just to let you know the service description document displays > metadata not description when searching "Phylogenetic", the first few > results Hmm, this seems to be the information that the service provider(s) have put in their WSDLs. We just parse the WSDL and store it as descriptions for the different parts of a service (the service itself, the operations, and input and output). > - The other thing was; there doesn't appear to be LIKE searching? > Searching for "Phylogenetics" returns 0 results, where "Phylogenetic" > returns 5. Yes, we need to improve this aspect. Looks like this particular thing can be fixed by handling pluralisations. One of the things we would also like to do is build a synonyms map that our search engine can use. Cheers, Jits > > Cheers, > > Sam. From noreply at rubyforge.org Mon Apr 27 08:59:04 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 27 Apr 2009 08:59:04 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2636] Stats page: filtered by time Message-ID: <20090427125904.833A7197857C@rubyforge.org> Task #2636 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Stats page: filtered by time Complete: 0% Status: Open Description: From Rodrigo: "Status during the last 24 hours - but I do realise you need to couple this within the scope of present possibilities - for the near future? " ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2636&group_id=6901&group_project_id=12540 From ericnzuo at ebi.ac.uk Mon Apr 27 08:21:29 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 27 Apr 2009 13:21:29 +0100 Subject: [BioCatalogue-developers] restrictions on test scripts Message-ID: <49F5A349.2000907@ebi.ac.uk> According to Steve, the restrictions that they have on the script provided in the embrace registry are - run in mode not allowing write permissions - use a safe file store What other restrictions do we want to place on the scripts? - set an upper bound on bandwidth usage ? - set max execution time and processor usage - restrict the languages of the scripts and require source ? ... Now what are the capabilities that the scripts should have apart from having access to the network? I need to give EBI systems a guidance note as to what our scripts should be able to to. Eric From jits at cs.man.ac.uk Mon Apr 27 10:34:16 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 27 Apr 2009 15:34:16 +0100 Subject: [BioCatalogue-developers] restrictions on test scripts In-Reply-To: <49F5A349.2000907@ebi.ac.uk> References: <49F5A349.2000907@ebi.ac.uk> Message-ID: <49F5C268.80408@cs.man.ac.uk> All those 5 things sound appropriate to me. I think we should start very restrictive and open up (if we need to) in a controlled manner. Cheers, Jits Eric Nzuobontane wrote: > According to Steve, the restrictions that they have on the script > provided in the embrace registry are > - run in mode not allowing write permissions > - use a safe file store > What other restrictions do we want to place on the scripts? > - set an upper bound on bandwidth usage ? > - set max execution time and processor usage > - restrict the languages of the scripts and require source ? > ... > > Now what are the capabilities that the scripts should have apart from > having access to the network? > > I need to give EBI systems a guidance note as to what our scripts > should be able to to. > > Eric > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From holger.lausen at seekda.com Mon Apr 27 10:23:07 2009 From: holger.lausen at seekda.com (Holger Lausen) Date: Mon, 27 Apr 2009 16:23:07 +0200 Subject: [BioCatalogue-developers] service availability on seekda/service finder In-Reply-To: <49F58189.8020708@ebi.ac.uk> References: <49F571BA.2040604@ebi.ac.uk> <49F57736.8070600@seekda.com> <49F58189.8020708@ebi.ac.uk> Message-ID: <49F5BFCB.6080607@seekda.com> >> Have you read >> http://seekda.com/blog/monitoring-the-availability-of-web-services/? > yes, I have. The post did tell me what you do and I think providing > more than just online/offline status information is quite interesting, > though like it is said it the post, these are representative measures > rather than definite ones. Because I want to integrate such metric in > biocatalogue, I am interested in how you achieve this as well. Sorry I do not understand. We are able to obtain the following measures for each check: - DNS resolution works/works not - IP reachable/not reachable - HTTP server running/not running - Endpoint adheres to SOAP Fault/does not adhere to SOAP fault. What do you mean by definite measures? >> What are your plans on going beyond what we have right now? > Some ideas have been tried in the context of the embrace > registry[http://www.embraceregistry.net] which we are also willing to > adopt. One of them is allowing a certain class of users, (hopefully > service providers ) to provide some tests that can be used to verify > the functionality of the service. We hope these could also go beyond > just calling an operation of the service but actually provide some > functional client of the service which can serve as a