From noreply at rubyforge.org Mon Jun 1 06:54:37 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Jun 2009 06:54:37 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2573] Improve perf by combining and compressing assets (JS/CSS) Message-ID: <20090601105437.B60051858110@rubyforge.org> Task #2573 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Improve perf by combining and compressing assets (JS/CSS) Complete: 100% Status: Closed Description: E.g: using the asset_packager plugin (see: http://railsillustrated.com/more-speed-improvements-with-asset_packager.html) Follow-Ups: ------------------------------------------------------- Date: 2009-06-01 10:54 By: jits Comment: Done! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2573&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 1 07:04:51 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Jun 2009 07:04:51 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2672] Change scripts to store logs in the /logs and to have timestamp Message-ID: <20090601110451.8504818580EA@rubyforge.org> Task #2672 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Change scripts to store logs in the /logs and to have timestamp Complete: 0% Status: Open Description: E.g: 'log/auto_tagger_{current_time}.log' ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2672&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 1 08:48:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Jun 2009 08:48:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2673] Investigate potential bug in search Message-ID: <20090601124802.EAD1B18581E7@rubyforge.org> Task #2673 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Investigate potential bug in search Complete: 0% Status: Open Description: The auto_tagger.rb script found about 350 services that are from BioMoby, but searching on the beta site only retrieves 180 or so. Look into this. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2673&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 1 10:20:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Jun 2009 10:20:45 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2575] Ratings in service listings Message-ID: <20090601142045.29E49185810F@rubyforge.org> Task #2575 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Ratings in service listings Complete: 0% Status: Closed Description: Show the overall rating and possibly the ratings breakdowns in the service listings. Follow-Ups: ------------------------------------------------------- Date: 2009-06-01 14:20 By: jits Comment: Not needed anymore ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2575&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 1 10:21:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Jun 2009 10:21:39 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2674] BioCatalogue wiki config sudden change Message-ID: <20090601142139.270D91858131@rubyforge.org> Task #2674 has been updated. Project: BioCatalogue Subproject: Pilot Summary: BioCatalogue wiki config sudden change Complete: 0% Status: Open Description: Investigate why the wki configuration for BioCatalogue change causing links to die. Put measures in place to prevent this from happening in the future ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2674&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 1 11:20:54 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Jun 2009 11:20:54 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2675] More informative WSDL parsing error message(s) Message-ID: <20090601152054.385441858112@rubyforge.org> Task #2675 has been updated. Project: BioCatalogue Subproject: Pilot Summary: More informative WSDL parsing error message(s) Complete: 0% Status: Open Description: As Carole mentioned ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2675&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Tue Jun 2 14:54:06 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 02 Jun 2009 19:54:06 +0100 Subject: [BioCatalogue-developers] Suggestions Message-ID: <4A25754E.6000801@cs.man.ac.uk> Hi guys, As we count down to a full public release, I have some suggestions to improve the overall user experience, and also to introduce more "social" type features, that I would like to run past you... 1. I propose a new "Explore" page in which we show the latest and aggregated information. This is much like myExperiment's "Home" page, where we can show things like the latest news, latest services, latest annotations (though we should use a better name for this) and so on. I'll also (possibly) move the tag cloud from the service index page to this new Explore page. This idea does mean we will have both "Explore" and "Browse" links, which may be confusing, so if you have any suggestions for naming these then please let me know! My suggestion would be "Explore" and "Services". 2. I'll implement a user messaging system, so users can send messages to each other (much like in myExperiment). 3. Have a "message this user" icon next to each user's name whenever a user is mentioned anywhere on the site. This allows one click access to the new message page. 4. RSS/ATOM feeds for pretty much everything - every box on the proposed "Explore" page, the services index, all filtering options on the services index, each service, each user, each provider etc etc. 5. Some users have complained that the site is "too green". The green on the top and sides seems to be a bit overpowering (especially on certain screens that show richer colours). I suggest we tone down these colours. 6. I am currently implementing a favouriting system (as a plugin similar to the annotations plugin so that it can be reused elsewhere). I'll need some feedback on this later. But in the meantime if you have any thoughts about favouriting please let me know. 7. We need some place to show new notifications, like when a user has new messages (and there probably will be new types of notifications in the future. Any suggestions? 8. The above point brings up a larger, important issue - a place to show user specific things (ie: a contextual sidebar like the one in myExp when you log in). We need some place where a user can access all their favourites, get to their latest messages and so on and so forth very easily. Any suggestions? I'll work on some ideas here. I believe these suggestions will give us significant added value over existing things like SeekDa and so on. What do you think? Thomas: what I'll do is start on these in a separate branch (apart from favouriting, which is in trunk), so as not to affect the main codebase and so that I can still take into account your feedback/ideas when you're back. Cheers, Jits From noreply at rubyforge.org Wed Jun 3 06:28:51 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Jun 2009 06:28:51 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2676] Searches beginning with * fail Message-ID: <20090603102851.AD5D01858114@rubyforge.org> Task #2676 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Searches beginning with * fail Complete: 0% Status: Open Description: Catch this and show an error message gracefully ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2676&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Wed Jun 3 17:34:31 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 03 Jun 2009 22:34:31 +0100 Subject: [BioCatalogue-developers] IMPORTANT change to development mode of codebase Message-ID: <4A26EC67.6020104@cs.man.ac.uk> Hi guys, I've made a change to the development mode configuration of our codebase (see revision: 745) to not reload classes each time, as this was causing me huge issues with some new stuff I've been developing, which seems to bring out a really nasty bug (ref: https://rails.lighthouseapp.com/projects/8994/tickets/1290 and https://rails.lighthouseapp.com/projects/8994/tickets/1339). Unfortunately this does mean that any changes to lib files, controllers, helpers and model will require a restart of your server to see the changes take effect. I think changes in views don't require a restart. I know this is a pain. Sorry. I'm afraid this is a necessary change. Apparently Rails 2.3.2 fixes the above mentioned issue, so hopefully we won't have to deal with this for too long. Cheers, Jits From jits at cs.man.ac.uk Wed Jun 3 17:38:12 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 03 Jun 2009 22:38:12 +0100 Subject: [BioCatalogue-developers] IMPORTANT change to development mode of codebase In-Reply-To: <4A26EC67.6020104@cs.man.ac.uk> References: <4A26EC67.6020104@cs.man.ac.uk> Message-ID: <4A26ED44.9070002@cs.man.ac.uk> I'm afraid even changes to views will require a server restart. Sorry about this! I'll look to move to Rails 2.3.2 VERY soon. On a plus side, development mode will generate the pages much faster.... Jits Jiten Bhagat wrote: > Hi guys, > > I've made a change to the development mode configuration of our > codebase (see revision: 745) to not reload classes each time, as this > was causing me huge issues with some new stuff I've been developing, > which seems to bring out a really nasty bug (ref: > https://rails.lighthouseapp.com/projects/8994/tickets/1290 and > https://rails.lighthouseapp.com/projects/8994/tickets/1339). > > Unfortunately this does mean that any changes to lib files, > controllers, helpers and model will require a restart of your server > to see the changes take effect. I think changes in views don't require > a restart. I know this is a pain. Sorry. I'm afraid this is a > necessary change. Apparently Rails 2.3.2 fixes the above mentioned > issue, so hopefully we won't have to deal with this for too long. > > Cheers, > Jits > From noreply at rubyforge.org Wed Jun 3 21:24:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Jun 2009 21:24:17 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2677] Tag cloud on services page shows incorrect ordering of tags Message-ID: <20090604012417.63748159802D@rubyforge.org> Task #2677 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Tag cloud on services page shows incorrect ordering of tags Complete: 0% Status: Open Description: From Rodrigo: "Check the tag cloud on http://beta.biocatalogue.org/services : the order of the top 20 is alphabetical(?!) and these are not the "Top 20 tags on BioCatalogue". " ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2677&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 4 07:09:03 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Jun 2009 07:09:03 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2678] IMPORTANT: updates event logging to take into account JMeter Message-ID: <20090604110903.A1E6118581E8@rubyforge.org> Task #2678 has been updated. Project: BioCatalogue Subproject: Pilot Summary: IMPORTANT: updates event logging to take into account JMeter Complete: 0% Status: Open Description: The load testing will causes lots of hits to the pages, which will cause lots of events to be logged. We need to update the event logging to exclude accesses from the load testing servers. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2678&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Thu Jun 4 07:16:24 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 04 Jun 2009 12:16:24 +0100 Subject: [BioCatalogue-developers] Beta site update on Wednesday Message-ID: <4A27AD08.7060803@cs.man.ac.uk> Hi guys, As we agreed in yesterday's telcon, we are aiming to do a full update to the beta site on Wednesday (10th June) after which Carole and Rodrigo will have a play and give us feedback. This means that trunk MUST be stable by Tuesday afternoon, so that we can focus on just bugfixes etc on Tuesday. If you are planning to work on anything that you think could take longer then please do this in a branch. In this email I will try and outline some of the actions we need to carry out before the update. This latest update will be a big one: - I'm hoping to migrate the codebase to Rails 2.3.2. - We will (hopefully) have a background processing mechanism in place. - The latest caching work will require a memcached server (preferably a couple of these) to be available to the beta site. - There are lots and lots of UI improvements and features. ACTION: Thomas - set up memcached server(s) for beta site. ACTION: Jits - to explain the steps required to update the beta site to all the new things (eg: the caching configuration set up, the asset packager setup and how to refresh the CSS and JS packaged files). ACTION: Eric, Thomas, Jits - to plan the set up of the background processing tasks and cron jobs for the tasks required for this updated (eg: "ping" tests, stats generations, metadata counts generation). Please can you document (or at least start documenting) stuff here: http://www.biocatalogue.org/wiki/doku.php?id=development:pilot_dev_notes, that might be relevant information in the future. I've been adding important stuff as I go along. ACTION: all - to document important aspects of the system (eg: brackground processing, what cron jobs will be set up). In terms of load testing, the plan is to carry this out on Monday and then also after the update on Wednesday, so we can do a before and after comparison. IMPORTANT: I need to update the event logging code to take into account accesses from the JMeter instances. ACTION: Eric - to give Jits information on the JMeter instances so that we can write code to filter out accesses from them. (Possibly by user agent string or something). ACTION: Eric - to run the load testing on the current beta site by Tuesday so we have data for a "before" profile. Please point out anything else I have missed. Thanks, Jits From noreply at rubyforge.org Thu Jun 4 07:31:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Jun 2009 07:31:40 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2677] Tag cloud on services page shows incorrect ordering of tags Message-ID: <20090604113140.5FD6318581EE@rubyforge.org> Task #2677 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Tag cloud on services page shows incorrect ordering of tags Complete: 100% Status: Closed Description: From Rodrigo: "Check the tag cloud on http://beta.biocatalogue.org/services : the order of the top 20 is alphabetical(?!) and these are not the "Top 20 tags on BioCatalogue". " Follow-Ups: ------------------------------------------------------- Date: 2009-06-04 11:31 By: jits Comment: Fixed. Revision: 755. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2677&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 4 07:32:22 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Jun 2009 07:32:22 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2678] IMPORTANT: update event logging to take into account JMeter Message-ID: <20090604113222.8B89218581EB@rubyforge.org> Task #2678 has been updated. Project: BioCatalogue Subproject: Pilot Summary: IMPORTANT: update event logging to take into account JMeter Complete: 0% Status: Open Description: The load testing will causes lots of hits to the pages, which will cause lots of events to be logged. We need to update the event logging to exclude accesses from the load testing servers. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2678&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 4 09:51:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Jun 2009 09:51:30 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2600] Add on-mouse-over message to service status icons Message-ID: <20090604135130.E7F0818581F4@rubyforge.org> Task #2600 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add on-mouse-over message to service status icons Complete: 100% Status: Closed Description: get info to display over that icon by setting the HTML "title" attribute to the returned contents of the "tooltip_title_attrib(..)" method in the application helper. (This uses a tooltip JS library to create the popup tooltip). E.g: <%= image_tag("success_icon.png", :title => tooltip_title_attrib("This service is alive! [Last checked: xxxxx]")) -%> Follow-Ups: ------------------------------------------------------- Date: 2009-06-04 13:51 By: ebontane Comment: done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2600&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 4 09:52:06 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Jun 2009 09:52:06 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2399] Refactor activate account action for users Message-ID: <20090604135206.3797D18581F4@rubyforge.org> Task #2399 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Refactor activate account action for users Complete: 100% Status: Closed Description: - use User.find_by_security_token(params[:security_token]), instead of User.find(:all) - the .update_attribute method bypasses validation checks so can be dangerous to use. Maybe a user.activate! method is better, thereby moving that logic into the model ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2399&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 4 09:58:50 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Jun 2009 09:58:50 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2673] Investigate potential bug in search Message-ID: <20090604135851.311F61858106@rubyforge.org> Task #2673 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Investigate potential bug in search Complete: 0% Status: Open Description: The auto_tagger.rb script found about 350 services that are from BioMoby, but searching on the beta site only retrieves 180 or so. Look into this. Follow-Ups: ------------------------------------------------------- Date: 2009-06-04 13:58 By: ebontane Comment: Search Related bug: ============ If the search box is used in IE & firefox on windows with search term clustalw for example, the skinning in the application is messed up. http://beta.biocatalogue.org/search?q=clustalw&commit= ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2673&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 5 07:06:09 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Jun 2009 07:06:09 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2679] Show correct datetimes to users in UI Message-ID: <20090605110610.02B9A18581E6@rubyforge.org> Task #2679 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show correct datetimes to users in UI Complete: 0% Status: Open Description: Currenly all datetime info is stored in UTC in the database and thus will be shown as UTC to users, in the UI. Allow users to specify what timezone they are in and ensure that all rendered datetime info is in the user's current timezone. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2679&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 5 07:09:18 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Jun 2009 07:09:18 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2680] provider link broken Message-ID: <20090605110918.985B8159802E@rubyforge.org> Task #2680 has been updated. Project: BioCatalogue Subproject: Pilot Summary: provider link broken Complete: 0% Status: Open Description: The provider links on the beta site is currently broken. ruby style error message when i click on a provider. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2680&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Fri Jun 5 12:52:14 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 05 Jun 2009 17:52:14 +0100 Subject: [BioCatalogue-developers] IMPORTANT: Timeouts in ruby Message-ID: <4A294D3E.6070301@cs.man.ac.uk> Hi Eric, I've just come across a rubygem called SystemTimer [1] which attempts to solve some of the issues with the existing timeout ruby library [2]. Remember how we were getting issues with hangs when doing geolocation etc etc? This should hopefully solve the problems. Please can you update all your scripts that require timeouts to use this new mechanism. For example usage look at the seekda_import.rb script. Essentially, never use: require 'timeout' ... instead use: require 'system_timer' and then instead of: Timeout::timeout(..) ... use: SystemTimer::timeout(..) The WSDL parser should also have this timeout functionality added to it (I believe at the moment there are no timeouts whatsoever on it). Cheers, Jits [1] - http://systemtimer.rubyforge.org/ [2] - http://ph7spot.com/articles/system_timer From noreply at rubyforge.org Fri Jun 5 14:07:57 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Jun 2009 14:07:57 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2681] Add suggestions auto complete for search Message-ID: <20090605180757.AFB0118581FD@rubyforge.org> Task #2681 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add suggestions auto complete for search Complete: 0% Status: Open Description: ... like we have for tags. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2681&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sat Jun 6 17:03:41 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sat, 6 Jun 2009 17:03:41 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2682] Main URL rewrite for main biocatalogue site Message-ID: <20090606210341.B8B8B18580E2@rubyforge.org> Task #2682 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Main URL rewrite for main biocatalogue site Complete: 0% Status: Open Description: Ensure that http://biocatalogue.org always rewrites to http://www.biocatalogue.org. This is crucial to the functioning of things like Disqus and bookmarking, as they work on absolute URLs. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2682&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sat Jun 6 18:15:34 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sat, 6 Jun 2009 18:15:34 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2683] Update filtering help text Message-ID: <20090606221534.69AAD159802A@rubyforge.org> Task #2683 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update filtering help text Complete: 0% Status: Open Description: Update the help text that explains what exactly the filtering does. Also possibly write a How To page on the public wiki for this. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2683&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Mon Jun 8 06:24:55 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 08 Jun 2009 11:24:55 +0100 Subject: [BioCatalogue-developers] Updgraded codebase to use Rails 2.3.2 Message-ID: <4A2CE6F7.5000801@cs.man.ac.uk> Please update your gems accordingly. Also check out new gems you will need, here: http://www.biocatalogue.org/wiki/doku.php?id=development:pilot_dev_notes Jits From jits at cs.man.ac.uk Mon Jun 8 06:25:50 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 08 Jun 2009 11:25:50 +0100 Subject: [BioCatalogue-developers] Caching using Memcache Message-ID: <4A2CE72E.3070104@cs.man.ac.uk> See: http://www.biocatalogue.org/wiki/doku.php?id=development:caching for more info. Jits From jits at cs.man.ac.uk Mon Jun 8 06:26:48 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 08 Jun 2009 11:26:48 +0100 Subject: [BioCatalogue-developers] Background processing Message-ID: <4A2CE768.8090101@cs.man.ac.uk> See: http://www.biocatalogue.org/wiki/doku.php?id=development:background_processing for more info. Jits From noreply at rubyforge.org Mon Jun 8 11:07:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Jun 2009 11:07:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2684] Page title should show filtering Message-ID: <20090608150702.1916D18581E9@rubyforge.org> Task #2684 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Page title should show filtering Complete: 0% Status: Open Description: When filtering, the page title should be updated to show the current filters. This is important for google etc indexing. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2684&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 9 08:56:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Jun 2009 08:56:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2678] IMPORTANT: update event logging to take into account JMeter Message-ID: <20090609125602.76E221678211@rubyforge.org> Task #2678 has been updated. Project: BioCatalogue Subproject: Pilot Summary: IMPORTANT: update event logging to take into account JMeter Complete: 80% Status: Open Description: The load testing will causes lots of hits to the pages, which will cause lots of events to be logged. We need to update the event logging to exclude accesses from the load testing servers. Follow-Ups: ------------------------------------------------------- Date: 2009-06-09 12:56 By: jits Comment: Added "JMeter" to list of robots that will be matched to the user agent string (so if the word "JMeter" is present it will match and ignore that request when it comes to recording events). This needs to be tested! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2678&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 10 10:35:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Jun 2009 10:35:11 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2685] Show viewed stats for services Message-ID: <20090610171138.5602D3C802A@rubyforge.org> Task #2685 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show viewed stats for services Complete: 0% Status: Open Description: This should be shown on the index, show and any other pages deemed necessary. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2685&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 10 10:37:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Jun 2009 10:37:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2666] Fix open search on beta site Message-ID: <20090610171138.8B186159802E@rubyforge.org> Task #2666 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fix open search on beta site Complete: 80% Status: Open Description: Open search is broken on beta site. Returns "Specify a search query... Examples "blast" "blast AND ebi" Follow-Ups: ------------------------------------------------------- Date: 2009-06-10 14:36 By: jits Comment: A fix has been put in place and needs testing. ------------------------------------------------------- Date: 2009-05-29 09:46 By: jits Comment: Ahh, this is because I changed the way queries are specified from &query=xxxx to &q=xxxx ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2666&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 10 10:36:54 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Jun 2009 10:36:54 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2666] Fix open search on beta site Message-ID: <20090610171139.5C3D91598077@rubyforge.org> Task #2666 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fix open search on beta site Complete: 80% Status: Open Description: Open search is broken on beta site. Returns "Specify a search query... Examples "blast" "blast AND ebi" Follow-Ups: ------------------------------------------------------- Date: 2009-06-10 14:36 By: jits Comment: A fix has been put in place and needs testing. ------------------------------------------------------- Date: 2009-05-29 09:46 By: jits Comment: Ahh, this is because I changed the way queries are specified from &query=xxxx to &q=xxxx ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2666&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Thu Jun 11 04:04:10 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 09:04:10 +0100 Subject: [BioCatalogue-developers] Psuedo synonyms Message-ID: <4A30BA7A.2040800@cs.man.ac.uk> If you're curious, here is the list of synonyms we have in SOLR right now: http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr/solr/conf/synonyms.txt Jits From ytanoh at cs.man.ac.uk Thu Jun 11 04:49:19 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Jun 2009 09:49:19 +0100 Subject: [BioCatalogue-developers] Psuedo synonyms In-Reply-To: <4A30BA7A.2040800@cs.man.ac.uk> Message-ID: Thanks Jits, Very useful page... Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 To: Franck Tanoh; biocatalogue-developers at rubyforge.org Subject: Psuedo synonyms If you're curious, here is the list of synonyms we have in SOLR right now: http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr /solr/conf/synonyms.txt Jits From ytanoh at cs.man.ac.uk Thu Jun 11 04:55:43 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Jun 2009 09:55:43 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: Message-ID: Hi guys, I'm doing an experiment ... I'm searching for term using the synonym list and keeping the number of hits so that I can compare the number of hit using the same terms once the site is updated. So please before you 'kill' the beta site let's me know.... Cheers, Franck -----Original Message----- From: biocatalogue-developers-bounces at rubyforge.org [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck Tanoh Sent: 11 June 2009 09:49 To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] Psuedo synonyms Thanks Jits, Very useful page... Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 To: Franck Tanoh; biocatalogue-developers at rubyforge.org Subject: Psuedo synonyms If you're curious, here is the list of synonyms we have in SOLR right now: http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr /solr/conf/synonyms.txt Jits _______________________________________________ BioCatalogue-developers mailing list BioCatalogue-developers at rubyforge.org http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Thu Jun 11 05:24:01 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 05:24:01 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2688] Look to changing the session store to memcache Message-ID: <20090611092401.79C1318581DD@rubyforge.org> Task #2688 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Look to changing the session store to memcache Complete: 0% Status: Open Description: Currently sessions are stored in the db. This is quite slow (but more secure than cookies). The best solution is to use memcache as the session store. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2688&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 11 06:21:46 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 06:21:46 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2689] Improve search results ordering Message-ID: <20090611102146.872D71858130@rubyforge.org> Task #2689 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Improve search results ordering Complete: 0% Status: Open Description: Right now the ordering of search results isn't great. Maybe use boosting to ensure that services that contain the word(s) in their names get higher up. Also MUST look to using the scores directly from SOLR when doing the reordering of results. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2689&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 11 06:27:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 06:27:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2690] Search indexing for annotations Message-ID: <20090611102702.6EF8E1858130@rubyforge.org> Task #2690 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Search indexing for annotations Complete: 0% Status: Open Description: 2 things here: 1. Make sure that when you do the categories work, that the ID (which is what is stored as the value) is not what gets indexed, rather, the actual category label itself! 2. Maybe certain types of annotations, like name aliases, should have a boost, when indexed. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2690&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Thu Jun 11 06:31:39 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 11:31:39 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: References: Message-ID: <4A30DD0B.5000205@cs.man.ac.uk> Looking very good Franck. Could you try the multiple word ones again, but this time with quotation marks around the whole phrase please? eg: you've done: protein sequence ... now do: "protein sequence" As that's only when many of the synonyms come into effect. Jits Franck Tanoh wrote: > I've finished with the first part of my experiment... you're free to 'kill' > the beta and bring it back to 'life' with a new 'smile' :-) > > Franck > > > -----Original Message----- > From: biocatalogue-developers-bounces at rubyforge.org > [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck > Tanoh > Sent: 11 June 2009 09:56 > To: biocatalogue-developers at rubyforge.org > Subject: [BioCatalogue-developers] before and after the synonyms .. > > Hi guys, > > I'm doing an experiment ... I'm searching for term using the synonym list > and keeping the number of hits so that I can compare the number of hit using > the same terms once the site is updated. So please before you 'kill' the > beta site let's me know.... > > Cheers, > Franck > > -----Original Message----- > From: biocatalogue-developers-bounces at rubyforge.org > [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck > Tanoh > Sent: 11 June 2009 09:49 > To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] Psuedo synonyms > > Thanks Jits, > > Very useful page... > > Franck > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 09:04 > To: Franck Tanoh; biocatalogue-developers at rubyforge.org > Subject: Psuedo synonyms > > If you're curious, here is the list of synonyms we have in SOLR right now: > > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > /solr/conf/synonyms.txt > > Jits > > > > _______________________________________________ > 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 > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ytanoh at cs.man.ac.uk Thu Jun 11 06:38:56 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Jun 2009 11:38:56 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: <4A30DD0B.5000205@cs.man.ac.uk> Message-ID: I tried but could find anything with the quotation ("") mark and most of the time with the underscore (_) as well. For example: gene expression database returns 4 hits but gene_expression_database and "gene expression database" return 0 hits. Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] before and after the synonyms .. Looking very good Franck. Could you try the multiple word ones again, but this time with quotation marks around the whole phrase please? eg: you've done: protein sequence ... now do: "protein sequence" As that's only when many of the synonyms come into effect. Jits Franck Tanoh wrote: > I've finished with the first part of my experiment... you're free to 'kill' > the beta and bring it back to 'life' with a new 'smile' :-) > > Franck > > > -----Original Message----- > From: biocatalogue-developers-bounces at rubyforge.org > [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck > Tanoh > Sent: 11 June 2009 09:56 > To: biocatalogue-developers at rubyforge.org > Subject: [BioCatalogue-developers] before and after the synonyms .. > > Hi guys, > > I'm doing an experiment ... I'm searching for term using the synonym list > and keeping the number of hits so that I can compare the number of hit using > the same terms once the site is updated. So please before you 'kill' the > beta site let's me know.... > > Cheers, > Franck > > -----Original Message----- > From: biocatalogue-developers-bounces at rubyforge.org > [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck > Tanoh > Sent: 11 June 2009 09:49 > To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] Psuedo synonyms > > Thanks Jits, > > Very useful page... > > Franck > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 09:04 > To: Franck Tanoh; biocatalogue-developers at rubyforge.org > Subject: Psuedo synonyms > > If you're curious, here is the list of synonyms we have in SOLR right now: > > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > /solr/conf/synonyms.txt > > Jits > > > > _______________________________________________ > 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 > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Thu Jun 11 06:41:52 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 11:41:52 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: References: Message-ID: <4A30DF70.7030106@cs.man.ac.uk> Is there anything in the BioCatalogue that actually has those phrases? Also, I have a suspicion that the search index for the beta site isnt completely up to date (eg: the biomoby case I reported 2 weeks ago). Jits Franck Tanoh wrote: > I tried but could find anything with the quotation ("") mark and most of the > time with the underscore (_) as well. > For example: gene expression database returns 4 hits but > gene_expression_database and "gene expression database" return 0 hits. > > Franck > > > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 11:32 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] before and after the synonyms .. > > Looking very good Franck. > > Could you try the multiple word ones again, but this time with quotation > marks around the whole phrase please? > > eg: you've done: > > protein sequence > > ... now do: > > "protein sequence" > > As that's only when many of the synonyms come into effect. > > Jits > > > Franck Tanoh wrote: > >> I've finished with the first part of my experiment... you're free to >> > 'kill' > >> the beta and bring it back to 'life' with a new 'smile' :-) >> >> Franck >> >> >> -----Original Message----- >> From: biocatalogue-developers-bounces at rubyforge.org >> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck >> Tanoh >> Sent: 11 June 2009 09:56 >> To: biocatalogue-developers at rubyforge.org >> Subject: [BioCatalogue-developers] before and after the synonyms .. >> >> Hi guys, >> >> I'm doing an experiment ... I'm searching for term using the synonym list >> and keeping the number of hits so that I can compare the number of hit >> > using > >> the same terms once the site is updated. So please before you 'kill' the >> beta site let's me know.... >> >> Cheers, >> Franck >> >> -----Original Message----- >> From: biocatalogue-developers-bounces at rubyforge.org >> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck >> Tanoh >> Sent: 11 June 2009 09:49 >> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >> >> Thanks Jits, >> >> Very useful page... >> >> Franck >> >> -----Original Message----- >> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] >> Sent: 11 June 2009 09:04 >> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >> Subject: Psuedo synonyms >> >> If you're curious, here is the list of synonyms we have in SOLR right now: >> >> >> > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > >> /solr/conf/synonyms.txt >> >> Jits >> >> >> >> _______________________________________________ >> 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 >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > > From jits at cs.man.ac.uk Thu Jun 11 06:42:49 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 11:42:49 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: <4A30DF70.7030106@cs.man.ac.uk> References: <4A30DF70.7030106@cs.man.ac.uk> Message-ID: <4A30DFA9.7060001@cs.man.ac.uk> If that last point is true, then your results of this experiment won't be accurate :-( Jits Jiten Bhagat wrote: > Is there anything in the BioCatalogue that actually has those phrases? > > Also, I have a suspicion that the search index for the beta site isnt > completely up to date (eg: the biomoby case I reported 2 weeks ago). > > Jits > > > Franck Tanoh wrote: >> I tried but could find anything with the quotation ("") mark and most >> of the >> time with the underscore (_) as well. For example: gene expression >> database returns 4 hits but >> gene_expression_database and "gene expression database" return 0 hits. >> Franck >> >> >> -----Original Message----- >> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >> To: Franck Tanoh >> Cc: biocatalogue-developers at rubyforge.org >> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >> >> Looking very good Franck. >> >> Could you try the multiple word ones again, but this time with >> quotation marks around the whole phrase please? >> >> eg: you've done: >> >> protein sequence >> >> ... now do: >> >> "protein sequence" >> >> As that's only when many of the synonyms come into effect. >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> I've finished with the first part of my experiment... you're free to >>> >> 'kill' >> >>> the beta and bring it back to 'life' with a new 'smile' :-) >>> >>> Franck >>> >>> -----Original Message----- >>> From: biocatalogue-developers-bounces at rubyforge.org >>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>> Franck >>> Tanoh >>> Sent: 11 June 2009 09:56 >>> To: biocatalogue-developers at rubyforge.org >>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>> >>> Hi guys, >>> I'm doing an experiment ... I'm searching for term using the synonym >>> list >>> and keeping the number of hits so that I can compare the number of hit >>> >> using >> >>> the same terms once the site is updated. So please before you 'kill' >>> the >>> beta site let's me know.... >>> >>> Cheers, Franck >>> >>> -----Original Message----- >>> From: biocatalogue-developers-bounces at rubyforge.org >>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>> Franck >>> Tanoh >>> Sent: 11 June 2009 09:49 >>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>> >>> Thanks Jits, >>> Very useful page... >>> Franck >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>> Subject: Psuedo synonyms >>> >>> If you're curious, here is the list of synonyms we have in SOLR >>> right now: >>> >>> >>> >> http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr >> >> >>> /solr/conf/synonyms.txt >>> >>> Jits >>> >>> >>> >>> _______________________________________________ >>> 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 >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> 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 ytanoh at cs.man.ac.uk Thu Jun 11 06:53:38 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Jun 2009 11:53:38 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: <4A30DFA9.7060001@cs.man.ac.uk> Message-ID: 1 more thing: and always give the same number of hit. So it looks like when you align the term together solr add 'AND' as default. But when I do the number of hits is different. When you add the quotation solr will look for the word with the quotation e.g. <"term1 term2"> not . Same thing happens with the underscore (_). For example: Protein sequence -> 96 hits protein AND sequence -> 96 hits protein OR sequence -> 480 hits "protein sequence" -> 0 hits Protein_sequence -> 18 hits The experiment could still be accurate if I ignore underscore and quotation mark :-) Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:43 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] before and after the synonyms .. If that last point is true, then your results of this experiment won't be accurate :-( Jits Jiten Bhagat wrote: > Is there anything in the BioCatalogue that actually has those phrases? > > Also, I have a suspicion that the search index for the beta site isnt > completely up to date (eg: the biomoby case I reported 2 weeks ago). > > Jits > > > Franck Tanoh wrote: >> I tried but could find anything with the quotation ("") mark and most >> of the >> time with the underscore (_) as well. For example: gene expression >> database returns 4 hits but >> gene_expression_database and "gene expression database" return 0 hits. >> Franck >> >> >> -----Original Message----- >> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >> To: Franck Tanoh >> Cc: biocatalogue-developers at rubyforge.org >> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >> >> Looking very good Franck. >> >> Could you try the multiple word ones again, but this time with >> quotation marks around the whole phrase please? >> >> eg: you've done: >> >> protein sequence >> >> ... now do: >> >> "protein sequence" >> >> As that's only when many of the synonyms come into effect. >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> I've finished with the first part of my experiment... you're free to >>> >> 'kill' >> >>> the beta and bring it back to 'life' with a new 'smile' :-) >>> >>> Franck >>> >>> -----Original Message----- >>> From: biocatalogue-developers-bounces at rubyforge.org >>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>> Franck >>> Tanoh >>> Sent: 11 June 2009 09:56 >>> To: biocatalogue-developers at rubyforge.org >>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>> >>> Hi guys, >>> I'm doing an experiment ... I'm searching for term using the synonym >>> list >>> and keeping the number of hits so that I can compare the number of hit >>> >> using >> >>> the same terms once the site is updated. So please before you 'kill' >>> the >>> beta site let's me know.... >>> >>> Cheers, Franck >>> >>> -----Original Message----- >>> From: biocatalogue-developers-bounces at rubyforge.org >>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>> Franck >>> Tanoh >>> Sent: 11 June 2009 09:49 >>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>> >>> Thanks Jits, >>> Very useful page... >>> Franck >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>> Subject: Psuedo synonyms >>> >>> If you're curious, here is the list of synonyms we have in SOLR >>> right now: >>> >>> >>> >> http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr >> >> >>> /solr/conf/synonyms.txt >>> >>> Jits >>> >>> >>> >>> _______________________________________________ >>> 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 >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> 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 Thu Jun 11 06:56:46 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 11:56:46 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: References: Message-ID: <4A30E2EE.2010909@cs.man.ac.uk> Franck Tanoh wrote: > 1 more thing: > > and always give the same number of hit. > So it looks like when you align the term together solr add 'AND' as default. > > But when I do the number of hits is different. > When you add the quotation solr will look for the word with the quotation > e.g. <"term1 term2"> not . Same thing happens with the > underscore (_). > > For example: > Protein sequence -> 96 hits > protein AND sequence -> 96 hits > protein OR sequence -> 480 hits > "protein sequence" -> 0 hits > Protein_sequence -> 18 hits > Interesting observations, thanks! I will look into this. > The experiment could still be accurate if I ignore underscore and quotation > mark :-) > No, what I was trying to say is that I think the content on the beta site hasn't been indexed properly, so when we do the update and the index is rebuilt, then if my thought is correct, more search results will be found (because its a bigger index than the incomplete one before). Jits > Franck > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 11:43 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] before and after the synonyms .. > > If that last point is true, then your results of this experiment won't > be accurate :-( > > Jits > > > Jiten Bhagat wrote: > >> Is there anything in the BioCatalogue that actually has those phrases? >> >> Also, I have a suspicion that the search index for the beta site isnt >> completely up to date (eg: the biomoby case I reported 2 weeks ago). >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> I tried but could find anything with the quotation ("") mark and most >>> of the >>> time with the underscore (_) as well. For example: gene expression >>> database returns 4 hits but >>> gene_expression_database and "gene expression database" return 0 hits. >>> Franck >>> >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >>> To: Franck Tanoh >>> Cc: biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >>> >>> Looking very good Franck. >>> >>> Could you try the multiple word ones again, but this time with >>> quotation marks around the whole phrase please? >>> >>> eg: you've done: >>> >>> protein sequence >>> >>> ... now do: >>> >>> "protein sequence" >>> >>> As that's only when many of the synonyms come into effect. >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> I've finished with the first part of my experiment... you're free to >>>> >>>> >>> 'kill' >>> >>> >>>> the beta and bring it back to 'life' with a new 'smile' :-) >>>> >>>> Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:56 >>>> To: biocatalogue-developers at rubyforge.org >>>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>>> >>>> Hi guys, >>>> I'm doing an experiment ... I'm searching for term using the synonym >>>> list >>>> and keeping the number of hits so that I can compare the number of hit >>>> >>>> >>> using >>> >>> >>>> the same terms once the site is updated. So please before you 'kill' >>>> the >>>> beta site let's me know.... >>>> >>>> Cheers, Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:49 >>>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>>> >>>> Thanks Jits, >>>> Very useful page... >>>> Franck >>>> >>>> -----Original Message----- >>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>>> Subject: Psuedo synonyms >>>> >>>> If you're curious, here is the list of synonyms we have in SOLR >>>> right now: >>>> >>>> >>>> >>>> > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > > >>> >>> >>>> /solr/conf/synonyms.txt >>>> >>>> Jits >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> ------------------------------------------------------------------------ >>>> > > >>>> _______________________________________________ >>>> 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 Thu Jun 11 07:52:32 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 07:52:32 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2691] Implement service categorisation Message-ID: <20090611115232.6E8511858136@rubyforge.org> Task #2691 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement service categorisation Complete: 0% Status: Open Description: Based on Francks service categories hierarchy. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2691&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 11 08:32:43 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 08:32:43 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2692] Use the service categories to implement "related services" Message-ID: <20090611123243.8FC5518580FD@rubyforge.org> Task #2692 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Use the service categories to implement "related services" Complete: 0% Status: Open Description: From Carole: "we can use the service categories to implement a "other services like this" option" ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2692&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 11 08:47:05 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 08:47:05 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2693] "Getting Started" and/or simple help/reference page. Message-ID: <20090611124705.44D8A1598076@rubyforge.org> Task #2693 has been updated. Project: BioCatalogue Subproject: Pilot Summary: "Getting Started" and/or simple help/reference page. Complete: 0% Status: Open Description: Needs to be done by ISMB. Need to consider things like: - legend/key to explain what the colours mean. - how to submit services. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2693&group_id=6901&group_project_id=12540 From ericnzuo at ebi.ac.uk Thu Jun 11 14:13:21 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 11 Jun 2009 19:13:21 +0100 Subject: [BioCatalogue-developers] Update of the beta Message-ID: <4A314941.5040603@ebi.ac.uk> Dear all, We have made an update of the beta site. http://beta.biocatalogue.org/ Unfortunately many things did not go according to plan but we have been working hard to make sure everything is in place. We are hoping that there are no major issues with this release as it has been quite a major one. Please play around with it bit and let us know as soon as possible if there are any issues. cheers, Eric From rls at ebi.ac.uk Thu Jun 11 15:34:26 2009 From: rls at ebi.ac.uk (Rodrigo Lopez) Date: Thu, 11 Jun 2009 20:34:26 +0100 Subject: [BioCatalogue-developers] Update of the beta In-Reply-To: <4A314941.5040603@ebi.ac.uk> References: <4A314941.5040603@ebi.ac.uk> Message-ID: <4A315C42.4040805@ebi.ac.uk> Dear All, Indeed well done to all! We will check and let you know if we encounter issues. I know this update has been hard and difficult, specially due to the failure of external dependencies. I would like to thank Dietmar (one of EBI's web admins) for his continuous help and support! We need to decide soon when beta moves to www BEFORE ISMB and ensure everything is working as expected. I dare suggest a date for this could be (at the latest!) one (1) week before we travel to ISMB. R:) Eric Nzuobontane wrote: > Dear all, > > We have made an update of the beta site. > > http://beta.biocatalogue.org/ > > Unfortunately many things did not go according to plan but we have been > working hard to make sure everything is in place. We are hoping that > there are no major issues with this release as it has been quite a major > one. Please play around with it bit and let us know as soon as possible > if there are any issues. > > cheers, > > Eric From jits at cs.man.ac.uk Thu Jun 11 15:54:44 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 20:54:44 +0100 Subject: [BioCatalogue-developers] Update of the beta In-Reply-To: <4A315C42.4040805@ebi.ac.uk> References: <4A314941.5040603@ebi.ac.uk> <4A315C42.4040805@ebi.ac.uk> Message-ID: <4A316104.2080305@cs.man.ac.uk> Rodrigo Lopez wrote: > Dear All, > > Indeed well done to all! We will check and let you know if we > encounter issues. I know this update has been hard and difficult, > specially due to the failure of external dependencies. I would like > to thank Dietmar (one of EBI's web admins) for his continuous help and > support! > > We need to decide soon when beta moves to www BEFORE ISMB and ensure > everything is working as expected. I dare suggest a date for this > could be (at the latest!) one (1) week before we travel to ISMB. That sounds like a good plan to me. There are certain things like google analytics, bookmarking widget, and change of URL of the Disqus commenting system that I will need to do after the move to www, so would be good to have plenty of time to do so. Cheers, Jits > > R:) > > Eric Nzuobontane wrote: >> Dear all, >> >> We have made an update of the beta site. >> >> http://beta.biocatalogue.org/ >> >> Unfortunately many things did not go according to plan but we have >> been working hard to make sure everything is in place. We are hoping >> that there are no major issues with this release as it has been quite >> a major one. Please play around with it bit and let us know as soon >> as possible if there are any issues. >> >> cheers, >> >> Eric > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Thu Jun 11 15:57:34 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 20:57:34 +0100 Subject: [BioCatalogue-developers] Update of the beta In-Reply-To: <4A314941.5040603@ebi.ac.uk> References: <4A314941.5040603@ebi.ac.uk> Message-ID: <4A3161AE.7040009@cs.man.ac.uk> Hi guys, I'm experiencing some weird behaviour - searching for "protein" brings back 0 results. Also, we need to run the seekda_cleanup and auto_tagger scripts tomorrow. Well done on getting the beta site updated! Jits Eric Nzuobontane wrote: > Dear all, > > We have made an update of the beta site. > > http://beta.biocatalogue.org/ > > Unfortunately many things did not go according to plan but we have > been working hard to make sure everything is in place. We are hoping > that there are no major issues with this release as it has been quite > a major one. Please play around with it bit and let us know as soon as > possible if there are any issues. > > cheers, > > Eric > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Thu Jun 11 16:13:21 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Jun 2009 21:13:21 +0100 Subject: [BioCatalogue-developers] Update of the beta In-Reply-To: <4A314941.5040603@ebi.ac.uk> References: <4A314941.5040603@ebi.ac.uk> Message-ID: <4A316561.9000604@cs.man.ac.uk> Please note, there is an issue with the search (to do with the pseudo synonyms work) and it may not return the results you expect. We're working on resolving this asap. Jits Eric Nzuobontane wrote: > Dear all, > > We have made an update of the beta site. > > http://beta.biocatalogue.org/ > > Unfortunately many things did not go according to plan but we have > been working hard to make sure everything is in place. We are hoping > that there are no major issues with this release as it has been quite > a major one. Please play around with it bit and let us know as soon as > possible if there are any issues. > > cheers, > > Eric > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Thu Jun 11 17:51:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Jun 2009 17:51:24 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2694] Implement OpenID sign on Message-ID: <20090611215124.445721858109@rubyforge.org> Task #2694 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement OpenID sign on Complete: 0% Status: Open Description: like in myexperiment ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2694&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Thu Jun 11 19:56:01 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Jun 2009 00:56:01 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: References: Message-ID: <4A319991.9030202@cs.man.ac.uk> Hi Franck and all, There's been a MAJOR change in the way I am doing the pseudo synonyms now (the ones we intend to use to aid in search). BEFORE this change: We built a synonyms list where we had mappings where each mapping had the format... [ a set of (related) terms that a user might search for ] => [ the list of pseudo synonyms that should be included in the user's search to broaden the search and get more useful results] So, these pseudo synonyms mapping were used at *query* time to aid in the search when a user provides a search query. Unfortunately, SOLR doesn't work this way with it's synonyms :-( :-( :-( There are three main issues here (ref: http://wiki.apache.org/solr/AnalyzersTokenizersTokenFilters#head-2c461ac74b4ddd82e453dc68fcfc92da77358d46).: - the pseudo synonyms get ANDed in the search which means that we get lesser or no results (trying searching for "protein" on the beta site right now). - SOLR doesn't handle multiple word queries very well. - The way SOLR parses the query breaks the synonyms search. I looked and looked but there was no way I could make SOLR play nice. So I've decided to do it differently (and this is the way that is recommended). NOW: I have changed the synonyms processing to happen at *index* time (ie: when indexing the services into SOLR for search later). This does mean that every time we update the synonyms list we need to reindex all the content. So now, the mappings are essentially used to enrich the index for each thing that is being indexed in SOLR. This is basically the opposite of the above, and the format is: [ a set of terms that may be in a service's metadata, or annotation, or whatever, when SOLR comes to indexing something ] => [ the list of terms that should be put into the index for that specific thing being indexed so that searches for any of these terms will match this item ] As you've probably guessed, this means we need to be very careful about what we have here. We CANNOT have things like this (which would be caused by ambiguous terms): Multiple Alignment => Multiple Alignment, Protein Sequence Analysis, Nucleotide Sequence Analysis ... because otherwise every service etc that has the words "multiple alignment" will also get the words "Protein Sequence Analysis" AND "Nucleotide Sequence Analysis" and one of those will be incorrect for that service. Based on this new knowledge, please can you verify the list of synonyms that we now have for SOLR - http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr/solr/conf/synonyms.txt. Note the ones I have commented out (with a '#') - this is because they are ambiguous. Note that you can still produce the raw synonyms list in the previous format because I have a script to convert it from the old format to the new (reversed) format. However there may be the danger of ambiguous terms so we should be vigilant about this. One added benefit to doing it this way is that we can use this to also suggest tags to users and better enrich the metadata of the services... Phew! Jits Franck Tanoh wrote: > 1 more thing: > > and always give the same number of hit. > So it looks like when you align the term together solr add 'AND' as default. > > But when I do the number of hits is different. > When you add the quotation solr will look for the word with the quotation > e.g. <"term1 term2"> not . Same thing happens with the > underscore (_). > > For example: > Protein sequence -> 96 hits > protein AND sequence -> 96 hits > protein OR sequence -> 480 hits > "protein sequence" -> 0 hits > Protein_sequence -> 18 hits > > The experiment could still be accurate if I ignore underscore and quotation > mark :-) > > Franck > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 11:43 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] before and after the synonyms .. > > If that last point is true, then your results of this experiment won't > be accurate :-( > > Jits > > > Jiten Bhagat wrote: > >> Is there anything in the BioCatalogue that actually has those phrases? >> >> Also, I have a suspicion that the search index for the beta site isnt >> completely up to date (eg: the biomoby case I reported 2 weeks ago). >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> I tried but could find anything with the quotation ("") mark and most >>> of the >>> time with the underscore (_) as well. For example: gene expression >>> database returns 4 hits but >>> gene_expression_database and "gene expression database" return 0 hits. >>> Franck >>> >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >>> To: Franck Tanoh >>> Cc: biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >>> >>> Looking very good Franck. >>> >>> Could you try the multiple word ones again, but this time with >>> quotation marks around the whole phrase please? >>> >>> eg: you've done: >>> >>> protein sequence >>> >>> ... now do: >>> >>> "protein sequence" >>> >>> As that's only when many of the synonyms come into effect. >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> I've finished with the first part of my experiment... you're free to >>>> >>>> >>> 'kill' >>> >>> >>>> the beta and bring it back to 'life' with a new 'smile' :-) >>>> >>>> Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:56 >>>> To: biocatalogue-developers at rubyforge.org >>>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>>> >>>> Hi guys, >>>> I'm doing an experiment ... I'm searching for term using the synonym >>>> list >>>> and keeping the number of hits so that I can compare the number of hit >>>> >>>> >>> using >>> >>> >>>> the same terms once the site is updated. So please before you 'kill' >>>> the >>>> beta site let's me know.... >>>> >>>> Cheers, Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:49 >>>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>>> >>>> Thanks Jits, >>>> Very useful page... >>>> Franck >>>> >>>> -----Original Message----- >>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>>> Subject: Psuedo synonyms >>>> >>>> If you're curious, here is the list of synonyms we have in SOLR >>>> right now: >>>> >>>> >>>> >>>> > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > > >>> >>> >>>> /solr/conf/synonyms.txt >>>> >>>> Jits >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> ------------------------------------------------------------------------ >>>> > > >>>> _______________________________________________ >>>> 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 ytanoh at cs.man.ac.uk Fri Jun 12 04:40:54 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 12 Jun 2009 09:40:54 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: <4A319991.9030202@cs.man.ac.uk> Message-ID: Hi Jits, Ok, so solar is not as clever as we thought :-(. The synonym list has changed a lot, has somebody else changed them. The idea of the synonyms is that if you type a general term you get all the specific terms associated to the general term. Reading the new list we seem to have lost the plot...:-(...who is the guilty man? I think if we go from general term to specific terms will remove most of the ambiguity in the current synonym list... Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 12 June 2009 00:56 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org; Eric Nzuobontane; Thomas Laurent Subject: Re: [BioCatalogue-developers] before and after the synonyms .. Hi Franck and all, There's been a MAJOR change in the way I am doing the pseudo synonyms now (the ones we intend to use to aid in search). BEFORE this change: We built a synonyms list where we had mappings where each mapping had the format... [ a set of (related) terms that a user might search for ] => [ the list of pseudo synonyms that should be included in the user's search to broaden the search and get more useful results] So, these pseudo synonyms mapping were used at *query* time to aid in the search when a user provides a search query. Unfortunately, SOLR doesn't work this way with it's synonyms :-( :-( :-( There are three main issues here (ref: http://wiki.apache.org/solr/AnalyzersTokenizersTokenFilters#head-2c461ac74b4 ddd82e453dc68fcfc92da77358d46).: - the pseudo synonyms get ANDed in the search which means that we get lesser or no results (trying searching for "protein" on the beta site right now). - SOLR doesn't handle multiple word queries very well. - The way SOLR parses the query breaks the synonyms search. I looked and looked but there was no way I could make SOLR play nice. So I've decided to do it differently (and this is the way that is recommended). NOW: I have changed the synonyms processing to happen at *index* time (ie: when indexing the services into SOLR for search later). This does mean that every time we update the synonyms list we need to reindex all the content. So now, the mappings are essentially used to enrich the index for each thing that is being indexed in SOLR. This is basically the opposite of the above, and the format is: [ a set of terms that may be in a service's metadata, or annotation, or whatever, when SOLR comes to indexing something ] => [ the list of terms that should be put into the index for that specific thing being indexed so that searches for any of these terms will match this item ] As you've probably guessed, this means we need to be very careful about what we have here. We CANNOT have things like this (which would be caused by ambiguous terms): Multiple Alignment => Multiple Alignment, Protein Sequence Analysis, Nucleotide Sequence Analysis ... because otherwise every service etc that has the words "multiple alignment" will also get the words "Protein Sequence Analysis" AND "Nucleotide Sequence Analysis" and one of those will be incorrect for that service. Based on this new knowledge, please can you verify the list of synonyms that we now have for SOLR - http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr /solr/conf/synonyms.txt. Note the ones I have commented out (with a '#') - this is because they are ambiguous. Note that you can still produce the raw synonyms list in the previous format because I have a script to convert it from the old format to the new (reversed) format. However there may be the danger of ambiguous terms so we should be vigilant about this. One added benefit to doing it this way is that we can use this to also suggest tags to users and better enrich the metadata of the services... Phew! Jits Franck Tanoh wrote: > 1 more thing: > > and always give the same number of hit. > So it looks like when you align the term together solr add 'AND' as default. > > But when I do the number of hits is different. > When you add the quotation solr will look for the word with the quotation > e.g. <"term1 term2"> not . Same thing happens with the > underscore (_). > > For example: > Protein sequence -> 96 hits > protein AND sequence -> 96 hits > protein OR sequence -> 480 hits > "protein sequence" -> 0 hits > Protein_sequence -> 18 hits > > The experiment could still be accurate if I ignore underscore and quotation > mark :-) > > Franck > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 11:43 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] before and after the synonyms .. > > If that last point is true, then your results of this experiment won't > be accurate :-( > > Jits > > > Jiten Bhagat wrote: > >> Is there anything in the BioCatalogue that actually has those phrases? >> >> Also, I have a suspicion that the search index for the beta site isnt >> completely up to date (eg: the biomoby case I reported 2 weeks ago). >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> I tried but could find anything with the quotation ("") mark and most >>> of the >>> time with the underscore (_) as well. For example: gene expression >>> database returns 4 hits but >>> gene_expression_database and "gene expression database" return 0 hits. >>> Franck >>> >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >>> To: Franck Tanoh >>> Cc: biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >>> >>> Looking very good Franck. >>> >>> Could you try the multiple word ones again, but this time with >>> quotation marks around the whole phrase please? >>> >>> eg: you've done: >>> >>> protein sequence >>> >>> ... now do: >>> >>> "protein sequence" >>> >>> As that's only when many of the synonyms come into effect. >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> I've finished with the first part of my experiment... you're free to >>>> >>>> >>> 'kill' >>> >>> >>>> the beta and bring it back to 'life' with a new 'smile' :-) >>>> >>>> Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:56 >>>> To: biocatalogue-developers at rubyforge.org >>>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>>> >>>> Hi guys, >>>> I'm doing an experiment ... I'm searching for term using the synonym >>>> list >>>> and keeping the number of hits so that I can compare the number of hit >>>> >>>> >>> using >>> >>> >>>> the same terms once the site is updated. So please before you 'kill' >>>> the >>>> beta site let's me know.... >>>> >>>> Cheers, Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:49 >>>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>>> >>>> Thanks Jits, >>>> Very useful page... >>>> Franck >>>> >>>> -----Original Message----- >>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>>> Subject: Psuedo synonyms >>>> >>>> If you're curious, here is the list of synonyms we have in SOLR >>>> right now: >>>> >>>> >>>> >>>> > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > > >>> >>> >>>> /solr/conf/synonyms.txt >>>> >>>> Jits >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> ------------------------------------------------------------------------ >>>> > > >>>> _______________________________________________ >>>> 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 ytanoh at cs.man.ac.uk Fri Jun 12 05:01:05 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 12 Jun 2009 10:01:05 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: Message-ID: Replying to myself here... Now I got the problem and the solution - thanks Jits Franck -----Original Message----- From: biocatalogue-developers-bounces at rubyforge.org [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Franck Tanoh Sent: 12 June 2009 09:41 To: 'Jiten Bhagat' Cc: biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] before and after the synonyms .. Hi Jits, Ok, so solar is not as clever as we thought :-(. The synonym list has changed a lot, has somebody else changed them. The idea of the synonyms is that if you type a general term you get all the specific terms associated to the general term. Reading the new list we seem to have lost the plot...:-(...who is the guilty man? I think if we go from general term to specific terms will remove most of the ambiguity in the current synonym list... Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 12 June 2009 00:56 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org; Eric Nzuobontane; Thomas Laurent Subject: Re: [BioCatalogue-developers] before and after the synonyms .. Hi Franck and all, There's been a MAJOR change in the way I am doing the pseudo synonyms now (the ones we intend to use to aid in search). BEFORE this change: We built a synonyms list where we had mappings where each mapping had the format... [ a set of (related) terms that a user might search for ] => [ the list of pseudo synonyms that should be included in the user's search to broaden the search and get more useful results] So, these pseudo synonyms mapping were used at *query* time to aid in the search when a user provides a search query. Unfortunately, SOLR doesn't work this way with it's synonyms :-( :-( :-( There are three main issues here (ref: http://wiki.apache.org/solr/AnalyzersTokenizersTokenFilters#head-2c461ac74b4 ddd82e453dc68fcfc92da77358d46).: - the pseudo synonyms get ANDed in the search which means that we get lesser or no results (trying searching for "protein" on the beta site right now). - SOLR doesn't handle multiple word queries very well. - The way SOLR parses the query breaks the synonyms search. I looked and looked but there was no way I could make SOLR play nice. So I've decided to do it differently (and this is the way that is recommended). NOW: I have changed the synonyms processing to happen at *index* time (ie: when indexing the services into SOLR for search later). This does mean that every time we update the synonyms list we need to reindex all the content. So now, the mappings are essentially used to enrich the index for each thing that is being indexed in SOLR. This is basically the opposite of the above, and the format is: [ a set of terms that may be in a service's metadata, or annotation, or whatever, when SOLR comes to indexing something ] => [ the list of terms that should be put into the index for that specific thing being indexed so that searches for any of these terms will match this item ] As you've probably guessed, this means we need to be very careful about what we have here. We CANNOT have things like this (which would be caused by ambiguous terms): Multiple Alignment => Multiple Alignment, Protein Sequence Analysis, Nucleotide Sequence Analysis ... because otherwise every service etc that has the words "multiple alignment" will also get the words "Protein Sequence Analysis" AND "Nucleotide Sequence Analysis" and one of those will be incorrect for that service. Based on this new knowledge, please can you verify the list of synonyms that we now have for SOLR - http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr /solr/conf/synonyms.txt. Note the ones I have commented out (with a '#') - this is because they are ambiguous. Note that you can still produce the raw synonyms list in the previous format because I have a script to convert it from the old format to the new (reversed) format. However there may be the danger of ambiguous terms so we should be vigilant about this. One added benefit to doing it this way is that we can use this to also suggest tags to users and better enrich the metadata of the services... Phew! Jits Franck Tanoh wrote: > 1 more thing: > > and always give the same number of hit. > So it looks like when you align the term together solr add 'AND' as default. > > But when I do the number of hits is different. > When you add the quotation solr will look for the word with the quotation > e.g. <"term1 term2"> not . Same thing happens with the > underscore (_). > > For example: > Protein sequence -> 96 hits > protein AND sequence -> 96 hits > protein OR sequence -> 480 hits > "protein sequence" -> 0 hits > Protein_sequence -> 18 hits > > The experiment could still be accurate if I ignore underscore and quotation > mark :-) > > Franck > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 June 2009 11:43 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] before and after the synonyms .. > > If that last point is true, then your results of this experiment won't > be accurate :-( > > Jits > > > Jiten Bhagat wrote: > >> Is there anything in the BioCatalogue that actually has those phrases? >> >> Also, I have a suspicion that the search index for the beta site isnt >> completely up to date (eg: the biomoby case I reported 2 weeks ago). >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> I tried but could find anything with the quotation ("") mark and most >>> of the >>> time with the underscore (_) as well. For example: gene expression >>> database returns 4 hits but >>> gene_expression_database and "gene expression database" return 0 hits. >>> Franck >>> >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >>> To: Franck Tanoh >>> Cc: biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >>> >>> Looking very good Franck. >>> >>> Could you try the multiple word ones again, but this time with >>> quotation marks around the whole phrase please? >>> >>> eg: you've done: >>> >>> protein sequence >>> >>> ... now do: >>> >>> "protein sequence" >>> >>> As that's only when many of the synonyms come into effect. >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> I've finished with the first part of my experiment... you're free to >>>> >>>> >>> 'kill' >>> >>> >>>> the beta and bring it back to 'life' with a new 'smile' :-) >>>> >>>> Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:56 >>>> To: biocatalogue-developers at rubyforge.org >>>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>>> >>>> Hi guys, >>>> I'm doing an experiment ... I'm searching for term using the synonym >>>> list >>>> and keeping the number of hits so that I can compare the number of hit >>>> >>>> >>> using >>> >>> >>>> the same terms once the site is updated. So please before you 'kill' >>>> the >>>> beta site let's me know.... >>>> >>>> Cheers, Franck >>>> >>>> -----Original Message----- >>>> From: biocatalogue-developers-bounces at rubyforge.org >>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>> Franck >>>> Tanoh >>>> Sent: 11 June 2009 09:49 >>>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>>> >>>> Thanks Jits, >>>> Very useful page... >>>> Franck >>>> >>>> -----Original Message----- >>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>>> Subject: Psuedo synonyms >>>> >>>> If you're curious, here is the list of synonyms we have in SOLR >>>> right now: >>>> >>>> >>>> >>>> > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > > >>> >>> >>>> /solr/conf/synonyms.txt >>>> >>>> Jits >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>>> ------------------------------------------------------------------------ >>>> > > >>>> _______________________________________________ >>>> 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 >> > > > _______________________________________________ BioCatalogue-developers mailing list BioCatalogue-developers at rubyforge.org http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Fri Jun 12 05:01:22 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Jun 2009 10:01:22 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: <4A32098F.50801@ebi.ac.uk> References: <4A319991.9030202@cs.man.ac.uk> <4A32098F.50801@ebi.ac.uk> Message-ID: <4A321962.9030103@cs.man.ac.uk> Good observation, BUT I want Franck to first check the synonyms to make sure they are okay. Please give us until after lunch, then we'll decide whether to go live with it or not. Jits Eric Nzuobontane wrote: > > I suppose this change means both the beta site and the test site need > to be updated and reindexed. > > Jiten Bhagat wrote: >> Hi Franck and all, >> >> There's been a MAJOR change in the way I am doing the pseudo synonyms >> now (the ones we intend to use to aid in search). >> >> BEFORE this change: >> >> We built a synonyms list where we had mappings where each mapping had >> the format... >> >> [ a set of (related) terms that a user might search for ] => [ the >> list of pseudo synonyms that should be included in the user's search >> to broaden the search and get more useful results] >> >> So, these pseudo synonyms mapping were used at *query* time to aid in >> the search when a user provides a search query. >> >> Unfortunately, SOLR doesn't work this way with it's synonyms :-( :-( >> :-( There are three main issues here (ref: >> http://wiki.apache.org/solr/AnalyzersTokenizersTokenFilters#head-2c461ac74b4ddd82e453dc68fcfc92da77358d46).: >> >> - the pseudo synonyms get ANDed in the search which means that we get >> lesser or no results (trying searching for "protein" on the beta site >> right now). >> - SOLR doesn't handle multiple word queries very well. >> - The way SOLR parses the query breaks the synonyms search. >> >> I looked and looked but there was no way I could make SOLR play nice. >> So I've decided to do it differently (and this is the way that is >> recommended). >> >> NOW: >> >> I have changed the synonyms processing to happen at *index* time (ie: >> when indexing the services into SOLR for search later). This does >> mean that every time we update the synonyms list we need to reindex >> all the content. >> >> So now, the mappings are essentially used to enrich the index for >> each thing that is being indexed in SOLR. This is basically the >> opposite of the above, and the format is: >> >> [ a set of terms that may be in a service's metadata, or annotation, >> or whatever, when SOLR comes to indexing something ] => [ the list of >> terms that should be put into the index for that specific thing being >> indexed so that searches for any of these terms will match this item ] >> >> As you've probably guessed, this means we need to be very careful >> about what we have here. We CANNOT have things like this (which would >> be caused by ambiguous terms): >> >> Multiple Alignment => Multiple Alignment, Protein Sequence Analysis, >> Nucleotide Sequence Analysis >> >> ... because otherwise every service etc that has the words "multiple >> alignment" will also get the words "Protein Sequence Analysis" AND >> "Nucleotide Sequence Analysis" and one of those will be incorrect for >> that service. >> >> Based on this new knowledge, please can you verify the list of >> synonyms that we now have for SOLR - >> http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr/solr/conf/synonyms.txt. >> Note the ones I have commented out (with a '#') - this is because >> they are ambiguous. >> >> Note that you can still produce the raw synonyms list in the previous >> format because I have a script to convert it from the old format to >> the new (reversed) format. However there may be the danger of >> ambiguous terms so we should be vigilant about this. >> >> One added benefit to doing it this way is that we can use this to >> also suggest tags to users and better enrich the metadata of the >> services... >> >> Phew! >> >> Jits >> >> >> >> Franck Tanoh wrote: >>> 1 more thing: >>> and always give the same number of >>> hit. So it looks like when you align the term together solr add >>> 'AND' as default. >>> >>> But when I do the number of hits is different. When >>> you add the quotation solr will look for the word with the quotation >>> e.g. <"term1 term2"> not . Same thing happens with the >>> underscore (_). >>> For example: Protein sequence -> 96 hits protein AND sequence -> 96 >>> hits protein OR sequence -> 480 hits "protein sequence" -> 0 hits >>> Protein_sequence -> 18 hits >>> >>> The experiment could still be accurate if I ignore underscore and >>> quotation >>> mark :-) >>> >>> Franck >>> >>> -----Original Message----- >>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:43 >>> To: Franck Tanoh >>> Cc: biocatalogue-developers at rubyforge.org >>> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >>> >>> If that last point is true, then your results of this experiment >>> won't be accurate :-( >>> >>> Jits >>> >>> >>> Jiten Bhagat wrote: >>> >>>> Is there anything in the BioCatalogue that actually has those phrases? >>>> >>>> Also, I have a suspicion that the search index for the beta site >>>> isnt completely up to date (eg: the biomoby case I reported 2 weeks >>>> ago). >>>> >>>> Jits >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>>> I tried but could find anything with the quotation ("") mark and >>>>> most of the >>>>> time with the underscore (_) as well. For example: gene expression >>>>> database returns 4 hits but >>>>> gene_expression_database and "gene expression database" return 0 >>>>> hits. >>>>> Franck >>>>> >>>>> >>>>> -----Original Message----- >>>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 >>>>> 11:32 >>>>> To: Franck Tanoh >>>>> Cc: biocatalogue-developers at rubyforge.org >>>>> Subject: Re: [BioCatalogue-developers] before and after the >>>>> synonyms .. >>>>> >>>>> Looking very good Franck. >>>>> >>>>> Could you try the multiple word ones again, but this time with >>>>> quotation marks around the whole phrase please? >>>>> >>>>> eg: you've done: >>>>> >>>>> protein sequence >>>>> >>>>> ... now do: >>>>> >>>>> "protein sequence" >>>>> >>>>> As that's only when many of the synonyms come into effect. >>>>> >>>>> Jits >>>>> >>>>> >>>>> Franck Tanoh wrote: >>>>> >>>>> >>>>>> I've finished with the first part of my experiment... you're free to >>>>>> >>>>> 'kill' >>>>> >>>>> >>>>>> the beta and bring it back to 'life' with a new 'smile' :-) >>>>>> >>>>>> Franck >>>>>> >>>>>> -----Original Message----- >>>>>> From: biocatalogue-developers-bounces at rubyforge.org >>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf >>>>>> Of Franck >>>>>> Tanoh >>>>>> Sent: 11 June 2009 09:56 >>>>>> To: biocatalogue-developers at rubyforge.org >>>>>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>>>>> >>>>>> Hi guys, >>>>>> I'm doing an experiment ... I'm searching for term using the >>>>>> synonym list >>>>>> and keeping the number of hits so that I can compare the number >>>>>> of hit >>>>>> >>>>> using >>>>> >>>>> >>>>>> the same terms once the site is updated. So please before you >>>>>> 'kill' the >>>>>> beta site let's me know.... >>>>>> >>>>>> Cheers, Franck >>>>>> >>>>>> -----Original Message----- >>>>>> From: biocatalogue-developers-bounces at rubyforge.org >>>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf >>>>>> Of Franck >>>>>> Tanoh >>>>>> Sent: 11 June 2009 09:49 >>>>>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>>>>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>>>>> >>>>>> Thanks Jits, >>>>>> Very useful page... >>>>>> Franck >>>>>> >>>>>> -----Original Message----- >>>>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 >>>>>> 09:04 >>>>>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>>>>> Subject: Psuedo synonyms >>>>>> >>>>>> If you're curious, here is the list of synonyms we have in SOLR >>>>>> right now: >>>>>> >>>>>> >>>>>> >>> http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr >>> >>> >>> >>>>> >>>>> >>>>>> /solr/conf/synonyms.txt >>>>>> >>>>>> Jits >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> ------------------------------------------------------------------------ >>>>>> >>>>>> >>> >>> >>>>>> _______________________________________________ >>>>>> 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 Fri Jun 12 05:05:02 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Jun 2009 10:05:02 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: References: Message-ID: <4A321A3E.9090700@cs.man.ac.uk> I am the guilty man :-) Guilty until 1am last night ;-) As I explained on the board, this new synonyms list works at *index* time, not at *query* time, so it's the other way around. Think of it in this way - the aim of the synonyms list is to add new metadata to services (but only in SOLR) when SOLR indexes the services (to make them searchable). Jits Franck Tanoh wrote: > Hi Jits, > > Ok, so solar is not as clever as we thought :-(. > The synonym list has changed a lot, has somebody else changed them. The > idea of the synonyms is that if you type a general term you get all the > specific terms associated to the general term. Reading the new list we seem > to have lost the plot...:-(...who is the guilty man? > I think if we go from general term to specific terms will remove most of the > ambiguity in the current synonym list... > > Franck > > > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 12 June 2009 00:56 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org; Eric Nzuobontane; Thomas Laurent > Subject: Re: [BioCatalogue-developers] before and after the synonyms .. > > Hi Franck and all, > > There's been a MAJOR change in the way I am doing the pseudo synonyms > now (the ones we intend to use to aid in search). > > BEFORE this change: > > We built a synonyms list where we had mappings where each mapping had > the format... > > [ a set of (related) terms that a user might search for ] => [ the list > of pseudo synonyms that should be included in the user's search to > broaden the search and get more useful results] > > So, these pseudo synonyms mapping were used at *query* time to aid in > the search when a user provides a search query. > > Unfortunately, SOLR doesn't work this way with it's synonyms :-( :-( :-( > There are three main issues here (ref: > http://wiki.apache.org/solr/AnalyzersTokenizersTokenFilters#head-2c461ac74b4 > ddd82e453dc68fcfc92da77358d46).: > - the pseudo synonyms get ANDed in the search which means that we get > lesser or no results (trying searching for "protein" on the beta site > right now). > - SOLR doesn't handle multiple word queries very well. > - The way SOLR parses the query breaks the synonyms search. > > I looked and looked but there was no way I could make SOLR play nice. So > I've decided to do it differently (and this is the way that is recommended). > > NOW: > > I have changed the synonyms processing to happen at *index* time (ie: > when indexing the services into SOLR for search later). This does mean > that every time we update the synonyms list we need to reindex all the > content. > > So now, the mappings are essentially used to enrich the index for each > thing that is being indexed in SOLR. This is basically the opposite of > the above, and the format is: > > [ a set of terms that may be in a service's metadata, or annotation, or > whatever, when SOLR comes to indexing something ] => [ the list of terms > that should be put into the index for that specific thing being indexed > so that searches for any of these terms will match this item ] > > As you've probably guessed, this means we need to be very careful about > what we have here. We CANNOT have things like this (which would be > caused by ambiguous terms): > > Multiple Alignment => Multiple Alignment, Protein Sequence Analysis, > Nucleotide Sequence Analysis > > ... because otherwise every service etc that has the words "multiple > alignment" will also get the words "Protein Sequence Analysis" AND > "Nucleotide Sequence Analysis" and one of those will be incorrect for > that service. > > Based on this new knowledge, please can you verify the list of synonyms > that we now have for SOLR - > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > /solr/conf/synonyms.txt. > Note the ones I have commented out (with a '#') - this is because they > are ambiguous. > > Note that you can still produce the raw synonyms list in the previous > format because I have a script to convert it from the old format to the > new (reversed) format. However there may be the danger of ambiguous > terms so we should be vigilant about this. > > One added benefit to doing it this way is that we can use this to also > suggest tags to users and better enrich the metadata of the services... > > Phew! > > Jits > > > > Franck Tanoh wrote: > >> 1 more thing: >> >> and always give the same number of hit. >> So it looks like when you align the term together solr add 'AND' as >> > default. > >> But when I do the number of hits is different. >> When you add the quotation solr will look for the word with the quotation >> e.g. <"term1 term2"> not . Same thing happens with the >> underscore (_). >> >> For example: >> Protein sequence -> 96 hits >> protein AND sequence -> 96 hits >> protein OR sequence -> 480 hits >> "protein sequence" -> 0 hits >> Protein_sequence -> 18 hits >> >> The experiment could still be accurate if I ignore underscore and >> > quotation > >> mark :-) >> >> Franck >> >> -----Original Message----- >> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] >> Sent: 11 June 2009 11:43 >> To: Franck Tanoh >> Cc: biocatalogue-developers at rubyforge.org >> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >> >> If that last point is true, then your results of this experiment won't >> be accurate :-( >> >> Jits >> >> >> Jiten Bhagat wrote: >> >> >>> Is there anything in the BioCatalogue that actually has those phrases? >>> >>> Also, I have a suspicion that the search index for the beta site isnt >>> completely up to date (eg: the biomoby case I reported 2 weeks ago). >>> >>> Jits >>> >>> >>> Franck Tanoh wrote: >>> >>> >>>> I tried but could find anything with the quotation ("") mark and most >>>> of the >>>> time with the underscore (_) as well. For example: gene expression >>>> database returns 4 hits but >>>> gene_expression_database and "gene expression database" return 0 hits. >>>> Franck >>>> >>>> >>>> -----Original Message----- >>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 11:32 >>>> To: Franck Tanoh >>>> Cc: biocatalogue-developers at rubyforge.org >>>> Subject: Re: [BioCatalogue-developers] before and after the synonyms .. >>>> >>>> Looking very good Franck. >>>> >>>> Could you try the multiple word ones again, but this time with >>>> quotation marks around the whole phrase please? >>>> >>>> eg: you've done: >>>> >>>> protein sequence >>>> >>>> ... now do: >>>> >>>> "protein sequence" >>>> >>>> As that's only when many of the synonyms come into effect. >>>> >>>> Jits >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>> >>>> >>>>> I've finished with the first part of my experiment... you're free to >>>>> >>>>> >>>>> >>>> 'kill' >>>> >>>> >>>> >>>>> the beta and bring it back to 'life' with a new 'smile' :-) >>>>> >>>>> Franck >>>>> >>>>> -----Original Message----- >>>>> From: biocatalogue-developers-bounces at rubyforge.org >>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>>> Franck >>>>> Tanoh >>>>> Sent: 11 June 2009 09:56 >>>>> To: biocatalogue-developers at rubyforge.org >>>>> Subject: [BioCatalogue-developers] before and after the synonyms .. >>>>> >>>>> Hi guys, >>>>> I'm doing an experiment ... I'm searching for term using the synonym >>>>> list >>>>> and keeping the number of hits so that I can compare the number of hit >>>>> >>>>> >>>>> >>>> using >>>> >>>> >>>> >>>>> the same terms once the site is updated. So please before you 'kill' >>>>> the >>>>> beta site let's me know.... >>>>> >>>>> Cheers, Franck >>>>> >>>>> -----Original Message----- >>>>> From: biocatalogue-developers-bounces at rubyforge.org >>>>> [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of >>>>> Franck >>>>> Tanoh >>>>> Sent: 11 June 2009 09:49 >>>>> To: 'Jiten Bhagat'; biocatalogue-developers at rubyforge.org >>>>> Subject: Re: [BioCatalogue-developers] Psuedo synonyms >>>>> >>>>> Thanks Jits, >>>>> Very useful page... >>>>> Franck >>>>> >>>>> -----Original Message----- >>>>> From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 June 2009 09:04 >>>>> To: Franck Tanoh; biocatalogue-developers at rubyforge.org >>>>> Subject: Psuedo synonyms >>>>> >>>>> If you're curious, here is the list of synonyms we have in SOLR >>>>> right now: >>>>> >>>>> >>>>> >>>>> >>>>> > http://biocatalogue.rubyforge.org/svn/trunk/vendor/plugins/acts_as_solr/solr > >> >> >>>> >>>> >>>> >>>>> /solr/conf/synonyms.txt >>>>> >>>>> Jits >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> > ------------------------------------------------------------------------ > >>>>> >>>>> >> >> >>>>> _______________________________________________ >>>>> 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 Fri Jun 12 12:19:53 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Jun 2009 17:19:53 +0100 Subject: [BioCatalogue-developers] beta features In-Reply-To: References: Message-ID: <4A328029.8080403@cs.man.ac.uk> Please remind me about this on Monday, I'll put together something. Jits Franck Tanoh wrote: > > Hi Guys, > > > > Well done for the new beta! Do you have the list of new features? I > need to send a mail on the friend list once the pseudo-synonym works. > > 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 Jun 12 12:45:16 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Jun 2009 17:45:16 +0100 Subject: [BioCatalogue-developers] before and after the synonyms .. In-Reply-To: References: Message-ID: <4A32861C.7010108@cs.man.ac.uk> Hi Eric, Thomas, After chatting with Franck about this, we need to do some more work on the synonyms, but I will still commit the current set of synonyms. So can one of you do an update to the beta (and maybe test) site(s) and do a full reindex please, on Monday morning, or whenever you can so that we can have a functional search. Then we'll hopefully have the new synonyms ready for Tuesday afternoon. Cheers, Jits From noreply at rubyforge.org Fri Jun 12 12:52:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Jun 2009 12:52:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2441] Better error handling when search server is down or errors Message-ID: <20090612165202.5C6791858130@rubyforge.org> Task #2441 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error handling when search server is down or errors Complete: 0% Status: Open Description: We need to catch any exceptions when searched are carried out and display appropriate messages to the end user. Follow-Ups: ------------------------------------------------------- Date: 2009-06-12 16:52 By: jits Comment: Currently if access to the search server fails then an exception is raised by results.total (since results is nil). Display a message to the user like: "Search is not available at this time. Please try again later." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2441&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sat Jun 13 09:25:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sat, 13 Jun 2009 09:25:28 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2695] Annotations plugin: better error handling for .create_annotations Message-ID: <20090613132528.72BFE1858109@rubyforge.org> Task #2695 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annotations plugin: better error handling for .create_annotations Complete: 0% Status: Open Description: The acts_as_annotatable#create_annotations method currently saves a bunch of data as annotation objects but there is no way to tell what has errored and why. Need to do 2 things: 1. Log all errors (probably in the Annotation model directly. 2. Have a way to get any errors generated in the .create_annotations method. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2695&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sat Jun 13 17:24:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sat, 13 Jun 2009 17:24:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2696] Add help icons all over the place Message-ID: <20090613212415.025D31858110@rubyforge.org> Task #2696 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add help icons all over the place Complete: 0% Status: Open Description: To explain all sections etc... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2696&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 14 10:45:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Jun 2009 10:45:39 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2697] Wrap the wsdl parsing in a timeout Message-ID: <20090614144539.8B6391598077@rubyforge.org> Task #2697 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Wrap the wsdl parsing in a timeout Complete: 0% Status: Open Description: Use SystemTimer instead of the built in Ruby timer. Look in /lib/bio_catalogue/util.rb for examples. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2697&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 14 14:03:05 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Jun 2009 14:03:05 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2580] my favorite services Message-ID: <20090614180305.B3C1B1598031@rubyforge.org> Task #2580 has been updated. Project: BioCatalogue Subproject: Pilot Summary: my favorite services Complete: 90% Status: Open Description: i want to group a number of services as my favorite services. Follow-Ups: ------------------------------------------------------- Date: 2009-06-14 18:03 By: jits Comment: Done. But need an easier way to get to "My Favourites". ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2580&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 14 14:03:55 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Jun 2009 14:03:55 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2562] Add hints to service submission page Message-ID: <20090614180355.2006A1858102@rubyforge.org> Task #2562 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add hints to service submission page Complete: 100% Status: Closed Description: From Marco: # It would be very helpful if there would be little hints on the page (little pieces of text and mouse-over info). * E.g. How will a 'name alias' be used? # Can I provide more than one alias? Follow-Ups: ------------------------------------------------------- Date: 2009-06-14 18:03 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2562&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 14 14:05:55 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Jun 2009 14:05:55 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2698] Service submission: add "my tags" Message-ID: <20090614180555.9EA941858110@rubyforge.org> Task #2698 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Service submission: add "my tags" Complete: 0% Status: Open Description: ... so that it is easy to add the tags that a user uses commonly. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2698&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 14 17:15:19 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Jun 2009 17:15:19 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2699] UI: Show the source of category annotations Message-ID: <20090614211519.DAB0D1858109@rubyforge.org> Task #2699 has been updated. Project: BioCatalogue Subproject: Pilot Summary: UI: Show the source of category annotations Complete: 0% Status: Open Description: (as in title) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2699&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 14 17:21:33 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Jun 2009 17:21:33 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2700] Implement deletion of categories Message-ID: <20090614212133.7503B1858110@rubyforge.org> Task #2700 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement deletion of categories Complete: 0% Status: Open Description: (as per title) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2700&group_id=6901&group_project_id=12540 From ericnzuo at ebi.ac.uk Mon Jun 15 05:55:10 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 15 Jun 2009 10:55:10 +0100 Subject: [BioCatalogue-developers] updating the test site Message-ID: <4A361A7E.9090206@ebi.ac.uk> Hi Guys, Does any one object to updating the test site? I have a fix for some parsing problems which I would like to test on the test site. In fact, Rodrigo would like to see this on the beta site as soon as possible. Also, I think there should be some search fixes checked in since the last update. Please let me know if I should not go ahead. Eric From noreply at rubyforge.org Mon Jun 15 07:14:35 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Jun 2009 07:14:35 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2701] Hitting enter on service submission dropdown should not submit Message-ID: <20090615111435.90E651858117@rubyforge.org> Task #2701 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Hitting enter on service submission dropdown should not submit Complete: 0% Status: Open Description: ... should add to list. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2701&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 05:34:54 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 05:34:54 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2444] service creation in a transaction Message-ID: <20090616093454.6B77F185811A@rubyforge.org> Task #2444 has been updated. Project: BioCatalogue Subproject: Pilot Summary: service creation in a transaction Complete: 100% Status: Closed Description: The entire service creation process should handled transactionally. post create and soap_service save are not handled in a transaction. That means it is possible to create a soap_service that has no reference to a parent service Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 09:34 By: ebontane Comment: done ------------------------------------------------------- Date: 2008-12-12 09:50 By: ebontane Comment: The service creation has been moved from the controller to the model (soap_service) and how handled in a transaction. soap_service save and post_create are now transactionally done. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2444&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 05:37:42 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 05:37:42 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2566] Investigate solr indexing in relation to application slowdown Message-ID: <20090616093742.5992B185811D@rubyforge.org> Task #2566 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Investigate solr indexing in relation to application slowdown Complete: 100% Status: Closed Description: It has been observed that when a service submission is made, solr reindexing is triggered and the respond from the submit is received only after the indexing is complete. This seems to enormously slow down the application. It will be of interest to possibly de-synchronize the indexing and the return of a submit response. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 09:37 By: ebontane Comment: the solution to this problem was decoupling indexing from submits to the database. Solr now handles it commits through configuration of the auto commit switch in the solr config file. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2566&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:17:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:17:31 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2438] add opensearch feature Message-ID: <20090616101731.E170B1598031@rubyforge.org> Task #2438 has been updated. Project: BioCatalogue Subproject: Pilot Summary: add opensearch feature Complete: 50% Status: Open Description: Use pagination for opensearch results and also use solr engine to generate the search results Follow-Ups: ------------------------------------------------------- Date: 2008-12-12 09:51 By: ebontane Comment: opensearch can now be used on the beta site from a browser. However programmatic use of opensearch is not available yet ------------------------------------------------------- Date: 2008-11-17 14:41 By: ebontane Comment: using solr search and pagination ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2438&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:17:52 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:17:52 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2440] Import content from EMBRACE Message-ID: <20090616101752.3A2B415B8020@rubyforge.org> Task #2440 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Import content from EMBRACE Complete: 0% Status: Open Description: Agree with embrace on harvesting embrace registry data ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2440&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:22:19 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:22:19 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2446] Better error message on fail of load_wsdl action Message-ID: <20090616102219.298221858117@rubyforge.org> Task #2446 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error message on fail of load_wsdl action Complete: 75% Status: Open Description: When the AJAX interaction returns back an error then an appropriate error message should be displayed in the UI (not the debug error page as now) and the error should be logged. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:22 By: jits Comment: Currently will display something like "WDL failed to load". But should have a more informative message with hints on what the user can do to solve the problem and maybe report it. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2446&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:26:33 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:26:33 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2446] Better error message on fail of load_wsdl action Message-ID: <20090616102633.59E4F18580ED@rubyforge.org> Task #2446 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error message on fail of load_wsdl action Complete: 75% Status: Open Description: When the AJAX interaction returns back an error then an appropriate error message should be displayed in the UI (not the debug error page as now) and the error should be logged. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:22 By: jits Comment: Currently will display something like "WDL failed to load". But should have a more informative message with hints on what the user can do to solve the problem and maybe report it. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2446&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:27:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:27:47 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2447] create custom error pages Message-ID: <20090616102747.DF1B818580ED@rubyforge.org> Task #2447 has been updated. Project: BioCatalogue Subproject: Pilot Summary: create custom error pages Complete: 0% Status: Deleted Description: create custom error pages with more helpful messages to the user Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:27 By: jits Comment: task too generic ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2447&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:29:44 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:29:44 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2449] fix parsing for ebisearch Message-ID: <20090616102944.7DB2015B8022@rubyforge.org> Task #2449 has been updated. Project: BioCatalogue Subproject: Pilot Summary: fix parsing for ebisearch Complete: 100% Status: Closed Description: the ebisearch wsdl does not parse with the current parser. The Hash.from_xml function does not return complete results Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:29 By: ebontane Comment: parsing fixed. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2449&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:33:51 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:33:51 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2456] Use rescue_exception in app controller Message-ID: <20090616103351.928C51598030@rubyforge.org> Task #2456 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Use rescue_exception in app controller Complete: 0% Status: Open Description: Use the rescue_exception method in the application_controller to catch any exception and then redirect to an error page (or something else user friendly). Follow-Ups: ------------------------------------------------------- Date: 2008-11-23 14:09 By: jits Comment: This should also log the error so it can be checked later by an admin. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2456&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:35:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:35:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2461] Improve login failure information Message-ID: <20090616103502.A8BE718580E3@rubyforge.org> Task #2461 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Improve login failure information Complete: 0% Status: Open Description: the login failure message should be different depending on if the login details are wrong or if the account hasn't been activated. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2461&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:35:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:35:58 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2441] Better error handling when search server is down or errors Message-ID: <20090616103559.07E5A1598031@rubyforge.org> Task #2441 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error handling when search server is down or errors Complete: 0% Status: Open Description: We need to catch any exceptions when searched are carried out and display appropriate messages to the end user. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:35 By: jits Comment: Catch the following errors individually and display different and appropriate messages: - When the search server is down. - When a user enters an invalid search term that causes solr to spit and shout. Excerpt from email thread: Jiten Bhagat wrote: > Could do... haven't looked in the exact errors being returned, just catching the base Exception at the moment and displaying that message. > > Jits > > > Thomas Laurent wrote: >> If a bad syntax is used doesn't SOLR throw an exception like "bad syntax" that we could trap to display a "bad syntax error" ? >> >> >> Jiten Bhagat wrote: >>> But like I said, the error could also be caused by someone typing in something like "service:blast:output", ie: bad syntax in the search. We probably shouldn't say that the search engine isnt available in that case! >>> >>> Jits >>> >>> >>> Thomas Laurent wrote: >>>> A more correct message would be "Search engine unreachable/unavailable, please try again or contact administrator" maybe ? >>>> >>>> >>>> Jiten Bhagat wrote: >>>>> Good point, that's exactly it. That message also shows when you've typed in a bad search query. Hence I tried to use an error message like that. >>>>> >>>>> But I also see Franck's point, it's a tad bit scary for the end user. Not sure what the best error message is in that case... >>>>> >>>>> Jits >>>>> >>>>> >>>>> Thomas Laurent wrote: >>>>>> I think there's a difference between the 2: when you get the "Search failed" it's in fact the search engine at the back throwing an exception (we have issues with it at the moment). I'm working on solving that pb at the moment. >>>>>> >>>>>> When the search doesn't match any docs you have the "Google style" : >>>>>> " Search query: "xcvzxvxcv~" returned 0 items " >>>>>> " No search results." >>>>>> >>>>>> Thomas ------------------------------------------------------- Date: 2009-06-12 16:52 By: jits Comment: Currently if access to the search server fails then an exception is raised by results.total (since results is nil). Display a message to the user like: "Search is not available at this time. Please try again later." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2441&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:36:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:36:11 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2462] Search engine error handling Message-ID: <20090616103611.453831598030@rubyforge.org> Task #2462 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Search engine error handling Complete: 0% Status: Deleted Description: Catch the following errors individually and display different and appropriate messages: - When the search server is down. - When a user enters an invalid search term that causes solr to spit and shout. Excerpt from email thread: Jiten Bhagat wrote: > Could do... haven't looked in the exact errors being returned, just catching the base Exception at the moment and displaying that message. > > Jits > > > Thomas Laurent wrote: >> If a bad syntax is used doesn't SOLR throw an exception like "bad syntax" that we could trap to display a "bad syntax error" ? >> >> >> Jiten Bhagat wrote: >>> But like I said, the error could also be caused by someone typing in something like "service:blast:output", ie: bad syntax in the search. We probably shouldn't say that the search engine isnt available in that case! >>> >>> Jits >>> >>> >>> Thomas Laurent wrote: >>>> A more correct message would be "Search engine unreachable/unavailable, please try again or contact administrator" maybe ? >>>> >>>> >>>> Jiten Bhagat wrote: >>>>> Good point, that's exactly it. That message also shows when you've typed in a bad search query. Hence I tried to use an error message like that. >>>>> >>>>> But I also see Franck's point, it's a tad bit scary for the end user. Not sure what the best error message is in that case... >>>>> >>>>> Jits >>>>> >>>>> >>>>> Thomas Laurent wrote: >>>>>> I think there's a difference between the 2: when you get the "Search failed" it's in fact the search engine at the back throwing an exception (we have issues with it at the moment). I'm working on solving that pb at the moment. >>>>>> >>>>>> When the search doesn't match any docs you have the "Google style" : >>>>>> " Search query: "xcvzxvxcv~" returned 0 items " >>>>>> " No search results." >>>>>> >>>>>> Thomas Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:36 By: jits Comment: Duplicate ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2462&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:37:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:37:30 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2465] Implement custom 404 page Message-ID: <20090616103730.71D5E1598031@rubyforge.org> Task #2465 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement custom 404 page Complete: 0% Status: Open Description: Instead of using the default 404 page, implement a better, more dynamic 404 page that will guide users in a better way. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:37 By: jits Comment: Use the rescue_exception method in the application_controller to catch any exception and then redirect to an error page (or something else user friendly). ------------------------------------------------------- Date: 2008-12-12 10:05 By: jits Comment: > should these 404s be logged in the DB? I don't think so, as they will be the file logs anyways. ------------------------------------------------------- Date: 2008-12-12 09:45 By: ebontane Comment: should these 404s be logged in the DB? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2465&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:37:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:37:39 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2465] Implement custom 404 etc pages Message-ID: <20090616103739.99A9718580E3@rubyforge.org> Task #2465 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement custom 404 etc pages Complete: 0% Status: Open Description: Instead of using the default 404 page, implement a better, more dynamic 404 page that will guide users in a better way. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:37 By: jits Comment: Use the rescue_exception method in the application_controller to catch any exception and then redirect to an error page (or something else user friendly). ------------------------------------------------------- Date: 2008-12-12 10:05 By: jits Comment: > should these 404s be logged in the DB? I don't think so, as they will be the file logs anyways. ------------------------------------------------------- Date: 2008-12-12 09:45 By: ebontane Comment: should these 404s be logged in the DB? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2465&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:38:54 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:38:54 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2504] Classification/type of service on submission Message-ID: <20090616103855.111A618580E3@rubyforge.org> Task #2504 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Classification/type of service on submission Complete: 50% Status: Open Description: Need to adapt annotations plugin to have constrained and use the choice based annotations (ie: seeds) Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:38 By: jits Comment: Implemented constraints. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2504&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:39:52 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:39:52 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2504] Classification/type of service on submission Message-ID: <20090616103952.3860A1858117@rubyforge.org> Task #2504 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Classification/type of service on submission Complete: 50% Status: Open Description: Need to adapt annotations plugin to have constrained and use the choice based annotations (ie: seeds) Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:39 By: jits Comment: Filtering and click through work remaining. ------------------------------------------------------- Date: 2009-06-16 10:38 By: jits Comment: Implemented constraints. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2504&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:40:15 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:40:15 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2504] Categorisation/classification/type of services Message-ID: <20090616104020.3D6C818580E3@rubyforge.org> Task #2504 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Categorisation/classification/type of services Complete: 50% Status: Open Description: Need to adapt annotations plugin to have constrained and use the choice based annotations (ie: seeds) Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:39 By: jits Comment: Filtering and click through work remaining. ------------------------------------------------------- Date: 2009-06-16 10:38 By: jits Comment: Implemented constraints. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2504&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:41:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:41:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2510] Make annotations editable Message-ID: <20090616104114.D518215B8022@rubyforge.org> Task #2510 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Make annotations editable Complete: 100% Status: Closed Description: As requested and discussed with Franck, annotations need to be editable by their owners, otherwise people will be pissed off that spelling mistakes etc cannot be edited! Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:41 By: jits Comment: Done ------------------------------------------------------- Date: 2009-01-29 14:56 By: jits Comment: Versioning done! Now need to show older versioning etc in the UI. ------------------------------------------------------- Date: 2009-01-27 14:14 By: jits Comment: Old versions of annotations need to be saved, so don't overwrite! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2510&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:43:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:43:47 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2516] Implement messaging/networking and other such features Message-ID: <20090616104347.719511598031@rubyforge.org> Task #2516 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement messaging/networking and other such features Complete: 10% Status: Open Description: As requested by Frnack: --- Hi, Yesterday, I wanted to contact a biocat user about a service he submitted ? but couldn?t. I said to myself; how will a biocat user contact a provider about his services then? Should he send us a mail first? Not a good idea? we are not service providers. We therefore need a way to enable communication between services provider/submitters/users/curators. My solution is to have an internal messaging system (myExperiment style)? leverage on existing technology :-) I know you guys have already a long list of requirements but I think we should have this system in place before the public release. Cheers Franck --- Should be able to drop in a plugin to achieve this. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2516&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:46:16 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:46:16 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2557] Annotations plugin: implement curation assertions Message-ID: <20090616104616.6565F15B8022@rubyforge.org> Task #2557 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annotations plugin: implement curation assertions Complete: 0% Status: Open Description: Make it generic, but for now the real use case is users being able to give a thumbs up or thumbs down for things. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2557&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:49:18 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:49:18 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2702] Feta: need to import the Soaplab services metadata Message-ID: <20090616104918.1BA91185811A@rubyforge.org> Task #2702 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Feta: need to import the Soaplab services metadata Complete: 0% Status: Open Description: ... as these could not be imported in the first instance. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2702&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:50:02 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:50:02 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2560] Show user name in all places instead of email address Message-ID: <20090616105002.CD6271858106@rubyforge.org> Task #2560 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show user name in all places instead of email address Complete: 0% Status: Open Description: ... like in the welcome messages. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:50 By: jits Comment: Emails are private data that should NEVER be divulged. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2560&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:50:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:50:30 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2703] User profile: allow users to register a public email Message-ID: <20090616105030.C495C18580ED@rubyforge.org> Task #2703 has been updated. Project: BioCatalogue Subproject: Pilot Summary: User profile: allow users to register a public email Complete: 0% Status: Open Description: ... or make their registered email address public. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2703&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:51:10 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:51:10 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2560] Show user name in all places instead of email address Message-ID: <20090616105110.2B43D18580ED@rubyforge.org> Task #2560 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show user name in all places instead of email address Complete: 0% Status: Open Description: ... like in the welcome messages. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:50 By: jits Comment: Emails are private data that should NEVER be divulged. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2560&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:55:27 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:55:27 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2560] Dealing with user's registered email address Message-ID: <20090616105527.DF2F7185811F@rubyforge.org> Task #2560 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Dealing with user's registered email address Complete: 80% Status: Open Description: ... like in the welcome messages. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 10:55 By: jits Comment: when showing user profiles, if you're viewing your own, you see your email... but its not obious that this will be hidden from others... so need to make it obvious that only you can see it ------------------------------------------------------- Date: 2009-06-16 10:50 By: jits Comment: Emails are private data that should NEVER be divulged. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2560&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:58:36 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:58:36 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2561] Scraping for services from a web page Message-ID: <20090616105836.9EE4E185811E@rubyforge.org> Task #2561 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Scraping for services from a web page Complete: 0% Status: Deleted Description: Look into possibly doing some page scraping of services. Is this worth it? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2561&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 06:59:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 06:59:17 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2568] unable to submit some services Message-ID: <20090616105917.EDB621858117@rubyforge.org> Task #2568 has been updated. Project: BioCatalogue Subproject: Pilot Summary: unable to submit some services Complete: 0% Status: Open Description: The registry treats these services as the same; so I can only register one of them. But in reality they are doing different things: http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl and http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1_ws0.wsdl http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws0.wsdl and http://www.cbs.dtu.dk/ws/BLASTatlas/BLASTatlas_1_0_ws2.wsdl http://www.cbs.dtu.dk/ws/NetGlycate/NetGlycate_1_0.wsdl and http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl http://www.cbs.dtu.dk/ws/NetNGlyc/NetNGlyc_1_0a_ws0.wsdl and http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl ?.. The provider: http://www.cbs.dtu.dk/ws/ ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2568&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:00:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:00:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2570] Add the addthis.com bookmarking widget Message-ID: <20090616110008.256C8185811E@rubyforge.org> Task #2570 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add the addthis.com bookmarking widget Complete: 0% Status: Open Description: Like on myexperiment ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2570&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:00:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:00:28 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2571] Add google analytics Message-ID: <20090616110028.BF31E185811E@rubyforge.org> Task #2571 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add google analytics Complete: 0% Status: Open Description: Need to add google analytics to the website Follow-Ups: ------------------------------------------------------- Date: 2009-03-11 13:02 By: jits Comment: Have the EBI registered for a Google Analytics account as Rodrigo mentioned? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2571&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:00:57 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:00:57 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2576] Annotations plugin: add constrained values config setting Message-ID: <20090616110059.5FA631858117@rubyforge.org> Task #2576 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Annotations plugin: add constrained values config setting Complete: 100% Status: Closed Description: So that certain annotations will only be created if the value falls within a constrained set of values (eg: for ratings, values can only be [1,2,3,4,5]) Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:00 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2576&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:02:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:02:17 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2578] Allow multiple name aliases to be provided Message-ID: <20090616110217.793DC185811E@rubyforge.org> Task #2578 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Allow multiple name aliases to be provided Complete: 100% Status: Closed Description: So maybe comma seperated in the one field during submission... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2578&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:04:06 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:04:06 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2582] Store extra log info during searches Message-ID: <20090616110406.472891858117@rubyforge.org> Task #2582 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Store extra log info during searches Complete: 0% Status: Open Description: Add search results count and any other info to ActivityLog after search... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2582&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:05:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:05:47 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2594] Tag frequency count fix for tags_box partial Message-ID: <20090616110547.8649E1858117@rubyforge.org> Task #2594 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Tag frequency count fix for tags_box partial Complete: 0% Status: Open Description: The partial annotations/_tags_box will currently only get a count of 1 per tag so all tags will be of the same size. In myexperiment, the size of the tag, even on individual tag clouds, always represents the frequency of that tag word on the whole site. Maybe this should be the same for the partial. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2594&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:08:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:08:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2595] Sourcing tags from ontology Message-ID: <20090616110808.09FB2185811A@rubyforge.org> Task #2595 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Sourcing tags from ontology Complete: 0% Status: Open Description: Sourcing tags from the myGrid ontology. This is the first step toward semantic annotation of web services. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:08 By: jits Comment: Added this to the tags autocomplete suggestions... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2595&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:09:42 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:09:42 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2704] Change ontology term tags to use namespaces instead of full URI Message-ID: <20090616110942.D3E1318580F0@rubyforge.org> Task #2704 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Change ontology term tags to use namespaces instead of full URI Complete: 0% Status: Open Description: eg: mygrid:simpleParamater ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2704&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:10:50 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:10:50 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2595] Sourcing tags from ontology Message-ID: <20090616111050.279DC1858117@rubyforge.org> Task #2595 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Sourcing tags from ontology Complete: 0% Status: Open Description: Sourcing tags from the myGrid ontology. This is the first step toward semantic annotation of web services. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:08 By: jits Comment: Added this to the tags autocomplete suggestions... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2595&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:11:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:11:38 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2596] 20 q: 1-number & type of service for a given provider Message-ID: <20090616111139.013921598030@rubyforge.org> Task #2596 has been updated. Project: BioCatalogue Subproject: Pilot Summary: 20 q: 1-number & type of service for a given provider Complete: 0% Status: Open Description: How many services has provider X? ?currently implemented but need to make sure it clear enough for users? How many of those are REST? How many of those are SOAP? ?different type of services should be clear on the site and users should know the number of each type after a search. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2596&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:13:56 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:13:56 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2597] 20 q: 2-number of submitter a given provider Message-ID: <20090616111356.BACEC185811F@rubyforge.org> Task #2597 has been updated. Project: BioCatalogue Subproject: Pilot Summary: 20 q: 2-number of submitter a given provider Complete: 0% Status: Open Description: How many submitters does provider X have??number of submitter from a provider must be clear ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2597&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:24:18 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:24:18 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2598] 20 q: 3- reliability profile of a service Message-ID: <20090616112418.85ACA185811E@rubyforge.org> Task #2598 has been updated. Project: BioCatalogue Subproject: Pilot Summary: 20 q: 3- reliability profile of a service Complete: 0% Status: Open Description: What is the reliability profile of service X? Can I see the usage history of service X? who is the provider? is it free? Each service should have a profile (reliability, history of use, free, licenses etc) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2598&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:25:09 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:25:09 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2612] Annotations: any finder should be able to take a list of options Message-ID: <20090616112509.8E888185811A@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 Tue Jun 16 07:26:01 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:26:01 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2618] Allow adding of example *sets* of inputs for operations Message-ID: <20090616112601.A254B185811A@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 Tue Jun 16 07:26:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:26:58 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2619] Investigate: no values for min_occurs and max_occurs Message-ID: <20090616112658.4057A185811E@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 Tue Jun 16 07:27:53 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:27:53 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2628] Write stats page Message-ID: <20090616112753.305101858117@rubyforge.org> Task #2628 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Write stats page Complete: 75% 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? Follow-Ups: ------------------------------------------------------- Date: 2009-05-31 16:26 By: jits Comment: Done, but what else is required on that page? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2628&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:30:00 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:30:00 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2634] Work on synonyms for search Message-ID: <20090616113000.A6C11185811A@rubyforge.org> Task #2634 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Work on synonyms for search Complete: 90% Status: Open Description: Work on synonyms for search Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:30 By: jits Comment: Franck to go through pseudo synonyms one more time. ------------------------------------------------------- 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 Tue Jun 16 07:30:59 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:30:59 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2635] Make stats calculations run as a background task Message-ID: <20090616113059.DF13D1858117@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 noreply at rubyforge.org Tue Jun 16 07:32:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:32:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2644] Add Admin features for curation like delete Message-ID: <20090616113207.6B19E185811A@rubyforge.org> Task #2644 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add Admin features for curation like delete Complete: 0% Status: Open Description: Add features to allow admins to curate/administrate the catalogue through the UI. This will permit people like Franck to go in and delete services ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2644&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:32:32 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:32:32 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2645] Tab persistency on user profile Message-ID: <20090616113232.F361F1858117@rubyforge.org> Task #2645 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Tab persistency on user profile Complete: 0% Status: Open Description: If you go to a user's page and click on the "services submitted", if you go to the "next" page, the tab goes back to "Profile". ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2645&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:34:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:34:45 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2646] Set up regular solr optimize Message-ID: <20090616113445.B92851858117@rubyforge.org> Task #2646 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Set up regular solr optimize Complete: 0% Status: Open Description: Set up a background task / cron job to regularly run the solr optimization Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:34 By: jits Comment: Possibly can just use cron to call a rake task to optimise. May need to write this rake task (see bottom of solr:reindex task to see how to optimize). ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2646&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:38:09 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:38:09 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2658] Improve page load in the event that Disqus fails Message-ID: <20090616113810.1A9711858117@rubyforge.org> Task #2658 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Improve page load in the event that Disqus fails Complete: 75% Status: Open Description: Right now, if Disqus fails or takes a long time to fetch, then tabs will not form properly... Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:38 By: jits Comment: Possibly use what Stuart has done in Sysmo ------------------------------------------------------- Date: 2009-05-19 16:33 By: jits Comment: Now the tabs will form properly and before the disqus thread tries to load. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2658&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:39:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:39:28 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2661] position status icons appropriate in view Message-ID: <20090616113928.2F8BD185811A@rubyforge.org> Task #2661 has been updated. Project: BioCatalogue Subproject: Pilot Summary: position status icons appropriate in view Complete: 100% Status: Closed Description: The service status and availability check icons needs to be position appropriate in the service show page and the monitoring tab Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:39 By: jits Comment: done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2661&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:39:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:39:40 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2662] Show source of tags and name aliases Message-ID: <20090616113940.42A45185811A@rubyforge.org> Task #2662 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show source of tags and name aliases Complete: 0% Status: Open Description: When you hover over tags and name aliases, show who submitted that... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2662&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:39:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:39:47 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2705] setup cron job to reindex on a regular basis Message-ID: <20090616113947.EC962185811A@rubyforge.org> Task #2705 has been updated. Project: BioCatalogue Subproject: Pilot Summary: setup cron job to reindex on a regular basis Complete: 0% Status: Open Description: the cron job would make the sure the index is fairly up to date ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2705&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:42:43 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:42:43 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2670] Perf: optimise filtering sidebar Message-ID: <20090616114243.74165185811A@rubyforge.org> Task #2670 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Perf: optimise filtering sidebar Complete: 0% Status: Open Description: The filtering sidebar takes a fair bit of time to render. Look into possibly optimising this. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2670&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:43:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:43:24 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2680] provider link broken Message-ID: <20090616114324.EC889185811E@rubyforge.org> Task #2680 has been updated. Project: BioCatalogue Subproject: Pilot Summary: provider link broken Complete: 0% Status: Closed Description: The provider links on the beta site is currently broken. ruby style error message when i click on a provider. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:43 By: jits Comment: fine now ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2680&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:45:09 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:45:09 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2673] Investigate potential bug in search Message-ID: <20090616114509.AB648185811A@rubyforge.org> Task #2673 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Investigate potential bug in search Complete: 0% Status: Closed Description: The auto_tagger.rb script found about 350 services that are from BioMoby, but searching on the beta site only retrieves 180 or so. Look into this. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:45 By: jits Comment: Fixed with reindex ------------------------------------------------------- Date: 2009-06-04 13:58 By: ebontane Comment: Search Related bug: ============ If the search box is used in IE & firefox on windows with search term clustalw for example, the skinning in the application is messed up. http://beta.biocatalogue.org/search?q=clustalw&commit= ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2673&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:47:00 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:47:00 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2700] Implement deletion of categories Message-ID: <20090616114700.2E9D31858117@rubyforge.org> Task #2700 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement deletion of categories Complete: 100% Status: Closed Description: (as per title) Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 11:46 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2700&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 07:47:59 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 07:47:59 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2674] BioCatalogue wiki config sudden change Message-ID: <20090616114759.904611858121@rubyforge.org> Task #2674 has been updated. Project: BioCatalogue Subproject: Pilot Summary: BioCatalogue wiki config sudden change Complete: 0% Status: Open Description: Investigate why the wki configuration for BioCatalogue change causing links to die. Put measures in place to prevent this from happening in the future ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2674&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 09:44:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 09:44:38 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2568] unable to submit some services Message-ID: <20090616134438.A27CF1598074@rubyforge.org> Task #2568 has been updated. Project: BioCatalogue Subproject: Pilot Summary: unable to submit some services Complete: 50% Status: Open Description: The registry treats these services as the same; so I can only register one of them. But in reality they are doing different things: http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl and http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1_ws0.wsdl http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws0.wsdl and http://www.cbs.dtu.dk/ws/BLASTatlas/BLASTatlas_1_0_ws2.wsdl http://www.cbs.dtu.dk/ws/NetGlycate/NetGlycate_1_0.wsdl and http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl http://www.cbs.dtu.dk/ws/NetNGlyc/NetNGlyc_1_0a_ws0.wsdl and http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl ?.. The provider: http://www.cbs.dtu.dk/ws/ Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 13:44 By: ebontane Comment: http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl need to still be verified for parse error. The rest have been tested to parse properly ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2568&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 09:46:36 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 09:46:36 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2674] BioCatalogue wiki config sudden change Message-ID: <20090616134636.30D581858106@rubyforge.org> Task #2674 has been updated. Project: BioCatalogue Subproject: Pilot Summary: BioCatalogue wiki config sudden change Complete: 100% Status: Closed Description: Investigate why the wki configuration for BioCatalogue change causing links to die. Put measures in place to prevent this from happening in the future Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 13:46 By: ebontane Comment: Base URL to wiki was changed. So some previously bookmarked URL may not work. To be closed now and maybe reopened if further problems arise. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2674&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 09:48:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 09:48:58 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2438] add opensearch feature Message-ID: <20090616134858.874BA1858122@rubyforge.org> Task #2438 has been updated. Project: BioCatalogue Subproject: Pilot Summary: add opensearch feature Complete: 50% Status: Open Description: Use pagination for opensearch results and also use solr engine to generate the search results Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 13:48 By: ebontane Comment: fix the existing opensearch functionality on the beta site or disable opensearch till after the pilot. ------------------------------------------------------- Date: 2008-12-12 09:51 By: ebontane Comment: opensearch can now be used on the beta site from a browser. However programmatic use of opensearch is not available yet ------------------------------------------------------- Date: 2008-11-17 14:41 By: ebontane Comment: using solr search and pagination ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2438&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Tue Jun 16 09:56:00 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 16 Jun 2009 14:56:00 +0100 Subject: [BioCatalogue-developers] features for the new beta release In-Reply-To: References: Message-ID: <4A37A470.2000004@cs.man.ac.uk> Hi Franck, Sorry, I did promise you I would put together a list. "Service monitoring: check for service availability via endpoint and wsdl file." ... should be: "Service monitoring: we regularly check the availability of the service by checking it's endpoint. We also check the WSDL location to make sure it is still available." And... "Service filtering by operations, inputs, outputs, providers and submitters." ... should be: "Service filtering by tags on services, operations, inputs, and outputs, as well as filtering by providers, submitters, and locations." I can't think of any other "new" features, which is a shame because it might make it look like we haven't really been doing much and not do justice to such a big update!! :-( You could rephrase what you say to say something like "We've been working hard on making the BioCatalogue more stable and friendly to use, as well as building in some cool new features. Some of the highlights of the new features are:..." Cheers, Jits Franck Tanoh wrote: > > Hi guys, > > Please complete the list of features so that I can send a mail on the > friend list? > > New features: > > - Search enhancement: when you search for a term, any related term > associated to it will be included in the search result. > > - Service monitoring: check for service availability via endpoint and > wsdl file. > > - Service categorisation: possibility to assign categories to services > during submission or after submission > > - Service filtering by operations, inputs, outputs, providers and > submitters. > > ? > > "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 tlaurent at ebi.ac.uk Tue Jun 16 10:12:29 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Tue, 16 Jun 2009 15:12:29 +0100 Subject: [BioCatalogue-developers] features for the new beta release In-Reply-To: References: Message-ID: <4A37A84D.9020306@ebi.ac.uk> You can also mention all the backend changes as well: - replaced mongrels with mod_rails on new dedicated Apache servers - moved the SOLR engine to dedicated Tomcat on separate machine These are pretty major moves to improve reliability and maintainability of the Biocatalogue setup. - installation of memcached servers to improve the speed of the application Thomas Franck Tanoh wrote: > Hi guys, > > > > Please complete the list of features so that I can send a mail on the > friend list? > > > > New features: > > - Search enhancement: when you search for a term, any related term > associated to it will be included in the search result. > > - Service monitoring: check for service availability via endpoint and > wsdl file. > > - Service categorisation: possibility to assign categories to services > during submission or after submission > > - Service filtering by operations, inputs, outputs, providers and > submitters. > > ? > > > > > > "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 noreply at rubyforge.org Tue Jun 16 10:19:08 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 10:19:08 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2706] "Help categorise this..." link should take into logged in or not Message-ID: <20090616141908.91BFC15B8020@rubyforge.org> Task #2706 has been updated. Project: BioCatalogue Subproject: Pilot Summary: "Help categorise this..." link should take into logged in or not Complete: 0% Status: Open Description: Currently will show the add annotation login box even if the person is not logged in! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2706&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 10:20:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 10:20:11 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2707] Fix alignment of text in the annotation source box Message-ID: <20090616142013.A1A6315B8023@rubyforge.org> Task #2707 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fix alignment of text in the annotation source box Complete: 0% Status: Open Description: Currently very badly aligned... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2707&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Tue Jun 16 10:42:46 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 16 Jun 2009 15:42:46 +0100 Subject: [BioCatalogue-developers] features for the new beta release In-Reply-To: <4A37A84D.9020306@ebi.ac.uk> References: <4A37A84D.9020306@ebi.ac.uk> Message-ID: <4A37AF66.1060805@cs.man.ac.uk> That is true. At first I thought users won't care about that, but I reckon some people would be interested to know. Jits Thomas Laurent wrote: > You can also mention all the backend changes as well: > - replaced mongrels with mod_rails on new dedicated Apache servers > - moved the SOLR engine to dedicated Tomcat on separate machine > > These are pretty major moves to improve reliability and > maintainability of the Biocatalogue setup. > > - installation of memcached servers to improve the speed of the > application > > Thomas > > Franck Tanoh wrote: >> Hi guys, >> >> >> >> Please complete the list of features so that I can send a mail on the >> friend list? >> >> >> >> New features: >> >> - Search enhancement: when you search for a term, any related term >> associated to it will be included in the search result. >> >> - Service monitoring: check for service availability via endpoint and >> wsdl file. >> >> - Service categorisation: possibility to assign categories to >> services during submission or after submission >> >> - Service filtering by operations, inputs, outputs, providers and >> submitters. >> >> ? >> >> >> >> >> >> "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 tlaurent at ebi.ac.uk Tue Jun 16 10:55:09 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Tue, 16 Jun 2009 15:55:09 +0100 Subject: [BioCatalogue-developers] features for the new beta release In-Reply-To: <4A37AF66.1060805@cs.man.ac.uk> References: <4A37A84D.9020306@ebi.ac.uk> <4A37AF66.1060805@cs.man.ac.uk> Message-ID: <4A37B24D.4050103@ebi.ac.uk> Sorry, I read Franck's email a bit quickly, I thought it was a summary for Carole. Jiten Bhagat wrote: > That is true. At first I thought users won't care about that, but I > reckon some people would be interested to know. > > Jits > > > Thomas Laurent wrote: >> You can also mention all the backend changes as well: >> - replaced mongrels with mod_rails on new dedicated Apache servers >> - moved the SOLR engine to dedicated Tomcat on separate machine >> >> These are pretty major moves to improve reliability and >> maintainability of the Biocatalogue setup. >> >> - installation of memcached servers to improve the speed of the >> application >> >> Thomas >> >> Franck Tanoh wrote: >>> Hi guys, >>> >>> >>> >>> Please complete the list of features so that I can send a mail on the >>> friend list? >>> >>> >>> >>> New features: >>> >>> - Search enhancement: when you search for a term, any related term >>> associated to it will be included in the search result. >>> >>> - Service monitoring: check for service availability via endpoint and >>> wsdl file. >>> >>> - Service categorisation: possibility to assign categories to >>> services during submission or after submission >>> >>> - Service filtering by operations, inputs, outputs, providers and >>> submitters. >>> >>> ? >>> >>> >>> >>> >>> >>> "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 ytanoh at cs.man.ac.uk Tue Jun 16 11:00:44 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 16 Jun 2009 16:00:44 +0100 Subject: [BioCatalogue-developers] features for the new beta release In-Reply-To: <4A37B24D.4050103@ebi.ac.uk> Message-ID: Still useful to know though...we have developers and users and the list. Cheers, Franck -----Original Message----- From: Thomas Laurent [mailto:tlaurent at ebi.ac.uk] Sent: 16 June 2009 15:55 To: Jiten Bhagat Cc: Franck Tanoh; biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] features for the new beta release Sorry, I read Franck's email a bit quickly, I thought it was a summary for Carole. Jiten Bhagat wrote: > That is true. At first I thought users won't care about that, but I > reckon some people would be interested to know. > > Jits > > > Thomas Laurent wrote: >> You can also mention all the backend changes as well: >> - replaced mongrels with mod_rails on new dedicated Apache servers >> - moved the SOLR engine to dedicated Tomcat on separate machine >> >> These are pretty major moves to improve reliability and >> maintainability of the Biocatalogue setup. >> >> - installation of memcached servers to improve the speed of the >> application >> >> Thomas >> >> Franck Tanoh wrote: >>> Hi guys, >>> >>> >>> >>> Please complete the list of features so that I can send a mail on the >>> friend list. >>> >>> >>> >>> New features: >>> >>> - Search enhancement: when you search for a term, any related term >>> associated to it will be included in the search result. >>> >>> - Service monitoring: check for service availability via endpoint and >>> wsdl file. >>> >>> - Service categorisation: possibility to assign categories to >>> services during submission or after submission >>> >>> - Service filtering by operations, inputs, outputs, providers and >>> submitters. >>> >>> . >>> >>> >>> >>> >>> >>> "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 noreply at rubyforge.org Tue Jun 16 11:09:04 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 11:09:04 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2708] Check that Registry display name is being shown, not name Message-ID: <20090616150904.705C4185812D@rubyforge.org> Task #2708 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Check that Registry display name is being shown, not name Complete: 0% Status: Open Description: (as per title) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2708&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 11:40:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 11:40:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2709] Update source in auto_tagger script Message-ID: <20090616154012.370EA185811F@rubyforge.org> Task #2709 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update source in auto_tagger script Complete: 0% Status: Open Description: Should use (and create) a "BioCatalogue" agent, as the source of new annotations. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2709&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 16:27:09 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 16:27:09 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2709] Update source in auto_tagger script Message-ID: <20090616202709.A5E4C1858123@rubyforge.org> Task #2709 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update source in auto_tagger script Complete: 100% Status: Closed Description: Should use (and create) a "BioCatalogue" agent, as the source of new annotations. Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 20:27 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2709&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 16:28:43 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 16:28:43 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2672] Change scripts to store logs in the /logs and to have timestamp Message-ID: <20090616202843.23B9A1678217@rubyforge.org> Task #2672 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Change scripts to store logs in the /logs and to have timestamp Complete: 100% Status: Closed Description: E.g: 'log/auto_tagger_{current_time}.log' Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 20:28 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2672&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 16:34:50 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 16:34:50 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2708] Check that Registry display name is being shown, not name Message-ID: <20090616203450.6E0CD1858136@rubyforge.org> Task #2708 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Check that Registry display name is being shown, not name Complete: 100% Status: Closed Description: (as per title) Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 20:34 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2708&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 18:13:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 18:13:29 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2664] Add "OR" back to filtering options of same type Message-ID: <20090616221329.8A2EF1858126@rubyforge.org> Task #2664 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add "OR" back to filtering options of same type Complete: 100% Status: Closed Description: Like before Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 22:13 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2664&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 18:14:05 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 18:14:05 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2707] Fix alignment of text in the annotation source box Message-ID: <20090616221405.666961779921@rubyforge.org> Task #2707 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fix alignment of text in the annotation source box Complete: 100% Status: Closed Description: Currently very badly aligned... Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 22:14 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2707&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 16 18:52:34 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Jun 2009 18:52:34 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2706] "Help categorise this..." link should take into logged in or not Message-ID: <20090616225234.6E70A1678217@rubyforge.org> Task #2706 has been updated. Project: BioCatalogue Subproject: Pilot Summary: "Help categorise this..." link should take into logged in or not Complete: 100% Status: Closed Description: Currently will show the add annotation login box even if the person is not logged in! Follow-Ups: ------------------------------------------------------- Date: 2009-06-16 22:52 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2706&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Wed Jun 17 05:46:14 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 17 Jun 2009 10:46:14 +0100 Subject: [BioCatalogue-developers] new features announcement. In-Reply-To: References: Message-ID: <4A38BB66.7010407@cs.man.ac.uk> Sound's good to me! Jits Franck Tanoh wrote: > > Hi guys, > > Please check my announcement for the friend list: > > << > > Hello everyone, > > We?ve been working hard on making the BioCatalogue more stable and > friendly to use, as well as building in some cool new features. Some > of the new features are: > > 1- Service monitoring: we regularly check the availability of the > service by checking its endpoint. We also check the WSDL location to > make sure it is still available. > > 2- Service filtering by tags on services, operations, inputs, and > outputs, as well as filtering by providers, submitters, and locations. > > 3- Search enhancement: when you search for a term, any related term > associated to it will be included in the search result. e.g. search > for Microarray and you get in your result any service tagged with > Affymetrix. > > 4- Service categorisation: possibility to assign categories to > services during submission or after submission. These categories > should allow a better filtering of services. > > We?ve also made a lot improvement on the server side to make sure the > BioCatalogue can handle your queries. For example: > > - replaced mongrels with mod_rails on new dedicated Apache servers > > - moved the SOLR engine to dedicated Tomcat on separate machine > > - installation of memcached servers to improve the speed of the > application. > > The BioCatalogue beta: http://beta.biocatalogue.org/ > > For support or bugs reports please email: > biocatalogue-support at rubyforge.org > > We look forward to working with you in developing the BioCatalogue > > Regards, > > The BioCatalogue Team > > >> > > 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 noreply at rubyforge.org Wed Jun 17 06:01:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 06:01:39 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2710] Add other types of annotations to service show page Message-ID: <20090617100139.A9E511598075@rubyforge.org> Task #2710 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add other types of annotations to service show page Complete: 0% Status: Open Description: Things like "usage conditions", "cost" etc etc ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2710&group_id=6901&group_project_id=12540 From tlaurent at ebi.ac.uk Wed Jun 17 06:23:56 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Wed, 17 Jun 2009 11:23:56 +0100 Subject: [BioCatalogue-developers] new features announcement. In-Reply-To: <4A38BB66.7010407@cs.man.ac.uk> References: <4A38BB66.7010407@cs.man.ac.uk> Message-ID: <4A38C43C.5000401@ebi.ac.uk> Yep, that's good for me as well. Thomas Jiten Bhagat wrote: > Sound's good to me! > > Jits > > > Franck Tanoh wrote: >> >> Hi guys, >> >> Please check my announcement for the friend list: >> >> << >> >> Hello everyone, >> >> We?ve been working hard on making the BioCatalogue more stable and >> friendly to use, as well as building in some cool new features. Some >> of the new features are: >> >> 1- Service monitoring: we regularly check the availability of the >> service by checking its endpoint. We also check the WSDL location to >> make sure it is still available. >> >> 2- Service filtering by tags on services, operations, inputs, and >> outputs, as well as filtering by providers, submitters, and locations. >> >> 3- Search enhancement: when you search for a term, any related term >> associated to it will be included in the search result. e.g. search >> for Microarray and you get in your result any service tagged with >> Affymetrix. >> >> 4- Service categorisation: possibility to assign categories to >> services during submission or after submission. These categories >> should allow a better filtering of services. >> >> We?ve also made a lot improvement on the server side to make sure the >> BioCatalogue can handle your queries. For example: >> >> - replaced mongrels with mod_rails on new dedicated Apache servers >> >> - moved the SOLR engine to dedicated Tomcat on separate machine >> >> - installation of memcached servers to improve the speed of the >> application. >> >> The BioCatalogue beta: http://beta.biocatalogue.org/ >> >> For support or bugs reports please email: >> biocatalogue-support at rubyforge.org >> >> We look forward to working with you in developing the BioCatalogue >> >> Regards, >> >> The BioCatalogue Team >> >> >> >> >> 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 noreply at rubyforge.org Wed Jun 17 06:48:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 06:48:40 -0400 (EDT) Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost Message-ID: <20090617104840.79AFE18581E8@rubyforge.org> Bugs item #26258, was opened at 2009-06-17 06:48 You can respond by visiting: http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 Category: None Group: None Status: Open Resolution: None Priority: 3 Submitted By: Nobody (None) Assigned to: Nobody (None) Summary: account confirmation email points to localhost Initial Comment: Content of the email I just received: Please, click on the following link to activate your account. http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951 ---------------------------------------------------------------------- You can respond by visiting: http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 From jits at cs.man.ac.uk Wed Jun 17 07:37:50 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 17 Jun 2009 12:37:50 +0100 Subject: [BioCatalogue-developers] [Fwd: [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost] Message-ID: <4A38D58E.2080007@cs.man.ac.uk> This needs to be sorted asap please (see below). Looking at the mailer templates: http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/registration_notification.html.erb http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/reset_password.html.erb ... the host name and port has been hard coded into the templates (!!). How have users been able to register and activate their account so far? One way of solving this problem is to automatically figure out the base_uri and then pass it into the mailer template. In myExperiment we do this by defining a method like this in the application_controller.rb: def base_host request.host_with_port end And then when calling the mailer we pass this into the template like eg: Mailer.deliver_account_confirmation(@user, confirmation_hash(@user.unconfirmed_email), base_host) And the final email template looks like this: http://myexperiment.rubyforge.org/svn/trunk/app/views/mailer/account_confirmation.rhtml Please can we fix this today and also do up the mail templates to look more professional. Thanks, Jits -------- Original Message -------- Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost Date: Wed, 17 Jun 2009 06:48:40 -0400 (EDT) From: To: noreply at rubyforge.org Bugs item #26258, was opened at 2009-06-17 06:48 You can respond by visiting: http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 Category: None Group: None Status: Open Resolution: None Priority: 3 Submitted By: Nobody (None) Assigned to: Nobody (None) Summary: account confirmation email points to localhost Initial Comment: Content of the email I just received: Please, click on the following link to activate your account. http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951 ---------------------------------------------------------------------- You can respond by visiting: http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 _______________________________________________ BioCatalogue-developers mailing list BioCatalogue-developers at rubyforge.org http://rubyforge.org/mailman/listinfo/biocatalogue-developers From tlaurent at ebi.ac.uk Wed Jun 17 09:02:01 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Wed, 17 Jun 2009 14:02:01 +0100 Subject: [BioCatalogue-developers] [Fwd: [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost] In-Reply-To: <4A38D58E.2080007@cs.man.ac.uk> References: <4A38D58E.2080007@cs.man.ac.uk> Message-ID: <4A38E949.4070301@ebi.ac.uk> It worked so far because they were using the right url. But I guess last week when we had the pb with svn, we removed the entire directory and checked it out again. The pb is I didn't want to check EBI specific urls, so what was checked in was the url using localhost. I'll put back the right urls. Jiten Bhagat wrote: > This needs to be sorted asap please (see below). > > Looking at the mailer templates: > > http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/registration_notification.html.erb > > http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/reset_password.html.erb > > > ... the host name and port has been hard coded into the templates (!!). > How have users been able to register and activate their account so far? > > One way of solving this problem is to automatically figure out the > base_uri and then pass it into the mailer template. > > In myExperiment we do this by defining a method like this in the > application_controller.rb: > > def base_host > request.host_with_port > end > > And then when calling the mailer we pass this into the template like eg: > > Mailer.deliver_account_confirmation(@user, > confirmation_hash(@user.unconfirmed_email), base_host) > > And the final email template looks like this: > > http://myexperiment.rubyforge.org/svn/trunk/app/views/mailer/account_confirmation.rhtml > > > Please can we fix this today and also do up the mail templates to look > more professional. > > Thanks, > Jits > > > -------- Original Message -------- > Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] > account confirmation email points to localhost > Date: Wed, 17 Jun 2009 06:48:40 -0400 (EDT) > From: > To: noreply at rubyforge.org > > > > Bugs item #26258, was opened at 2009-06-17 06:48 > You can respond by visiting: > http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 > > > Category: None > Group: None > Status: Open > Resolution: None > Priority: 3 > Submitted By: Nobody (None) > Assigned to: Nobody (None) > Summary: account confirmation email points to localhost > > Initial Comment: > Content of the email I just received: > > Please, click on the following link to activate your account. > http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951 > > > ---------------------------------------------------------------------- > > You can respond by visiting: > http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Wed Jun 17 09:06:50 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 17 Jun 2009 14:06:50 +0100 Subject: [BioCatalogue-developers] [Fwd: [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost] In-Reply-To: <4A38E949.4070301@ebi.ac.uk> References: <4A38D58E.2080007@cs.man.ac.uk> <4A38E949.4070301@ebi.ac.uk> Message-ID: <4A38EA6A.5050103@cs.man.ac.uk> Okay, I figured that would be the case. But the "right" way to do it, and its fairly simple, is what I suggested in my email below. That will ensure it works on any deployment. Locally modifying svn'ed files is a recipe for disaster :-( Jits Thomas Laurent wrote: > It worked so far because they were using the right url. > But I guess last week when we had the pb with svn, we removed the > entire directory and checked it out again. The pb is I didn't want to > check EBI specific urls, so what was checked in was the url using > localhost. > > I'll put back the right urls. > > Jiten Bhagat wrote: >> This needs to be sorted asap please (see below). >> >> Looking at the mailer templates: >> >> http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/registration_notification.html.erb >> >> http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/reset_password.html.erb >> >> >> ... the host name and port has been hard coded into the templates >> (!!). How have users been able to register and activate their account >> so far? >> >> One way of solving this problem is to automatically figure out the >> base_uri and then pass it into the mailer template. >> >> In myExperiment we do this by defining a method like this in the >> application_controller.rb: >> >> def base_host >> request.host_with_port >> end >> >> And then when calling the mailer we pass this into the template like eg: >> >> Mailer.deliver_account_confirmation(@user, >> confirmation_hash(@user.unconfirmed_email), base_host) >> >> And the final email template looks like this: >> >> http://myexperiment.rubyforge.org/svn/trunk/app/views/mailer/account_confirmation.rhtml >> >> >> Please can we fix this today and also do up the mail templates to >> look more professional. >> >> Thanks, >> Jits >> >> >> -------- Original Message -------- >> Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] >> account confirmation email points to localhost >> Date: Wed, 17 Jun 2009 06:48:40 -0400 (EDT) >> From: >> To: noreply at rubyforge.org >> >> >> >> Bugs item #26258, was opened at 2009-06-17 06:48 >> You can respond by visiting: >> http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 >> >> >> Category: None >> Group: None >> Status: Open >> Resolution: None >> Priority: 3 >> Submitted By: Nobody (None) >> Assigned to: Nobody (None) >> Summary: account confirmation email points to localhost >> >> Initial Comment: >> Content of the email I just received: >> >> Please, click on the following link to activate your account. >> http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951 >> >> >> ---------------------------------------------------------------------- >> >> You can respond by visiting: >> http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Wed Jun 17 09:17:25 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 09:17:25 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2438] add opensearch feature Message-ID: <20090617131725.DA20718580F4@rubyforge.org> Task #2438 has been updated. Project: BioCatalogue Subproject: Pilot Summary: add opensearch feature Complete: 55% Status: Open Description: Use pagination for opensearch results and also use solr engine to generate the search results Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 13:17 By: ebontane Comment: BioCatalogue search can now be added to your list of search engines for browsers that support open search. ------------------------------------------------------- Date: 2009-06-16 13:48 By: ebontane Comment: fix the existing opensearch functionality on the beta site or disable opensearch till after the pilot. ------------------------------------------------------- Date: 2008-12-12 09:51 By: ebontane Comment: opensearch can now be used on the beta site from a browser. However programmatic use of opensearch is not available yet ------------------------------------------------------- Date: 2008-11-17 14:41 By: ebontane Comment: using solr search and pagination ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2438&group_id=6901&group_project_id=12540 From tlaurent at ebi.ac.uk Wed Jun 17 09:16:47 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Wed, 17 Jun 2009 14:16:47 +0100 Subject: [BioCatalogue-developers] [Fwd: [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost] In-Reply-To: <4A38EA6A.5050103@cs.man.ac.uk> References: <4A38D58E.2080007@cs.man.ac.uk> <4A38E949.4070301@ebi.ac.uk> <4A38EA6A.5050103@cs.man.ac.uk> Message-ID: <4A38ECBF.8080406@ebi.ac.uk> Jits, I've never said anywhere in my mail (I've re-read it to check) that I was not going to implement it the way you described in your email. The thing is as it's a pretty urgent matter, I prefer putting it back in my hacky "unprofessional" way to have it sorted quickly, and then once people can register again I'm going to implement the base_uri lookup. Thomas Jiten Bhagat wrote: > Okay, I figured that would be the case. > > But the "right" way to do it, and its fairly simple, is what I suggested > in my email below. That will ensure it works on any deployment. > > Locally modifying svn'ed files is a recipe for disaster :-( > > Jits > > > Thomas Laurent wrote: >> It worked so far because they were using the right url. >> But I guess last week when we had the pb with svn, we removed the >> entire directory and checked it out again. The pb is I didn't want to >> check EBI specific urls, so what was checked in was the url using >> localhost. >> >> I'll put back the right urls. >> >> Jiten Bhagat wrote: >>> This needs to be sorted asap please (see below). >>> >>> Looking at the mailer templates: >>> >>> http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/registration_notification.html.erb >>> >>> http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/reset_password.html.erb >>> >>> >>> ... the host name and port has been hard coded into the templates >>> (!!). How have users been able to register and activate their account >>> so far? >>> >>> One way of solving this problem is to automatically figure out the >>> base_uri and then pass it into the mailer template. >>> >>> In myExperiment we do this by defining a method like this in the >>> application_controller.rb: >>> >>> def base_host >>> request.host_with_port >>> end >>> >>> And then when calling the mailer we pass this into the template like eg: >>> >>> Mailer.deliver_account_confirmation(@user, >>> confirmation_hash(@user.unconfirmed_email), base_host) >>> >>> And the final email template looks like this: >>> >>> http://myexperiment.rubyforge.org/svn/trunk/app/views/mailer/account_confirmation.rhtml >>> >>> >>> Please can we fix this today and also do up the mail templates to >>> look more professional. >>> >>> Thanks, >>> Jits >>> >>> >>> -------- Original Message -------- >>> Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] >>> account confirmation email points to localhost >>> Date: Wed, 17 Jun 2009 06:48:40 -0400 (EDT) >>> From: >>> To: noreply at rubyforge.org >>> >>> >>> >>> Bugs item #26258, was opened at 2009-06-17 06:48 >>> You can respond by visiting: >>> http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 >>> >>> >>> Category: None >>> Group: None >>> Status: Open >>> Resolution: None >>> Priority: 3 >>> Submitted By: Nobody (None) >>> Assigned to: Nobody (None) >>> Summary: account confirmation email points to localhost >>> >>> Initial Comment: >>> Content of the email I just received: >>> >>> Please, click on the following link to activate your account. >>> http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951 >>> >>> >>> ---------------------------------------------------------------------- >>> >>> You can respond by visiting: >>> http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Wed Jun 17 09:23:49 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 17 Jun 2009 14:23:49 +0100 Subject: [BioCatalogue-developers] [Fwd: [ biocatalogue-Bugs-26258 ] account confirmation email points to localhost] In-Reply-To: <4A38ECBF.8080406@ebi.ac.uk> References: <4A38D58E.2080007@cs.man.ac.uk> <4A38E949.4070301@ebi.ac.uk> <4A38EA6A.5050103@cs.man.ac.uk> <4A38ECBF.8080406@ebi.ac.uk> Message-ID: <4A38EE65.40008@cs.man.ac.uk> Thomas Laurent wrote: > Jits, I've never said anywhere in my mail (I've re-read it to check) > that I was not going to implement it the way you described in your email. Yeap, you definitely didn't say that, and I wasn't assuming that (sorry it sounded that way). I was just reiterating my point so that this doesn't get lost in all the other tasks we have to do. As it's pretty crucial (as you are well aware). > The thing is as it's a pretty urgent matter, I prefer putting it back > in my hacky "unprofessional" way to have it sorted quickly, and then > once people can register again I'm going to implement the base_uri > lookup. That's absolutely the right thing to do, to solve the immediate problem :-) You also probably know this already but I'd rather state it explicitly - when you do make the changes and then update the server, be on the look out for svn conflicts on the mailer template(s). Cheers, Jits > > Thomas > > Jiten Bhagat wrote: >> Okay, I figured that would be the case. >> >> But the "right" way to do it, and its fairly simple, is what I >> suggested in my email below. That will ensure it works on any >> deployment. >> >> Locally modifying svn'ed files is a recipe for disaster :-( >> >> Jits >> >> >> Thomas Laurent wrote: >>> It worked so far because they were using the right url. >>> But I guess last week when we had the pb with svn, we removed the >>> entire directory and checked it out again. The pb is I didn't want >>> to check EBI specific urls, so what was checked in was the url using >>> localhost. >>> >>> I'll put back the right urls. >>> >>> Jiten Bhagat wrote: >>>> This needs to be sorted asap please (see below). >>>> >>>> Looking at the mailer templates: >>>> >>>> http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/registration_notification.html.erb >>>> >>>> http://biocatalogue.rubyforge.org/svn/trunk/app/views/user_mailer/reset_password.html.erb >>>> >>>> >>>> ... the host name and port has been hard coded into the templates >>>> (!!). How have users been able to register and activate their >>>> account so far? >>>> >>>> One way of solving this problem is to automatically figure out the >>>> base_uri and then pass it into the mailer template. >>>> >>>> In myExperiment we do this by defining a method like this in the >>>> application_controller.rb: >>>> >>>> def base_host >>>> request.host_with_port >>>> end >>>> >>>> And then when calling the mailer we pass this into the template >>>> like eg: >>>> >>>> Mailer.deliver_account_confirmation(@user, >>>> confirmation_hash(@user.unconfirmed_email), base_host) >>>> >>>> And the final email template looks like this: >>>> >>>> http://myexperiment.rubyforge.org/svn/trunk/app/views/mailer/account_confirmation.rhtml >>>> >>>> >>>> Please can we fix this today and also do up the mail templates to >>>> look more professional. >>>> >>>> Thanks, >>>> Jits >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: [BioCatalogue-developers] [ biocatalogue-Bugs-26258 ] >>>> account confirmation email points to localhost >>>> Date: Wed, 17 Jun 2009 06:48:40 -0400 (EDT) >>>> From: >>>> To: noreply at rubyforge.org >>>> >>>> >>>> >>>> Bugs item #26258, was opened at 2009-06-17 06:48 >>>> You can respond by visiting: >>>> http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 >>>> >>>> >>>> Category: None >>>> Group: None >>>> Status: Open >>>> Resolution: None >>>> Priority: 3 >>>> Submitted By: Nobody (None) >>>> Assigned to: Nobody (None) >>>> Summary: account confirmation email points to localhost >>>> >>>> Initial Comment: >>>> Content of the email I just received: >>>> >>>> Please, click on the following link to activate your account. >>>> http://localhost:3005/activate_account/ff874b7dfa115620b077d24cf7f1553640294951 >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> You can respond by visiting: >>>> http://rubyforge.org/tracker/?func=detail&atid=26756&aid=26258&group_id=6901 >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Wed Jun 17 13:50:34 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 13:50:34 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2690] Search indexing for annotations Message-ID: <20090617175034.BCF5418581E7@rubyforge.org> Task #2690 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Search indexing for annotations Complete: 50% Status: Open Description: 2 things here: 1. Make sure that when you do the categories work, that the ID (which is what is stored as the value) is not what gets indexed, rather, the actual category label itself! 2. Maybe certain types of annotations, like name aliases, should have a boost, when indexed. Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 17:50 By: jits Comment: 1. is done. Need to look into boosting. This is dependant on task 2689. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2690&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 13:51:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 13:51:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2691] Implement service categorisation Message-ID: <20090617175114.F093218581E7@rubyforge.org> Task #2691 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement service categorisation Complete: 50% Status: Open Description: Based on Francks service categories hierarchy. Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 17:51 By: jits Comment: Initial implementation done. Working on filtering now. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2691&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 13:52:34 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 13:52:34 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2465] Implement custom 404 etc pages Message-ID: <20090617175234.3FA5A18581E7@rubyforge.org> Task #2465 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement custom 404 etc pages Complete: 75% Status: Open Description: Instead of using the default 404 page, implement a better, more dynamic 404 page that will guide users in a better way. Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 17:52 By: jits Comment: Done, using the exception_notified plugin. For the future: have more useful error pages with links/suggestions/etc ------------------------------------------------------- Date: 2009-06-16 10:37 By: jits Comment: Use the rescue_exception method in the application_controller to catch any exception and then redirect to an error page (or something else user friendly). ------------------------------------------------------- Date: 2008-12-12 10:05 By: jits Comment: > should these 404s be logged in the DB? I don't think so, as they will be the file logs anyways. ------------------------------------------------------- Date: 2008-12-12 09:45 By: ebontane Comment: should these 404s be logged in the DB? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2465&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 13:54:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 13:54:24 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2683] Update filtering help text and write How To page Message-ID: <20090617175424.CDCF21858104@rubyforge.org> Task #2683 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update filtering help text and write How To page Complete: 70% Status: Open Description: Update the help text that explains what exactly the filtering does. Also possibly write a How To page on the public wiki for this. Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 17:54 By: jits Comment: 1st part done. Need to write a How To page ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2683&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 18:21:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 18:21:31 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2711] Ability to make announcements on services Message-ID: <20090617222131.6710E3C802E@rubyforge.org> Task #2711 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Ability to make announcements on services Complete: 0% Status: Open Description: Potentially using the annotations plugin, implement a way for users to make announcements on services, in order to inform people about things. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2711&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 19:13:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 19:13:58 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2712] Implement "Include tag filters" Message-ID: <20090617231358.88D711858117@rubyforge.org> Task #2712 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement "Include tag filters" Complete: 0% Status: Open Description: In order to improve performance, by default don't show the tag filtering options. Provide the option to do so if users want. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2712&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 20:09:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 20:09:45 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2712] Implement "Include tag filters" Message-ID: <20090618000945.DF90A185811F@rubyforge.org> Task #2712 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement "Include tag filters" Complete: 100% Status: Closed Description: In order to improve performance, by default don't show the tag filtering options. Provide the option to do so if users want. Follow-Ups: ------------------------------------------------------- Date: 2009-06-18 00:09 By: jits Comment: Done. Revision 836. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2712&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 20:11:25 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 20:11:25 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2691] Implement service categorisation Message-ID: <20090618001125.BD0463C8040@rubyforge.org> Task #2691 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement service categorisation Complete: 100% Status: Closed Description: Based on Francks service categories hierarchy. Follow-Ups: ------------------------------------------------------- Date: 2009-06-18 00:11 By: jits Comment: Filtering done. ------------------------------------------------------- Date: 2009-06-17 17:51 By: jits Comment: Initial implementation done. Working on filtering now. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2691&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 17 20:12:06 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Jun 2009 20:12:06 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2713] Possibly implement show category page Message-ID: <20090618001206.689073C8032@rubyforge.org> Task #2713 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Possibly implement show category page Complete: 0% Status: Open Description: This page can allow users to easily traverse the category tree and get the results. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2713&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 18 09:30:21 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Jun 2009 09:30:21 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2697] Wrap the wsdl parsing in a timeout Message-ID: <20090618133021.6673A1D787E6@rubyforge.org> Task #2697 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Wrap the wsdl parsing in a timeout Complete: 0% Status: Open Description: Use SystemTimer instead of the built in Ruby timer. Look in /lib/bio_catalogue/util.rb for examples. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2697&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 06:41:00 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 06:41:00 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2714] Update auto_tagger script to do tags -> categories Message-ID: <20090619104100.E015E18581E3@rubyforge.org> Task #2714 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update auto_tagger script to do tags -> categories Complete: 0% Status: Open Description: For categories with unambiguous labels, we can find tags with those labels and add categories automatically. (As suggested by Katy) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2714&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 06:52:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 06:52:38 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2670] Perf: optimise filtering sidebar Message-ID: <20090619105239.0336F18581DE@rubyforge.org> Task #2670 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Perf: optimise filtering sidebar Complete: 50% Status: Open Description: The filtering sidebar takes a fair bit of time to render. Look into possibly optimising this. Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 10:52 By: jits Comment: 1st step - disabled the tag filters by default. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2670&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 06:53:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 06:53:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2662] Show source of tags, categories and name aliases Message-ID: <20090619105314.DCE3118581E3@rubyforge.org> Task #2662 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show source of tags, categories and name aliases Complete: 0% Status: Open Description: When you hover over tags and name aliases, show who submitted that... Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 10:53 By: jits Comment: Also, categories... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2662&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 09:43:57 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 09:43:57 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2715] Implement feedback form Message-ID: <20090619134358.1E0D2185811D@rubyforge.org> Task #2715 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement feedback form Complete: 0% Status: Open Description: Like in myexperiment ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2715&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 12:20:53 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 12:20:53 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2716] Further consolidate controller search logic Message-ID: <20090619162053.D701218581E0@rubyforge.org> Task #2716 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Further consolidate controller search logic Complete: 0% Status: Open Description: Right now, some search logic is still repeated between the search controller and services controller. Instead, have the type specific searches still happen within the search controller and not as a separate search action. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2716&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 12:38:21 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 12:38:21 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2717] Fragment cache service listings Message-ID: <20090619163822.20B7D185811A@rubyforge.org> Task #2717 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fragment cache service listings Complete: 0% Status: Open Description: Fragment cache each listing item (with appropriate cache invalidation) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2717&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 12:40:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 12:40:29 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2441] Better error handling when search server is down or errors Message-ID: <20090619164029.611B0185811A@rubyforge.org> Task #2441 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error handling when search server is down or errors Complete: 100% Status: Open Description: We need to catch any exceptions when searched are carried out and display appropriate messages to the end user. Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 16:40 By: jits Comment: Done ------------------------------------------------------- Date: 2009-06-16 10:35 By: jits Comment: Catch the following errors individually and display different and appropriate messages: - When the search server is down. - When a user enters an invalid search term that causes solr to spit and shout. Excerpt from email thread: Jiten Bhagat wrote: > Could do... haven't looked in the exact errors being returned, just catching the base Exception at the moment and displaying that message. > > Jits > > > Thomas Laurent wrote: >> If a bad syntax is used doesn't SOLR throw an exception like "bad syntax" that we could trap to display a "bad syntax error" ? >> >> >> Jiten Bhagat wrote: >>> But like I said, the error could also be caused by someone typing in something like "service:blast:output", ie: bad syntax in the search. We probably shouldn't say that the search engine isnt available in that case! >>> >>> Jits >>> >>> >>> Thomas Laurent wrote: >>>> A more correct message would be "Search engine unreachable/unavailable, please try again or contact administrator" maybe ? >>>> >>>> >>>> Jiten Bhagat wrote: >>>>> Good point, that's exactly it. That message also shows when you've typed in a bad search query. Hence I tried to use an error message like that. >>>>> >>>>> But I also see Franck's point, it's a tad bit scary for the end user. Not sure what the best error message is in that case... >>>>> >>>>> Jits >>>>> >>>>> >>>>> Thomas Laurent wrote: >>>>>> I think there's a difference between the 2: when you get the "Search failed" it's in fact the search engine at the back throwing an exception (we have issues with it at the moment). I'm working on solving that pb at the moment. >>>>>> >>>>>> When the search doesn't match any docs you have the "Google style" : >>>>>> " Search query: "xcvzxvxcv~" returned 0 items " >>>>>> " No search results." >>>>>> >>>>>> Thomas ------------------------------------------------------- Date: 2009-06-12 16:52 By: jits Comment: Currently if access to the search server fails then an exception is raised by results.total (since results is nil). Display a message to the user like: "Search is not available at this time. Please try again later." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2441&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 12:40:46 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 12:40:46 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2441] Better error handling when search server is down or errors Message-ID: <20090619164046.351E218581E4@rubyforge.org> Task #2441 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error handling when search server is down or errors Complete: 100% Status: Closed Description: We need to catch any exceptions when searched are carried out and display appropriate messages to the end user. Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 16:40 By: jits Comment: Done ------------------------------------------------------- Date: 2009-06-16 10:35 By: jits Comment: Catch the following errors individually and display different and appropriate messages: - When the search server is down. - When a user enters an invalid search term that causes solr to spit and shout. Excerpt from email thread: Jiten Bhagat wrote: > Could do... haven't looked in the exact errors being returned, just catching the base Exception at the moment and displaying that message. > > Jits > > > Thomas Laurent wrote: >> If a bad syntax is used doesn't SOLR throw an exception like "bad syntax" that we could trap to display a "bad syntax error" ? >> >> >> Jiten Bhagat wrote: >>> But like I said, the error could also be caused by someone typing in something like "service:blast:output", ie: bad syntax in the search. We probably shouldn't say that the search engine isnt available in that case! >>> >>> Jits >>> >>> >>> Thomas Laurent wrote: >>>> A more correct message would be "Search engine unreachable/unavailable, please try again or contact administrator" maybe ? >>>> >>>> >>>> Jiten Bhagat wrote: >>>>> Good point, that's exactly it. That message also shows when you've typed in a bad search query. Hence I tried to use an error message like that. >>>>> >>>>> But I also see Franck's point, it's a tad bit scary for the end user. Not sure what the best error message is in that case... >>>>> >>>>> Jits >>>>> >>>>> >>>>> Thomas Laurent wrote: >>>>>> I think there's a difference between the 2: when you get the "Search failed" it's in fact the search engine at the back throwing an exception (we have issues with it at the moment). I'm working on solving that pb at the moment. >>>>>> >>>>>> When the search doesn't match any docs you have the "Google style" : >>>>>> " Search query: "xcvzxvxcv~" returned 0 items " >>>>>> " No search results." >>>>>> >>>>>> Thomas ------------------------------------------------------- Date: 2009-06-12 16:52 By: jits Comment: Currently if access to the search server fails then an exception is raised by results.total (since results is nil). Display a message to the user like: "Search is not available at this time. Please try again later." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2441&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 12:41:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 12:41:38 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2456] Use rescue_exception in app controller Message-ID: <20090619164138.A3EBD18581E4@rubyforge.org> Task #2456 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Use rescue_exception in app controller Complete: 0% Status: Closed Description: Use the rescue_exception method in the application_controller to catch any exception and then redirect to an error page (or something else user friendly). Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 16:41 By: jits Comment: Done, using the exception notification plugin. ------------------------------------------------------- Date: 2008-11-23 14:09 By: jits Comment: This should also log the error so it can be checked later by an admin. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2456&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 12:42:46 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 12:42:46 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2412] Catch mail send exception Message-ID: <20090619164246.52D2B185811A@rubyforge.org> Task #2412 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Catch mail send exception Complete: 0% Status: Open Description: When sending the account activation email, if the mail sending fails then an exception is thrown and the user will get a generic error. We need to catch this exception and take appropriate action (such as logging the error so that the mail can be sent manually later). The user shouldn't need to know that the exception was ever raised. Follow-Ups: ------------------------------------------------------- Date: 2009-03-05 15:26 By: ebontane Comment: Thomas, I think this is done? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2412&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 13:00:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 13:00:31 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2446] Better error message on fail of load_wsdl action Message-ID: <20090619170031.B7BA5185811F@rubyforge.org> Task #2446 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Better error message on fail of load_wsdl action Complete: 100% Status: Closed Description: When the AJAX interaction returns back an error then an appropriate error message should be displayed in the UI (not the debug error page as now) and the error should be logged. Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 17:00 By: jits Comment: Done ------------------------------------------------------- Date: 2009-06-16 10:22 By: jits Comment: Currently will display something like "WDL failed to load". But should have a more informative message with hints on what the user can do to solve the problem and maybe report it. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2446&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 14:56:53 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 14:56:53 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2504] Categorisation/classification/type of services Message-ID: <20090619185653.982A41858125@rubyforge.org> Task #2504 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Categorisation/classification/type of services Complete: 100% Status: Closed Description: Need to adapt annotations plugin to have constrained and use the choice based annotations (ie: seeds) Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 18:56 By: jits Comment: Initial implementation of filtering and click through done. ------------------------------------------------------- Date: 2009-06-16 10:39 By: jits Comment: Filtering and click through work remaining. ------------------------------------------------------- Date: 2009-06-16 10:38 By: jits Comment: Implemented constraints. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2504&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 19 15:41:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Jun 2009 15:41:39 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2560] Dealing with user's registered email address Message-ID: <20090619194139.DAFFE18581E4@rubyforge.org> Task #2560 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Dealing with user's registered email address Complete: 100% Status: Closed Description: ... like in the welcome messages. Follow-Ups: ------------------------------------------------------- Date: 2009-06-19 19:41 By: jits Comment: Done ------------------------------------------------------- Date: 2009-06-16 10:55 By: jits Comment: when showing user profiles, if you're viewing your own, you see your email... but its not obious that this will be hidden from others... so need to make it obvious that only you can see it ------------------------------------------------------- Date: 2009-06-16 10:50 By: jits Comment: Emails are private data that should NEVER be divulged. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2560&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Fri Jun 19 17:12:27 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 19 Jun 2009 22:12:27 +0100 Subject: [BioCatalogue-developers] Tool for look into memcache servers Message-ID: <4A3BFF3B.10201@cs.man.ac.uk> Hi guys, If you need a way to look into memcache servers, I've come across this tool: http://github.com/rama/statsproxy/tree/master I haven't installed it yet but it sounds very very useful! If you don't want to install something additional, you can also use something like: memcached-tool 127.0.0.1:11211 dump > ~/memcache_dump.txt Cheers, Jits From jits at cs.man.ac.uk Sat Jun 20 18:10:26 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sat, 20 Jun 2009 23:10:26 +0100 Subject: [BioCatalogue-developers] [871] trunk: Initial work on the integration of the cache-money plugin, which takes care of caching AR models in memory, across requests (Rails' query cache only stores per request). In-Reply-To: <20090620220307.3FE51159802D@rubyforge.org> References: <20090620220307.3FE51159802D@rubyforge.org> Message-ID: <4A3D5E52.8030209@cs.man.ac.uk> Hi guys, Note that this change, when it goes live, will need updates to both the memcache.yml and the biocat_local.rb files (see their respective .pre files). Cheers, Jits noreply at rubyforge.org wrote: > > Revision > 871 > Author > jits > Date > 2009-06-20 18:03:06 -0400 (Sat, 20 Jun 2009) > > > Log Message > > Initial work on the integration of the cache-money plugin, which takes care of caching AR models in memory, across requests (Rails' query cache only stores per request). > > NOTE: we are using Onyx's version of cache-money, not the original one by nkallen. > > Please the biocat_local.rb.pre config file for a new setting. > > > Modified Paths > > * trunk/app/models/agent.rb <#trunkappmodelsagentrb> > * trunk/app/models/annotation.rb <#trunkappmodelsannotationrb> > * trunk/app/models/category.rb <#trunkappmodelscategoryrb> > * trunk/app/models/favourite.rb <#trunkappmodelsfavouriterb> > * trunk/app/models/registry.rb <#trunkappmodelsregistryrb> > * trunk/app/models/relationship.rb <#trunkappmodelsrelationshiprb> > * trunk/app/models/rest_method.rb <#trunkappmodelsrest_methodrb> > * trunk/app/models/rest_method_parameter.rb > <#trunkappmodelsrest_method_parameterrb> > * trunk/app/models/rest_method_representation.rb > <#trunkappmodelsrest_method_representationrb> > * trunk/app/models/rest_parameter.rb <#trunkappmodelsrest_parameterrb> > * trunk/app/models/rest_representation.rb > <#trunkappmodelsrest_representationrb> > * trunk/app/models/rest_resource.rb <#trunkappmodelsrest_resourcerb> > * trunk/app/models/rest_service.rb <#trunkappmodelsrest_servicerb> > * trunk/app/models/service.rb <#trunkappmodelsservicerb> > * trunk/app/models/service_deployment.rb > <#trunkappmodelsservice_deploymentrb> > * trunk/app/models/service_provider.rb > <#trunkappmodelsservice_providerrb> > * trunk/app/models/service_version.rb > <#trunkappmodelsservice_versionrb> > * trunk/app/models/soap_input.rb <#trunkappmodelssoap_inputrb> > * trunk/app/models/soap_operation.rb <#trunkappmodelssoap_operationrb> > * trunk/app/models/soap_output.rb <#trunkappmodelssoap_outputrb> > * trunk/app/models/soap_service.rb <#trunkappmodelssoap_servicerb> > * trunk/app/models/soaplab_server.rb <#trunkappmodelssoaplab_serverrb> > * trunk/app/models/test_result.rb <#trunkappmodelstest_resultrb> > * trunk/app/models/url_monitor.rb <#trunkappmodelsurl_monitorrb> > * trunk/app/models/user.rb <#trunkappmodelsuserrb> > * trunk/config/environment.rb <#trunkconfigenvironmentrb> > * trunk/config/initializers/biocat_local.rb.pre > <#trunkconfiginitializersbiocat_localrbpre> > * trunk/config/memcache.yml.pre <#trunkconfigmemcacheymlpre> > * trunk/lib/bio_catalogue/cache_helper.rb > <#trunklibbio_cataloguecache_helperrb> > * trunk/vendor/gems/disqus-1.0.1/.specification > <#trunkvendorgemsdisqus101specification> > * trunk/vendor/gems/geokit-1.3.2/.specification > <#trunkvendorgemsgeokit132specification> > * trunk/vendor/gems/mperham-memcache-client-1.7.4/.specification > <#trunkvendorgemsmperhammemcacheclient174specification> > > > Added Paths > > * trunk/app/models/annotation_attribute.rb > <#trunkappmodelsannotation_attributerb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/.specification > <#trunkvendorgemsonyxcachemoney0261specification> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/README > <#trunkvendorgemsonyxcachemoney0261README> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/TODO > <#trunkvendorgemsonyxcachemoney0261TODO> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/UNSUPPORTED_FEATURES > <#trunkvendorgemsonyxcachemoney0261UNSUPPORTED_FEATURES> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/config/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/config/environment.rb > <#trunkvendorgemsonyxcachemoney0261configenvironmentrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/config/memcache.yml > <#trunkvendorgemsonyxcachemoney0261configmemcacheyml> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/db/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/db/schema.rb > <#trunkvendorgemsonyxcachemoney0261dbschemarb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cache_money.rb > <#trunkvendorgemsonyxcachemoney0261libcache_moneyrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/accessor.rb > <#trunkvendorgemsonyxcachemoney0261libcashaccessorrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/buffered.rb > <#trunkvendorgemsonyxcachemoney0261libcashbufferedrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/config.rb > <#trunkvendorgemsonyxcachemoney0261libcashconfigrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/finders.rb > <#trunkvendorgemsonyxcachemoney0261libcashfindersrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/index.rb > <#trunkvendorgemsonyxcachemoney0261libcashindexrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/local.rb > <#trunkvendorgemsonyxcachemoney0261libcashlocalrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/lock.rb > <#trunkvendorgemsonyxcachemoney0261libcashlockrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/mock.rb > <#trunkvendorgemsonyxcachemoney0261libcashmockrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/query/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/query/abstract.rb > <#trunkvendorgemsonyxcachemoney0261libcashqueryabstractrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/query/calculation.rb > <#trunkvendorgemsonyxcachemoney0261libcashquerycalculationrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/query/primary_key.rb > <#trunkvendorgemsonyxcachemoney0261libcashqueryprimary_keyrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/query/select.rb > <#trunkvendorgemsonyxcachemoney0261libcashqueryselectrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/request.rb > <#trunkvendorgemsonyxcachemoney0261libcashrequestrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/transactional.rb > <#trunkvendorgemsonyxcachemoney0261libcashtransactionalrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/util/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/util/array.rb > <#trunkvendorgemsonyxcachemoney0261libcashutilarrayrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/util/marshal.rb > <#trunkvendorgemsonyxcachemoney0261libcashutilmarshalrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/lib/cash/write_through.rb > <#trunkvendorgemsonyxcachemoney0261libcashwrite_throughrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/ > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/accessor_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashaccessor_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/active_record_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashactive_record_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/calculations_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashcalculations_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/config_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashconfig_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/finders_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashfinders_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/lock_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashlock_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/marshal_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashmarshal_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/order_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashorder_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/transactional_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashtransactional_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/window_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashwindow_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/cash/write_through_spec.rb > <#trunkvendorgemsonyxcachemoney0261speccashwrite_through_specrb> > * trunk/vendor/gems/onyx-cache-money-0.2.6.1/spec/spec_helper.rb > <#trunkvendorgemsonyxcachemoney0261specspec_helperrb> > > > Diff > > > Modified: trunk/app/models/agent.rb (870 => 871) > > > --- trunk/app/models/agent.rb 2009-06-20 18:06:43 UTC (rev 870) > +++ trunk/app/models/agent.rb 2009-06-20 22:03:06 UTC (rev 871) > @@ -5,6 +5,11 @@ > # See license.txt for details > > class Agent < ActiveRecord::Base > + if ENABLE_CACHE_MONEY > + is_cached :repository => $cache > + index :name > + end > + > acts_as_trashable > > acts_as_annotation_source > > > Modified: trunk/app/models/annotation.rb (870 => 871) > > > --- trunk/app/models/annotation.rb 2009-06-20 18:06:43 UTC (rev 870) > +++ trunk/app/models/annotation.rb 2009-06-20 22:03:06 UTC (rev 871) > @@ -11,6 +11,13 @@ > require_dependency RAILS_ROOT + '/vendor/plugins/annotations/lib/app/models/annotation' > > class Annotation < ActiveRecord::Base > +# if ENABLE_CACHE_MONEY > +# is_cached :repository => $cache > +# [snipped] From noreply at rubyforge.org Sat Jun 20 20:38:27 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sat, 20 Jun 2009 20:38:27 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2582] Store extra log info during searches Message-ID: <20090621003827.BD6611598030@rubyforge.org> Task #2582 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Store extra log info during searches Complete: 0% Status: Open Description: Add search results count and any other info to ActivityLog after search... ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2582&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 09:31:00 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 09:31:00 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2689] Improve search results ordering Message-ID: <20090621133100.3D26A185810C@rubyforge.org> Task #2689 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Improve search results ordering Complete: 0% Status: Open Description: Right now the ordering of search results isn't great. Maybe use boosting to ensure that services that contain the word(s) in their names get higher up. Also MUST look to using the scores directly from SOLR when doing the reordering of results. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2689&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 09:31:22 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 09:31:22 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2690] Search indexing for annotations Message-ID: <20090621133122.3BD94185810C@rubyforge.org> Task #2690 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Search indexing for annotations Complete: 50% Status: Open Description: 2 things here: 1. Make sure that when you do the categories work, that the ID (which is what is stored as the value) is not what gets indexed, rather, the actual category label itself! 2. Maybe certain types of annotations, like name aliases, should have a boost, when indexed. Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 17:50 By: jits Comment: 1. is done. Need to look into boosting. This is dependant on task 2689. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2690&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 09:33:18 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 09:33:18 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2690] Search indexing for annotations Message-ID: <20090621133318.59FED1858111@rubyforge.org> Task #2690 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Search indexing for annotations Complete: 50% Status: Open Description: 2 things here: 1. Make sure that when you do the categories work, that the ID (which is what is stored as the value) is not what gets indexed, rather, the actual category label itself! 2. Maybe certain types of annotations, like name aliases, should have a boost, when indexed. Follow-Ups: ------------------------------------------------------- Date: 2009-06-17 17:50 By: jits Comment: 1. is done. Need to look into boosting. This is dependant on task 2689. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2690&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 09:33:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 09:33:40 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2689] Improve search results ordering Message-ID: <20090621133340.72D8A1858117@rubyforge.org> Task #2689 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Improve search results ordering Complete: 0% Status: Open Description: Right now the ordering of search results isn't great. Maybe use boosting to ensure that services that contain the word(s) in their names get higher up. Also MUST look to using the scores directly from SOLR when doing the reordering of results. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2689&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 10:51:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 10:51:11 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2685] Show viewed stats for services Message-ID: <20090621145111.81CBF1858117@rubyforge.org> Task #2685 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Show viewed stats for services Complete: 100% Status: Closed Description: This should be shown on the index, show and any other pages deemed necessary. Follow-Ups: ------------------------------------------------------- Date: 2009-06-21 14:51 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2685&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Sun Jun 21 10:56:12 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 21 Jun 2009 15:56:12 +0100 Subject: [BioCatalogue-developers] contact@biocatalogue.org Message-ID: <4A3E4A0C.1020101@cs.man.ac.uk> Can we get contact at biocatalogue.org to forward to biocatalogue-developers at rubyforge.org for now please? Cheers, Jits From noreply at rubyforge.org Sun Jun 21 12:42:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 12:42:11 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2715] Implement feedback form Message-ID: <20090621164211.E76D41858112@rubyforge.org> Task #2715 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement feedback form Complete: 100% Status: Closed Description: Like in myexperiment Follow-Ups: ------------------------------------------------------- Date: 2009-06-21 16:42 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2715&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Sun Jun 21 14:17:41 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 21 Jun 2009 19:17:41 +0100 Subject: [BioCatalogue-developers] New caching work + decision required In-Reply-To: <4A3E1A2F.2030505@cs.man.ac.uk> References: <4A3E1A2F.2030505@cs.man.ac.uk> Message-ID: <4A3E7945.8030500@cs.man.ac.uk> I spoke too soon :-( I did some more testing today and it turns out that cache-money is affecting a number of things (like service submission and loading up categories at startup). So, very important: set ENABLE_CACHE_MONEY to false for now. I will try and resolve this by ISMB (it's possible that another fork of cache-money won't be as buggy). Jits Jiten Bhagat wrote: > [cc'ing to e-lab hackers list as an FYI] > > Hi guys, > > I've been working on some caching this weekend and I've implemented a > number of things. The main thing I wanted to bring up is the > integration of the cache-money plugin [1] and my findings on this, so > that we can make a decision on whether to enable it or disable on the > beta site. (I've integrated it in such a way that it can easily be > switched on or off). > > Cache-money was originally developed at Twitter [2]. What it does is > cache whole ActiveRecord model object collections in memcache [2] in > an indexed fashion (like DB indexes), across requests, so as to save > the trips to the database. It automatically updates the cache whenever > creates/updates/deletes are made to models. > > This was the thing I mentioned in the meetings that is likely to allow > us to scale, IF the DB is the main bottleneck. > > Attached is a report on the before and after performance benchmarks I > carried out (specific to the BioCatalogue codebase). Summary is... > > With cache-money enabled: > - SIGNIFICANTLY less time is spent accessing the DB. > - More time is spent in the views processing (probably due to > generating cache keys, checking cache etc). > - Only in some cases is the overall performance actually faster. > > BUT please note: > - The server I was running this on is a Virtual Private Server that > shares CPU, memory, etc with other VPSes, so the actual CPU > performance is likely to be very low in comparison to dedicated > servers and likely to have fluctuated, and hence could be the cause of > the slowish view processing in general. > - CPU and memory resource is much more scalable than DB and file > resources (in most cases). So even though individual requests might be > slower (we're talking less than a second slower), at least we could > potentially scale up to many more requests at the same time, without > the potential DB bottleneck. > > My thinking is this: > - IF the DB is a potential bottleneck (i.e.: if we cannot scale to x > requests per second because the DB is causing the slowdown [due to > saturated resources]), AND > - IF we're confident that there is still room for CPU, memory etc to > scale (i.e.: it's an underused resource at the moment), > > ... then we should definitely have cache-money enabled. It's better to > have slightly slower single requests if it means we can scale to many > concurrent requests, rather then fast single requests but the > inability to scale. > > Note that this is also highly dependent on the exact deployment > infrastructure and setup, such as latency times to the memcache > server(s), latency times to the DB, machine resources the DB has, and > so on. So the ultimate decision is up to you guys :-) > > Of course, the load testing will give us the real results here. > > If we do enable cache-money, when it comes to the API, which will have > very little view processing, this beast is really going to fly :-) > > Cheers, > Jits > > [1] I'm using this specific fork: > http://github.com/onyx/cache-money/tree/master > [2] > http://magicscalingsprinkles.wordpress.com/2008/12/11/introducing-cache-money/ > > [3] Note that we don't enable cache-money for all models in the > BioCatalogue codebase. Currently the Annotation and > AnnotationAttribute models aren't cached using cache-money as I was > getting "stack too deep" errors. If I could get it working for > annotations then this would further reduce load on the DB and greatly > improve scalability. But this can be a task for after ISMB. From noreply at rubyforge.org Sun Jun 21 15:37:49 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 15:37:49 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2681] Add suggestions auto complete for search Message-ID: <20090621193749.457811858111@rubyforge.org> Task #2681 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add suggestions auto complete for search Complete: 100% Status: Closed Description: ... like we have for tags. Follow-Ups: ------------------------------------------------------- Date: 2009-06-21 19:37 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2681&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 15:38:19 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 15:38:19 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2676] Searches beginning with * fail Message-ID: <20090621193819.D677E1858117@rubyforge.org> Task #2676 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Searches beginning with * fail Complete: 0% Status: Open Description: Catch this and show an error message gracefully ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2676&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 15:50:44 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 15:50:44 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2676] Searches beginning with * fail Message-ID: <20090621195044.543B01598030@rubyforge.org> Task #2676 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Searches beginning with * fail Complete: 100% Status: Closed Description: Catch this and show an error message gracefully Follow-Ups: ------------------------------------------------------- Date: 2009-06-21 19:50 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2676&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 17:42:26 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 17:42:26 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2716] Further consolidate controller search logic Message-ID: <20090621214226.A5A471858112@rubyforge.org> Task #2716 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Further consolidate controller search logic Complete: 100% Status: Closed Description: Right now, some search logic is still repeated between the search controller and services controller. Instead, have the type specific searches still happen within the search controller and not as a separate search action. Follow-Ups: ------------------------------------------------------- Date: 2009-06-21 21:42 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2716&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Jun 21 18:08:49 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 18:08:49 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2701] Hitting enter on service submission dropdown should not submit Message-ID: <20090621220849.58E1E1858111@rubyforge.org> Task #2701 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Hitting enter on service submission dropdown should not submit Complete: 100% Status: Closed Description: ... should add to list. Follow-Ups: ------------------------------------------------------- Date: 2009-06-21 22:08 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2701&group_id=6901&group_project_id=12540 From twitter-welcome-biocatalogue-developers=rubyforge.org at postmaster.twitter.com Sun Jun 21 18:21:46 2009 From: twitter-welcome-biocatalogue-developers=rubyforge.org at postmaster.twitter.com (Twitter) Date: Sun, 21 Jun 2009 22:21:46 +0000 Subject: [BioCatalogue-developers] Welcome to Twitter! Message-ID: <4a3eb27a9ab81_281315a4bb4987f0230311f@mx006.twitter.com.tmail> Hello, new Twitter-er! Using Twitter is going to change the way you think about staying in touch with friends and family. Did you know you can send and receive Twitter updates via mobile texting or the web? To do that, you'll want to visit your settings page (and you'll want to invite some friends). Activate Phone: http://twitter.com/devices Invite Your Friends: http://twitter.com/invite The New York Times calls Twitter "one of the fastest-growing phenomena on the Internet." TIME Magazine says, "Twitter is on its way to becoming the next killer app," and Newsweek noted that "Suddenly, it seems as though all the world's a-twitter." What will you think? http://twitter.com Thanks again for signing up! - Biz Stone and The Twitter Team http://twitter.com/biz -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Jun 21 20:46:48 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 21 Jun 2009 20:46:48 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2718] Move tweets to a delayed job Message-ID: <20090622004648.815BF1858111@rubyforge.org> Task #2718 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Move tweets to a delayed job Complete: 0% Status: Open Description: (as per title) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2718&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Mon Jun 22 05:46:07 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 22 Jun 2009 10:46:07 +0100 Subject: [BioCatalogue-developers] Server updates + background processing Message-ID: <4A3F52DF.2030604@cs.man.ac.uk> Hi guys, I don't think I've explicitly mentioned this... Every time you do an update to the servers (or locally), you need to restart the worker script: ruby script/worker stop ... then: ruby script/worker start As that way the worker will run on the latest codebase (incl picking up the latest Jobs). Also, if things don't seem right with the background processing, check the delayed_jobs table. Failed jobs stay in there and are logged. If too many jobs are piling up in this table then they should be cleared: rake jobs:clear Otherwise all of them will be carried out! Cheers, Jits From noreply at rubyforge.org Mon Jun 22 08:43:22 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 08:43:22 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2668] Change metadata counts calcuation to a background task Message-ID: <20090622124322.E51771598075@rubyforge.org> Task #2668 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Change metadata counts calcuation to a background task Complete: 0% Status: Open Description: Currently, metadata counts are calculated and cached for 60 mins. Change this to have a table to store metadata counts, that get refreshed "offline" via a background task, so as not to affect user requests. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2668&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 08:46:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 08:46:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2570] Add the addthis.com bookmarking widget Message-ID: <20090622124607.C6F44159807B@rubyforge.org> Task #2570 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add the addthis.com bookmarking widget Complete: 100% Status: Closed Description: Like on myexperiment Follow-Ups: ------------------------------------------------------- Date: 2009-06-22 12:46 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2570&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 08:49:18 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 08:49:18 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2717] Fragment cache service listings Message-ID: <20090622124918.2B7621598075@rubyforge.org> Task #2717 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fragment cache service listings Complete: 30% Status: Open Description: Fragment cache each listing item (with appropriate cache invalidation) Follow-Ups: ------------------------------------------------------- Date: 2009-06-22 12:49 By: jits Comment: The flat tags lists are now cached. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2717&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 09:42:56 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 09:42:56 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2719] get to the same page after logging Message-ID: <20090622134256.137E91598074@rubyforge.org> Task #2719 has been updated. Project: BioCatalogue Subproject: Pilot Summary: get to the same page after logging Complete: 0% Status: Open Description: link without logging, the logging form appears asking me to logging before i carry on. Once i enter ma logging details, i expect the site to take me to the description page so that i can add my description. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2719&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 09:46:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 09:46:29 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2720] get to the same page after logging Message-ID: <20090622134629.A258A1598074@rubyforge.org> Task #2720 has been updated. Project: BioCatalogue Subproject: Pilot Summary: get to the same page after logging Complete: 0% Status: Open Description: To return to the same page when you sign in. e.g. I select the description link without logging, the logging form appears asking me to logging before i carry on. Once i enter ma logging details, i expect the site to take me to the description page so that i can add my description. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2720&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 09:56:22 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 09:56:22 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2692] Use the service categories to implement "related services" Message-ID: <20090622135622.12ABB159807A@rubyforge.org> Task #2692 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Use the service categories to implement "related services" Complete: 100% Status: Closed Description: From Carole: "we can use the service categories to implement a "other services like this" option" Follow-Ups: ------------------------------------------------------- Date: 2009-06-22 13:56 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2692&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 13:32:25 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 13:32:25 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2721] Implement some basic RSS feeds Message-ID: <20090622173225.D0D54159807A@rubyforge.org> Task #2721 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement some basic RSS feeds Complete: 0% Status: Open Description: Mainly for latest services ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2721&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Jun 22 19:04:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Jun 2009 19:04:45 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2717] Fragment cache service listings Message-ID: <20090622230445.457AF1858124@rubyforge.org> Task #2717 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Fragment cache service listings Complete: 100% Status: Closed Description: Fragment cache each listing item (with appropriate cache invalidation) Follow-Ups: ------------------------------------------------------- Date: 2009-06-22 23:04 By: jits Comment: Now the name aliases, categories and descriptions are also cached. Not much else I can do there! ------------------------------------------------------- Date: 2009-06-22 12:49 By: jits Comment: The flat tags lists are now cached. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2717&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 23 10:26:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Jun 2009 10:26:40 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2730] BioMoby service tag and note Message-ID: <20090623142640.32DD0197858D@rubyforge.org> Task #2730 has been updated. Project: BioCatalogue Subproject: Pilot Summary: BioMoby service tag and note Complete: 0% Status: Open Description: Need to tag all BioMoby services as 'BioMoby' and add a note that proper support for these services are coming soon. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2730&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 23 10:26:43 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Jun 2009 10:26:43 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2731] Allow users to register themselves as "contacts" for a service Message-ID: <20090623142644.07A74197858D@rubyforge.org> Task #2731 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Allow users to register themselves as "contacts" for a service Complete: 0% Status: Open Description: These can then be shown in the "Contacts" annotations section above all free text annotations. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2731&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 23 10:27:25 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Jun 2009 10:27:25 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2580] my favorite services Message-ID: <20090623142725.84EFE197858D@rubyforge.org> Task #2580 has been updated. Project: BioCatalogue Subproject: Pilot Summary: my favorite services Complete: 100% Status: Closed Description: i want to group a number of services as my favorite services. Follow-Ups: ------------------------------------------------------- Date: 2009-06-23 14:27 By: jits Comment: Added "My Favourites" link to top of the page when logged in. ------------------------------------------------------- Date: 2009-06-14 18:03 By: jits Comment: Done. But need an easier way to get to "My Favourites". ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2580&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 23 10:41:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Jun 2009 10:41:11 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2710] Add other types of annotations to service show page Message-ID: <20090623144111.977551779932@rubyforge.org> Task #2710 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add other types of annotations to service show page Complete: 80% Status: Open Description: Things like "usage conditions", "cost" etc etc Follow-Ups: ------------------------------------------------------- Date: 2009-06-23 14:41 By: jits Comment: Cost, licenses and contact info added. Not sure about "usage conditions" yet. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2710&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Tue Jun 23 11:39:48 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 23 Jun 2009 16:39:48 +0100 Subject: [BioCatalogue-developers] sign up page In-Reply-To: References: Message-ID: <4A40F744.8020204@cs.man.ac.uk> Franck Tanoh wrote: > > Hi guys, > > Can you please make the required information on the sign up page > obvious please? > > http://beta.biocatalogue.org/signup > > Something like this ?*? to show that an information is required. At > the moment not sure what is mandatory or optional. > > I?ve also pointed out to Jits that it?s not obvious from the home page > where to sign up for an account ; a ?sign in / register? is clearer > than just a ?sign in? button. > For this I have added a "Sign up" link next to "Sign in". Cheers, Jits > Cheers, > > Franck > > -- > > Yangoran Franck Tanoh > > myGrid team > > ESNW 1.17 Kilburn Building > > University of Manchester > > +44(0)1612750145 > > "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 ytanoh at cs.man.ac.uk Tue Jun 23 11:42:03 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 23 Jun 2009 16:42:03 +0100 Subject: [BioCatalogue-developers] sign up page In-Reply-To: <4A40F744.8020204@cs.man.ac.uk> Message-ID: >For this I have added a "Sign up" link next to "Sign in". Thanks Jits, Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 23 June 2009 16:40 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] sign up page Franck Tanoh wrote: > > Hi guys, > > Can you please make the required information on the sign up page > obvious please? > > http://beta.biocatalogue.org/signup > > Something like this '*' to show that an information is required. At > the moment not sure what is mandatory or optional. > > I've also pointed out to Jits that it's not obvious from the home page > where to sign up for an account ; a 'sign in / register' is clearer > than just a 'sign in' button. > For this I have added a "Sign up" link next to "Sign in". Cheers, Jits > Cheers, > > Franck > > -- > > Yangoran Franck Tanoh > > myGrid team > > ESNW 1.17 Kilburn Building > > University of Manchester > > +44(0)1612750145 > > "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 noreply at rubyforge.org Tue Jun 23 13:20:34 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Jun 2009 13:20:34 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2732] enable tag filter Message-ID: <20090623172034.633B818581E5@rubyforge.org> Task #2732 has been updated. Project: BioCatalogue Subproject: Pilot Summary: enable tag filter Complete: 0% Status: Open Description: the 'enable tag filter' doesn't stay. i have to keep on clicking on it anytime i want to browse for new services...very frustrating. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2732&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 23 19:17:21 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Jun 2009 19:17:21 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2721] Implement some RSS/atom feeds Message-ID: <20090623231721.BEE6618581F0@rubyforge.org> Task #2721 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Implement some RSS/atom feeds Complete: 50% Status: Open Description: Mainly for latest services Follow-Ups: ------------------------------------------------------- Date: 2009-06-23 23:17 By: jits Comment: Implemented feeds for latest services and filter results. Still to do: - Individual service feeds - General activity feeds ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2721&group_id=6901&group_project_id=12540 From tlaurent at ebi.ac.uk Wed Jun 24 04:27:53 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Wed, 24 Jun 2009 09:27:53 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: References: Message-ID: <4A41E389.5010906@ebi.ac.uk> The beta site won't be updated until we've got the go ahead from Jits and you, who are currently testing the update of the test site. Once you're happy with the state of the test site is in, let us know and we'll update the beta site. Jits, I don't expect that there'll be more new functionalities checked in, and that the only things which will be checked in now are bug fixes, minor layout changes or speed/reliability improvements ? Thomas Franck Tanoh wrote: > Hi Eric and Thomas, > > > > What?s happening with the beta site? I have a rehearsal tomorrow @11.00 > ? not sure what to expect. Or will the old beta still available? > > > > 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 ytanoh at cs.man.ac.uk Wed Jun 24 04:40:04 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 24 Jun 2009 09:40:04 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: <4A41E389.5010906@ebi.ac.uk> Message-ID: Hi, Sorry didn't manage to test the test site as I found out that it's been updated only at around 6pm yesterday...would have appreciated a quick mail when it was done :-(. I'll try and test it later on today but for now it's all about soaplab and rehearsal...Will to the rehearsal with the current beta then. Cheers, Franck -----Original Message----- From: Thomas Laurent [mailto:tlaurent at ebi.ac.uk] Sent: 24 June 2009 09:28 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] beta site update The beta site won't be updated until we've got the go ahead from Jits and you, who are currently testing the update of the test site. Once you're happy with the state of the test site is in, let us know and we'll update the beta site. Jits, I don't expect that there'll be more new functionalities checked in, and that the only things which will be checked in now are bug fixes, minor layout changes or speed/reliability improvements ? Thomas Franck Tanoh wrote: > Hi Eric and Thomas, > > > > What's happening with the beta site? I have a rehearsal tomorrow @11.00 > . not sure what to expect. Or will the old beta still available? > > > > 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 tlaurent at ebi.ac.uk Wed Jun 24 04:54:54 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Wed, 24 Jun 2009 09:54:54 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: References: Message-ID: <4A41E9DE.7060905@ebi.ac.uk> Sorry Franck, there's been misunderstanding then... We were skyping with Jits during all the update process, and when we finished, Jits told me you were at lunch and that you'd test it when you'd be back. That's why I didn't send an email, I assumed you were already doing it. Thomas Franck Tanoh wrote: > Hi, > Sorry didn't manage to test the test site as I found out that it's been > updated only at around 6pm yesterday...would have appreciated a quick mail > when it was done :-(. > I'll try and test it later on today but for now it's all about soaplab and > rehearsal...Will to the rehearsal with the current beta then. > > Cheers, > Franck > > -----Original Message----- > From: Thomas Laurent [mailto:tlaurent at ebi.ac.uk] > Sent: 24 June 2009 09:28 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] beta site update > > The beta site won't be updated until we've got the go ahead from Jits > and you, who are currently testing the update of the test site. > > Once you're happy with the state of the test site is in, let us know and > we'll update the beta site. > > Jits, I don't expect that there'll be more new functionalities checked > in, and that the only things which will be checked in now are bug fixes, > minor layout changes or speed/reliability improvements ? > > Thomas > > Franck Tanoh wrote: >> Hi Eric and Thomas, >> >> >> >> What's happening with the beta site? I have a rehearsal tomorrow @11.00 >> . not sure what to expect. Or will the old beta still available? >> >> >> >> 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 noreply at rubyforge.org Wed Jun 24 05:06:07 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Jun 2009 05:06:07 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2710] Add other types of annotations to service show page Message-ID: <20090624090607.F22D71858112@rubyforge.org> Task #2710 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add other types of annotations to service show page Complete: 80% Status: Open Description: Things like "usage conditions", "cost" etc etc Follow-Ups: ------------------------------------------------------- Date: 2009-06-23 14:41 By: jits Comment: Cost, licenses and contact info added. Not sure about "usage conditions" yet. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2710&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Jun 24 05:07:03 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Jun 2009 05:07:03 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2711] Ability to make announcements on services Message-ID: <20090624090703.BF2381858112@rubyforge.org> Task #2711 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Ability to make announcements on services Complete: 0% Status: Open Description: Potentially using the annotations plugin, implement a way for users to make announcements on services, in order to inform people about things. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2711&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Wed Jun 24 05:08:16 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 24 Jun 2009 10:08:16 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: <4A41E9DE.7060905@ebi.ac.uk> References: <4A41E9DE.7060905@ebi.ac.uk> Message-ID: <4A41ED00.5070209@cs.man.ac.uk> Thomas Laurent wrote: > Sorry Franck, there's been misunderstanding then... We were skyping > with Jits during all the update process, and when we finished, Jits > told me you were at lunch and that you'd test it when you'd be back. > That's why I didn't send an email, I assumed you were already doing it. Sorry about this, my mistake. It completely skipped my mind whilst I was dealing with the other stuff going on :-( Jits > > Thomas > > Franck Tanoh wrote: >> Hi, Sorry didn't manage to test the test site as I found out that >> it's been >> updated only at around 6pm yesterday...would have appreciated a quick >> mail >> when it was done :-(. I'll try and test it later on today but for now >> it's all about soaplab and >> rehearsal...Will to the rehearsal with the current beta then. >> Cheers, Franck >> >> -----Original Message----- >> From: Thomas Laurent [mailto:tlaurent at ebi.ac.uk] Sent: 24 June 2009 >> 09:28 >> To: Franck Tanoh >> Cc: biocatalogue-developers at rubyforge.org >> Subject: Re: [BioCatalogue-developers] beta site update >> >> The beta site won't be updated until we've got the go ahead from Jits >> and you, who are currently testing the update of the test site. >> >> Once you're happy with the state of the test site is in, let us know >> and we'll update the beta site. >> >> Jits, I don't expect that there'll be more new functionalities >> checked in, and that the only things which will be checked in now are >> bug fixes, minor layout changes or speed/reliability improvements ? >> >> Thomas >> >> Franck Tanoh wrote: >>> Hi Eric and Thomas, >>> >>> >>> What's happening with the beta site? I have a rehearsal tomorrow >>> @11.00 . not sure what to expect. Or will the old beta still >>> available? >>> >>> >>> 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 jits at cs.man.ac.uk Wed Jun 24 05:12:14 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 24 Jun 2009 10:12:14 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: <4A41E389.5010906@ebi.ac.uk> References: <4A41E389.5010906@ebi.ac.uk> Message-ID: <4A41EDEE.6010404@cs.man.ac.uk> Thomas Laurent wrote: > The beta site won't be updated until we've got the go ahead from Jits > and you, who are currently testing the update of the test site. > > Once you're happy with the state of the test site is in, let us know > and we'll update the beta site. Okay, lets aim to do this just after lunch if we can. Could you update the test site again in the meantime please. > > Jits, I don't expect that there'll be more new functionalities checked > in, and that the only things which will be checked in now are bug > fixes, minor layout changes or speed/reliability improvements ? You are largely correct, BUT they are a few things that I am aiming to get done by Thursday night: 1. EMBRACE import script. 2. Changing the way the ontology terms show in the tag cloud. I've been asked to do something like: mygrid:simpleParameter (ie: namespace them) instead of using the different colours. 3. Adding help info across the site in the form of info icons with a tooltip. 4. A "getting started" page. 5. Improve the service show page loading when disqus is taking a while to respond. 6. Show source of tags, categories and name aliases 7. Allow users to register a public email (or make their existing one public). I know this is very last minute... I will be doing all the new things in a branch and will only bring it back to trunk (prob Thursday night) IF it's as stable as I can get it to be (thankfully we don't have a huge number of pages to test). Lets tag the update we do this evening so we can revert if required! Hope this is okay! Jits > > Thomas > > Franck Tanoh wrote: >> Hi Eric and Thomas, >> >> >> What?s happening with the beta site? I have a rehearsal tomorrow >> @11.00 ? not sure what to expect. Or will the old beta still available? >> >> >> 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 jits at cs.man.ac.uk Wed Jun 24 05:15:39 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 24 Jun 2009 10:15:39 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: <4A41EDEE.6010404@cs.man.ac.uk> References: <4A41E389.5010906@ebi.ac.uk> <4A41EDEE.6010404@cs.man.ac.uk> Message-ID: <4A41EEBB.2070809@cs.man.ac.uk> Oh and 8. Add Google Analytics script to layout Jits Jiten Bhagat wrote: > Thomas Laurent wrote: >> The beta site won't be updated until we've got the go ahead from Jits >> and you, who are currently testing the update of the test site. >> >> Once you're happy with the state of the test site is in, let us know >> and we'll update the beta site. > > Okay, lets aim to do this just after lunch if we can. Could you update > the test site again in the meantime please. > >> >> Jits, I don't expect that there'll be more new functionalities >> checked in, and that the only things which will be checked in now are >> bug fixes, minor layout changes or speed/reliability improvements ? > > You are largely correct, BUT they are a few things that I am aiming to > get done by Thursday night: > 1. EMBRACE import script. > 2. Changing the way the ontology terms show in the tag cloud. I've > been asked to do something like: mygrid:simpleParameter (ie: namespace > them) instead of using the different colours. > 3. Adding help info across the site in the form of info icons with a > tooltip. > 4. A "getting started" page. > 5. Improve the service show page loading when disqus is taking a while > to respond. > 6. Show source of tags, categories and name aliases > > > 7. Allow users to register a public email (or make their existing one > public). > > I know this is very last minute... I will be doing all the new things > in a branch and will only bring it back to trunk (prob Thursday night) > IF it's as stable as I can get it to be (thankfully we don't have a > huge number of pages to test). > > Lets tag the update we do this evening so we can revert if required! > > Hope this is okay! > > Jits > > >> >> Thomas >> >> Franck Tanoh wrote: >>> Hi Eric and Thomas, >>> >>> What?s happening with the beta site? I have a rehearsal tomorrow >>> @11.00 ? not sure what to expect. Or will the old beta still >>> available? >>> >>> 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 > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From tlaurent at ebi.ac.uk Wed Jun 24 05:52:02 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Wed, 24 Jun 2009 10:52:02 +0100 Subject: [BioCatalogue-developers] beta site update In-Reply-To: <4A41EDEE.6010404@cs.man.ac.uk> References: <4A41E389.5010906@ebi.ac.uk> <4A41EDEE.6010404@cs.man.ac.uk> Message-ID: <4A41F742.2040000@ebi.ac.uk> Waouh, I didn't realise there was still so much to put in... Ok then, and most of all, good luck ! That's a very good idea to put it in a branch. Thomas Jiten Bhagat wrote: > Thomas Laurent wrote: >> The beta site won't be updated until we've got the go ahead from Jits >> and you, who are currently testing the update of the test site. >> >> Once you're happy with the state of the test site is in, let us know >> and we'll update the beta site. > > Okay, lets aim to do this just after lunch if we can. Could you update > the test site again in the meantime please. > >> >> Jits, I don't expect that there'll be more new functionalities checked >> in, and that the only things which will be checked in now are bug >> fixes, minor layout changes or speed/reliability improvements ? > > You are largely correct, BUT they are a few things that I am aiming to > get done by Thursday night: > 1. EMBRACE import script. > 2. Changing the way the ontology terms show in the tag cloud. I've been > asked to do something like: mygrid:simpleParameter (ie: namespace them) > instead of using the different colours. > 3. Adding help info across the site in the form of info icons with a > tooltip. > 4. A "getting started" page. > 5. Improve the service show page loading when disqus is taking a while > to respond. > 6. Show source of tags, categories and name aliases > > > 7. Allow users to register a public email (or make their existing one > public). > > I know this is very last minute... I will be doing all the new things in > a branch and will only bring it back to trunk (prob Thursday night) IF > it's as stable as I can get it to be (thankfully we don't have a huge > number of pages to test). > > Lets tag the update we do this evening so we can revert if required! > > Hope this is okay! > > Jits > > >> >> Thomas >> >> Franck Tanoh wrote: >>> Hi Eric and Thomas, >>> >>> What?s happening with the beta site? I have a rehearsal tomorrow >>> @11.00 ? not sure what to expect. Or will the old beta still >>> available? >>> >>> 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 noreply at rubyforge.org Wed Jun 24 09:59:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Jun 2009 09:59:30 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2733] allow the submitter to select a display name for a service Message-ID: <20090624135930.ED9D515B8023@rubyforge.org> Task #2733 has been updated. Project: BioCatalogue Subproject: Pilot Summary: allow the submitter to select a display name for a service Complete: 0% Status: Open Description: <> posted by Andrew on the Biocat support list ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2733&group_id=6901&group_project_id=12540 From tlaurent at ebi.ac.uk Thu Jun 25 05:48:45 2009 From: tlaurent at ebi.ac.uk (Thomas Laurent) Date: Thu, 25 Jun 2009 10:48:45 +0100 Subject: [BioCatalogue-developers] when are we moving to biocatalogue.org? In-Reply-To: References: Message-ID: <4A4347FD.7000104@ebi.ac.uk> Next attempt is today if the update of the beta site goes smoothly. Thomas Franck Tanoh wrote: > Hi guys, > > > > Are we ?migrating? to biocatalogue.org today? It wasn?t possible on > Wednesday for obvious reasons. > > So when is the next attempt? > > > > 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 Thu Jun 25 07:12:34 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 25 Jun 2009 12:12:34 +0100 Subject: [BioCatalogue-developers] A question on integrating Disqus In-Reply-To: <49B8DBFD.9090500@cs.man.ac.uk> References: <49B7D5F9.8050602@cs.man.ac.uk> <919995550903111130j3137d602lbcfff48006397c4f@mail.gmail.com> <49B8DBFD.9090500@cs.man.ac.uk> Message-ID: <4A435BA2.3090003@cs.man.ac.uk> Hello Gianni, We're looking to launch the public BioCatalogue website next week Wednesday (July 1st). Would it be possible to update your database so that all comments on pages starting with the URL "http://beta.biocatalogue.org" should now start with "http://www.biocatalogue.org" instead please? Username is: biocatalogue Many thanks, Jiten Bhagat Jiten Bhagat wrote: > Okay, thanks Giannii. > > Jiten > > > Giannii Calvert wrote: >> Jiten, >> >> When you're ready to switch over give us a 24 hours notice and we'll >> change the permalinks to reflect the new site url. >> >> Giannii >> DISQUS >> Community Manager >> giannii at disqus.com >> http://twitter.com/giannii >> >> On Wed, Mar 11, 2009 at 8:17 AM, Jiten Bhagat > > wrote: >> >> Hello, >> >> Firstly, let me say, I love the concept of Disqus and I think you >> guys are doing great :-) >> >> I have a question I was hoping you could help with. Apologies if >> this question has already been answered on your help pages or forum. >> >> I work on the BioCatalogue project (http://www.biocatalogue.org) >> and we are looking to use your service for commenting/discussing >> on the BioCatalogue. For now we have a private beta site >> (http://beta.biocatalogue.org) which will use Disqus. However, we >> plan on moving to a public beta site fairly soon which will be at >> the URL http://www.biocatalogue.org/. My concern is that we will >> lose all comments made on http://beta.biocatalogue.org when we do >> so. Will it be possible, in the future, to change the hostname of >> all the things that have comment threads on them? >> >> Thanks, >> Jits >> >> >> >> >> -- >> > > From noreply at rubyforge.org Thu Jun 25 09:59:42 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Jun 2009 09:59:42 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2703] User profile: allow users to register a public email Message-ID: <20090625135943.017911779932@rubyforge.org> Task #2703 has been updated. Project: BioCatalogue Subproject: Pilot Summary: User profile: allow users to register a public email Complete: 100% Status: Closed Description: ... or make their registered email address public. Follow-Ups: ------------------------------------------------------- Date: 2009-06-25 13:59 By: jits Comment: Done ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2703&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Jun 25 12:01:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Jun 2009 12:01:47 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2734] bug in soap services populate method Message-ID: <20090625160147.3ED3B1779933@rubyforge.org> Task #2734 has been updated. Project: BioCatalogue Subproject: Pilot Summary: bug in soap services populate method Complete: 0% Status: Open Description: the basic error is when it gets a hash that doesnt follow the structure it expects (partly wsdl parsing fault as that is returning an incorrect hash) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2734&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 26 05:12:06 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Jun 2009 05:12:06 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2739] Curating services Message-ID: <20090626091207.091631779930@rubyforge.org> Task #2739 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Curating services Complete: 0% Status: Open Description: From Steve: "Perhaps a wikipedia-like approach, where something gets marked for deletion and gets a big warning badge in the meantime, giving people a chance to comment / complain before it goes in the bin. " ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2739&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Jun 26 05:13:59 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Jun 2009 05:13:59 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2739] Curating services Message-ID: <20090626091401.0F4B6159807C@rubyforge.org> Task #2739 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Curating services Complete: 0% Status: Open Description: From Steve: "Perhaps a wikipedia-like approach, where something gets marked for deletion and gets a big warning badge in the meantime, giving people a chance to comment / complain before it goes in the bin. " Follow-Ups: ------------------------------------------------------- Date: 2009-06-26 09:13 By: jits Comment: >From Carole: "We will eventually need a functionality for being able to list all services removed from the catalogue." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2739&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 30 08:30:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Jun 2009 08:30:28 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2742] set expiry time for sessions Message-ID: <20090630123055.DB0901779931@rubyforge.org> Task #2742 has been updated. Project: BioCatalogue Subproject: Pilot Summary: set expiry time for sessions Complete: 0% Status: Open Description: set up expiry time for cookies and delete expired sessions from the db ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2742&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 30 08:33:12 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Jun 2009 08:33:12 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2743] contact form subject problem Message-ID: <20090630123312.F30E0177992F@rubyforge.org> Task #2743 has been updated. Project: BioCatalogue Subproject: Pilot Summary: contact form subject problem Complete: 0% Status: Open Description: a problem with the contact form is that we are loosing the subject of the message, it's replaced with "BioCatalogue feedback from: User Name ("email address"), ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2743&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Jun 30 08:36:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Jun 2009 08:36:14 -0400 (EDT) Subject: [BioCatalogue-developers] [Task #2705] setup cron job to reindex on a regular basis Message-ID: <20090630123615.5FB56177992F@rubyforge.org> Task #2705 has been updated. Project: BioCatalogue Subproject: Pilot Summary: setup cron job to reindex on a regular basis Complete: 0% Status: Open Description: the cron job would make the sure the index is fairly up to date Follow-Ups: ------------------------------------------------------- Date: 2009-06-30 12:36 By: ebontane Comment: rake solr:reindex fails on optimize. For that reason, it would not be a good idea set up a cron to run the reindexing. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2705&group_id=6901&group_project_id=12540