From noreply at rubyforge.org Mon Dec 1 09:15:17 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Dec 2008 09:15:17 -0500 (EST) Subject: [BioCatalogue-developers] [311] branches/annotations/vendor/plugins/annotations: Annotations plugin. Message-ID: <20081201141518.345461588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 1 10:40:11 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Dec 2008 10:40:11 -0500 (EST) Subject: [BioCatalogue-developers] [312] branches/annotations/vendor/plugins/annotations: Annotations plugin. Message-ID: <20081201154011.32D291588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 1 12:03:36 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Dec 2008 12:03:36 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2465] Implement custom 404 page Message-ID: <20081201170336.7E6D21588057@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. ------------------------------------------------------- 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 Dec 2 04:23:49 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Dec 2008 04:23:49 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2466] Add table indexes Message-ID: <20081202092353.5E3F11858186@rubyforge.org> Task #2466 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Add table indexes Complete: 0% Status: Open Description: See for example the migration script in the annotations plugin. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2466&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Dec 2 08:08:52 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Dec 2008 08:08:52 -0500 (EST) Subject: [BioCatalogue-developers] [313] branches/annotations/vendor/plugins/annotations: Annotations plugin. Message-ID: <20081202130852.856831858184@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 2 12:04:35 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Dec 2008 12:04:35 -0500 (EST) Subject: [BioCatalogue-developers] [314] branches/annotations/vendor/plugins/annotations: Annotations plugin. Message-ID: <20081202170435.69E091858190@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 2 18:33:39 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Dec 2008 18:33:39 -0500 (EST) Subject: [BioCatalogue-developers] [315] branches/annotations: Annotations plugin. Message-ID: <20081202233339.E5B681588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 04:38:55 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 04:38:55 -0500 (EST) Subject: [BioCatalogue-developers] [316] branches/annotations/app/controllers/services_controller.rb: Updated the disable_action method to return a 404 instead of redirecting. Message-ID: <20081203093855.7D085185818C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 04:41:18 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 04:41:18 -0500 (EST) Subject: [BioCatalogue-developers] [317] branches/annotations/app/controllers/application.rb: ( Previous commit message was incorrect). Message-ID: <20081203094118.5F18E1588059@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 06:42:58 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 06:42:58 -0500 (EST) Subject: [BioCatalogue-developers] [318] branches/annotations: Annotations plugin. Message-ID: <20081203114258.7C05216780DB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 07:00:18 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 07:00:18 -0500 (EST) Subject: [BioCatalogue-developers] [319] branches/annotations/db/migrate: Db migrations to remove old annotations table and use new annotations migration . Message-ID: <20081203120018.82E6C1858196@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 10:26:54 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 10:26:54 -0500 (EST) Subject: [BioCatalogue-developers] [320] trunk/app/views/services/_listing.html.erb: check that a service is not null before trying to display anything Message-ID: <20081203152654.DA56A1588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 10:29:56 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 10:29:56 -0500 (EST) Subject: [BioCatalogue-developers] [321] branches/annotations: Annotations work. Message-ID: <20081203152956.A7CC91858181@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 3 11:35:05 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Dec 2008 11:35:05 -0500 (EST) Subject: [BioCatalogue-developers] [322] trunk/app/views/home/index.html.erb: fix typo Message-ID: <20081203163505.E34E51858188@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Dec 4 05:52:21 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 04 Dec 2008 10:52:21 +0000 Subject: [BioCatalogue-developers] beta site Message-ID: <4937B665.6030906@cs.man.ac.uk> Hi guys, Was just thinking... I think we should run the beta site now in production mode? It will be significantly faster + users won't see the ugly debugging pages (though they will see a slightly less ugly default 404 page ;-)) Cheers, Jits From noreply at rubyforge.org Thu Dec 4 06:18:53 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Dec 2008 06:18:53 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2474] After log in, redirect to previous page user was on Message-ID: <20081204111853.574C81858186@rubyforge.org> Task #2474 has been updated. Project: BioCatalogue Subproject: Pilot Summary: After log in, redirect to previous page user was on Complete: 0% Status: Open Description: Currently when a user logs in from the login widget at the top right, they are redirected to the user index page. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2474&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Dec 4 06:19:37 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Dec 2008 06:19:37 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2474] After log in, redirect to previous page user was on Message-ID: <20081204111937.A9BF8185818B@rubyforge.org> Task #2474 has been updated. Project: BioCatalogue Subproject: Pilot Summary: After log in, redirect to previous page user was on Complete: 0% Status: Open Description: Currently when a user logs in from the login widget at the top right, they are redirected to the user index page. Follow-Ups: ------------------------------------------------------- Date: 2008-12-04 11:19 By: jits Comment: OOPS... this task already exists. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2474&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Dec 4 06:19:50 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Dec 2008 06:19:50 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2474] After log in, redirect to previous page user was on Message-ID: <20081204111950.35B201858186@rubyforge.org> Task #2474 has been updated. Project: BioCatalogue Subproject: Pilot Summary: After log in, redirect to previous page user was on Complete: 0% Status: Deleted Description: Currently when a user logs in from the login widget at the top right, they are redirected to the user index page. Follow-Ups: ------------------------------------------------------- Date: 2008-12-04 11:19 By: jits Comment: OOPS... this task already exists. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2474&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Dec 4 06:22:28 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Dec 2008 06:22:28 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2413] Secure delete actions Message-ID: <20081204112229.18266185818C@rubyforge.org> Task #2413 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Secure delete actions Complete: 95% Status: Open Description: Need to secure/disable all delete actions on resources Follow-Ups: ------------------------------------------------------- Date: 2008-12-04 11:22 By: jits Comment: Done. But needs more testing to make sure ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2413&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Dec 4 06:35:58 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Dec 2008 06:35:58 -0500 (EST) Subject: [BioCatalogue-developers] [323] branches/annotations: Annotations work. Message-ID: <20081204113558.EC6DD185818B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Dec 4 13:01:46 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Dec 2008 13:01:46 -0500 (EST) Subject: [BioCatalogue-developers] [324] branches/annotations: Annotations work. Message-ID: <20081204180146.96B6B1588057@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Fri Dec 5 12:30:22 2008 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 05 Dec 2008 17:30:22 +0000 Subject: [BioCatalogue-developers] opensearch Message-ID: <4939652E.3040605@ebi.ac.uk> Hey Guys! Thomas and I enabled the opensearch thing which has been available for some time now on the beta site. So you can add BioCatalogue search engine to you list of search engines now :). I find this quite convenient, not having to go to the beta site to find something. I talked to Rodrigo about it and he liked it as well :) . So simple things like this can make a huge difference... Eric -------------- next part -------------- A non-text attachment was scrubbed... Name: ericnzuo.vcf Type: text/x-vcard Size: 238 bytes Desc: not available URL: From jits at cs.man.ac.uk Sat Dec 6 05:42:35 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sat, 06 Dec 2008 10:42:35 +0000 Subject: [BioCatalogue-developers] opensearch In-Reply-To: <4939652E.3040605@ebi.ac.uk> References: <4939652E.3040605@ebi.ac.uk> Message-ID: <493A571B.2020700@cs.man.ac.uk> Awesome! Nice one guys! Jits Eric Nzuobontane wrote: > Hey Guys! > Thomas and I enabled the opensearch thing which has been available for > some time now on the beta site. So you can add BioCatalogue search > engine to you list of search engines now :). I find this quite > convenient, not having to go to the beta site to find something. I > talked to Rodrigo about it and he liked it as well :) . So simple > things like this can make a huge difference... > > Eric > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Sun Dec 7 12:41:56 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 7 Dec 2008 12:41:56 -0500 (EST) Subject: [BioCatalogue-developers] [325] branches/annotations: Annotations work. Message-ID: <20081207174158.B6BF41858188@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Dec 7 12:50:58 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 7 Dec 2008 12:50:58 -0500 (EST) Subject: [BioCatalogue-developers] [326] branches/annotations/app/views/annotations/new_popup.html.erb: Annotations work. Message-ID: <20081207175058.47C391588059@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Dec 7 16:04:42 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 7 Dec 2008 16:04:42 -0500 (EST) Subject: [BioCatalogue-developers] [327] branches/annotations: Annnotations work. Message-ID: <20081207210442.28E9D1858283@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Dec 7 16:13:20 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 7 Dec 2008 16:13:20 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2426] Paginate acts_as_solr results with will_paginate Message-ID: <20081207211321.17E25158805E@rubyforge.org> Task #2426 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Paginate acts_as_solr results with will_paginate Complete: 0% Status: Open Description: Based on: http://henrik.nyh.se/2007/06/using-will_paginate-with-acts_as_solr ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2426&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Sun Dec 7 16:46:07 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 07 Dec 2008 21:46:07 +0000 Subject: [BioCatalogue-developers] WSDL parser Message-ID: <493C441F.7080505@cs.man.ac.uk> Turns out this: http://bioruby.org/ has a WSDL parser for Ruby... did we try it out? It also has a DAS parser... Jits From jits at cs.man.ac.uk Sun Dec 7 16:58:11 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 07 Dec 2008 21:58:11 +0000 Subject: [BioCatalogue-developers] WSDL parser In-Reply-To: <493C441F.7080505@cs.man.ac.uk> References: <493C441F.7080505@cs.man.ac.uk> Message-ID: <493C46F3.2020103@cs.man.ac.uk> They even have an EBI SOAP parser! Jits Jiten Bhagat wrote: > Turns out this: http://bioruby.org/ has a WSDL parser for Ruby... did > we try it out? > > It also has a DAS parser... > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Sun Dec 7 17:01:27 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 07 Dec 2008 22:01:27 +0000 Subject: [BioCatalogue-developers] WSDL parser In-Reply-To: <493C46F3.2020103@cs.man.ac.uk> References: <493C441F.7080505@cs.man.ac.uk> <493C46F3.2020103@cs.man.ac.uk> Message-ID: <493C47B7.6060702@cs.man.ac.uk> Okay so looks like their soap wsdl thingee creates a "live" proxy that can be used to invoke operations! Methinks this could be highly useful..... Jits Jiten Bhagat wrote: > They even have an EBI SOAP parser! > > Jits > > > Jiten Bhagat wrote: >> Turns out this: http://bioruby.org/ has a WSDL parser for Ruby... did >> we try it out? >> >> It also has a DAS parser... >> >> 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 From ericnzuo at ebi.ac.uk Mon Dec 8 05:53:01 2008 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 08 Dec 2008 10:53:01 +0000 Subject: [BioCatalogue-developers] WSDL parser In-Reply-To: <493C441F.7080505@cs.man.ac.uk> References: <493C441F.7080505@cs.man.ac.uk> Message-ID: <493CFC8D.5010306@ebi.ac.uk> No Jits, we did not, I would say I did not. I did not even know it existed. I will be more than happy to replace our current parser if there one that does a better job. Eric Jiten Bhagat wrote: > Turns out this: http://bioruby.org/ has a WSDL parser for Ruby... did > we try it out? > > It also has a DAS parser... > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- A non-text attachment was scrubbed... Name: ericnzuo.vcf Type: text/x-vcard Size: 238 bytes Desc: not available URL: From jits at cs.man.ac.uk Mon Dec 8 05:56:34 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 08 Dec 2008 10:56:34 +0000 Subject: [BioCatalogue-developers] WSDL parser In-Reply-To: <493CFC8D.5010306@ebi.ac.uk> References: <493C441F.7080505@cs.man.ac.uk> <493CFC8D.5010306@ebi.ac.uk> Message-ID: <493CFD62.3050705@cs.man.ac.uk> Could you download the code and/or install the gem and investigate? (Instructions here: http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_notes, in the gems section). I had a look last night and it seemed to have many useful things. Jits Eric Nzuobontane wrote: > No Jits, we did not, I would say I did not. I did not even know it > existed. I will be more than happy to replace our current parser if > there one that does a better job. > > Eric > > > Jiten Bhagat wrote: >> Turns out this: http://bioruby.org/ has a WSDL parser for Ruby... did >> we try it out? >> >> It also has a DAS parser... >> >> Jits >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Mon Dec 8 08:29:35 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 08:29:35 -0500 (EST) Subject: [BioCatalogue-developers] [328] branches/annotations: Reordering of search results tabs so that services always show first. Message-ID: <20081208132935.E12361588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 08:41:54 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 08:41:54 -0500 (EST) Subject: [BioCatalogue-developers] [329] branches/annotations/app: Search results work. Message-ID: <20081208134154.B359B185818C@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Dec 8 09:34:27 2008 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 8 Dec 2008 14:34:27 -0000 Subject: [BioCatalogue-developers] opensearch In-Reply-To: <4939652E.3040605@ebi.ac.uk> References: <4939652E.3040605@ebi.ac.uk> Message-ID: <4B0C77D0E6F945B89EE14126DF7F010B@franckPC> I've just tried it ... very useful!! Well done. Franck -----Original Message----- From: biocatalogue-developers-bounces at rubyforge.org [mailto:biocatalogue-developers-bounces at rubyforge.org] On Behalf Of Eric Nzuobontane Sent: 05 December 2008 17:30 To: biocatalogue-developers at rubyforge.org Subject: [BioCatalogue-developers] opensearch Hey Guys! Thomas and I enabled the opensearch thing which has been available for some time now on the beta site. So you can add BioCatalogue search engine to you list of search engines now :). I find this quite convenient, not having to go to the beta site to find something. I talked to Rodrigo about it and he liked it as well :) . So simple things like this can make a huge difference... Eric From ytanoh at cs.man.ac.uk Mon Dec 8 09:43:21 2008 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 8 Dec 2008 14:43:21 -0000 Subject: [BioCatalogue-developers] FW: myGrid and BiologyCat.org Message-ID: Any answer to that? Jits, check out myExperiment on programmableweb Franck -----Original Message----- From: John Musser [mailto:john at programmableweb.com] Sent: 05 December 2008 18:30 To: Franck Tanoh Subject: Re: myGrid and BiologyCat.org Hi Franck, Thanks for sending along the links. Very helpful. I've now subscribed to the mailing list. FYI, we've now added a link to the myExperiment API on PW http://www.programmableweb.com/api/myexperiment BioCatalogue looks like it will be quite useful to the community. Anything we can do to help? I'd be happy to provide input on the advisory side; we can export or import web services via RSS and our own API; I suspect we can integrate directly with myExperiment fairly easily; or we could setup one a 'topic area' to create a bio-centric version of PW for your community. Look forward to hearing from you. Cheers, John On Tue, Nov 11, 2008 at 5:02 AM, Franck Tanoh wrote: > Hi John, > > Thanks for your interest in the BioCatalogue project. > >>Are there more background on the project online >>somewhere? > BioCatalogue started 5 months ago so we're at the early stage. The aim of > the project is to build a registry of annotated biological web services. > For information on the project and what's currently going on, check our > newly set up public wiki @ www.biocatalogue.org/wiki . > To get involved or received updates on the project, please join our mailing > list: > http://listserv.manchester.ac.uk/cgi-bin/wa?SUBED1=biocatalogue-friends&A=1 > You might also be interested in the myExperiment project: > http://www.myexperiment.org/ , a repository of workflow. > The myGrid website has a number a project you might also find useful: > http://www.mygrid.org.uk/ > > Look forward to hearing from you > > Cheers, > > Franck > > > > -----Original Message----- > From: John Musser [mailto:john at programmableweb.com] > Sent: 10 November 2008 21:36 > To: ytanoh at cs.man.ac.uk > Subject: myGrid and BiologyCat.org > > Hi Frank, > > I wanted to introduce myself and let you know that I've just come > across your myGrid and BioCatalogue projects and think they're quite > interesting. They certainly related to a number of things we're > working here at ProgrammableWeb, like our vertical topic areas and our > own API (I'd be happy to discuss if of interest). > > I'd love to learn more about BioCatalogue. I don't see a lot of docs on > the site itself. Are there more background on the project online > somewhere? > > Cheers, > John > > From noreply at rubyforge.org Mon Dec 8 12:15:31 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 12:15:31 -0500 (EST) Subject: [BioCatalogue-developers] [330] branches/annotations: - New layout for the show service page - split out overview and operations into 2 tabs . Message-ID: <20081208171531.BB63C185818C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 12:23:07 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 12:23:07 -0500 (EST) Subject: [BioCatalogue-developers] [331] trunk/app/models/soap_service.rb: create entire service structure in a transaction Message-ID: <20081208172307.96A3C1858283@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 12:24:09 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 12:24:09 -0500 (EST) Subject: [BioCatalogue-developers] [332] trunk/app/controllers/soap_services_controller.rb: create entire service structure in a transaction Message-ID: <20081208172409.4878B185818B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 17:43:49 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 17:43:49 -0500 (EST) Subject: [BioCatalogue-developers] [333] branches/annotations: Annotations work. Message-ID: <20081208224349.9D04E158805E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 17:52:54 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 17:52:54 -0500 (EST) Subject: [BioCatalogue-developers] [334] branches/annotations: Annotations work. Message-ID: <20081208225254.E9A691588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 18:02:43 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 18:02:43 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2415] Login shouldn't redirect to users index page Message-ID: <20081208230243.BE1A41588057@rubyforge.org> Task #2415 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Login shouldn't redirect to users index page Complete: 0% Status: Open Description: When you login using the login widget at the top of the page, it should take you back to the page you were on. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2415&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Dec 8 18:56:31 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 18:56:31 -0500 (EST) Subject: [BioCatalogue-developers] [335] branches/annotations: Improvements for login/authentication. Message-ID: <20081208235631.6067F1588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Dec 8 18:57:25 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Dec 2008 18:57:25 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2415] Login shouldn't redirect to users index page Message-ID: <20081208235725.51B061588057@rubyforge.org> Task #2415 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Login shouldn't redirect to users index page Complete: 100% Status: Closed Description: When you login using the login widget at the top of the page, it should take you back to the page you were on. Follow-Ups: ------------------------------------------------------- Date: 2008-12-08 23:57 By: jits Comment: DONE!! In revision 335 :-) :-) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2415&group_id=6901&group_project_id=12540 From jits at cs.man.ac.uk Tue Dec 9 04:58:00 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 09 Dec 2008 09:58:00 +0000 Subject: [BioCatalogue-developers] FW: myGrid and BiologyCat.org In-Reply-To: References: Message-ID: <493E4128.6010406@cs.man.ac.uk> That's great stuff... tell him I said THANKS! for registering the myExp API :-) Sounds like this could be a very useful collaboration BUT I think you need to speak to Carole and Dave (De Roure) about this first. Tell them you've been approached by this guy and mention the stuff below. Then, if this is something fruitful for us they can resource it :-) Jits Franck Tanoh wrote: > Any answer to that? > > Jits, check out myExperiment on programmableweb > > Franck > > -----Original Message----- > From: John Musser [mailto:john at programmableweb.com] > Sent: 05 December 2008 18:30 > To: Franck Tanoh > Subject: Re: myGrid and BiologyCat.org > > Hi Franck, > > Thanks for sending along the links. Very helpful. I've now subscribed > to the mailing list. > > FYI, we've now added a link to the myExperiment API on PW > > http://www.programmableweb.com/api/myexperiment > > BioCatalogue looks like it will be quite useful to the community. > Anything we can do to help? I'd be happy to provide input on the > advisory side; we can export or import web services via RSS and our > own API; I suspect we can integrate directly with myExperiment fairly > easily; or we could setup one a 'topic area' to create a bio-centric > version of PW for your community. > > Look forward to hearing from you. > Cheers, > John > > > > On Tue, Nov 11, 2008 at 5:02 AM, Franck Tanoh wrote: > >> Hi John, >> >> Thanks for your interest in the