basis for other > client development and/or integration into other applications. In the general case that is very difficult. Even if you have a request/response pair that is created by a provider, you still can not simply take this as a functional unittest: (1) will the request remain valid over time (e.g. if you ask for the whether of (2009-04-28) this will not be a valid request in future. Or other way around: what parts of the request need to be adopted when repeating it? (2) you must assure that a unit test does not have unintended site effects (e.g. a real world transaction like reserving a hotel room). (3) you must provide a way of stating some assertions on the output, since only in a few cases the input can remain static for a meaningful test this means you need a language that is capable of stating some relation between inputs and outputs. Do you have any ideas on above problems? /holger -- Holger Lausen seekda GmbH Museumstr. 21/302, 6020 Innsbruck, Austria Tel: +43 1 2365084, Fax: +43 1 2365084-99 Registration Number: FN323499i Registration Court: Innsbruck Web: http://seekda.com Jabber/Mail: holger.lausen at seekda.com From ericnzuo at ebi.ac.uk Tue Apr 28 06:47:58 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 28 Apr 2009 11:47:58 +0100 Subject: [BioCatalogue-developers] service testing and monitoring Message-ID: <49F6DEDE.5040706@ebi.ac.uk> Hi Guys, I have started this page on service testing and monitoring. Could you please have a look and let me know if there is some missing or that you do not understand? http://www.biocatalogue.org/wiki/doku.php?id=development:service_testing Hopefully as development progresses we will be able to update this page so that questions from people like Carole monitoring can be answered here. Eric From jits at cs.man.ac.uk Tue Apr 28 08:48:19 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 28 Apr 2009 13:48:19 +0100 Subject: [BioCatalogue-developers] service testing and monitoring In-Reply-To: <49F6DEDE.5040706@ebi.ac.uk> References: <49F6DEDE.5040706@ebi.ac.uk> Message-ID: <49F6FB13.8050002@cs.man.ac.uk> Thanks Eric, this is looking good. I'll have more time later to have a detailed look. Right now, it's time to interview some intern candidates! :-D Jits Eric Nzuobontane wrote: > Hi Guys, > I have started this page on service testing and monitoring. Could you > please have a look and let me know if there is some missing or that > you do not understand? > > http://www.biocatalogue.org/wiki/doku.php?id=development:service_testing > > Hopefully as development progresses we will be able to update this > page so that questions from people like Carole monitoring can be > answered here. > > Eric > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Wed Apr 29 07:07:06 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 29 Apr 2009 12:07:06 +0100 Subject: [BioCatalogue-developers] service testing and monitoring In-Reply-To: <49F6FB13.8050002@cs.man.ac.uk> References: <49F6DEDE.5040706@ebi.ac.uk> <49F6FB13.8050002@cs.man.ac.uk> Message-ID: <49F834DA.9040503@cs.man.ac.uk> Comments below: - Firstly, I've added some "public" facing test on service monitoring on the public roadmap page - http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=public:roadmap. We need to make sure this is aligned with what we do / intend to do. - Would be useful to write up what we mean by the "traffic light system" and what the different icons mean (eg: see bottom of http://www.embraceregistry.net/content/understanding-service-statuses). Then in requirement 1 for Testing, you can link to this info. - Re: "(note by eric : this contradicts the requirement that only selected users, ie owners of the service should submit test scripts)" - yeah, EMBRACE allow the service submitter to provide test scripts. In our case I'm not sure what our policy should be. Maybe start with service submitter? And then when we have proper ownership management in place we could look to restrict it? - The requirements for Monitoring need to be elaborated to mention that we need to test different things like the hostname (for both endpoints and description doc location), endpoint HTTP GET, SOAP execution of endpoint, etc, and that these need to be combined into a single visual measure (or set of measures). - Do we allow more than 1 test script per service? If so, how do we manage the different test scripts, and how do we collate the different results from the different scripts? What if one test script is less useful or more complex than another? Apart from that I think it captures the current state of discussions/issues very well. I understand that there is still a lot of work to be done in this area still, so please don't see any of my comments as criticism :-) Jits Jiten Bhagat wrote: > Thanks Eric, this is looking good. I'll have more time later to have a > detailed look. Right now, it's time to interview some intern > candidates! :-D > > Jits > > > Eric Nzuobontane wrote: >> Hi Guys, >> I have started this page on service testing and monitoring. Could you >> please have a