BioCatalogue project. >> >> >>> Are there more background on the project online >>> somewhere? >>> >> BioCatalogue started 5 months ago so we're at the early stage. The aim of >> the project is to build a registry of annotated biological web services. >> For information on the project and what's currently going on, check our >> newly set up public wiki @ www.biocatalogue.org/wiki . >> To get involved or received updates on the project, please join our >> > mailing > >> list: >> >> > http://listserv.manchester.ac.uk/cgi-bin/wa?SUBED1=biocatalogue-friends&A=1 > >> You might also be interested in the myExperiment project: >> http://www.myexperiment.org/ , a repository of workflow. >> The myGrid website has a number a project you might also find useful: >> http://www.mygrid.org.uk/ >> >> Look forward to hearing from you >> >> Cheers, >> >> Franck >> >> >> >> -----Original Message----- >> From: John Musser [mailto:john at programmableweb.com] >> Sent: 10 November 2008 21:36 >> To: ytanoh at cs.man.ac.uk >> Subject: myGrid and BiologyCat.org >> >> Hi Frank, >> >> I wanted to introduce myself and let you know that I've just come >> across your myGrid and BioCatalogue projects and think they're quite >> interesting. They certainly related to a number of things we're >> working here at ProgrammableWeb, like our vertical topic areas and our >> own API (I'd be happy to discuss if of interest). >> >> I'd love to learn more about BioCatalogue. I don't see a lot of docs on >> the site itself. Are there more background on the project online >> somewhere? >> >> Cheers, >> John >> >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Tue Dec 9 06:30:00 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 06:30:00 -0500 (EST) Subject: [BioCatalogue-developers] [336] branches/annotations: Annotations work. Message-ID: <20081209113000.B644A18585B8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 06:57:35 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 06:57:35 -0500 (EST) Subject: [BioCatalogue-developers] [337] branches/annotations: Annotations work. Message-ID: <20081209115735.44B011588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 08:32:23 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 08:32:23 -0500 (EST) Subject: [BioCatalogue-developers] [338] trunk: Merged annotations branch to trunk, fixed conflicts and made some tweaks. Message-ID: <20081209133225.758CE1858181@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 11:22:17 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 11:22:17 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2478] Update rails to 2.2.2 on beta server Message-ID: <20081209162217.E4CF61588057@rubyforge.org> Task #2478 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update rails to 2.2.2 on beta server Complete: 0% Status: Open Description: Update rails to 2.2.2 on beta server ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2478&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Dec 9 11:22:25 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 11:22:25 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2478] Update rails to 2.2.2 on beta server Message-ID: <20081209162225.39B0D18585B1@rubyforge.org> Task #2478 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update rails to 2.2.2 on beta server Complete: 0% Status: Open Description: Update rails to 2.2.2 on beta server ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2478&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Dec 9 11:37:09 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 11:37:09 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2478] Update rails to 2.2.2 on beta server Message-ID: <20081209163709.D5AF91588059@rubyforge.org> Task #2478 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update rails to 2.2.2 on beta server Complete: 0% Status: Open Description: Update rails to 2.2.2 on beta server Follow-Ups: ------------------------------------------------------- Date: 2008-12-09 16:37 By: jits Comment: Note also that Rails 2.2.2 requires rubygems v1.3.1 to work. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2478&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Dec 9 12:01:06 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 12:01:06 -0500 (EST) Subject: [BioCatalogue-developers] [339] trunk: Upgraded to Rails 2.2.2 which required some modification etc ( eg: country_select was deprecated and now relies on a plugin). Message-ID: <20081209170107.12E721588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 12:33:41 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 12:33:41 -0500 (EST) Subject: [BioCatalogue-developers] [340] trunk/app/views/services: Added tags to service listings, and changed display of these. Message-ID: <20081209173341.F2F3A1858190@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 12:42:54 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 12:42:54 -0500 (EST) Subject: [BioCatalogue-developers] [341] trunk/app/controllers/search_controller.rb: Disabled fuzzy search for now. Message-ID: <20081209174254.B9D46185818C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 12:53:39 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 12:53:39 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2479] URLs should be indexed and searchable Message-ID: <20081209175339.435CE1858283@rubyforge.org> Task #2479 has been updated. Project: BioCatalogue Subproject: Pilot Summary: URLs should be indexed and searchable Complete: 0% Status: Open Description: Like WSDL urls and so on ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2479&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Dec 9 13:02:19 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 13:02:19 -0500 (EST) Subject: [BioCatalogue-developers] [342] trunk/app/models: Annotations should now be indexed. Message-ID: <20081209180219.1A6A21858283@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 9 13:09:51 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Dec 