look and let me know if there is some missing or that >> you do not understand? >> >> http://www.biocatalogue.org/wiki/doku.php?id=development:service_testing >> >> Hopefully as development progresses we will be able to update this >> page so that questions from people like Carole monitoring can be >> answered here. >> >> 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 jits at cs.man.ac.uk Wed Apr 29 07:42:04 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 29 Apr 2009 12:42:04 +0100 Subject: [BioCatalogue-developers] service testing and monitoring In-Reply-To: <49F836CA.8070907@ebi.ac.uk> References: <49F6DEDE.5040706@ebi.ac.uk> <49F6FB13.8050002@cs.man.ac.uk> <49F834DA.9040503@cs.man.ac.uk> <49F836CA.8070907@ebi.ac.uk> Message-ID: <49F83D0C.1000703@cs.man.ac.uk> :-) Eric Nzuobontane wrote: > thanks for the comments! They are very welcome. I learned during a > management course that critism is not the right word to mention when > giving feedback. The right would should be feedback as feedback is > neutral, critism is negative. So every kind of feedback in welcome. > > Eric > > > Jiten Bhagat wrote: >> Comments below: >> >> - Firstly, I've added some "public" facing test on service monitoring >> on the public roadmap page - >> http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=public:roadmap. >> We need to make sure this is aligned with what we do / intend to do. >> >> - Would be useful to write up what we mean by the "traffic light >> system" and what the different icons mean (eg: see bottom of >> http://www.embraceregistry.net/content/understanding-service-statuses). >> Then in requirement 1 for Testing, you can link to this info. >> >> - Re: "(note by eric : this contradicts the requirement that only >> selected users, ie owners of the service should submit test scripts)" >> - yeah, EMBRACE allow the service submitter to provide test scripts. >> In our case I'm not sure what our policy should be. Maybe start with >> service submitter? And then when we have proper ownership management >> in place we could look to restrict it? >> >> - The requirements for Monitoring need to be elaborated to mention >> that we need to test different things like the hostname (for both >> endpoints and description doc location), endpoint HTTP GET, SOAP >> execution of endpoint, etc, and that these need to be combined into a >> single visual measure (or set of measures). >> >> - Do we allow more than 1 test script per service? If so, how do we >> manage the different test scripts, and how do we collate the >> different results from the different scripts? What if one test script >> is less useful or more complex than another? >> >> Apart from that I think it captures the current state of >> discussions/issues very well. >> >> I understand that there is still a lot of work to be done in this >> area still, so please don't see any of my comments as criticism :-) >> >> Jits >> >> >> >> Jiten Bhagat wrote: >>> Thanks Eric, this is looking good. I'll have more time later to have >>> a detailed look. Right now, it's time to interview some intern >>> candidates! :-D >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>>> Hi Guys, >>>> I have started this page on service testing and monitoring. Could >>>> you please have a look and let me know if there is some missing or >>>> that you do not understand? >>>> >>>> http://www.biocatalogue.org/wiki/doku.php?id=development:service_testing >>>> >>>> >>>> Hopefully as development progresses we will be able to update this >>>> page so that questions from people like Carole monitoring can be >>>> answered here. >>>> >>>> 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 noreply at rubyforge.org Wed Apr 29 09:41:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 29 Apr 2009 09:41:47 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2637] Add viewings for services Message-ID: <20090429134147.9B0E518581DD@rubyforge.org> Task #2637 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add viewings for services Complete: 0% Status: Open Description: Possibly just store an ActivityLog entry ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2637&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Wed Apr 29 12:24:17 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 29 Apr 2009 17:24:17 +0100 Subject: [BioCatalogue-developers] myExp+BioCat hackathon Message-ID: <49F87F31.908@cs.man.ac.uk> [Apologies for resending this - i got an email saying ericnzuo at ebi.ac.uk is an unknown user!] Hi guys, Are you available on the 14th and 15th of May for a hackathon in Southampton between the myExp and BioCat teams? We can take this opportunity to discuss things like controlled vocabularies etc as well as get advise on and discuss the service monitoring work, face to face? (Ofcourse, we shall take this opportunity to get some good food and alcohol too :-)) We'll also be discussing BioCat integration within myExperiment. How does this sound? If there is anything specific you guys would like to discuss then let me (or Dave De Roure) know. Thanks, Jits