2008 13:09:51 -0500 (EST) Subject: [BioCatalogue-developers] [343] trunk/app/models: Some fixes + additions for the fields that are indexed for models. Message-ID: <20081209180951.877201858183@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 05:48:49 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 05:48:49 -0500 (EST) Subject: [BioCatalogue-developers] [344] trunk/app/controllers/search_controller.rb: Fixed typo and increased total search results limit to 1000. Message-ID: <20081210104850.26E5218581B0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 05:49:14 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 05:49:14 -0500 (EST) Subject: [BioCatalogue-developers] [345] trunk/lib/util.rb: Added extra logging. Message-ID: <20081210104915.241201588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 06:51:04 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 06:51:04 -0500 (EST) Subject: [BioCatalogue-developers] [346] trunk/app: - Redid the way parameters are passed into the annotation_add_by_popup_link helper method , so now it is much easier to configure and use. Message-ID: <20081210115104.DE33918581B8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 09:12:40 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 09:12:40 -0500 (EST) Subject: [BioCatalogue-developers] [347] trunk: - Refactored descriptions annotations UI into a single helper that can be reused anywhere that descriptions need to be shown and annotated! Message-ID: <20081210141241.7343C1858181@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 09:46:06 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 09:46:06 -0500 (EST) Subject: [BioCatalogue-developers] [348] trunk/app/models/annotation.rb: Updated activity log configuration for annotation model to record the source and annotatable as culprit and referenced respectively . Message-ID: <20081210144607.078C3185818C@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 17:32:51 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 17:32:51 -0500 (EST) Subject: [BioCatalogue-developers] [349] trunk: Removed old files that are not needed now. Message-ID: <20081210223251.757A618585AB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 18:08:18 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 18:08:18 -0500 (EST) Subject: [BioCatalogue-developers] [350] trunk: Annotations plugin can now be configured so that the values of annotations with certain attribute names will always get lowercased or uppercased automatically ( this is useful for things like tags where the policy could be to have all lowercase phrases ). Message-ID: <20081210230818.4BDF11588057@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Dec 10 18:12:47 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Dec 2008 18:12:47 -0500 (EST) Subject: [BioCatalogue-developers] [351] trunk/app/views/services: Tags on service listings and service page are now sorted alphabetically and duplicates are removed . Message-ID: <20081210231247.8964F18585A9@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Dec 11 06:36:19 2008 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Dec 2008 11:36:19 -0000 Subject: [BioCatalogue-developers] roadMap Message-ID: Hi guys, I need your comment on the public pilot roadmap: http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_ planning Franck -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Dec 11 06:39:44 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Dec 2008 11:39:44 +0000 Subject: [BioCatalogue-developers] roadMap In-Reply-To: References: Message-ID: <4940FC00.4020508@cs.man.ac.uk> Hi Franck, Is that the roadmap document or the planning document? These should be two different things since the roadmap is a list of *features* that end users and public will see whereas the planning doc should be a list of *tasks* for our internal usage. Jits Franck Tanoh wrote: > > Hi guys, > > > > I need your comment on the public pilot roadmap: > > http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_planning > > > > > Franck > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ytanoh at cs.man.ac.uk Thu Dec 11 06:53:25 2008 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Dec 2008 11:53:25 -0000 Subject: [BioCatalogue-developers] roadMap In-Reply-To: <4940FC00.4020508@cs.man.ac.uk> References: <4940FC00.4020508@cs.man.ac.uk> Message-ID: <0F5FCB41DF3C4C7085756BBB3A78DA6F@franckPC> Hum ... sorry for my lack of knowledge :-( It's a planning document then but it's meant to be external... we already have a roadmap (which need to be update) I guess. Actually I can add some date to the internal planning document without any polishing. Franck -----Original Message----- From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] Sent: 11 December 2008 11:40 To: Franck Tanoh Cc: biocatalogue-developers at rubyforge.org Subject: Re: [BioCatalogue-developers] roadMap Hi Franck, Is that the roadmap document or the planning document? These should be two different things since the roadmap is a list of *features* that end users and public will see whereas the planning doc should be a list of *tasks* for our internal usage. Jits Franck Tanoh wrote: > > Hi guys, > > > > I need your comment on the public pilot roadmap: > > http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_ planning > > > > > Franck > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Thu Dec 11 07:03:23 2008 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 11 Dec 2008 12:03:23 +0000 Subject: [BioCatalogue-developers] roadMap In-Reply-To: <0F5FCB41DF3C4C7085756BBB3A78DA6F@franckPC> References: <4940FC00.4020508@cs.man.ac.uk> <0F5FCB41DF3C4C7085756BBB3A78DA6F@franckPC> Message-ID: <4941018B.7080004@ebi.ac.uk> As Jits said, some of those task may not necessarily translate to user visible features, and the road map that is visible to users should only tell them about features visible to them. Franck Tanoh wrote: > Hum ... sorry for my lack of knowledge :-( > It's a planning document then but it's meant to be external... we already > have a roadmap (which need to be update) I guess. > Actually I can add some date to the internal planning document without any > polishing. > > Franck > > > -----Original Message----- > From: Jiten Bhagat [mailto:jits at cs.man.ac.uk] > Sent: 11 December 2008 11:40 > To: Franck Tanoh > Cc: biocatalogue-developers at rubyforge.org > Subject: Re: [BioCatalogue-developers] roadMap > > Hi Franck, > > Is that the roadmap document or the planning document? These should be > two different things since the roadmap is a list of *features* that end > users and public will see whereas the planning doc should be a list of > *tasks* for our internal usage. > > Jits > > > Franck Tanoh wrote: > >> Hi guys, >> >> >> >> I need your comment on the public pilot roadmap: >> >> >> > http://www.ebi.ac.uk/ebiwiki/biocatalogue/doku.php?id=development:pilot_dev_ > planning > >> >> >> Franck >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > -------------- next part -------------- A non-text attachment was scrubbed... Name: ericnzuo.vcf Type: text/x-vcard Size: 238 bytes Desc: not available URL: From noreply at rubyforge.org Thu Dec 11 09:22:59 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Dec 2008 09:22:59 -0500 (EST) Subject: [BioCatalogue-developers] [352] trunk: Major reworking and tweaks for search! Message-ID: <20081211142259.DA34816780DC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Dec 11 10:51:51 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Dec 2008 10:51:51 -0500 (EST) Subject: [BioCatalogue-developers] [353] trunk/lib/util.rb: Some nil checks in case data becomes inconsistent. Message-ID: <20081211155151.86C0E1858183@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Dec 11 11:19:22 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Dec 2008 11:19:22 -0500 (EST) Subject: [BioCatalogue-developers] [354] trunk/lib/slugalizer.rb: Fixed an issue that cropped up after upgrading to Rails 2.2.2. Message-ID: <20081211161922.36BE1185818C@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Dec 11 12:14:59 2008 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Dec 2008 17:14:59 +0000 Subject: [BioCatalogue-developers] Beta site updated Message-ID: <49414A93.604@cs.man.ac.uk> This is mainly for Franck... Hi Franck, Just to let you know we've updated the beta site with the latest annotations and search work. Could you have a play and give us your feedback? Note: i'm off from tomorrow... finally :-) So have a great Christmas and New Years! Cheers Jits From noreply at rubyforge.org Thu Dec 11 12:21:31 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Dec 2008 12:21:31 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2479] URLs should be indexed and searchable Message-ID: <20081211172132.1FAAC158805E@rubyforge.org> Task #2479 has been updated. Project: BioCatalogue Subproject: Pilot Summary: URLs should be indexed and searchable Complete: 100% Status: Open Description: Like WSDL urls and so on Follow-Ups: ------------------------------------------------------- Date: 2008-12-11 17:21 By: jits Comment: Done. This required modifying the acts_as_solr plugin since it was appending "_t" after each value before a ":" (this is for the way it determines the fields in the index). This changes means that specific searches won't work! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2479&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Dec 11 13:06:24 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Dec 2008 13:06:24 -0500 (EST) Subject: [BioCatalogue-developers] [355] trunk: Description and tag annotations for soap operations, soap inputs and soap outputs. Message-ID: <20081211180624.C199118581BB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 12 04:43:41 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 04:43:41 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2478] Update rails to 2.2.2 on beta server Message-ID: <20081212094341.C5A4518585B1@rubyforge.org> Task #2478 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Update rails to 2.2.2 on beta server Complete: 100% Status: Closed Description: Update rails to 2.2.2 on beta server Follow-Ups: ------------------------------------------------------- Date: 2008-12-12 09:43 By: ebontane Comment: done ------------------------------------------------------- Date: 2008-12-09 16:37 By: jits Comment: Note also that Rails 2.2.2 requires rubygems v1.3.1 to work. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2478&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Dec 12 04:45:30 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 04:45:30 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2465] Implement custom 404 page Message-ID: <20081212094530.5B33E18585A0@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: 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 Fri Dec 12 04:50:02 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 04:50:02 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2444] service creation in a transaction Message-ID: <20081212095006.09D5C18585B1@rubyforge.org> Task #2444 has been updated. Project: BioCatalogue Subproject: Pilot Summary: service creation in a transaction Complete: 30% Status: Open 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: 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 Fri Dec 12 04:51:53 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 04:51:53 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2438] add opensearch feature Message-ID: <20081212095209.4B43818585B8@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 Fri Dec 12 04:52:43 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 04:52:43 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2426] Paginate acts_as_solr results with will_paginate Message-ID: <20081212095243.6C20318585A2@rubyforge.org> Task #2426 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Paginate acts_as_solr results with will_paginate Complete: 100% Status: Closed Description: Based on: http://henrik.nyh.se/2007/06/using-will_paginate-with-acts_as_solr ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2426&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Dec 12 04:53:51 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 04:53:51 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2444] service creation in a transaction Message-ID: <20081212095351.7ABF618585A0@rubyforge.org> Task #2444 has been updated. Project: BioCatalogue Subproject: Pilot Summary: service creation in a transaction Complete: 50% Status: Open 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: 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 Fri Dec 12 05:05:48 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 05:05:48 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2465] Implement custom 404 page Message-ID: <20081212100548.EE56F18585A7@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: 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 Fri Dec 12 05:07:10 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 05:07:10 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2426] Paginate acts_as_solr results with will_paginate Message-ID: <20081212100710.CF3E918585B1@rubyforge.org> Task #2426 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Paginate acts_as_solr results with will_paginate Complete: 0% Status: Closed Description: Based on: http://henrik.nyh.se/2007/06/using-will_paginate-with-acts_as_solr Follow-Ups: ------------------------------------------------------- Date: 2008-12-12 10:07 By: jits Comment: When was this completed?? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2426&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Dec 12 05:57:17 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 05:57:17 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2426] Paginate acts_as_solr results with will_paginate Message-ID: <20081212105717.E9C1018585AA@rubyforge.org> Task #2426 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Paginate acts_as_solr results with will_paginate Complete: 0% Status: Open Description: Based on: http://henrik.nyh.se/2007/06/using-will_paginate-with-acts_as_solr Follow-Ups: ------------------------------------------------------- Date: 2008-12-12 10:07 By: jits Comment: When was this completed?? ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2426&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Dec 12 06:36:34 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 06:36:34 -0500 (EST) Subject: [BioCatalogue-developers] [356] trunk/vendor/plugins/annotations: Added methods to allow specific annotatable objects to be found that have a specified attribute name AND value . Message-ID: <20081212113634.A74BC18585A2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 12 07:28:13 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 07:28:13 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2480] Allow tags during service submission Message-ID: <20081212122813.3EC0E18585A7@rubyforge.org> Task #2480 has been updated. Project: BioCatalogue Subproject: Pilot Summary: Allow tags during service submission Complete: 0% Status: Open Description: This needs to use the special way of creating multiple annotations from one value. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2480&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Dec 12 07:32:18 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 07:32:18 -0500 (EST) Subject: [BioCatalogue-developers] [357] trunk/app: Implemeted annotations creation at service submission, so now submitter can add a new name alias, description and documentation URL. Message-ID: <20081212123218.91CC518585A7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 12 08:11:34 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 08:11:34 -0500 (EST) Subject: [BioCatalogue-developers] [358] trunk: - Extended Annotation model (in the app, not the plugin) so that all values are white_listed (ie: bad tags/ scripts are explcitly removed). Message-ID: <20081212131134.6CE8718585A2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 12 08:27:48 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 08:27:48 -0500 (EST) Subject: [BioCatalogue-developers] [359] trunk/lib/wsdl_parser.rb: Endpoint URL is now normalised. Message-ID: <20081212132748.A8BD918585AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 12 08:29:13 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 08:29:13 -0500 (EST) Subject: [BioCatalogue-developers] [360] trunk/lib/wsdl_parser.rb: Forgot require. Message-ID: <20081212132917.6B6B418585AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Dec 12 08:43:12 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Dec 2008 08:43:12 -0500 (EST) Subject: [BioCatalogue-developers] [361] trunk/app: Reworked duplication check so that both wsdl url and endpoint are checked. Message-ID: <20081212134312.ABF4918585AB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 16 06:19:54 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Dec 2008 06:19:54 -0500 (EST) Subject: [BioCatalogue-developers] [362] trunk/app/models/soaplab_server.rb: fix for the interface change in soap_service. create_service to take care of annotations Message-ID: <20081216111954.C4CAA167820F@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 16 06:20:32 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Dec 2008 06:20:32 -0500 (EST) Subject: [BioCatalogue-developers] [363] trunk/app/controllers/soaplab_servers_controller.rb: Message-ID: <20081216112033.0F2581588059@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Dec 16 12:06:37 2008 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Dec 2008 12:06:37 -0500 (EST) Subject: [BioCatalogue-developers] [364] trunk/app/controllers/application.rb: filter the logging of plain text passwords Message-ID: <20081216170637.6DB9D1588057@rubyforge.org> An HTML attachment was scrubbed... URL: