From ericnzuo at ebi.ac.uk Mon Mar 1 04:17:04 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 01 Mar 2010 09:17:04 +0000 Subject: [BioCatalogue-developers] Important Rails vulnerability - we need to fix for this release In-Reply-To: <4B8ABBFA.3070900@cs.man.ac.uk> References: <4B8ABBFA.3070900@cs.man.ac.uk> Message-ID: <4B8B8610.70906@ebi.ac.uk> Hi Jits, What I would suggest is that we apply the patch in the release. For the next release, freeze all gems in vendor and and apply the patch and maybe plan for upgrade. Eric Jiten Bhagat wrote: > Hi Eric, > > I brought this up a while back; there's been a severe vulnerability in > Rails 2.x for a while now to do with Unicode characters and XSS injection. > > See: > http://weblog.rubyonrails.org/2009/9/4/xss-vulnerability-in-ruby-on-rails > http://tomcopeland.blogs.com/juniordeveloper/2009/09/applying-the-rails-xss-vulnerability-patch.html > > We need to urgently patch the live and test systems to fix this. * > > I have a hunch that the recent error emails we have been getting is to > do with this. So we should fix this asap. > > * Note: I have tried to upgrade our codebase to Rails 2.3.4+, which has > fixed this vulnerability, but was unsuccessful. More time would be > required to upgrade. In the meantime we should at least apply the patches. > > Jits > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Mar 1 05:16:11 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 01 Mar 2010 10:16:11 +0000 Subject: [BioCatalogue-developers] Important Rails vulnerability - we need to fix for this release In-Reply-To: <4B8B8610.70906@ebi.ac.uk> References: <4B8ABBFA.3070900@cs.man.ac.uk> <4B8B8610.70906@ebi.ac.uk> Message-ID: <4B8B93EB.9030307@cs.man.ac.uk> Eric Nzuobontane wrote: > Hi Jits, > What I would suggest is that we apply the patch in the release. For > the next release, freeze all gems in vendor and and apply the patch > and maybe plan for upgrade. The patch needs to be applied to the Rails core code (ie: the ActionPack gems etc), as per the blog posts. Can this be done on the live and test servers? Jits > > Eric > > > > Jiten Bhagat wrote: >> Hi Eric, >> >> I brought this up a while back; there's been a severe vulnerability in >> Rails 2.x for a while now to do with Unicode characters and XSS >> injection. >> >> See: >> http://weblog.rubyonrails.org/2009/9/4/xss-vulnerability-in-ruby-on-rails >> >> http://tomcopeland.blogs.com/juniordeveloper/2009/09/applying-the-rails-xss-vulnerability-patch.html >> >> >> We need to urgently patch the live and test systems to fix this. * >> >> I have a hunch that the recent error emails we have been getting is to >> do with this. So we should fix this asap. >> >> * Note: I have tried to upgrade our codebase to Rails 2.3.4+, which has >> fixed this vulnerability, but was unsuccessful. More time would be >> required to upgrade. In the meantime we should at least apply the >> patches. >> >> Jits >> > > From ericnzuo at ebi.ac.uk Mon Mar 1 05:32:26 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 01 Mar 2010 10:32:26 +0000 Subject: [BioCatalogue-developers] Important Rails vulnerability - we need to fix for this release In-Reply-To: <4B8B93EB.9030307@cs.man.ac.uk> References: <4B8ABBFA.3070900@cs.man.ac.uk> <4B8B8610.70906@ebi.ac.uk> <4B8B93EB.9030307@cs.man.ac.uk> Message-ID: <4B8B97BA.8090706@ebi.ac.uk> Both, the test and live site are running on the same rails core, so applying to test should fix both sites. Let me see if I can get the system guys to apply the patch. Eric Jiten Bhagat wrote: > Eric Nzuobontane wrote: > >> Hi Jits, >> What I would suggest is that we apply the patch in the release. For >> the next release, freeze all gems in vendor and and apply the patch >> and maybe plan for upgrade. >> > > The patch needs to be applied to the Rails core code (ie: the ActionPack > gems etc), as per the blog posts. Can this be done on the live and test > servers? > > Jits > > >> Eric >> >> >> >> Jiten Bhagat wrote: >> >>> Hi Eric, >>> >>> I brought this up a while back; there's been a severe vulnerability in >>> Rails 2.x for a while now to do with Unicode characters and XSS >>> injection. >>> >>> See: >>> http://weblog.rubyonrails.org/2009/9/4/xss-vulnerability-in-ruby-on-rails >>> >>> http://tomcopeland.blogs.com/juniordeveloper/2009/09/applying-the-rails-xss-vulnerability-patch.html >>> >>> >>> We need to urgently patch the live and test systems to fix this. * >>> >>> I have a hunch that the recent error emails we have been getting is to >>> do with this. So we should fix this asap. >>> >>> * Note: I have tried to upgrade our codebase to Rails 2.3.4+, which has >>> fixed this vulnerability, but was unsuccessful. More time would be >>> required to upgrade. In the meantime we should at least apply the >>> patches. >>> >>> Jits >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Mar 1 05:34:39 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 01 Mar 2010 10:34:39 +0000 Subject: [BioCatalogue-developers] Important Rails vulnerability - we need to fix for this release In-Reply-To: <4B8B97BA.8090706@ebi.ac.uk> References: <4B8ABBFA.3070900@cs.man.ac.uk> <4B8B8610.70906@ebi.ac.uk> <4B8B93EB.9030307@cs.man.ac.uk> <4B8B97BA.8090706@ebi.ac.uk> Message-ID: <4B8B983F.4000308@cs.man.ac.uk> OK Eric Nzuobontane wrote: > Both, the test and live site are running on the same rails core, so > applying to test should fix both sites. Let me see if I can get the > system guys to apply the patch. > > Eric > > > Jiten Bhagat wrote: >> Eric Nzuobontane wrote: >> >>> Hi Jits, >>> What I would suggest is that we apply the patch in the release. For >>> the next release, freeze all gems in vendor and and apply the patch >>> and maybe plan for upgrade. >>> >> >> The patch needs to be applied to the Rails core code (ie: the ActionPack >> gems etc), as per the blog posts. Can this be done on the live and test >> servers? >> >> Jits >> >> >>> Eric >>> >>> >>> >>> Jiten Bhagat wrote: >>> >>>> Hi Eric, >>>> >>>> I brought this up a while back; there's been a severe vulnerability in >>>> Rails 2.x for a while now to do with Unicode characters and XSS >>>> injection. >>>> >>>> See: >>>> http://weblog.rubyonrails.org/2009/9/4/xss-vulnerability-in-ruby-on-rails >>>> >>>> >>>> http://tomcopeland.blogs.com/juniordeveloper/2009/09/applying-the-rails-xss-vulnerability-patch.html >>>> >>>> >>>> >>>> We need to urgently patch the live and test systems to fix this. * >>>> >>>> I have a hunch that the recent error emails we have been getting is to >>>> do with this. So we should fix this asap. >>>> >>>> * Note: I have tried to upgrade our codebase to Rails 2.3.4+, which >>>> has >>>> fixed this vulnerability, but was unsuccessful. More time would be >>>> required to upgrade. In the meantime we should at least apply the >>>> patches. >>>> >>>> Jits >>>> >>> > > From ericnzuo at ebi.ac.uk Mon Mar 1 05:51:36 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 01 Mar 2010 10:51:36 +0000 Subject: [BioCatalogue-developers] about blocking an ip Message-ID: <4B8B9C38.4040802@ebi.ac.uk> Here is what the systems people told when I asked the ip below could be blocked? --------------------------------------------- Re: 84.12.145.138 First of all I would not block this IP because it belongs to an ISP, so another user could be allocated it. But why would you want to block it anyway? It was by far your best customer on 26/2/2010, and behaved very well, only using 2 connections at a time and making legitimate requests. We only block access where a client program has gone beserk, or is disobeying clearly stated rules. I do not see anything banning programmed download of the biocatalogue. On that day it did make 10K hits, but googlebot made nearly 16K. Some of the google requests download huge amounts of data, so I have now blocked dynamic queries in the robots.txt. They did not appear in the google index anyway. I assume you are having problems so I have blocked spamming robots that give us no referrals in your robots.txt. The only problem I see with requests from 84.12.145.138 is that there were some timeouts, so I have increased the timeout at the loadbalancer. I would strongly suggest that you turn off debugging on your production server. Your error and production logs are enormous, and writing them will slow down your service. ------------------------------------------------- We really should have investigated the IP a bit more. Anyway, the advise is that there is no need to block this IP for reasons stated above. -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Mar 1 06:03:21 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 01 Mar 2010 11:03:21 +0000 Subject: [BioCatalogue-developers] about blocking an ip In-Reply-To: <4B8B9C38.4040802@ebi.ac.uk> References: <4B8B9C38.4040802@ebi.ac.uk> Message-ID: <4B8B9EF9.5000607@cs.man.ac.uk> Those are fair points from the systems people. The only information I have at hand are the error emails I keep getting. And what I could deduce from those were some kind of collation errors, which may have been a potential unicode XSS injection attack (based on the Rails vulnerability I have mentioned before). Regarding some of the points... > Some of the google requests download huge amounts of data, so I have > now blocked dynamic queries in the robots.txt. This does mean that none of the filtered pages will be indexed. Which is a shame, but I can see their point of view. Note: that I have been able to restrict some of these combinations of filters via the Google Webmaster Tools, but other bots would have still been crawling everything. > I would strongly suggest that you turn off debugging on your production > server. Your error and production logs are enormous, and writing them > will slow down your service. Can they not archive these on a regular basis? Since we don't have any proper instrumentation in place, we need these logs in order to be able to see the real world performance etc. BTW, you may want to commit this new robots.txt file back into the codebase. Jits Eric Nzuobontane wrote: > Here is what the systems people told when I asked the ip below could > be blocked? > --------------------------------------------- > > Re: 84.12.145.138 > > First of all I would not block this IP because it belongs to an ISP, so > another user could be allocated it. > > But why would you want to block it anyway? It was by far your best > customer on 26/2/2010, and behaved very well, only using 2 connections > at a time and making legitimate requests. We only block access where > a client program has gone beserk, or is disobeying clearly stated > rules. I do not see anything banning programmed download of the > biocatalogue. > > On that day it did make 10K hits, but googlebot made nearly 16K. Some > of the google requests download huge amounts of data, so I have now > blocked dynamic queries in the robots.txt. They did not appear in the > google index anyway. I assume you are having problems so I have > blocked spamming robots that give us no referrals in your robots.txt. > > The only problem I see with requests from 84.12.145.138 is that there > were some timeouts, so I have increased the timeout at the loadbalancer. > > I would strongly suggest that you turn off debugging on your production > server. Your error and production logs are enormous, and writing them > will slow down your service. > > ------------------------------------------------- > > We really should have investigated the IP a bit more. Anyway, the > advise is that there is no need to block this IP for reasons stated > above. > From noreply at rubyforge.org Mon Mar 1 10:52:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Mar 2010 10:52:42 -0500 (EST) Subject: [BioCatalogue-developers] [1643] trunk/app/controllers/search_controller.rb: Bugfix for search by data link Message-ID: <20100301155242.746B618582DA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 1 11:58:36 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Mar 2010 11:58:36 -0500 (EST) Subject: [BioCatalogue-developers] [1644] trunk: Various style fixes. Message-ID: <20100301165836.8249718582D4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 1 12:26:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 1 Mar 2010 12:26:17 -0500 (EST) Subject: [BioCatalogue-developers] [1645] trunk/app/controllers/favourites_controller.rb: Disabled remembering of tab after adding a favourite. Message-ID: <20100301172617.5AB49158806E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 05:23:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 05:23:19 -0500 (EST) Subject: [BioCatalogue-developers] [1646] trunk/app/helpers/application_helper.rb: Bugfix for links in contributors box on homepage. Message-ID: <20100302102319.E1F82185830A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 05:32:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 05:32:25 -0500 (EST) Subject: [BioCatalogue-developers] [1647] trunk/public/stylesheets/styles.css: Style fix Message-ID: <20100302103225.7B6EA1858310@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 05:39:44 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 05:39:44 -0500 (EST) Subject: [BioCatalogue-developers] [1648] trunk/script/biocatalogue/api/tests/json_tests.rb: Fixed typo Message-ID: <20100302103944.D9D32185830B@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 06:04:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 06:04:19 -0500 (EST) Subject: [BioCatalogue-developers] [1649] trunk/license.txt: Updated copyright dates on licenses Message-ID: <20100302110419.5D70718582EE@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Mar 2 06:21:33 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 02 Mar 2010 11:21:33 +0000 Subject: [BioCatalogue-developers] Tasks list Message-ID: <4B8CF4BD.1080706@cs.man.ac.uk> Hi guys, I'm going to migrate the Rubyforge task list to JIRA in the next few days. So please don't add any more new tasks on Rubyforge. Cheers, Jits From noreply at rubyforge.org Tue Mar 2 07:07:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 07:07:07 -0500 (EST) Subject: [BioCatalogue-developers] [1650] trunk/app/models/user.rb: Fix for users annotations collection Message-ID: <20100302120707.725141588062@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 07:47:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 07:47:20 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2927] filters disappear when I switch between different views Message-ID: <20100302124721.06CAC18582E7@rubyforge.org> Task #2927 has been updated. Project: BioCatalogue Subproject: Main Summary: filters disappear when I switch between different views Complete: 0% Status: Open Description: when i filter services (e.g by provider, location etc.) and switch to simple view for example, it clears off all the selected filters. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2927&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Tue Mar 2 11:19:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 11:19:51 -0500 (EST) Subject: [BioCatalogue-developers] [1651] trunk/app/models/test_script.rb: allow all plain text files to be uploaded as scripts Message-ID: <20100302161951.D426718582E2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 11:48:59 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 11:48:59 -0500 (EST) Subject: [BioCatalogue-developers] [1652] trunk/app/models/test_script.rb: Added 'application/x-ruby' to list of allowed content types for test script. Message-ID: <20100302164859.A2A6E1858317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 12:41:00 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 12:41:00 -0500 (EST) Subject: [BioCatalogue-developers] [1653] trunk: REST API work: implemented XML for Message-ID: <20100302174100.8B60018582EF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 12:49:55 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 12:49:55 -0500 (EST) Subject: [BioCatalogue-developers] [1654] trunk/app/controllers/application_controller.rb: Point API consumers to the api docs when an error occurs Message-ID: <20100302174955.B94BA18582DE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 2 13:16:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 2 Mar 2010 13:16:42 -0500 (EST) Subject: [BioCatalogue-developers] [1655] trunk: REST API work: modifications of the results API endpoint (XML), and added to schema. Message-ID: <20100302181642.300BD185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Mar 3 04:48:54 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 3 Mar 2010 09:48:54 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4B8CF4BD.1080706@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> Message-ID: Hi Jits, Maybe we need to go through the list and see which one are completed, not relevant or need to be updated (ownership/content) before the migration. We did it a while ago. Franck On 2 March 2010 11:21, Jiten Bhagat wrote: > Hi guys, > > I'm going to migrate the Rubyforge task list to JIRA in the next few > days. So please don't add any more new tasks on Rubyforge. > > Cheers, > Jits > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Mar 3 05:22:16 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 03 Mar 2010 10:22:16 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: References: <4B8CF4BD.1080706@cs.man.ac.uk> Message-ID: <4B8E3858.6020008@cs.man.ac.uk> Franck Tanoh wrote: > Hi Jits, > > Maybe we need to go through the list and see which one are completed, > not relevant or need to be updated (ownership/content) before the > migration. We did it a while ago. I'll be doing a full import (including stuff that was completed / deleted), so that we have the full history in JIRA. After the import we can go through that process. Right now we need to focus on the release. It's 2 weeks late! Jits > > Franck > > On 2 March 2010 11:21, Jiten Bhagat > wrote: > > Hi guys, > > I'm going to migrate the Rubyforge task list to JIRA in the next few > days. So please don't add any more new tasks on Rubyforge. > > Cheers, > Jits > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From ytanoh at cs.man.ac.uk Wed Mar 3 05:48:40 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 3 Mar 2010 10:48:40 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4B8E3858.6020008@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B8E3858.6020008@cs.man.ac.uk> Message-ID: >I'll be doing a full import (including stuff that was completed / >deleted), so that we have the full history in JIRA. After the import we >can go through that process. I see >Right now we need to focus on the release. It's 2 weeks late! We'll get there. my tests haven't revealed any more issues but I'm still playing around with. Franck On 3 March 2010 10:22, Jiten Bhagat wrote: > Franck Tanoh wrote: > > Hi Jits, > > > > Maybe we need to go through the list and see which one are completed, > > not relevant or need to be updated (ownership/content) before the > > migration. We did it a while ago. > > I'll be doing a full import (including stuff that was completed / > deleted), so that we have the full history in JIRA. After the import we > can go through that process. > > Right now we need to focus on the release. It's 2 weeks late! > > Jits > > > > > > Franck > > > > On 2 March 2010 11:21, Jiten Bhagat > > wrote: > > > > Hi guys, > > > > I'm going to migrate the Rubyforge task list to JIRA in the next few > > days. So please don't add any more new tasks on Rubyforge. > > > > Cheers, > > Jits > > > > > > > > > > -- > > "Science knows no country, because knowledge belongs to humanity, and > > is the torch which illuminates the world." - Louis Pasteur > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Mar 3 05:51:17 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 03 Mar 2010 10:51:17 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B8E3858.6020008@cs.man.ac.uk> Message-ID: <4B8E3F25.40008@cs.man.ac.uk> Thanks Franck! Jits Franck Tanoh wrote: > >I'll be doing a full import (including stuff that was completed / > >deleted), so that we have the full history in JIRA. After the import we > >can go through that process. > I see > > >Right now we need to focus on the release. It's 2 weeks late! > We'll get there. my tests haven't revealed any more issues but I'm > still playing around with. > > Franck > > On 3 March 2010 10:22, Jiten Bhagat > wrote: > > Franck Tanoh wrote: > > Hi Jits, > > > > Maybe we need to go through the list and see which one are > completed, > > not relevant or need to be updated (ownership/content) before the > > migration. We did it a while ago. > > I'll be doing a full import (including stuff that was completed / > deleted), so that we have the full history in JIRA. After the > import we > can go through that process. > > Right now we need to focus on the release. It's 2 weeks late! > > Jits > > > > > > Franck > > > > On 2 March 2010 11:21, Jiten Bhagat > > >> wrote: > > > > Hi guys, > > > > I'm going to migrate the Rubyforge task list to JIRA in the > next few > > days. So please don't add any more new tasks on Rubyforge. > > > > Cheers, > > Jits > > > > > > > > > > -- > > "Science knows no country, because knowledge belongs to > humanity, and > > is the torch which illuminates the world." - Louis Pasteur > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Wed Mar 3 06:04:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Mar 2010 06:04:39 -0500 (EST) Subject: [BioCatalogue-developers] [1656] trunk: add submitter to test scripts and show submitter in UI Message-ID: <20100303110439.8674018582DE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 3 07:54:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Mar 2010 07:54:29 -0500 (EST) Subject: [BioCatalogue-developers] [1657] trunk: REST API work: added to index. Message-ID: <20100303125429.E9B0E18582F3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 3 08:14:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Mar 2010 08:14:20 -0500 (EST) Subject: [BioCatalogue-developers] [1658] trunk/app/views: Various fixes for test scripts work. Message-ID: <20100303131420.CA4AC1588079@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 3 09:26:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Mar 2010 09:26:29 -0500 (EST) Subject: [BioCatalogue-developers] [1659] trunk/script/biocatalogue/embrace_test_scripts_import.rb: add default activated_at time for imported scripts Message-ID: <20100303142629.EB5D71858307@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 3 10:22:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Mar 2010 10:22:08 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2928] Add soap_operations to search results web UI Message-ID: <20100303152209.10FDD18582F8@rubyforge.org> Task #2928 has been updated. Project: BioCatalogue Subproject: Main Summary: Add soap_operations to search results web UI Complete: 0% Status: Open Description: Currently, soap_operations are available in the search via the API. Build this into the web UI for search too. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2928&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Mar 3 11:26:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 3 Mar 2010 11:26:02 -0500 (EST) Subject: [BioCatalogue-developers] [1660] trunk: Added soap_operations to search results. Message-ID: <20100303162602.ADC9E1598081@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Mar 4 04:46:04 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 04 Mar 2010 09:46:04 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org Message-ID: <4B8F815C.6050103@cs.man.ac.uk> Eric - I'm assuming that the error notification is not configured properly on test.biocatalogue.org? Or is it just you who gets the error emails? Franck - would you be able to perform some basic testing on http://sandbox.biocatalogue.org please, so I can catch any error notifications that come out it? Thanks, Jits From ytanoh at cs.man.ac.uk Thu Mar 4 05:34:40 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 4 Mar 2010 10:34:40 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org In-Reply-To: <4B8F815C.6050103@cs.man.ac.uk> References: <4B8F815C.6050103@cs.man.ac.uk> Message-ID: I've tested it, even tried to create some error on purpose... did you get any notifications? Franck On 4 March 2010 09:46, Jiten Bhagat wrote: > Eric - I'm assuming that the error notification is not configured > properly on test.biocatalogue.org? Or is it just you who gets the error > emails? > > Franck - would you be able to perform some basic testing on > http://sandbox.biocatalogue.org please, so I can catch any error > notifications that come out it? > > Thanks, > Jits > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Mar 4 05:37:09 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 04 Mar 2010 10:37:09 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org In-Reply-To: References: <4B8F815C.6050103@cs.man.ac.uk> Message-ID: <4B8F8D55.7060909@cs.man.ac.uk> Hi Franck, Franck Tanoh wrote: > I've tested it, even tried to create some error on purpose... did you > get any notifications? Yeap, I got some for some duplicate annotations you were trying to add. Though I meant that you should test the functionality out in case of any bugs. I had already set up the error notification on sandbox a while back and knew it was working :-) Thanks for testing! Cheers, Jits > > Franck > > On 4 March 2010 09:46, Jiten Bhagat > wrote: > > Eric - I'm assuming that the error notification is not configured > properly on test.biocatalogue.org ? > Or is it just you who gets the error > emails? > > Franck - would you be able to perform some basic testing on > http://sandbox.biocatalogue.org please, so I can catch any error > notifications that come out it? > > Thanks, > Jits > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Thu Mar 4 05:51:10 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 04 Mar 2010 10:51:10 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org In-Reply-To: References: <4B8F815C.6050103@cs.man.ac.uk> Message-ID: <4B8F909E.3040800@ebi.ac.uk> Franck Tanoh wrote: > I've tested it, even tried to create some error on purpose... did you > get any notifications? > > Franck > > On 4 March 2010 09:46, Jiten Bhagat > wrote: > > Eric - I'm assuming that the error notification is not configured > properly on test.biocatalogue.org ? > Or is it just you who gets the error > I switched off emailing so you would not not get any error notifications. That was on purpose to run the embrace scripts and I think emailing should be normally switched off in dev unless it the emailing process itself that is being tested. Now I am also wondering whether sending email on every error occurrence is a good idea. We can easily become spammers though to ourselves. Maybe we need to look at a way of recording errors and maybe generating an email on a regular basis in case of errors. That way we may be able to configure at what rate we receive the mails. Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu Mar 4 06:02:26 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 04 Mar 2010 11:02:26 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org In-Reply-To: <4B8F909E.3040800@ebi.ac.uk> References: <4B8F815C.6050103@cs.man.ac.uk> <4B8F909E.3040800@ebi.ac.uk> Message-ID: <4B8F9342.4020802@cs.man.ac.uk> Eric, Eric Nzuobontane wrote: > Franck Tanoh wrote: >> I've tested it, even tried to create some error on purpose... did you >> get any notifications? >> >> Franck >> >> On 4 March 2010 09:46, Jiten Bhagat > > wrote: >> >> Eric - I'm assuming that the error notification is not configured >> properly on test.biocatalogue.org ? >> Or is it just you who gets the error >> > > I switched off emailing so you would not not get any error > notifications. That was on purpose to run the embrace scripts and I > think emailing should be normally switched off in dev unless it the > emailing process itself that is being tested. The immediate concern is on testing this release, and error notifications are essential for this (this is how I caught the bugs for the API, during Sergey's use of sandbox). In the case of sending emails, yes, it should be switched off in *dev* environments, but we need to think about test environments a bit more... E.g: in a test environment, I want to be able to test that user sign ups are working. Therefore I need to be able to receive the signup email. Or I may want to test some other feature that relies on emails being sent. My opinion is that test environments should very closely mimic live environments. Otherwise you're not sure to be testing things properly. But in cases of the EMBRACE import it makes sense to switch emailing off *temporarily*. Another best practice is to scramble/reset all real emails in the db (I have written a script [or rake task] to do that). Therefore no real emails will ever be sent emails. > > Now I am also wondering whether sending email on every error > occurrence is a good idea. We can easily become spammers though to > ourselves. Maybe we need to look at a way of recording errors and > maybe generating an email on a regular basis in case of errors. That > way we may be able to configure at what rate we receive the mails. Feel free to dedicate some time to doing this if you want. For now, the current system I put in place does the job but it could be tweaked (or replaced). I don't see that we have the resources to do this though. We need a way of getting error reports, otherwise we reduce the chances of catching bugs during testing and live production (as we then only get the ones people are bothered to inform us about). Jits > > Eric > > > From ericnzuo at ebi.ac.uk Thu Mar 4 06:15:14 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 04 Mar 2010 11:15:14 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org In-Reply-To: <4B8F9342.4020802@cs.man.ac.uk> References: <4B8F815C.6050103@cs.man.ac.uk> <4B8F909E.3040800@ebi.ac.uk> <4B8F9342.4020802@cs.man.ac.uk> Message-ID: <4B8F9642.2000304@ebi.ac.uk> OK. I have switched on the emailing now. If you do not mind Franck, could you on purpose attempt to generate the errors again? Eric Jiten Bhagat wrote: > Eric, > > Eric Nzuobontane wrote: > >> Franck Tanoh wrote: >> >>> I've tested it, even tried to create some error on purpose... did you >>> get any notifications? >>> >>> Franck >>> >>> On 4 March 2010 09:46, Jiten Bhagat >> > wrote: >>> >>> Eric - I'm assuming that the error notification is not configured >>> properly on test.biocatalogue.org ? >>> Or is it just you who gets the error >>> >>> >> I switched off emailing so you would not not get any error >> notifications. That was on purpose to run the embrace scripts and I >> think emailing should be normally switched off in dev unless it the >> emailing process itself that is being tested. >> > > The immediate concern is on testing this release, and error > notifications are essential for this (this is how I caught the bugs for > the API, during Sergey's use of sandbox). > > In the case of sending emails, yes, it should be switched off in *dev* > environments, but we need to think about test environments a bit more... > > E.g: in a test environment, I want to be able to test that user sign ups > are working. Therefore I need to be able to receive the signup email. Or > I may want to test some other feature that relies on emails being sent. > > My opinion is that test environments should very closely mimic live > environments. Otherwise you're not sure to be testing things properly. > But in cases of the EMBRACE import it makes sense to switch emailing off > *temporarily*. Another best practice is to scramble/reset all real > emails in the db (I have written a script [or rake task] to do that). > Therefore no real emails will ever be sent emails. > > >> Now I am also wondering whether sending email on every error >> occurrence is a good idea. We can easily become spammers though to >> ourselves. Maybe we need to look at a way of recording errors and >> maybe generating an email on a regular basis in case of errors. That >> way we may be able to configure at what rate we receive the mails. >> > > Feel free to dedicate some time to doing this if you want. For now, the > current system I put in place does the job but it could be tweaked (or > replaced). I don't see that we have the resources to do this though. > > We need a way of getting error reports, otherwise we reduce the chances > of catching bugs during testing and live production (as we then only get > the ones people are bothered to inform us about). > > Jits > > >> Eric >> >> >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Thu Mar 4 06:24:29 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 4 Mar 2010 11:24:29 +0000 Subject: [BioCatalogue-developers] Fwd: "Linked Data is merely more data" paper In-Reply-To: <4B8F823F.5040201@cs.man.ac.uk> References: <4B8F823F.5040201@cs.man.ac.uk> Message-ID: You might find this useful Franck ---------- Forwarded message ---------- From: Paolo Missier Date: 4 March 2010 09:49 Subject: "Linked Data is merely more data" paper To: Robert Stevens , Sean Bechhofer < sean.bechhofer at manchester.ac.uk>, Carole Goble < carole.goble at manchester.ac.uk>, khalidb at cs.man.ac.uk, Katy Wolstencroft < katy at cs.man.ac.uk>, Peter Li , Matthew Gamble < matthew.gamble at gmail.com>, Norman Paton , Jiten Bhagat < jits at cs.man.ac.uk>, Franck Tanoh , David De Roure < dder at ecs.soton.ac.uk> as mentioned in today's meeting: http://dl.dropbox.com/u/2533177/linkedai2010_submission_13.pdf just a short position paper, but an interesting position -Paolo -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pmissier.vcf Type: text/x-vcard Size: 398 bytes Desc: not available URL: From jits at cs.man.ac.uk Thu Mar 4 06:30:17 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 04 Mar 2010 11:30:17 +0000 Subject: [BioCatalogue-developers] Testing on test.biocatalogue.org In-Reply-To: <4B8F9642.2000304@ebi.ac.uk> References: <4B8F815C.6050103@cs.man.ac.uk> <4B8F909E.3040800@ebi.ac.uk> <4B8F9342.4020802@cs.man.ac.uk> <4B8F9642.2000304@ebi.ac.uk> Message-ID: <4B8F99C9.2050002@cs.man.ac.uk> Eric Nzuobontane wrote: > OK. I have switched on the emailing now. If you do not mind Franck, > could you on purpose attempt to generate the errors again? http://test.biocatalogue.org/fail/500 can be used to purposely generate an error. Jits > > Eric > > > > > Jiten Bhagat wrote: >> Eric, >> >> Eric Nzuobontane wrote: >> >>> Franck Tanoh wrote: >>> >>>> I've tested it, even tried to create some error on purpose... did you >>>> get any notifications? >>>> >>>> Franck >>>> >>>> On 4 March 2010 09:46, Jiten Bhagat >>> > wrote: >>>> >>>> Eric - I'm assuming that the error notification is not configured >>>> properly on test.biocatalogue.org ? >>>> Or is it just you who gets the error >>>> >>>> >>> I switched off emailing so you would not not get any error >>> notifications. That was on purpose to run the embrace scripts and I >>> think emailing should be normally switched off in dev unless it the >>> emailing process itself that is being tested. >>> >> >> The immediate concern is on testing this release, and error >> notifications are essential for this (this is how I caught the bugs for >> the API, during Sergey's use of sandbox). >> >> In the case of sending emails, yes, it should be switched off in *dev* >> environments, but we need to think about test environments a bit more... >> >> E.g: in a test environment, I want to be able to test that user sign ups >> are working. Therefore I need to be able to receive the signup email. Or >> I may want to test some other feature that relies on emails being sent. >> >> My opinion is that test environments should very closely mimic live >> environments. Otherwise you're not sure to be testing things properly. >> But in cases of the EMBRACE import it makes sense to switch emailing off >> *temporarily*. Another best practice is to scramble/reset all real >> emails in the db (I have written a script [or rake task] to do that). >> Therefore no real emails will ever be sent emails. >> >> >>> Now I am also wondering whether sending email on every error >>> occurrence is a good idea. We can easily become spammers though to >>> ourselves. Maybe we need to look at a way of recording errors and >>> maybe generating an email on a regular basis in case of errors. That >>> way we may be able to configure at what rate we receive the mails. >>> >> >> Feel free to dedicate some time to doing this if you want. For now, the >> current system I put in place does the job but it could be tweaked (or >> replaced). I don't see that we have the resources to do this though. >> >> We need a way of getting error reports, otherwise we reduce the chances >> of catching bugs during testing and live production (as we then only get >> the ones people are bothered to inform us about). >> >> Jits >> >> >>> Eric >>> >>> >>> >>> > > From noreply at rubyforge.org Thu Mar 4 06:49:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 06:49:42 -0500 (EST) Subject: [BioCatalogue-developers] [1662] trunk/app/views/services/_index_filters.html.erb: Reduced the number of filters shown for tags, to improve perf. Message-ID: <20100304114942.E12A618582D0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 4 06:53:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 06:53:11 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2929] Add caching to filters in filtering sidebar Message-ID: <20100304115311.C32C918582BF@rubyforge.org> Task #2929 has been updated. Project: BioCatalogue Subproject: Main Summary: Add caching to filters in filtering sidebar Complete: 0% Status: Open Description: Currently the filtering sidebar is generated on each request. This is not scalable. Some caching work is required. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2929&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Mar 4 06:55:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 06:55:08 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2930] Tag filters limiting not working properly Message-ID: <20100304115508.5ABB718582D2@rubyforge.org> Task #2930 has been updated. Project: BioCatalogue Subproject: Main Summary: Tag filters limiting not working properly Complete: 0% Status: Open Description: There is a bug in the tag filters limiting which causes incorrect limiting of tags. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2930&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Thu Mar 4 06:56:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 06:56:22 -0500 (EST) Subject: [BioCatalogue-developers] [1663] trunk/app/views/services/_index_filters.html.erb: Reverted previous change to tag filters limiting due to a bug in the tag filters limiting code . Message-ID: <20100304115622.6221518582D3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 4 07:43:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 07:43:47 -0500 (EST) Subject: [BioCatalogue-developers] [1664] trunk/app/models/test_script.rb: Test Scripts work : bug fix Message-ID: <20100304124348.12A6918582D2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 4 07:51:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 07:51:10 -0500 (EST) Subject: [BioCatalogue-developers] [1665] trunk/vendor/embrace_scripts/src: run only activated scripts Message-ID: <20100304125110.2768818582E4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 4 08:37:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 08:37:10 -0500 (EST) Subject: [BioCatalogue-developers] [1666] trunk/lib/bio_catalogue/filtering/services.rb: Minor fix Message-ID: <20100304133710.8DE9B18582E4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 4 09:23:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 09:23:05 -0500 (EST) Subject: [BioCatalogue-developers] [1667] branches/integration-jan10: NEW REST SUPPORT WORK ( done after prep for first March release) Message-ID: <20100304142305.43AB818582DC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 4 12:15:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 4 Mar 2010 12:15:54 -0500 (EST) Subject: [BioCatalogue-developers] [1668] trunk/lib/bio_catalogue/search.rb: Search should only happen is search is actually on! Message-ID: <20100304171554.C9BE218582F7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 03:08:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 03:08:33 -0500 (EST) Subject: [BioCatalogue-developers] [1669] trunk: Message-ID: <20100305080833.18FE515B8029@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Fri Mar 5 03:14:11 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 05 Mar 2010 08:14:11 +0000 Subject: [BioCatalogue-developers] Maintenance message Message-ID: <4B90BD53.9070206@cs.man.ac.uk> Eric, As discussed earlier this morning... I've committed (in rev 1669) a new way of easily adding maintenance messages and other important announcements to the site. All you need to do now is set something like (in the biocat_local.rb config file): HEADER_MESSAGE = "The BioCatalogue will be undergoing maintenance on Tuesday March 9th 2010 between 16:00-19:00 GMT" ... and this will automatically show up on the top of every page. Note that you can add any HTML within this message (like tags etc). By default the text is in a maroon colour. Please can you update *ONLY* the following file on the live server: app/views/layouts/application_wide.html.erb And then add the above config line to: config/initializers/biocat_local.rb Then restart the app server(s). Jits From noreply at rubyforge.org Fri Mar 5 04:00:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 04:00:09 -0500 (EST) Subject: [BioCatalogue-developers] [1670] trunk: REST API work: implemented /soap_operations index ( with tag filtering) and /soap_operations/filters. Message-ID: <20100305090009.A78DF15B8029@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 04:23:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 04:23:50 -0500 (EST) Subject: [BioCatalogue-developers] [1671] trunk: REST API work: added to the related links for . Message-ID: <20100305092350.4CC1418582DF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 05:56:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 05:56:45 -0500 (EST) Subject: [BioCatalogue-developers] [1672] trunk/app/views/layouts/application_wide.html.erb: Made the header message bigger and also search engine friendly (it won' t get revealed to search engines). Message-ID: <20100305105645.B1E9215B8029@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 06:02:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 06:02:10 -0500 (EST) Subject: [BioCatalogue-developers] [1673] trunk: REST API work: renamed to , and < hostedVersion> in to . Message-ID: <20100305110210.6F51B15B8029@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 06:09:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 06:09:39 -0500 (EST) Subject: [BioCatalogue-developers] [1674] trunk/script/biocatalogue/api/tests: REST API work: added tests for service deployment. Message-ID: <20100305110939.1A90318582EA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 06:14:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 06:14:30 -0500 (EST) Subject: [BioCatalogue-developers] [1675] trunk/lib/bio_catalogue/filtering/soap_operations.rb: Disabled some debugging comments. Message-ID: <20100305111430.9FFDA18582EA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 06:24:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 06:24:02 -0500 (EST) Subject: [BioCatalogue-developers] [1676] trunk: REST API work: fixes. Message-ID: <20100305112402.DD62918582DD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 09:33:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 09:33:49 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2931] Refactor filtering UI to use new filters code Message-ID: <20100305143349.BC9D118582E1@rubyforge.org> Task #2931 has been updated. Project: BioCatalogue Subproject: Main Summary: Refactor filtering UI to use new filters code Complete: 0% Status: Open Description: A new mechanism has been implemented to load up all available filter groups for a resource type. See: BioCatalogue::Filtering.get_all_filter_groups_for The filtering in the services index needs to be updated to use this instead of loading up filters in the views. That way caching, etc can be done in one place. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2931&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Mar 5 09:34:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 09:34:26 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2932] Add link to "filter these services" on search Message-ID: <20100305143426.5490A18582DD@rubyforge.org> Task #2932 has been updated. Project: BioCatalogue Subproject: Main Summary: Add link to "filter these services" on search Complete: 0% Status: Open Description: For services in the search results, add a button to "filter these services" ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2932&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Mar 5 09:55:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 09:55:56 -0500 (EST) Subject: [BioCatalogue-developers] [1677] trunk/app/views: Work on service discovery and filtering: now there is the option to "filter these services" after a search is done, which will take the user to the services index with the search already applied and filters ready for use . Message-ID: <20100305145556.ECBDC18582D6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 10:58:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 10:58:54 -0500 (EST) Subject: [BioCatalogue-developers] [1678] trunk/app/views/search/show.html.erb: Disabled the " filter these services" link on search, for now. Message-ID: <20100305155854.4062718582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 5 11:12:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 11:12:23 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2933] show filters pop up when 'filterservice' is selected Message-ID: <20100305161223.6D80E18582EA@rubyforge.org> Task #2933 has been updated. Project: BioCatalogue Subproject: Main Summary: show filters pop up when 'filterservice' is selected Complete: 0% Status: Open Description: When users select 'filter these services' they will be presented with a filter pop up menu. They can then select the required filters. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2933&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Mar 5 12:20:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 5 Mar 2010 12:20:17 -0500 (EST) Subject: [BioCatalogue-developers] [1679] trunk: REST API work: the structure of the top level resource and in parameters have been changed to something like this: Message-ID: <20100305172017.CA70E18582CB@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Mon Mar 8 04:46:12 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 08 Mar 2010 09:46:12 +0000 Subject: [BioCatalogue-developers] [Biocatalogue-support] - Functional testing for BioCatalogue In-Reply-To: References: <36813.86.1.40.156.1267244864.squirrel@webmail.ebi.ac.uk> <41824.86.1.40.156.1267272020.squirrel@webmail.ebi.ac.uk> <48160.86.1.40.156.1267321933.squirrel@webmail.ebi.ac.uk> <4B8BA6D2.8040107@ebi.ac.uk> Message-ID: <4B94C764.5010705@ebi.ac.uk> Hi Franck, I have been looking around over the weekend for a tool that could help us with functional testing of the BioCatalogue. There are a host of tools available as can be seen from this list http://www.opensourcetesting.org/functional.php . At the EBI some groups are also currently considering some of these tools for testing other EBI applications/resources. There is an inclination towards selenium and as far as I have seen, it does satisfy our basic requirement. This basic requirements in my opinion is being able to record the most critical scenarios and replaying them each time there is an update. Selenium has a firefox plugin with an IDE for recording browser activity and the possibility to export these into scripts, with many languages supported including ruby. These can be collected as a set of functional tests. I would suggest we try to build our functional testing around selenium http://seleniumhq.org/ , at least for the start and if it becomes inadequate we may move to something else, though I doubt we have the resource to push it to its limits. So we can start with Franck's DRAMA to build out first set of functional tests. What do you guys think? Eric Franck Tanoh wrote: > Good point. We need proper test infrastructures and possibly automate > some of the process. > Do you know any software or tools around we may use in the process? > > Usually my manual test is around those 5 elements: (DRAMA) Discover, > Register, Annotate, Monitor, AOB > I'll write it down. > > I wonder what myExperiment team does for testing - Jits do you have > the answer? > > Franck > > On 1 March 2010 11:36, Eric Nzuobontane > wrote: > > Hi Franck, > > Thanks for those comments. As the application is growing so will > the number of things to test. And updating and checking all of > those things may not always possible especially if one has no > 'written test cases'. Would it be possible for you to write down > these test cases so that with every update we will remember to go > through them and have more confidence on the application status? > > Eric > > Franck Tanoh wrote: > > Hi Eric, > > Some more issues: > 1-Search within doesn't work > 2-latest service out of the box (homepage), same issue with > the latest activity box but seems to have disappeared. > 3-could not submit that service: > http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl > > 4-search by data link doesn't work > 5-anytime i add a service to my favorite the site takes me to > the operation page. > 6-couldn't enable tag filter carried out by the server> > 7-when i filter services (e.g by provider, location etc.) and > switch to simple view for example, it clears off all the > selected filters. > > Everything else seems to be working fine for now... > > Cheers, > Franck > > > On 28 February 2010 01:52, >> wrote: > > > Hi Franck, > That problem should be fixed now. Please test to confirm. Also > please let > me know as soon as you spot anything else. > > Eric > > > Hi Eric, > > > > While checking the test site I've noticed that I am unable to > add/register > > anything (description, tags, new services, etc). > > > > Franck > > > > On 27 February 2010 12:00, > >> wrote: > > > >> Hi Franck, > >> I could send you a script but I think a good test would > be to just > >> download one from the embrace registry and add it > against the > >> corresponding service in BioCatalogue. Possibly one of the > soaplab ones. > >> Another test is to try to upload a file that is not, python, > perl, ruby, > >> xml or zip. It should not allow you. > >> > >> I will run the embrace import on the test site this > afternoon > and the > >> import of the embrace scripts afterwards. > >> > >> Eric > >> > >> > >> > Good job guys, > >> > > >> > Eric, I'll take a look later on. Anything particular i > should > pay more > >> > attention to? > >> > For the test script bit I don't have any script to > check that > feature; > >> do > >> > you think you could supply me with some? > >> > > >> > Franck > >> > > >> > On 27 February 2010 04:27, > >> wrote: > >> > > >> >> Hi Guys, > >> >> OK, it has been a long evening but the test site is now > updated. Not > >> >> really test that everything works as expected...that > is for this > >> >> afternoon. Would be great if Franck in particular could > test.. later > >> >> > >> >> Eric > >> >> > >> >> _______________________________________________ > >> >> Biocatalogue-support mailing list > >> >> Biocatalogue-support at rubyforge.org > > > > > >> >> > http://rubyforge.org/mailman/listinfo/biocatalogue-support > >> >> > >> > > >> > > >> > > >> > -- > >> > "Science knows no country, because knowledge belongs to > humanity, and > >> is > >> > the > >> > torch which illuminates the world." - Louis Pasteur > >> > > >> > >> > >> > > > > > > -- > > "Science knows no country, because knowledge belongs to > humanity, and is > > the > > torch which illuminates the world." - Louis Pasteur > > > > > > > > -- > "Science knows no country, because knowledge belongs to > humanity, and is the torch which illuminates the world." - > Louis Pasteur > > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Mar 8 05:39:18 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 08 Mar 2010 10:39:18 +0000 Subject: [BioCatalogue-developers] [Biocatalogue-support] - Functional testing for BioCatalogue In-Reply-To: <4B94C764.5010705@ebi.ac.uk> References: <36813.86.1.40.156.1267244864.squirrel@webmail.ebi.ac.uk> <41824.86.1.40.156.1267272020.squirrel@webmail.ebi.ac.uk> <48160.86.1.40.156.1267321933.squirrel@webmail.ebi.ac.uk> <4B8BA6D2.8040107@ebi.ac.uk> <4B94C764.5010705@ebi.ac.uk> Message-ID: <4B94D3D6.2000008@cs.man.ac.uk> Eric, Good idea. Selenium is a tried and tested tool and we should definitely use it (it's been on my list for a testing the UI for a while now). Franck, if you could try out this plugin to record your steps and then send us the scripts that would be very useful! Cheers, Jits Eric Nzuobontane wrote: > Hi Franck, > > I have been looking around over the weekend for a tool that could help > us with functional testing of the BioCatalogue. There are a host of > tools available as can be seen from this list > http://www.opensourcetesting.org/functional.php . At the EBI some > groups are also currently considering some of these tools for testing > other EBI applications/resources. There is an inclination towards > selenium and as far as I have seen, it does satisfy our basic > requirement. This basic requirements in my opinion is being able to > record the most critical scenarios and replaying them each time there > is an update. > > Selenium has a firefox plugin with an IDE for recording browser > activity and the possibility to export these into scripts, with many > languages supported including ruby. These can be collected as a set of > functional tests. I would suggest we try to build our functional > testing around selenium http://seleniumhq.org/ , at least for the > start and if it becomes inadequate we may move to something else, > though I doubt we have the resource to push it to its limits. So we > can start with Franck's DRAMA to build out first set of functional tests. > > What do you guys think? > > Eric > > > > Franck Tanoh wrote: >> Good point. We need proper test infrastructures and possibly automate >> some of the process. >> Do you know any software or tools around we may use in the process? >> >> Usually my manual test is around those 5 elements: (DRAMA) Discover, >> Register, Annotate, Monitor, AOB >> I'll write it down. >> >> I wonder what myExperiment team does for testing - Jits do you have >> the answer? >> >> Franck >> >> On 1 March 2010 11:36, Eric Nzuobontane > > wrote: >> >> Hi Franck, >> >> Thanks for those comments. As the application is growing so will >> the number of things to test. And updating and checking all of >> those things may not always possible especially if one has no >> 'written test cases'. Would it be possible for you to write down >> these test cases so that with every update we will remember to go >> through them and have more confidence on the application status? >> >> Eric >> >> Franck Tanoh wrote: >> >> Hi Eric, >> >> Some more issues: >> 1-Search within doesn't work >> 2-latest service out of the box (homepage), same issue with >> the latest activity box but seems to have disappeared. >> 3-could not submit that service: >> http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap.cgi?wsdl >> >> 4-search by data link doesn't work >> 5-anytime i add a service to my favorite the site takes me to >> the operation page. >> 6-couldn't enable tag filter > carried out by the server> >> 7-when i filter services (e.g by provider, location etc.) and >> switch to simple view for example, it clears off all the >> selected filters. >> >> Everything else seems to be working fine for now... >> >> Cheers, >> Franck >> >> >> On 28 February 2010 01:52, > > >> wrote: >> >> >> Hi Franck, >> That problem should be fixed now. Please test to confirm. >> Also >> please let >> me know as soon as you spot anything else. >> >> Eric >> >> > Hi Eric, >> > >> > While checking the test site I've noticed that I am >> unable to >> add/register >> > anything (description, tags, new services, etc). >> > >> > Franck >> > >> > On 27 February 2010 12:00, > >> >> >> wrote: >> > >> >> Hi Franck, >> >> I could send you a script but I think a good test would >> be to just >> >> download one from the embrace registry and add it >> against the >> >> corresponding service in BioCatalogue. Possibly one of the >> soaplab ones. >> >> Another test is to try to upload a file that is not, >> python, >> perl, ruby, >> >> xml or zip. It should not allow you. >> >> >> >> I will run the embrace import on the test site this >> afternoon >> and the >> >> import of the embrace scripts afterwards. >> >> >> >> Eric >> >> >> >> >> >> > Good job guys, >> >> > >> >> > Eric, I'll take a look later on. Anything particular i >> should >> pay more >> >> > attention to? >> >> > For the test script bit I don't have any script to >> check that >> feature; >> >> do >> >> > you think you could supply me with some? >> >> > >> >> > Franck >> >> > >> >> > On 27 February 2010 04:27, > >> >> >> wrote: >> >> > >> >> >> Hi Guys, >> >> >> OK, it has been a long evening but the test site is now >> updated. Not >> >> >> really test that everything works as expected...that >> is for this >> >> >> afternoon. Would be great if Franck in particular could >> test.. later >> >> >> >> >> >> Eric >> >> >> >> >> >> _______________________________________________ >> >> >> Biocatalogue-support mailing list >> >> >> Biocatalogue-support at rubyforge.org >> >> > > >> >> >> >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-support >> >> >> >> >> > >> >> > >> >> > >> >> > -- >> >> > "Science knows no country, because knowledge belongs to >> humanity, and >> >> is >> >> > the >> >> > torch which illuminates the world." - Louis Pasteur >> >> > >> >> >> >> >> >> >> > >> > >> > -- >> > "Science knows no country, because knowledge belongs to >> humanity, and is >> > the >> > torch which illuminates the world." - Louis Pasteur >> > >> >> >> >> >> >> -- "Science knows no country, because knowledge >> belongs to >> humanity, and is the torch which illuminates the world." - >> Louis Pasteur >> >> >> >> -- Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur > > From noreply at rubyforge.org Mon Mar 8 07:34:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Mar 2010 07:34:08 -0500 (EST) Subject: [BioCatalogue-developers] [1680] trunk/vendor/embrace_scripts/src/testscript_runner.py: send only status message back to app, not log Message-ID: <20100308123408.1D37618582DA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 8 07:34:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 8 Mar 2010 07:34:25 -0500 (EST) Subject: [BioCatalogue-developers] [1681] branches/integration-jan10/app: REST SUPPORT WORK Message-ID: <20100308123425.408F818582DC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 9 06:56:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Mar 2010 06:56:43 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2934] ATOM feed for latest activity feed Message-ID: <20100309115643.CAC781598084@rubyforge.org> Task #2934 has been updated. Project: BioCatalogue Subproject: Main Summary: ATOM feed for latest activity feed Complete: 0% Status: Open Description: Implement an ATOM feed for the latest activity ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2934&group_id=6901&group_project_id=12540 From ytanoh at cs.man.ac.uk Tue Mar 9 11:39:51 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 9 Mar 2010 16:39:51 +0000 Subject: [BioCatalogue-developers] Biocat developer list Message-ID: Hi Steve, As agreed yesterday, please subscribe the biocatalogue developer list (cc) to the Embrace developer list so that we can be notified of any service/test updates in the Embrace Registry. Thanks, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Tue Mar 9 16:28:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 9 Mar 2010 16:28:21 -0500 (EST) Subject: [BioCatalogue-developers] [1682] trunk/app/views/api/show.xml.builder: REST API work: added soap_operations index and it's filters to the root document. Message-ID: <20100309212822.02B3F18582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Mar 9 19:28:13 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 10 Mar 2010 00:28:13 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4B8CF4BD.1080706@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> Message-ID: <4B96E79D.4040206@cs.man.ac.uk> Hi guys, I've finally received the data dump for the tasks list from the Rubyforge guys. So hopefully in the next week or so I'll have it migrated. So from now on please don't add any new tasks to Rubyforge. These won't make it to JIRA and will be lost when we (eventually) delete the Rubyforge tasks list. Cheers, Jits Jiten Bhagat wrote: > Hi guys, > > I'm going to migrate the Rubyforge task list to JIRA in the next few > days. So please don't add any more new tasks on Rubyforge. > > Cheers, > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Wed Mar 10 05:07:36 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 10 Mar 2010 10:07:36 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4B96E79D.4040206@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B96E79D.4040206@cs.man.ac.uk> Message-ID: <4B976F68.7080600@ebi.ac.uk> OK. Does that mean we can start using Jira? Eric Jiten Bhagat wrote: > Hi guys, > > I've finally received the data dump for the tasks list from the > Rubyforge guys. So hopefully in the next week or so I'll have it migrated. > > So from now on please don't add any new tasks to Rubyforge. These won't > make it to JIRA and will be lost when we (eventually) delete the > Rubyforge tasks list. > > Cheers, > Jits > > > Jiten Bhagat wrote: > >> Hi guys, >> >> I'm going to migrate the Rubyforge task list to JIRA in the next few >> days. So please don't add any more new tasks on Rubyforge. >> >> Cheers, >> Jits >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Wed Mar 10 05:11:25 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 10 Mar 2010 10:11:25 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4B976F68.7080600@ebi.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B96E79D.4040206@cs.man.ac.uk> <4B976F68.7080600@ebi.ac.uk> Message-ID: <4B97704D.6040107@cs.man.ac.uk> Yeap, you can put *new* tasks in there, but I still need to migrate the existing ones into there. Please can anyone who needs an account for JIRA let me know (giving me their preferred email address). Cheers, Jits Eric Nzuobontane wrote: > OK. Does that mean we can start using Jira? > > Eric > > > > Jiten Bhagat wrote: >> Hi guys, >> >> I've finally received the data dump for the tasks list from the >> Rubyforge guys. So hopefully in the next week or so I'll have it >> migrated. >> >> So from now on please don't add any new tasks to Rubyforge. These won't >> make it to JIRA and will be lost when we (eventually) delete the >> Rubyforge tasks list. >> >> Cheers, >> Jits >> >> >> Jiten Bhagat wrote: >> >>> Hi guys, >>> >>> I'm going to migrate the Rubyforge task list to JIRA in the next few >>> days. So please don't add any more new tasks on Rubyforge. >>> >>> Cheers, >>> Jits >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > > From ericnzuo at ebi.ac.uk Wed Mar 10 05:13:30 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 10 Mar 2010 10:13:30 +0000 Subject: [BioCatalogue-developers] BioCatalogue update Message-ID: <4B9770CA.5090506@ebi.ac.uk> Hi guys, I updated the code last night but because of connectivity issues I had from home, I could not run the imports. I did not think it wise to send a mail to the list stating this I suspected it could create unnecessary anxiety. I will do the imports now and restart the servers. There will be no downtime as the import do run while the application is up. I will restart of the application when the import is done but I do not expect users to notice anything. cheers, Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Wed Mar 10 06:24:13 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 10 Mar 2010 11:24:13 +0000 Subject: [BioCatalogue-developers] BioCatalogue update In-Reply-To: <4B9770CA.5090506@ebi.ac.uk> References: <4B9770CA.5090506@ebi.ac.uk> Message-ID: Hi Eric, Thanks for the updates. I'm giving a tutorial tomorrow with over 20 people who may use the biocat at once. So if we could finish the updates today that will be extremely good. It will also give me the time to do some testing. Franck On 10 March 2010 10:13, Eric Nzuobontane wrote: > Hi guys, > > I updated the code last night but because of connectivity issues I had from > home, I could not run the imports. I did not think it wise to send a mail to > the list stating this ?I suspected it could create unnecessary anxiety. I > will do the imports now and restart the servers. There ?will be no downtime > as the import do run while the application is up. I will restart of the > application when the import is done but I do not expect users to notice > anything. > > cheers, > > Eric > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Wed Mar 10 06:32:49 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 10 Mar 2010 11:32:49 +0000 Subject: [BioCatalogue-developers] BioCatalogue update In-Reply-To: References: <4B9770CA.5090506@ebi.ac.uk> Message-ID: <4B978361.5020506@ebi.ac.uk> Yes, the update will be complete today. The embrace services import is running now. As soon as it is done, I will run the test script import and that should be it with the import. Then it is a matter of making sure that all services are functioning as expected. Eric Franck Tanoh wrote: > Hi Eric, > > Thanks for the updates. > I'm giving a tutorial tomorrow with over 20 people who may use the > biocat at once. So if we could finish the updates today that will be > extremely good. It will also give me the time to do some testing. > > Franck > > On 10 March 2010 10:13, Eric Nzuobontane wrote: > >> Hi guys, >> >> I updated the code last night but because of connectivity issues I had from >> home, I could not run the imports. I did not think it wise to send a mail to >> the list stating this I suspected it could create unnecessary anxiety. I >> will do the imports now and restart the servers. There will be no downtime >> as the import do run while the application is up. I will restart of the >> application when the import is done but I do not expect users to notice >> anything. >> >> cheers, >> >> Eric >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Wed Mar 10 07:09:14 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Mar 2010 07:09:14 -0500 (EST) Subject: [BioCatalogue-developers] [1683] branches/integration-jan10: REST SUPPORT WORK Message-ID: <20100310120914.7455B18582CB@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 10 07:42:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Mar 2010 07:42:58 -0500 (EST) Subject: [BioCatalogue-developers] [1684] trunk/app/views/services/show.xml.builder: bugfix : show_versions -> show_variants Message-ID: <20100310124258.2BB5B18582DC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 10 09:49:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Mar 2010 09:49:38 -0500 (EST) Subject: [BioCatalogue-developers] [1685] branches/integration-jan10/app/views/rest_parameters: REST SUPPORT WORK Message-ID: <20100310144938.14B3618582E4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 10 10:29:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Mar 2010 10:29:23 -0500 (EST) Subject: [BioCatalogue-developers] [1686] trunk/app/views/soap_services/deployments.xml.builder: REST API work : bugfix for /soap_services/{id}/deployments Message-ID: <20100310152923.A456318582F1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 10 10:38:26 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Mar 2010 10:38:26 -0500 (EST) Subject: [BioCatalogue-developers] [1687] trunk/lib/bio_catalogue/util.rb: REST API work: implemented finders for SoapInput and SoapOutput for /lookup Message-ID: <20100310153826.E821618582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 10 10:47:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 10 Mar 2010 10:47:48 -0500 (EST) Subject: [BioCatalogue-developers] [1688] trunk/lib/bio_catalogue/stats.rb: Bugfix for stats generation Message-ID: <20100310154748.3995318582EE@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Mar 11 04:26:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 11 Mar 2010 09:26:47 +0000 Subject: [BioCatalogue-developers] embrace test harness Message-ID: <4B98B757.30506@ebi.ac.uk> Hi Steve/Phil, I am seeing some discrepancies between test results on the embrace and biocatalogue registries. They are mostly to do with the INB services. An example is http://www.embraceregistry.net/test/inbmmbpcbubesplotfeatureaasequence1 and http://www.biocatalogue.org/services/2613-plotfeatureaasequenceservice_7718 According to the embrace logs, the last time this test was run was a day ago. So the status may have changed since the last run. What I am not sure about is how frequently these tests are run on the embrace registry. If I look at this service http://www.embraceregistry.net/test/inbinbbscesrunembossdigestfromsequence1 http://www.biocatalogue.org/services/2609-runembossdigestfromsequenceservice_339328 although current status(failure) is consistent between biocatalogue and embrace, the most recent embrace log is from one month ago. Am I missing something here? I only run them once a day on the biocatalogue. Help will be appreciated... Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Thu Mar 11 10:29:26 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 11 Mar 2010 15:29:26 +0000 Subject: [BioCatalogue-developers] Request to register web components Message-ID: <4B990C56.6010604@ebi.ac.uk> Hi Guys, I have been speaking to Paula de Mato who is a member of the chembi team here at EBI. They have some pieces of software or components within their team that they would like to see reused by other groups. They were therefore looking for a place to register these components so they came to BioCatalogue. I advised that these could be registered as rest services are they are essentially URIs. However, according to the advise on our site http://www.biocatalogue.org/rest_services/new it would have meant that they will have the same URL as they all share the same base url and there is no way to register different resources/parameters at the moment. So these components have not be registered yet, but I did say to Paula that we are working on better REST support and that I will contact her when that is released. I know that Mannie did work on this so what I was thinking was playing around with Mannie's work, possibly with Paula so we may be sure we can satisfy their requirement. Mannie could you let me know what I need to do in order to enable the new rest support? -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu Mar 11 11:14:27 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 11 Mar 2010 16:14:27 +0000 Subject: [BioCatalogue-developers] Request to register web components In-Reply-To: <4B990C56.6010604@ebi.ac.uk> References: <4B990C56.6010604@ebi.ac.uk> Message-ID: <4B9916E3.3040207@cs.man.ac.uk> Hi Eric, You can play around with this right now on: http://rpc232.cs.man.ac.uk:81/ But please note that things (esp the UI) will change a fair bit in the next couple of weeks before it is released. It sounds like she just needs to register one REST service and add different endpoints. This will be a good test of this feature before we release it! Cheers, Jits Eric Nzuobontane wrote: > Hi Guys, > > I have been speaking to Paula de Mato who is a member of the chembi > team here at EBI. They have some pieces of software or components > within their team that they would like to see reused by other groups. > They were therefore looking for a place to register these components > so they came to BioCatalogue. > > I advised that these could be registered as rest services are they are > essentially URIs. However, according to the advise on our site > http://www.biocatalogue.org/rest_services/new it would have meant that > they will have the same URL as they all share the same base url and > there is no way to register different resources/parameters at the moment. > > So these components have not be registered yet, but I did say to Paula > that we are working on better REST support and that I will contact her > when that is released. I know that Mannie did work on this so what I > was thinking was playing around with Mannie's work, possibly with > Paula so we may be sure we can satisfy their requirement. > > Mannie could you let me know what I need to do in order to enable the > new rest support? > From ytanoh at cs.man.ac.uk Thu Mar 11 12:10:40 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 11 Mar 2010 17:10:40 +0000 Subject: [BioCatalogue-developers] confirmation e-mail Message-ID: Hi guys, I've just finished a taverna/biocatalogue/myExperiment tutorial... Lot of people didn't get their confirmation email when they sign up. Could you check if it's something to do with Newcastle University or a problem with us. Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Thu Mar 11 12:26:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 11 Mar 2010 12:26:12 -0500 (EST) Subject: [BioCatalogue-developers] [1689] trunk: Rest API work: moved the service types data to the root of < service>. Message-ID: <20100311172612.41A6718582F9@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Mar 11 13:20:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 11 Mar 2010 18:20:38 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMultiPairwiseMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/783 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Mar 11 12:38:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 11 Mar 2010 17:38:59 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/781 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Fri Mar 12 04:27:03 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 12 Mar 2010 09:27:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: References: Message-ID: Hi, The status of this service doesn't seem to have changed in the BioCatalogue: http://www.biocatalogue.org/services/2311-runmetaalignmentgffservice_790349#overview . Is it because we have not run the monitor test yet? Eric - can you take a look please? It will be useful if we can synchronize our daily test with the Embrace one if that's the case. Franck On 11 March 2010 17:38, wrote: > This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: > ? ?http://embraceregistry.net/node/781 > > If you have any questions, please reply to this email. > > Yours, > The EMBRACE Registry Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Fri Mar 12 05:11:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 12 Mar 2010 10:11:43 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: References: Message-ID: <4B9A135F.8020003@ebi.ac.uk> Hi Franck, I had the same questions and took a look at http://www.biocatalogue.org/services/2315-runmultipairwisemetaalignmentgffservice_726543#monitoring Since the monitoring on embrace and biocatalogue is not synchronised, we are going to have some of these differences. As you can see from the posted service, I re-ran the monitoring for that service and yes it did succeed. So the problem does not seem to be with the framework but rather with the timing of the runs. At least that is what I have seen sofar. I sent a mail to embrace people yesterday to ask how often they run the monitoring because I could not work it out from the website. So to answer your question, think the problem the timing of the monitoring runs and the change of status of the services. Eric Franck Tanoh wrote: > Hi, > The status of this service doesn't seem to have changed in the > BioCatalogue: http://www.biocatalogue.org/services/2311-runmetaalignmentgffservice_790349#overview > . > Is it because we have not run the monitor test yet? Eric - can you > take a look please? It will be useful if we can synchronize our daily > test with the Embrace one if that's the case. > > Franck > > On 11 March 2010 17:38, wrote: > >> This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: >> http://embraceregistry.net/node/781 >> >> If you have any questions, please reply to this email. >> >> Yours, >> The EMBRACE Registry Team >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From mannie.tags at googlemail.com Fri Mar 12 05:21:16 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Fri, 12 Mar 2010 10:21:16 +0000 Subject: [BioCatalogue-developers] Request to register web components In-Reply-To: <4B9916E3.3040207@cs.man.ac.uk> References: <4B990C56.6010604@ebi.ac.uk> <4B9916E3.3040207@cs.man.ac.uk> Message-ID: <9AACC8E8-8D20-4EBA-AA78-DB3F85185D19@gmail.com> Hi Jits, I was going to tell you that the REST stuff is in the integration branch and is enabled. I guess you already figured that out :) Mannie On 11 Mar 2010, at 16:14, Jiten Bhagat wrote: > Hi Eric, > > You can play around with this right now on: > http://rpc232.cs.man.ac.uk:81/ > > But please note that things (esp the UI) will change a fair bit in the > next couple of weeks before it is released. > > It sounds like she just needs to register one REST service and add > different endpoints. > > This will be a good test of this feature before we release it! > > Cheers, > Jits > > > Eric Nzuobontane wrote: >> Hi Guys, >> >> I have been speaking to Paula de Mato who is a member of the chembi >> team here at EBI. They have some pieces of software or components >> within their team that they would like to see reused by other groups. >> They were therefore looking for a place to register these components >> so they came to BioCatalogue. >> >> I advised that these could be registered as rest services are they are >> essentially URIs. However, according to the advise on our site >> http://www.biocatalogue.org/rest_services/new it would have meant that >> they will have the same URL as they all share the same base url and >> there is no way to register different resources/parameters at the moment. >> >> So these components have not be registered yet, but I did say to Paula >> that we are working on better REST support and that I will contact her >> when that is released. I know that Mannie did work on this so what I >> was thinking was playing around with Mannie's work, possibly with >> Paula so we may be sure we can satisfy their requirement. >> >> Mannie could you let me know what I need to do in order to enable the >> new rest support? >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Fri Mar 12 05:28:15 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 12 Mar 2010 10:28:15 +0000 Subject: [BioCatalogue-developers] Request to register web components In-Reply-To: <9AACC8E8-8D20-4EBA-AA78-DB3F85185D19@gmail.com> References: <4B990C56.6010604@ebi.ac.uk> <4B9916E3.3040207@cs.man.ac.uk> <9AACC8E8-8D20-4EBA-AA78-DB3F85185D19@gmail.com> Message-ID: <4B9A173F.8060206@ebi.ac.uk> hmmm, I already deleted that branch locally... My understanding was that development in that branch was going to cease? Or maybe I missed something... Eric Mannie Tagarira wrote: > Hi Jits, > > I was going to tell you that the REST stuff is in the integration branch and is enabled. I guess you already figured that out :) > > Mannie > > > > On 11 Mar 2010, at 16:14, Jiten Bhagat wrote: > > >> Hi Eric, >> >> You can play around with this right now on: >> http://rpc232.cs.man.ac.uk:81/ >> >> But please note that things (esp the UI) will change a fair bit in the >> next couple of weeks before it is released. >> >> It sounds like she just needs to register one REST service and add >> different endpoints. >> >> This will be a good test of this feature before we release it! >> >> Cheers, >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> Hi Guys, >>> >>> I have been speaking to Paula de Mato who is a member of the chembi >>> team here at EBI. They have some pieces of software or components >>> within their team that they would like to see reused by other groups. >>> They were therefore looking for a place to register these components >>> so they came to BioCatalogue. >>> >>> I advised that these could be registered as rest services are they are >>> essentially URIs. However, according to the advise on our site >>> http://www.biocatalogue.org/rest_services/new it would have meant that >>> they will have the same URL as they all share the same base url and >>> there is no way to register different resources/parameters at the moment. >>> >>> So these components have not be registered yet, but I did say to Paula >>> that we are working on better REST support and that I will contact her >>> when that is released. I know that Mannie did work on this so what I >>> was thinking was playing around with Mannie's work, possibly with >>> Paula so we may be sure we can satisfy their requirement. >>> >>> Mannie could you let me know what I need to do in order to enable the >>> new rest support? >>> >>> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Fri Mar 12 05:52:59 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 12 Mar 2010 10:52:59 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> References: <4B9A135F.8020003@ebi.ac.uk> <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> Message-ID: <4B9A1D0B.8020805@ebi.ac.uk> > We should be able to sync these painlessly -- it won't be perfect, but if we just arrange for the tests to run at the same time (or within a few minutes of one another) it'll give us a good indication of whether things are behaving sensibly. I agree > I believe the EMBRACE tests run every 12 hours now, but I have no idea at what time -- I'm sure Dave can tell us. > OK, let me know One thing I do not understand is what recent logs go the embrace website. I see that the most recent log for http://embraceregistry.net/test/inbinbbscesrunembossdigestfromsequence1 is a month ago. Does that mean the last change of status was a month ago or the last time the test was run was a month ago? Eric > Steve > > >> As you can see from the posted service, I re-ran the monitoring for that service and yes it did succeed. So the problem does not seem to be with the framework but rather with the timing of the runs. At least that is what I have seen sofar. I sent a mail to embrace people yesterday to ask how often they run the monitoring because I could not work it out from the website. >> >> So to answer your question, think the problem the timing of the monitoring runs and the change of status of the services. >> >> Eric >> >> >> >> Franck Tanoh wrote: >> >>> Hi, >>> The status of this service doesn't seem to have changed in the >>> BioCatalogue: http://www.biocatalogue.org/services/2311-runmetaalignmentgffservice_790349#overview >>> . >>> Is it because we have not run the monitor test yet? Eric - can you >>> take a look please? It will be useful if we can synchronize our daily >>> test with the Embrace one if that's the case. >>> >>> Franck >>> >>> On 11 March 2010 17:38, wrote: >>> >>> >>>> This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: >>>> http://embraceregistry.net/node/781 >>>> >>>> If you have any questions, please reply to this email. >>>> >>>> Yours, >>>> The EMBRACE Registry Team >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >>>> >>> >>> >>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Fri Mar 12 07:16:53 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 12 Mar 2010 12:16:53 +0000 Subject: [BioCatalogue-developers] Request to register web components In-Reply-To: <624A1E91-5B46-464F-9D19-913F4AF3DE94@gmail.com> References: <4B990C56.6010604@ebi.ac.uk> <4B9916E3.3040207@cs.man.ac.uk> <9AACC8E8-8D20-4EBA-AA78-DB3F85185D19@gmail.com> <4B9A173F.8060206@ebi.ac.uk> <624A1E91-5B46-464F-9D19-913F4AF3DE94@gmail.com> Message-ID: <4B9A30B5.5070602@ebi.ac.uk> OK. Mannie Tagarira wrote: > It had; I had a big chunk of work that needed to be committed. I could not commit this into the trunk as preparations for the release were being made. Besides, my work was not in a fully stable state for the trunk; I needed a place to keep the code. This was a more viable option than creating a new branch for me based on the not-so-stable trunk at that moment in time; and since there is going to be another branch for UI stuff soon, this was going to create a lot of unnecessary work... > > Mannie > > On 12 Mar 2010, at 10:28, Eric Nzuobontane wrote: > > >> hmmm, I already deleted that branch locally... My understanding was that development in that branch was going to cease? Or maybe I missed something... >> >> Eric >> >> >> Mannie Tagarira wrote: >> >>> Hi Jits, >>> >>> I was going to tell you that the REST stuff is in the integration branch and is enabled. I guess you already figured that out :) >>> >>> Mannie >>> >>> >>> >>> On 11 Mar 2010, at 16:14, Jiten Bhagat wrote: >>> >>> >>> >>>> Hi Eric, >>>> >>>> You can play around with this right now on: >>>> http://rpc232.cs.man.ac.uk:81/ >>>> >>>> But please note that things (esp the UI) will change a fair bit in the >>>> next couple of weeks before it is released. >>>> >>>> It sounds like she just needs to register one REST service and add >>>> different endpoints. >>>> >>>> This will be a good test of this feature before we release it! >>>> >>>> Cheers, >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>>> Hi Guys, >>>>> >>>>> I have been speaking to Paula de Mato who is a member of the chembi >>>>> team here at EBI. They have some pieces of software or components >>>>> within their team that they would like to see reused by other groups. >>>>> They were therefore looking for a place to register these components >>>>> so they came to BioCatalogue. >>>>> >>>>> I advised that these could be registered as rest services are they are >>>>> essentially URIs. However, according to the advise on our site >>>>> http://www.biocatalogue.org/rest_services/new it would have meant that >>>>> they will have the same URL as they all share the same base url and >>>>> there is no way to register different resources/parameters at the moment. >>>>> >>>>> So these components have not be registered yet, but I did say to Paula >>>>> that we are working on better REST support and that I will contact her >>>>> when that is released. I know that Mannie did work on this so what I >>>>> was thinking was playing around with Mannie's work, possibly with >>>>> Paula so we may be sure we can satisfy their requirement. >>>>> >>>>> Mannie could you let me know what I need to do in order to enable the >>>>> new rest support? >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >>> >>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From mannie.tags at googlemail.com Fri Mar 12 07:13:01 2010 From: mannie.tags at googlemail.com (Mannie Tagarira) Date: Fri, 12 Mar 2010 12:13:01 +0000 Subject: [BioCatalogue-developers] Request to register web components In-Reply-To: <4B9A173F.8060206@ebi.ac.uk> References: <4B990C56.6010604@ebi.ac.uk> <4B9916E3.3040207@cs.man.ac.uk> <9AACC8E8-8D20-4EBA-AA78-DB3F85185D19@gmail.com> <4B9A173F.8060206@ebi.ac.uk> Message-ID: <624A1E91-5B46-464F-9D19-913F4AF3DE94@gmail.com> It had; I had a big chunk of work that needed to be committed. I could not commit this into the trunk as preparations for the release were being made. Besides, my work was not in a fully stable state for the trunk; I needed a place to keep the code. This was a more viable option than creating a new branch for me based on the not-so-stable trunk at that moment in time; and since there is going to be another branch for UI stuff soon, this was going to create a lot of unnecessary work... Mannie On 12 Mar 2010, at 10:28, Eric Nzuobontane wrote: > hmmm, I already deleted that branch locally... My understanding was that development in that branch was going to cease? Or maybe I missed something... > > Eric > > > Mannie Tagarira wrote: >> Hi Jits, >> >> I was going to tell you that the REST stuff is in the integration branch and is enabled. I guess you already figured that out :) >> >> Mannie >> >> >> >> On 11 Mar 2010, at 16:14, Jiten Bhagat wrote: >> >> >>> Hi Eric, >>> >>> You can play around with this right now on: >>> http://rpc232.cs.man.ac.uk:81/ >>> >>> But please note that things (esp the UI) will change a fair bit in the >>> next couple of weeks before it is released. >>> >>> It sounds like she just needs to register one REST service and add >>> different endpoints. >>> >>> This will be a good test of this feature before we release it! >>> >>> Cheers, >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> Hi Guys, >>>> >>>> I have been speaking to Paula de Mato who is a member of the chembi >>>> team here at EBI. They have some pieces of software or components >>>> within their team that they would like to see reused by other groups. >>>> They were therefore looking for a place to register these components >>>> so they came to BioCatalogue. >>>> >>>> I advised that these could be registered as rest services are they are >>>> essentially URIs. However, according to the advise on our site >>>> http://www.biocatalogue.org/rest_services/new it would have meant that >>>> they will have the same URL as they all share the same base url and >>>> there is no way to register different resources/parameters at the moment. >>>> >>>> So these components have not be registered yet, but I did say to Paula >>>> that we are working on better REST support and that I will contact her >>>> when that is released. I know that Mannie did work on this so what I >>>> was thinking was playing around with Mannie's work, possibly with >>>> Paula so we may be sure we can satisfy their requirement. >>>> >>>> Mannie could you let me know what I need to do in order to enable the >>>> new rest support? >>>> >>>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > From jits at cs.man.ac.uk Fri Mar 12 07:27:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Mar 2010 12:27:49 +0000 Subject: [BioCatalogue-developers] Request to register web components In-Reply-To: <4B9A30B5.5070602@ebi.ac.uk> References: <4B990C56.6010604@ebi.ac.uk> <4B9916E3.3040207@cs.man.ac.uk> <9AACC8E8-8D20-4EBA-AA78-DB3F85185D19@gmail.com> <4B9A173F.8060206@ebi.ac.uk> <624A1E91-5B46-464F-9D19-913F4AF3DE94@gmail.com> <4B9A30B5.5070602@ebi.ac.uk> Message-ID: <4B9A3345.9000807@cs.man.ac.uk> Just to confirm that I agreed with Mannie that the best way was to continue with the integration branch and get it to a stable state and then merge back into trunk (hopefully next week). Jits Eric Nzuobontane wrote: > OK. > > > Mannie Tagarira wrote: >> It had; I had a big chunk of work that needed to be committed. I >> could not commit this into the trunk as preparations for the release >> were being made. Besides, my work was not in a fully stable state >> for the trunk; I needed a place to keep the code. This was a more >> viable option than creating a new branch for me based on the >> not-so-stable trunk at that moment in time; and since there is going >> to be another branch for UI stuff soon, this was going to create a >> lot of unnecessary work... >> >> Mannie >> >> On 12 Mar 2010, at 10:28, Eric Nzuobontane wrote: >> >> >>> hmmm, I already deleted that branch locally... My understanding was >>> that development in that branch was going to cease? Or maybe I >>> missed something... >>> >>> Eric >>> >>> >>> Mannie Tagarira wrote: >>> >>>> Hi Jits, >>>> >>>> I was going to tell you that the REST stuff is in the integration >>>> branch and is enabled. I guess you already figured that out :) >>>> >>>> Mannie >>>> >>>> >>>> >>>> On 11 Mar 2010, at 16:14, Jiten Bhagat wrote: >>>> >>>> >>>> >>>>> Hi Eric, >>>>> >>>>> You can play around with this right now on: >>>>> http://rpc232.cs.man.ac.uk:81/ >>>>> >>>>> But please note that things (esp the UI) will change a fair bit in >>>>> the >>>>> next couple of weeks before it is released. >>>>> >>>>> It sounds like she just needs to register one REST service and add >>>>> different endpoints. >>>>> >>>>> This will be a good test of this feature before we release it! >>>>> >>>>> Cheers, >>>>> Jits >>>>> >>>>> >>>>> Eric Nzuobontane wrote: >>>>> >>>>>> Hi Guys, >>>>>> >>>>>> I have been speaking to Paula de Mato who is a member of the chembi >>>>>> team here at EBI. They have some pieces of software or components >>>>>> within their team that they would like to see reused by other >>>>>> groups. >>>>>> They were therefore looking for a place to register these components >>>>>> so they came to BioCatalogue. >>>>>> >>>>>> I advised that these could be registered as rest services are >>>>>> they are >>>>>> essentially URIs. However, according to the advise on our site >>>>>> http://www.biocatalogue.org/rest_services/new it would have meant >>>>>> that >>>>>> they will have the same URL as they all share the same base url and >>>>>> there is no way to register different resources/parameters at the >>>>>> moment. >>>>>> >>>>>> So these components have not be registered yet, but I did say to >>>>>> Paula >>>>>> that we are working on better REST support and that I will >>>>>> contact her >>>>>> when that is released. I know that Mannie did work on this so what I >>>>>> was thinking was playing around with Mannie's work, possibly with >>>>>> Paula so we may be sure we can satisfy their requirement. >>>>>> >>>>>> Mannie could you let me know what I need to do in order to enable >>>>>> the >>>>>> new rest support? >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>> >>>> >>>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >> >> > > From utopia at cs.man.ac.uk Thu Mar 11 17:53:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 11 Mar 2010 22:53:25 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:unzipTrajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:unzipTrajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1172 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 12 01:59:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 12 Mar 2010 06:59:56 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getProdomDomainsFromUniProt' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getProdomDomainsFromUniProt' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1060 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 12 06:38:27 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 12 Mar 2010 11:38:27 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1128 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Fri Mar 12 08:58:01 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 12 Mar 2010 13:58:01 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: <4B9A1D0B.8020805@ebi.ac.uk> References: <4B9A135F.8020003@ebi.ac.uk> <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> <4B9A1D0B.8020805@ebi.ac.uk> Message-ID: Hi Eric, I find those automatic messages quite useful. Do we have something like that in place for biocatalogue which will inform us+ providers when a service status changes? Franck On 12 March 2010 10:52, Eric Nzuobontane wrote: > >> We should be able to sync these painlessly -- it won't be perfect, but if >> we just arrange for the tests to run at the same time (or within a few >> minutes of one another) it'll give us a good indication of whether things >> are behaving sensibly. > > I agree >> >> I believe the EMBRACE tests run every 12 hours now, but I have no idea at >> what time -- I'm sure Dave can tell us. >> > > OK, let me know > > One thing I do not understand is what recent logs go the embrace website. I > see that the most recent log for > http://embraceregistry.net/test/inbinbbscesrunembossdigestfromsequence1 > is a month ago. Does that mean the last change of status was a month ago or > the last time the test was run was a month ago? > > Eric > >> Steve >> >> >>> >>> As you can see from the posted service, I re-ran the monitoring for that >>> service and yes it did succeed. So the problem does not seem to be with the >>> framework but rather with the timing of the runs. At least that is what I >>> have seen sofar. I sent a mail to embrace people yesterday to ask how often >>> they run the monitoring because I could not work it out from the website. >>> >>> So to answer your question, ?think the problem the timing of the >>> monitoring runs and the change of status of the services. >>> >>> Eric >>> >>> >>> >>> Franck Tanoh wrote: >>> >>>> >>>> Hi, >>>> The status of this service doesn't seem to have changed in the >>>> BioCatalogue: >>>> http://www.biocatalogue.org/services/2311-runmetaalignmentgffservice_790349#overview >>>> . >>>> Is it because we have not run the monitor test yet? Eric - can you >>>> take a look please? It will be useful if we can synchronize our daily >>>> test with the Embrace one if that's the case. >>>> >>>> Franck >>>> >>>> On 11 March 2010 17:38, ? wrote: >>>> >>>>> >>>>> This is an automatic notification to let you know that your service >>>>> 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to >>>>> 'Passed'. Follow the link to investigate: >>>>> ?http://embraceregistry.net/node/781 >>>>> >>>>> If you have any questions, please reply to this email. >>>>> >>>>> Yours, >>>>> The EMBRACE Registry Team >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>> >>>>> >>>> >>>> >>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel ? : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> >>> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From jits at cs.man.ac.uk Fri Mar 12 09:12:57 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 12 Mar 2010 14:12:57 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: References: <4B9A135F.8020003@ebi.ac.uk> <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> <4B9A1D0B.8020805@ebi.ac.uk> Message-ID: <4B9A4BE9.8070807@cs.man.ac.uk> Franck Tanoh wrote: > Hi Eric, > > I find those automatic messages quite useful. Do we have something > like that in place for biocatalogue which will inform us+ providers > when a service status changes? > We are recording these status changes now in the db and the aim is to make available email notifications, feeds, etc in the future. Jits > Franck > > On 12 March 2010 10:52, Eric Nzuobontane wrote: > >>> We should be able to sync these painlessly -- it won't be perfect, but if >>> we just arrange for the tests to run at the same time (or within a few >>> minutes of one another) it'll give us a good indication of whether things >>> are behaving sensibly. >>> >> I agree >> >>> I believe the EMBRACE tests run every 12 hours now, but I have no idea at >>> what time -- I'm sure Dave can tell us. >>> >>> >> OK, let me know >> >> One thing I do not understand is what recent logs go the embrace website. I >> see that the most recent log for >> http://embraceregistry.net/test/inbinbbscesrunembossdigestfromsequence1 >> is a month ago. Does that mean the last change of status was a month ago or >> the last time the test was run was a month ago? >> >> Eric >> >> >>> Steve >>> >>> >>> >>>> As you can see from the posted service, I re-ran the monitoring for that >>>> service and yes it did succeed. So the problem does not seem to be with the >>>> framework but rather with the timing of the runs. At least that is what I >>>> have seen sofar. I sent a mail to embrace people yesterday to ask how often >>>> they run the monitoring because I could not work it out from the website. >>>> >>>> So to answer your question, think the problem the timing of the >>>> monitoring runs and the change of status of the services. >>>> >>>> Eric >>>> >>>> >>>> >>>> Franck Tanoh wrote: >>>> >>>> >>>>> Hi, >>>>> The status of this service doesn't seem to have changed in the >>>>> BioCatalogue: >>>>> http://www.biocatalogue.org/services/2311-runmetaalignmentgffservice_790349#overview >>>>> . >>>>> Is it because we have not run the monitor test yet? Eric - can you >>>>> take a look please? It will be useful if we can synchronize our daily >>>>> test with the Embrace one if that's the case. >>>>> >>>>> Franck >>>>> >>>>> On 11 March 2010 17:38, wrote: >>>>> >>>>> >>>>>> This is an automatic notification to let you know that your service >>>>>> 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to >>>>>> 'Passed'. Follow the link to investigate: >>>>>> http://embraceregistry.net/node/781 >>>>>> >>>>>> If you have any questions, please reply to this email. >>>>>> >>>>>> Yours, >>>>>> The EMBRACE Registry Team >>>>>> _______________________________________________ >>>>>> BioCatalogue-developers mailing list >>>>>> BioCatalogue-developers at rubyforge.org >>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>> >>>>>> >>>>>> >>>>> >>>> -- >>>> Eric Nzuobontane >>>> ================================== >>>> European Bioinformatics Institute >>>> Wellcome Trust Genome Campus >>>> Hinxton, Cambridge >>>> CB10 1SD >>>> United Kingdom >>>> >>>> Tel : +44 1223 492654 >>>> email : ericnzuo at ebi.ac.uk >>>> ================================== >>>> >>>> >>>> >>>> >>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > > > From utopia at cs.man.ac.uk Fri Mar 12 10:14:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 12 Mar 2010 15:14:16 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossPepcoilFromSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossPepcoilFromSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/822 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 12 12:21:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 12 Mar 2010 12:21:23 -0500 (EST) Subject: [BioCatalogue-developers] [1690] trunk/lib/bio_catalogue/monitoring/status.rb: changed label for successful tests from "Success" to "Passed" to make it consistent with embrace terminology Message-ID: <20100312172123.F013518582F6@rubyforge.org> An HTML attachment was scrubbed... URL: From steve.pettifer at manchester.ac.uk Fri Mar 12 05:30:49 2010 From: steve.pettifer at manchester.ac.uk (Steve Pettifer) Date: Fri, 12 Mar 2010 10:30:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: <4B9A135F.8020003@ebi.ac.uk> References: <4B9A135F.8020003@ebi.ac.uk> Message-ID: <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> > Since the monitoring on embrace and biocatalogue is not synchronised, we are going to have some of these differences. We should be able to sync these painlessly -- it won't be perfect, but if we just arrange for the tests to run at the same time (or within a few minutes of one another) it'll give us a good indication of whether things are behaving sensibly. I believe the EMBRACE tests run every 12 hours now, but I have no idea at what time -- I'm sure Dave can tell us. Steve > As you can see from the posted service, I re-ran the monitoring for that service and yes it did succeed. So the problem does not seem to be with the framework but rather with the timing of the runs. At least that is what I have seen sofar. I sent a mail to embrace people yesterday to ask how often they run the monitoring because I could not work it out from the website. > > So to answer your question, think the problem the timing of the monitoring runs and the change of status of the services. > > Eric > > > > Franck Tanoh wrote: >> Hi, >> The status of this service doesn't seem to have changed in the >> BioCatalogue: http://www.biocatalogue.org/services/2311-runmetaalignmentgffservice_790349#overview >> . >> Is it because we have not run the monitor test yet? Eric - can you >> take a look please? It will be useful if we can synchronize our daily >> test with the Embrace one if that's the case. >> >> Franck >> >> On 11 March 2010 17:38, wrote: >> >>> This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignmentGFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: >>> http://embraceregistry.net/node/781 >>> >>> If you have any questions, please reply to this email. >>> >>> Yours, >>> The EMBRACE Registry Team >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >> >> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > From utopia at cs.man.ac.uk Fri Mar 12 20:10:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 01:10:55 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossConsFromAlignment' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossConsFromAlignment' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/811 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 12 23:01:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 04:01:42 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossDigestFromSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossDigestFromSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/872 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 01:27:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 06:27:22 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:plotArrayXYData' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:plotArrayXYData' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/925 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 06:36:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 11:36:09 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getTermsFromProduct' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getTermsFromProduct' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/931 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 11:40:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 16:40:34 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getActiveSiteInterfaceFromPDBId' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getActiveSiteInterfaceFromPDBId' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1109 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 14:13:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 19:13:18 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runPratt' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runPratt' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/930 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 16:11:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 21:11:06 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:parseSecondaryStructureFromPHDText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:parseSecondaryStructureFromPHDText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1101 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 17:51:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 13 Mar 2010 22:51:10 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPDBIdsFromLigandId' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPDBIdsFromLigandId' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1107 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 19:32:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 14 Mar 2010 00:32:08 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1840 The test was aborted because it did not complete within 1800 seconds. As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 19:42:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 14 Mar 2010 00:42:29 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:frommmCifToNDBText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:frommmCifToNDBText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/934 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 20:24:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 14 Mar 2010 01:24:24 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runNucleosomePotential' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runNucleosomePotential' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1112 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 21:12:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 14 Mar 2010 02:12:30 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:displayAlignmentFromTreeDetAnnotation' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:displayAlignmentFromTreeDetAnnotation' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1091 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 13 21:15:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 14 Mar 2010 02:15:59 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runTTSFinder' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runTTSFinder' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1104 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Sun Mar 14 15:00:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Mar 2010 15:00:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1691] trunk: REST API work: implemented /soap_operations/{id}/annotations. xml?include=inputs, outputs Message-ID: <20100314190045.A5309185828D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Mar 14 15:46:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Mar 2010 15:46:18 -0400 (EDT) Subject: [BioCatalogue-developers] [1692] trunk: REST API work: updated monitoring status labels. Message-ID: <20100314194619.0435818582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Mar 14 15:53:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Mar 2010 15:53:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1693] trunk: REST API work: further updates to monitoring status labels. Message-ID: <20100314195358.1F50818582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Mar 14 15:59:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Mar 2010 15:59:11 -0400 (EDT) Subject: [BioCatalogue-developers] [1694] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: schema updates for root resource. Message-ID: <20100314195911.F2E8718582D5@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Sun Mar 14 16:01:53 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sun, 14 Mar 2010 20:01:53 +0000 Subject: [BioCatalogue-developers] [Fwd: [Biocatalogue-support] Warning: could not send message for past 3 hours] Message-ID: <4B9D40B1.4030901@cs.man.ac.uk> What's this all about??? Jits -------- Original Message -------- Subject: [Biocatalogue-support] Warning: could not send message for past 3 hours Date: Fri, 12 Mar 2010 20:40:36 GMT From: Mail Delivery Subsystem To: ********************************************** ** THIS IS A WARNING MESSAGE ONLY ** ** YOU DO NOT NEED TO RESEND YOUR MESSAGE ** ********************************************** The original message was received at Fri, 12 Mar 2010 17:14:44 GMT from eric.windows.ebi.ac.uk [172.22.69.205] ----- Transcript of session follows ----- <782005351 at example.com>... Deferred: Connection timed out with example.com. Warning: message still undelivered after 3 hours Will keep trying until message is 3 days old -------------- next part -------------- An embedded message was scrubbed... From: biocatalogue-support at rubyforge.org Subject: Someone would like to take responsibility for a service you are currently responsible for Date: Fri, 12 Mar 2010 17:14:44 +0000 Size: 1072 URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: Attached Message Part URL: From david.thorne at manchester.ac.uk Fri Mar 12 05:47:24 2010 From: david.thorne at manchester.ac.uk (David Thorne) Date: Fri, 12 Mar 2010 10:47:24 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignmentGFF' changed to Passed In-Reply-To: <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> References: <4B9A135F.8020003@ebi.ac.uk> <91455707-4C3F-4E7F-834D-87316755BA2A@manchester.ac.uk> Message-ID: Yes, every 12 hours, 10am and 10pm... D On 12 Mar 2010, at 10:30, Steve Pettifer wrote: > I believe the EMBRACE tests run every 12 hours now, but I have no > idea at what time -- I'm sure Dave can tell us. From noreply at rubyforge.org Sun Mar 14 18:14:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 14 Mar 2010 18:14:52 -0400 (EDT) Subject: [BioCatalogue-developers] [1695] trunk: REST API work: requests to the first page of tags is now cached for 5 mins (only for API) . Message-ID: <20100314221452.77747185828E@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Mar 15 01:18:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 15 Mar 2010 05:18:48 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromFSSP' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromFSSP' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/790 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Mar 15 05:38:46 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 15 Mar 2010 09:38:46 +0000 Subject: [BioCatalogue-developers] [Fwd: [Biocatalogue-support] Warning: could not send message for past 3 hours] In-Reply-To: <4B9D40B1.4030901@cs.man.ac.uk> References: <4B9D40B1.4030901@cs.man.ac.uk> Message-ID: <4B9E0026.6030006@ebi.ac.uk> Hi Jits, It is nothing to worry about. When Franck was doing his course and some people did not get their account activation mail, I did not get any mail delivery failure errors either. So I was testing that error messages are generated when there is a failed delivery but had mistakenly left in the contact email instead of my personal mail in biocat_local file. But that was changed so you should not get any errors generated by my local code. As for the message itself, I am also starting work on allowing people to make a request to take responsibility for a service. This is something we have talked about and that I have had to do manually for one EBI service that was registered by someone not maintaining the service, though still from EBI. There was a new version of the service available and they did not want people using the old version but did not have the rights to remove the old one from BioCatalogue as it was registered by someone else. At the moment we do no have a process in place. My thinking is that we should at least have something allowing people to make a request and also that we know what happens when a request is made. Eric Jiten Bhagat wrote: > What's this all about??? > > Jits > > > -------- Original Message -------- > Subject: [Biocatalogue-support] Warning: could not send message for > past 3 hours > Date: Fri, 12 Mar 2010 20:40:36 GMT > From: Mail Delivery Subsystem > To: > > > > ********************************************** > ** THIS IS A WARNING MESSAGE ONLY ** > ** YOU DO NOT NEED TO RESEND YOUR MESSAGE ** > ********************************************** > > The original message was received at Fri, 12 Mar 2010 17:14:44 GMT > from eric.windows.ebi.ac.uk [172.22.69.205] > > ----- Transcript of session follows ----- > <782005351 at example.com>... Deferred: Connection timed out with example.com. > Warning: message still undelivered after 3 hours > Will keep trying until message is 3 days old > > > > ------------------------------------------------------------------------ > > Subject: > Someone would like to take responsibility for a service you are > currently responsible for > From: > biocatalogue-support at rubyforge.org > Date: > Fri, 12 Mar 2010 17:14:44 +0000 > To: > 782005351 at example.com > > To: > 782005351 at example.com > > > > > > Hi ericnzuo, > > We have received a request from http://localhost:3000/users/index/1 > > that they would like to take responsibility for the http://localhost:3000/services/index/406 > for which you are currently responsible. > > If you would like to grant this request, please click the link (grant) > > Or if you do not wish to grant this request, please click the link and kindly give us a reason why. > > Kind regards, > > - The BioCatalogue Team > http://localhost:3000 > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Mon Mar 15 05:48:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 15 Mar 2010 09:48:58 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getHSSPIDsFromUniprot' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getHSSPIDsFromUniprot' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/907 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Mar 15 06:08:31 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 15 Mar 2010 10:08:31 +0000 Subject: [BioCatalogue-developers] http://rpc232.cs.man.ac.uk:81/ Message-ID: <4B9E071F.70500@ebi.ac.uk> Not able to connect to http://rpc232.cs.man.ac.uk:81/ Do I need to do anything from my end? Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Mar 15 06:59:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 15 Mar 2010 10:59:59 +0000 Subject: [BioCatalogue-developers] [Fwd: [Biocatalogue-support] Warning: could not send message for past 3 hours] In-Reply-To: <4B9E0026.6030006@ebi.ac.uk> References: <4B9D40B1.4030901@cs.man.ac.uk> <4B9E0026.6030006@ebi.ac.uk> Message-ID: <4B9E132F.2040801@cs.man.ac.uk> Hi Eric, Eric Nzuobontane wrote: > Hi Jits, > It is nothing to worry about. When Franck was doing his course and > some people did not get their account activation mail, I did not get > any mail delivery failure errors either. So I was testing that error > messages are generated when there is a failed delivery but had > mistakenly left in the contact email instead of my personal mail in > biocat_local file. But that was changed so you should not get any > errors generated by my local code. OK. > > As for the message itself, I am also starting work on allowing people > to make a request to take responsibility for a service. This is > something we have talked about and that I have had to do manually for > one EBI service that was registered by someone not maintaining the > service, though still from EBI. There was a new version of the service > available and they did not want people using the old version but did > not have the rights to remove the old one from BioCatalogue as it was > registered by someone else. Ahh, yes, that's what it seemed like from the email's content. Which slightly worried me. It would have been good if you could have let us know that you were working on this (though I understand that you're probably doing exploratory work more than anything). Firstly, so we could plan it (and design it) with the rest of the tasks (it's not on the roadmap until the next quarter), and secondly because this shouldn't just be a case of overwriting the submitter fields! I.e.: it's a bigger task than it looks. Also, it can be used to spam others so needs safe checks (like, only one request per service per user, etc). > > At the moment we do no have a process in place. My thinking is that we > should at least have something allowing people to make a request and > also that we know what happens when a request is made. Yes. that's a good start to the ownership work. We also need to consider how this fits in with the ServiceProviders stuff. I.e: is it better just to have one User as "owner" or a service, or can you also assign a ServiceProvider, and then Users can be assigned to ServiceProviders? Though for the first instance it's probably best just to keep it simple and have one User as "owner". One thing to consider is having a separate OwnershipRequests table that can capture these requests and when approved maybe an "owner_id" field can set in the top level Service model. Jits > > > Eric > > > > > Jiten Bhagat wrote: >> What's this all about??? >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [Biocatalogue-support] Warning: could not send message for >> past 3 hours >> Date: Fri, 12 Mar 2010 20:40:36 GMT >> From: Mail Delivery Subsystem >> To: >> >> >> >> ********************************************** >> ** THIS IS A WARNING MESSAGE ONLY ** >> ** YOU DO NOT NEED TO RESEND YOUR MESSAGE ** >> ********************************************** >> >> The original message was received at Fri, 12 Mar 2010 17:14:44 GMT >> from eric.windows.ebi.ac.uk [172.22.69.205] >> >> ----- Transcript of session follows ----- >> <782005351 at example.com>... Deferred: Connection timed out with >> example.com. >> Warning: message still undelivered after 3 hours >> Will keep trying until message is 3 days old >> >> >> >> ------------------------------------------------------------------------ >> >> Subject: >> Someone would like to take responsibility for a service you are >> currently responsible for >> From: >> biocatalogue-support at rubyforge.org >> Date: >> Fri, 12 Mar 2010 17:14:44 +0000 >> To: >> 782005351 at example.com >> >> To: >> 782005351 at example.com >> >> >> >> >> >> Hi ericnzuo, >> >> We have received a request from http://localhost:3000/users/index/1 >> that they would like to take responsibility for the >> http://localhost:3000/services/index/406 for which you are currently >> responsible. >> >> If you would like to grant this request, please click the link (grant) >> >> Or if you do not wish to grant this request, please click the link >> and kindly give us a reason why. >> >> Kind regards, >> >> - The BioCatalogue Team >> http://localhost:3000 >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > From jits at cs.man.ac.uk Mon Mar 15 07:05:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 15 Mar 2010 11:05:49 +0000 Subject: [BioCatalogue-developers] http://rpc232.cs.man.ac.uk:81/ In-Reply-To: <4B9E071F.70500@ebi.ac.uk> References: <4B9E071F.70500@ebi.ac.uk> Message-ID: <4B9E148D.8030408@cs.man.ac.uk> Ah, the Uni is probably blocking that port. Let me try moving it to 8080. Jits Eric Nzuobontane wrote: > > Not able to connect to http://rpc232.cs.man.ac.uk:81/ > > Do I need to do anything from my end? > > Eric > > From jits at cs.man.ac.uk Mon Mar 15 07:11:06 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 15 Mar 2010 11:11:06 +0000 Subject: [BioCatalogue-developers] http://rpc232.cs.man.ac.uk:81/ In-Reply-To: <4B9E148D.8030408@cs.man.ac.uk> References: <4B9E071F.70500@ebi.ac.uk> <4B9E148D.8030408@cs.man.ac.uk> Message-ID: <4B9E15CA.0@cs.man.ac.uk> Please try: http://rpc232.cs.man.ac.uk:8080/ Jits Jiten Bhagat wrote: > Ah, the Uni is probably blocking that port. > > Let me try moving it to 8080. > > Jits > > > Eric Nzuobontane wrote: > >> Not able to connect to http://rpc232.cs.man.ac.uk:81/ >> >> Do I need to do anything from my end? >> >> Eric >> >> >> > > > From ericnzuo at ebi.ac.uk Mon Mar 15 08:35:34 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 15 Mar 2010 12:35:34 +0000 Subject: [BioCatalogue-developers] [Fwd: [Biocatalogue-support] Warning: could not send message for past 3 hours] In-Reply-To: <4B9E132F.2040801@cs.man.ac.uk> References: <4B9D40B1.4030901@cs.man.ac.uk> <4B9E0026.6030006@ebi.ac.uk> <4B9E132F.2040801@cs.man.ac.uk> Message-ID: <4B9E2996.6000705@ebi.ac.uk> Hi Jits, > Hi Eric, > > Eric Nzuobontane wrote: > >> Hi Jits, >> It is nothing to worry about. When Franck was doing his course and >> some people did not get their account activation mail, I did not get >> any mail delivery failure errors either. So I was testing that error >> messages are generated when there is a failed delivery but had >> mistakenly left in the contact email instead of my personal mail in >> biocat_local file. But that was changed so you should not get any >> errors generated by my local code. >> > > OK. > > >> As for the message itself, I am also starting work on allowing people >> to make a request to take responsibility for a service. This is >> something we have talked about and that I have had to do manually for >> one EBI service that was registered by someone not maintaining the >> service, though still from EBI. There was a new version of the service >> available and they did not want people using the old version but did >> not have the rights to remove the old one from BioCatalogue as it was >> registered by someone else. >> > > Ahh, yes, that's what it seemed like from the email's content. Which > slightly worried me. It would have been good if you could have let us > know that you were working on this (though I understand that you're > probably doing exploratory work more than anything). Firstly, so we > could plan it (and design it) with the rest of the tasks (it's not on > the roadmap until the next quarter), and secondly because this shouldn't > just be a case of overwriting the submitter fields! I.e.: it's a bigger > task than it looks. > Yes, it was more exploratory and I was going to have a chat about it this morning, then I saw your mail. > Also, it can be used to spam others so needs safe checks (like, only one > request per service per user, etc). > > That has been a concern. My first thought was just have a manual process in place. So if a request is made for example, it just goes into a queue and someone will then have to make sure those requests are acted upon. Then I thought, maybe it is good to let the requester & us know via mail that the request was successfully received. For the person that submitted the service or currently responsible for the service, I was not sure about an automated mail. >> At the moment we do no have a process in place. My thinking is that we >> should at least have something allowing people to make a request and >> also that we know what happens when a request is made. >> > > Yes. that's a good start to the ownership work. We also need to consider > how this fits in with the ServiceProviders stuff. I.e: is it better just > to have one User as "owner" or a service, or can you also assign a > ServiceProvider, and then Users can be assigned to ServiceProviders? > > Though for the first instance it's probably best just to keep it simple > and have one User as "owner". > > One thing to consider is having a separate OwnershipRequests table that > can capture these requests and when approved maybe an "owner_id" field > can set in the top level Service model. > Good points. I have considered the ownership or responsibility request table. My thinking was that this would just serve as a queue for managing requests. So if and when a request is approved, the requester(User) will be added to the responsibility list. And for the list, I thought we could just add a relationship entry with a predicate like 'hasResponsible'. That way several users could be responsible for a service and we may not have to change the service structure. So the original submitter remains as the submitter and the responsible(s) would be given privileges on the services using our auth module. I thought that would be simple enough for a start and get us some distance. What do you think? Eric > Jits > > >> Eric >> >> >> >> >> Jiten Bhagat wrote: >> >>> What's this all about??? >>> >>> Jits >>> >>> >>> -------- Original Message -------- >>> Subject: [Biocatalogue-support] Warning: could not send message for >>> past 3 hours >>> Date: Fri, 12 Mar 2010 20:40:36 GMT >>> From: Mail Delivery Subsystem >>> To: >>> >>> >>> >>> ********************************************** >>> ** THIS IS A WARNING MESSAGE ONLY ** >>> ** YOU DO NOT NEED TO RESEND YOUR MESSAGE ** >>> ********************************************** >>> >>> The original message was received at Fri, 12 Mar 2010 17:14:44 GMT >>> from eric.windows.ebi.ac.uk [172.22.69.205] >>> >>> ----- Transcript of session follows ----- >>> <782005351 at example.com>... Deferred: Connection timed out with >>> example.com. >>> Warning: message still undelivered after 3 hours >>> Will keep trying until message is 3 days old >>> >>> >>> >>> ------------------------------------------------------------------------ >>> >>> Subject: >>> Someone would like to take responsibility for a service you are >>> currently responsible for >>> From: >>> biocatalogue-support at rubyforge.org >>> Date: >>> Fri, 12 Mar 2010 17:14:44 +0000 >>> To: >>> 782005351 at example.com >>> >>> To: >>> 782005351 at example.com >>> >>> >>> >>> >>> >>> Hi ericnzuo, >>> >>> We have received a request from http://localhost:3000/users/index/1 >>> that they would like to take responsibility for the >>> http://localhost:3000/services/index/406 for which you are currently >>> responsible. >>> >>> If you would like to grant this request, please click the link (grant) >>> >>> Or if you do not wish to grant this request, please click the link >>> and kindly give us a reason why. >>> >>> Kind regards, >>> >>> - The BioCatalogue Team >>> http://localhost:3000 >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Mon Mar 15 12:01:41 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 15 Mar 2010 16:01:41 +0000 Subject: [BioCatalogue-developers] New biocatalogue-hackers list Message-ID: <4B9E59E5.1040901@cs.man.ac.uk> Hi guys, I've created a new biocatalogue-hackers list - http://rubyforge.org/mailman/listinfo/biocatalogue-hackers The description of the list is as follows: " This mailing list is for any developer, hacker, coder, scripter, and so on, who is interested in the BioCatalogue API and/or the BioCatalogue codebase. Feel free to post questions, feedback, ideas and have discussions. But please keep things civil and be respectful of others. " Note that this is a public facing list and open to anyone to sign up. Please join this list if you're interested. Jits From jits at cs.man.ac.uk Mon Mar 15 12:30:05 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 15 Mar 2010 16:30:05 +0000 Subject: [BioCatalogue-developers] [Fwd: [Biocatalogue-support] Warning: could not send message for past 3 hours] In-Reply-To: <4B9E2996.6000705@ebi.ac.uk> References: <4B9D40B1.4030901@cs.man.ac.uk> <4B9E0026.6030006@ebi.ac.uk> <4B9E132F.2040801@cs.man.ac.uk> <4B9E2996.6000705@ebi.ac.uk> Message-ID: <4B9E608D.2010603@cs.man.ac.uk> Hi Eric, > That has been a concern. My first thought was just have a manual > process in place. So if a request is made for example, it just goes > into a queue and someone will then have to make sure those requests > are acted upon. Then I thought, maybe it is good to let the requester > & us know via mail that the request was successfully received. For the > person that submitted the service or currently responsible for the > service, I was not sure about an automated mail. I wonder, wouldn't it be better to have a process where the original submitter can click on a link to allow this ownership (much like the activation link)? Or should a curator get involved as well? To be honest, I don't know what the right answers are here! > Good points. I have considered the ownership or responsibility request > table. My thinking was that this would just serve as a queue for > managing requests. Yeap. It's also a provenance thing - a way of tracking when these ownership things happened, and also a way of checking what existing requests are pending. > So if and when a request is approved, the requester(User) will be > added to the responsibility list. And for the list, I thought we could > just add a relationship entry with a predicate like 'hasResponsible'. > That way several users could be responsible for a service and we may > not have to change the service structure. So the original submitter > remains as the submitter and the responsible(s) would be given > privileges on the services using our auth module. > > I thought that would be simple enough for a start and get us some > distance. What do you think? I would really try to avoid using the Relationship model here. It may seem like a quick win, but ultimately the Relationships things was more about layering in *secondary* and *arbitrary* relationships, rather than to be used for *core* functionality. I think this is too important and might be worth having an "owner_id" field in the Service model (to start with?) OR a separate ServiceOwners table which has a 1..* mapping to Service. By doing it separately we ensure that future changes, as well as performance optimisations, can be done in a manageable way. What do you think? Cheers, Jits Eric Nzuobontane wrote: > Hi Jits, >> Hi Eric, >> >> Eric Nzuobontane wrote: >> >>> Hi Jits, >>> It is nothing to worry about. When Franck was doing his course and >>> some people did not get their account activation mail, I did not get >>> any mail delivery failure errors either. So I was testing that error >>> messages are generated when there is a failed delivery but had >>> mistakenly left in the contact email instead of my personal mail in >>> biocat_local file. But that was changed so you should not get any >>> errors generated by my local code. >>> >> >> OK. >> >> >>> As for the message itself, I am also starting work on allowing people >>> to make a request to take responsibility for a service. This is >>> something we have talked about and that I have had to do manually for >>> one EBI service that was registered by someone not maintaining the >>> service, though still from EBI. There was a new version of the service >>> available and they did not want people using the old version but did >>> not have the rights to remove the old one from BioCatalogue as it was >>> registered by someone else. >>> >> >> Ahh, yes, that's what it seemed like from the email's content. Which >> slightly worried me. It would have been good if you could have let us >> know that you were working on this (though I understand that you're >> probably doing exploratory work more than anything). Firstly, so we >> could plan it (and design it) with the rest of the tasks (it's not on >> the roadmap until the next quarter), and secondly because this shouldn't >> just be a case of overwriting the submitter fields! I.e.: it's a bigger >> task than it looks. >> > Yes, it was more exploratory and I was going to have a chat about it > this morning, then I saw your mail. >> Also, it can be used to spam others so needs safe checks (like, only one >> request per service per user, etc). >> >> > That has been a concern. My first thought was just have a manual > process in place. So if a request is made for example, it just goes > into a queue and someone will then have to make sure those requests > are acted upon. Then I thought, maybe it is good to let the requester > & us know via mail that the request was successfully received. For the > person that submitted the service or currently responsible for the > service, I was not sure about an automated mail. >>> At the moment we do no have a process in place. My thinking is that we >>> should at least have something allowing people to make a request and >>> also that we know what happens when a request is made. >>> >> >> Yes. that's a good start to the ownership work. We also need to consider >> how this fits in with the ServiceProviders stuff. I.e: is it better just >> to have one User as "owner" or a service, or can you also assign a >> ServiceProvider, and then Users can be assigned to ServiceProviders? >> >> Though for the first instance it's probably best just to keep it simple >> and have one User as "owner". >> >> One thing to consider is having a separate OwnershipRequests table that >> can capture these requests and when approved maybe an "owner_id" field >> can set in the top level Service model. >> > Good points. I have considered the ownership or responsibility request > table. My thinking was that this would just serve as a queue for > managing requests. So if and when a request is approved, the > requester(User) will be added to the responsibility list. And for the > list, I thought we could just add a relationship entry with a > predicate like 'hasResponsible'. That way several users could be > responsible for a service and we may not have to change the service > structure. So the original submitter remains as the submitter and the > responsible(s) would be given privileges on the services using our > auth module. > > I thought that would be simple enough for a start and get us some > distance. What do you think? > > Eric > > > > >> Jits >> >> >>> Eric >>> >>> >>> >>> >>> Jiten Bhagat wrote: >>> >>>> What's this all about??? >>>> >>>> Jits >>>> >>>> >>>> -------- Original Message -------- >>>> Subject: [Biocatalogue-support] Warning: could not send message >>>> for >>>> past 3 hours >>>> Date: Fri, 12 Mar 2010 20:40:36 GMT >>>> From: Mail Delivery Subsystem >>>> To: >>>> >>>> >>>> >>>> ********************************************** >>>> ** THIS IS A WARNING MESSAGE ONLY ** >>>> ** YOU DO NOT NEED TO RESEND YOUR MESSAGE ** >>>> ********************************************** >>>> >>>> The original message was received at Fri, 12 Mar 2010 17:14:44 GMT >>>> from eric.windows.ebi.ac.uk [172.22.69.205] >>>> >>>> ----- Transcript of session follows ----- >>>> <782005351 at example.com>... Deferred: Connection timed out with >>>> example.com. >>>> Warning: message still undelivered after 3 hours >>>> Will keep trying until message is 3 days old >>>> >>>> >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> Subject: >>>> Someone would like to take responsibility for a service you are >>>> currently responsible for >>>> From: >>>> biocatalogue-support at rubyforge.org >>>> Date: >>>> Fri, 12 Mar 2010 17:14:44 +0000 >>>> To: >>>> 782005351 at example.com >>>> >>>> To: >>>> 782005351 at example.com >>>> >>>> >>>> >>>> >>>> >>>> Hi ericnzuo, >>>> >>>> We have received a request from http://localhost:3000/users/index/1 >>>> that they would like to take responsibility for the >>>> http://localhost:3000/services/index/406 for which you are currently >>>> responsible. >>>> >>>> If you would like to grant this request, please click the link (grant) >>>> >>>> Or if you do not wish to grant this request, please click the link >>>> and kindly give us a reason why. >>>> >>>> Kind regards, >>>> >>>> - The BioCatalogue Team >>>> http://localhost:3000 >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>> > > From noreply at rubyforge.org Mon Mar 15 13:11:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 13:11:24 -0400 (EDT) Subject: [BioCatalogue-developers] [1696] trunk/app/views: REST API work: always show the section when showing resources as result items. Message-ID: <20100315171124.95F2618582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 13:12:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 13:12:04 -0400 (EDT) Subject: [BioCatalogue-developers] [1697] trunk/app/views/soap_operations/api/_result_item.xml.builder: REST API work: missing from previous commit. Message-ID: <20100315171204.9A15918582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 13:35:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 13:35:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1698] trunk/app: REST API work: implemented include= all query parameter so you can ask for all sections for that resource. Message-ID: <20100315173522.7B6D318582EF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 13:44:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 13:44:29 -0400 (EDT) Subject: [BioCatalogue-developers] [1699] trunk: REST API work: added link to for . Message-ID: <20100315174430.0748018582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 13:49:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 13:49:23 -0400 (EDT) Subject: [BioCatalogue-developers] [1700] trunk: REST API work: added to for < soapOperation>. Message-ID: <20100315174923.253681D790F5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 13:55:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 13:55:30 -0400 (EDT) Subject: [BioCatalogue-developers] [1701] trunk/app: REST API work: changed /soap_operations/{id}/annotations? include=inputs, outputs to /soap_operations/{id}/annotations?also=inputs, outputs ... Message-ID: <20100315175530.2920718582EA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 14:06:36 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 14:06:36 -0400 (EDT) Subject: [BioCatalogue-developers] [1702] trunk: REST API work: for all filterable indexes, introduced < filtersFromHere> to distinguish between a 'clean' link to the filters vs one that can be used to build up filters. Message-ID: <20100315180636.A507E18582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 15 14:14:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 15 Mar 2010 14:14:54 -0400 (EDT) Subject: [BioCatalogue-developers] [1703] trunk: REST API work: added more links to the services index. Message-ID: <20100315181454.362F01D790F5@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Mar 15 22:02:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 16 Mar 2010 02:02:36 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getTermsFromProduct' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getTermsFromProduct' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/931 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Tue Mar 16 05:37:48 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 16 Mar 2010 09:37:48 +0000 Subject: [BioCatalogue-developers] Some comments from Hamish on BioCatalogue Message-ID: <4B9F516C.9040800@ebi.ac.uk> Hi Guys, As mentioned in the meeting yesterday, I had a discussion with Hamish and he pointed out a few things to me on BioCatalogue. Find what I gathered from the discussion below: 1. When the list of alternative names becomes long enough so that it fills the whole width of the window (page) then the page wrap constantly flickers that it make it hard to add even more names. You could ask why one service should be known by so many names, but unfortunately that seems to exist 2. When adding alternatives names, it is not possible to add multiple names at once 3. Rendering of service show page sometimes breaks when the alternative is clicked before the complete page has been rendered 4. When view is switched from detailed to simple, one is always taken to the first page irrespective of what page one was at 5. There is a signup link shown to users even when they are logged in. This is visible on the users listing even after login 6. Some annotations for complex types are not picked up by the wsdl parsing 7. There are many duplicate services in BioCatalogue and there is not mechanism to group/associate these 8. There is no mechanism to hand over responsibility of a service to some other user 9. There is no machanism to group providers. Since BioCatalogue generates an automatic provider based on the host domain/subdomain of the service many services from the same provider do appear as if coming from different providers. It would nice of there was a way of grouping all of these under the same umbrella. Those are the points that were raised. I believe we have UI revamp on our road map and many of these thing would fit in there though not all. Well, our task list keeps growing... -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Tue Mar 16 07:00:46 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 16 Mar 2010 11:00:46 +0000 Subject: [BioCatalogue-developers] Some comments from Hamish on BioCatalogue In-Reply-To: <4B9F516C.9040800@ebi.ac.uk> References: <4B9F516C.9040800@ebi.ac.uk> Message-ID: <4B9F64DE.7030003@cs.man.ac.uk> Thanks Eric. These are very useful points. Jits Eric Nzuobontane wrote: > Hi Guys, > As mentioned in the meeting yesterday, I had a discussion with Hamish > and he pointed out a few things to me on BioCatalogue. Find what I > gathered from the discussion below: > > 1. When the list of alternative names becomes long enough so that it > fills the whole width of the window (page) then the page wrap > constantly flickers that it make it hard to add even more names. > You could ask why one service should be known by so many names, > but unfortunately that seems to exist > 2. When adding alternatives names, it is not possible to add multiple > names at once > 3. Rendering of service show page sometimes breaks when the > alternative is clicked before the complete page has been rendered > 4. When view is switched from detailed to simple, one is always taken > to the first page irrespective of what page one was at > 5. There is a signup link shown to users even when they are logged > in. This is visible on the users listing even after login > 6. Some annotations for complex types are not picked up by the wsdl > parsing > 7. There are many duplicate services in BioCatalogue and there is not > mechanism to group/associate these > 8. There is no mechanism to hand over responsibility of a service to > some other user > 9. There is no machanism to group providers. Since BioCatalogue > generates an automatic provider based on the host domain/subdomain > of the service many services from the same provider do appear as > if coming from different providers. It would nice of there was a > way of grouping all of these under the same umbrella. > > Those are the points that were raised. I believe we have UI revamp on > our road map and many of these thing would fit in there though not > all. Well, our task list keeps growing... > From noreply at rubyforge.org Tue Mar 16 07:50:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Mar 2010 07:50:43 -0400 (EDT) Subject: [BioCatalogue-developers] [1704] trunk/app/controllers: Better error handling when a search exception occurs. Message-ID: <20100316115043.C1CFF18582E9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 16 07:55:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Mar 2010 07:55:51 -0400 (EDT) Subject: [BioCatalogue-developers] [1705] trunk: REST API work: renamed to < filtersOnCurrentResults>. Message-ID: <20100316115551.1707B18582F8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 16 07:57:41 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Mar 2010 07:57:41 -0400 (EDT) Subject: [BioCatalogue-developers] [1706] trunk: REST API work: renamed to . Message-ID: <20100316115741.78B7818582E9@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Mar 16 08:16:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 16 Mar 2010 12:16:08 +0000 Subject: [BioCatalogue-developers] announcement on the friend list Message-ID: Hi Guys, Correct me if i'm wrong but i think we decided the make an announcement about the new release (API excluded) on the Friend list. If that the case, Eric can you make it, please. It's more about the Embrace stuff. Also, We need documentation and some help text for the test script bit. Currently it is not clear what it is and what it is for. Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From jits at cs.man.ac.uk Tue Mar 16 08:19:27 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 16 Mar 2010 12:19:27 +0000 Subject: [BioCatalogue-developers] announcement on the friend list In-Reply-To: References: Message-ID: <4B9F774F.1070006@cs.man.ac.uk> Franck Tanoh wrote: > Hi Guys, > > Correct me if i'm wrong but i think we decided the make an > announcement about the new release (API excluded) on the Friend list. > If that the case, Eric can you make it, please. It's more about the > Embrace stuff. > No, we agreed that we could FIRST contact Steve to sort out the EMBRACE stuff first! Jits > Also, We need documentation and some help text for the test script > bit. Currently it is not clear what it is and what it is for. > > Franck > > From noreply at rubyforge.org Tue Mar 16 08:23:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 16 Mar 2010 08:23:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1707] trunk: REST API work: some changes to the related links for Message-ID: <20100316122309.C30B41858304@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Mar 16 08:52:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 16 Mar 2010 12:52:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1155 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Tue Mar 16 09:05:50 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 16 Mar 2010 13:05:50 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Passed In-Reply-To: References: Message-ID: Hi Eric I've noticed that the service below was always up in the BioCatalogue: http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502 Is it still a sync problem or sth that need more attention? Franck On 16 March 2010 12:52, wrote: > This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: > ? ?http://embraceregistry.net/node/1155 > > If you have any questions, please reply to this email. > > Yours, > The EMBRACE Registry Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ytanoh at cs.man.ac.uk Tue Mar 16 09:07:22 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 16 Mar 2010 13:07:22 +0000 Subject: [BioCatalogue-developers] announcement on the friend list In-Reply-To: <4B9F774F.1070006@cs.man.ac.uk> References: <4B9F774F.1070006@cs.man.ac.uk> Message-ID: OK. I've emailed Steve Franck On 16 March 2010 12:19, Jiten Bhagat wrote: > Franck Tanoh wrote: >> Hi Guys, >> >> Correct me if i'm wrong but i think we decided the make an >> announcement about the new release (API excluded) on the Friend list. >> If that the case, Eric can you make it, please. It's more about the >> Embrace stuff. >> > > No, we agreed that we could FIRST contact Steve to sort out the EMBRACE > stuff first! > > Jits > >> Also, We need documentation and some help text for the test script >> bit. Currently it is not clear what it is and what it is for. >> >> Franck >> >> > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From jits at cs.man.ac.uk Tue Mar 16 09:27:41 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 16 Mar 2010 13:27:41 +0000 Subject: [BioCatalogue-developers] announcement on the friend list In-Reply-To: References: <4B9F774F.1070006@cs.man.ac.uk> Message-ID: <4B9F874D.3080808@cs.man.ac.uk> Thanks Franck Tanoh wrote: > OK. > I've emailed Steve > > Franck > > On 16 March 2010 12:19, Jiten Bhagat wrote: > >> Franck Tanoh wrote: >> >>> Hi Guys, >>> >>> Correct me if i'm wrong but i think we decided the make an >>> announcement about the new release (API excluded) on the Friend list. >>> If that the case, Eric can you make it, please. It's more about the >>> Embrace stuff. >>> >>> >> No, we agreed that we could FIRST contact Steve to sort out the EMBRACE >> stuff first! >> >> Jits >> >> >>> Also, We need documentation and some help text for the test script >>> bit. Currently it is not clear what it is and what it is for. >>> >>> Franck >>> >>> >>> >> > > > > From utopia at cs.man.ac.uk Tue Mar 16 21:12:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 01:12:57 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPHDFromBLASTText' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPHDFromBLASTText' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1003 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 16 23:05:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 03:05:09 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runPrank' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runPrank' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1095 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 17 01:16:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 05:16:22 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossWaterFromSequences' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossWaterFromSequences' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/831 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Wed Mar 17 09:38:49 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 17 Mar 2010 13:38:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Passed In-Reply-To: References: Message-ID: <4BA0DB69.9000803@ebi.ac.uk> Hi Franck, From what I could see from the embrace logs, the last time this failed was a month ago. So I do not see any inconsistency with biocatalogue or are we looking at different things? http://embraceregistry.net/test/inb-devmmbpcbubesgetcollectivityindexesfrompczreport1 http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502#overview Eric Franck Tanoh wrote: > Hi Eric > I've noticed that the service below was always up in the BioCatalogue: > http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502 > Is it still a sync problem or sth that need more attention? > > Franck > > On 16 March 2010 12:52, wrote: > >> This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: >> http://embraceregistry.net/node/1155 >> >> If you have any questions, please reply to this email. >> >> Yours, >> The EMBRACE Registry Team >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From utopia at cs.man.ac.uk Wed Mar 17 11:08:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 15:08:39 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFFCollection' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFFCollection' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/777 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 17 11:52:32 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 15:52:32 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:parseMWfromMWAnnotatedAASequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:parseMWfromMWAnnotatedAASequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/927 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 17 12:40:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 16:40:28 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getUniprotIDsFromGOTerm' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getUniprotIDsFromGOTerm' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/894 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Mar 17 13:05:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 17 Mar 2010 13:05:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1708] branches/integration-jan10: REST SUPPORT WORK Message-ID: <20100317170509.82EF91D793E1@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 17 18:51:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 17 Mar 2010 22:51:01 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseFeatureAASequenceFromFSOLVText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseFeatureAASequenceFromFSOLVText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/991 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Thu Mar 18 06:59:36 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 18 Mar 2010 10:59:36 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Passed In-Reply-To: <4BA0DB69.9000803@ebi.ac.uk> References: <4BA0DB69.9000803@ebi.ac.uk> Message-ID: Hi Eric, Thanks for the clarification. It looks like these messages are delivered very late. This one for example is delivered one month after the service status changed. Franck On 17 March 2010 13:38, Eric Nzuobontane wrote: > Hi Franck, > > From what I could see from the embrace logs, the last time this failed was a > month ago. So I do not see any inconsistency with biocatalogue or are we > looking at different things? > http://embraceregistry.net/test/inb-devmmbpcbubesgetcollectivityindexesfrompczreport1 > http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502#overview > > Eric > > > Franck Tanoh wrote: >> >> Hi Eric >> I've noticed that the service below was always up in the BioCatalogue: >> >> http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502 >> Is it still a sync problem or sth that need more attention? >> >> Franck >> >> On 16 March 2010 12:52, ? wrote: >> >>> >>> This is an automatic notification to let you know that your service >>> 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed >>> status from 'Failed' to 'Passed'. Follow the link to investigate: >>> ? http://embraceregistry.net/node/1155 >>> >>> If you have any questions, please reply to this email. >>> >>> Yours, >>> The EMBRACE Registry Team >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >> >> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Thu Mar 18 07:40:53 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 18 Mar 2010 11:40:53 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Passed In-Reply-To: References: <4BA0DB69.9000803@ebi.ac.uk> Message-ID: <4BA21145.4030007@ebi.ac.uk> Franck Tanoh wrote: > Hi Eric, > > Thanks for the clarification. > It looks like these messages are delivered very late. This one for > example is delivered one month after the service status changed. > I suspect instead that they are not putting up all the logs, though I have asked the question several times but did not get an answer. Eric > Franck > > On 17 March 2010 13:38, Eric Nzuobontane wrote: > >> Hi Franck, >> >> From what I could see from the embrace logs, the last time this failed was a >> month ago. So I do not see any inconsistency with biocatalogue or are we >> looking at different things? >> http://embraceregistry.net/test/inb-devmmbpcbubesgetcollectivityindexesfrompczreport1 >> http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502#overview >> >> Eric >> >> >> Franck Tanoh wrote: >> >>> Hi Eric >>> I've noticed that the service below was always up in the BioCatalogue: >>> >>> http://www.biocatalogue.org/services/2333-getcollectivityindexesfrompcz_reportservice_771502 >>> Is it still a sync problem or sth that need more attention? >>> >>> Franck >>> >>> On 16 March 2010 12:52, wrote: >>> >>> >>>> This is an automatic notification to let you know that your service >>>> 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed >>>> status from 'Failed' to 'Passed'. Follow the link to investigate: >>>> http://embraceregistry.net/node/1155 >>>> >>>> If you have any questions, please reply to this email. >>>> >>>> Yours, >>>> The EMBRACE Registry Team >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>>> >>>> >>> >>> >>> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Mar 18 10:13:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 10:13:40 -0400 (EDT) Subject: [BioCatalogue-developers] [1709] trunk: REST API work: added Agents to API. Message-ID: <20100318141341.0A8081598084@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 18 10:33:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 10:33:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1710] trunk/script/biocatalogue/api/tests/config.yml.pre: REST API work: fixed minor typo in tests config file template. Message-ID: <20100318143317.D538B18582E1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 18 11:00:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 11:00:27 -0400 (EDT) Subject: [BioCatalogue-developers] [1711] trunk: REST API work: added more useful related links to . Message-ID: <20100318150027.AF93818582E2@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Mar 18 11:12:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 18 Mar 2010 15:12:15 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runSGP2GFF' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runSGP2GFF' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/770 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Mar 18 10:50:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 18 Mar 2010 14:50:55 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/188 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Mar 18 12:07:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 18 Mar 2010 16:07:06 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:fromNDBTextTommCif' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:fromNDBTextTommCif' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/936 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Thu Mar 18 12:14:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 12:14:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1712] trunk/app/views: REST API work: cleaned up some sections, and also deleted some unnecessary views. Message-ID: <20100318161445.AA58518582E2@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 18 12:20:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 12:20:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1713] trunk/app/views/soap_inputs/api/_related_links.xml.builder: Bugfix Message-ID: <20100318162005.ED63718582E2@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Mar 18 12:28:50 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 18 Mar 2010 16:28:50 +0000 Subject: [BioCatalogue-developers] Dev chat Message-ID: <4BA254C2.8020902@cs.man.ac.uk> Hi guys, Can we set up a dev chat for tomorrow, say 14:30 please? We have a couple of pieces of work that need merging and planning for a release. Franck: you can join if you're interested in knowing what's coming in the next release :-) Jits From jits at cs.man.ac.uk Thu Mar 18 12:54:08 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 18 Mar 2010 16:54:08 +0000 Subject: [BioCatalogue-developers] Dev chat In-Reply-To: <4BA254C2.8020902@cs.man.ac.uk> References: <4BA254C2.8020902@cs.man.ac.uk> Message-ID: <4BA25AB0.3020504@cs.man.ac.uk> Actually, can we do this at 11am tomorrow please? Jits Jiten Bhagat wrote: > Hi guys, > > Can we set up a dev chat for tomorrow, say 14:30 please? > > We have a couple of pieces of work that need merging and planning for a > release. > > Franck: you can join if you're interested in knowing what's coming in > the next release :-) > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ytanoh at cs.man.ac.uk Thu Mar 18 12:56:11 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 18 Mar 2010 16:56:11 +0000 Subject: [BioCatalogue-developers] Dev chat In-Reply-To: <4BA254C2.8020902@cs.man.ac.uk> References: <4BA254C2.8020902@cs.man.ac.uk> Message-ID: Fine with me ... I'll be watching :-) Franck On 18 March 2010 16:28, Jiten Bhagat wrote: > Hi guys, > > Can we set up a dev chat for tomorrow, say 14:30 please? > > We have a couple of pieces of work that need merging and planning for a > release. > > Franck: you can join if you're interested in knowing what's coming in > the next release :-) > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Thu Mar 18 12:59:00 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 18 Mar 2010 16:59:00 +0000 Subject: [BioCatalogue-developers] Dev chat In-Reply-To: <4BA254C2.8020902@cs.man.ac.uk> References: <4BA254C2.8020902@cs.man.ac.uk> Message-ID: <4BA25BD4.3020805@ebi.ac.uk> Good idea. It was something on my mind as well. I am fine with the time too. May need to step away for a few minutes to grab a tea @3pm... :) Eric Jiten Bhagat wrote: > Hi guys, > > Can we set up a dev chat for tomorrow, say 14:30 please? > > We have a couple of pieces of work that need merging and planning for a > release. > > Franck: you can join if you're interested in knowing what's coming in > the next release :-) > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Thu Mar 18 13:00:10 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 18 Mar 2010 17:00:10 +0000 Subject: [BioCatalogue-developers] Dev chat In-Reply-To: <4BA25AB0.3020504@cs.man.ac.uk> References: <4BA254C2.8020902@cs.man.ac.uk> <4BA25AB0.3020504@cs.man.ac.uk> Message-ID: <4BA25C1A.2020707@ebi.ac.uk> Still fine by me. Eric Jiten Bhagat wrote: > Actually, can we do this at 11am tomorrow please? > > Jits > > > Jiten Bhagat wrote: > >> Hi guys, >> >> Can we set up a dev chat for tomorrow, say 14:30 please? >> >> We have a couple of pieces of work that need merging and planning for a >> release. >> >> Franck: you can join if you're interested in knowing what's coming in >> the next release :-) >> >> 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 > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Mar 18 13:07:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 13:07:40 -0400 (EDT) Subject: [BioCatalogue-developers] [1714] branches/integration-jan10: REST SUPPORT WORK Message-ID: <20100318170740.7A63C1598086@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 18 13:50:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 18 Mar 2010 13:50:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1715] branches/integration-jan10/app/views/rest_methods/show.html.erb: REST support work: changes to the REST method show view ( still to be tested). Message-ID: <20100318175009.96B4A18582DD@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Thu Mar 18 16:29:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 18 Mar 2010 20:29:49 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getPrositeAnnStructureFromPDBID' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getPrositeAnnStructureFromPDBID' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/915 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Mar 18 16:49:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 18 Mar 2010 20:49:58 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getPubMed' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getPubMed' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1090 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Mar 18 18:01:05 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 18 Mar 2010 22:01:05 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runGenewise' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runGenewise' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/836 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 19 01:11:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 05:11:10 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossGetorfFromSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossGetorfFromSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/816 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 19 02:29:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 06:29:20 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLAST blastp protein similarity search (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'BLAST blastp protein similarity search (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/92 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 19 06:36:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 06:36:24 -0400 (EDT) Subject: [BioCatalogue-developers] [1716] branches/integration-jan10/app: REST support work Message-ID: <20100319103624.2AA5B1598086@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 19 07:18:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 11:18:36 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1840 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 19 07:56:36 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 11:56:36 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryBfactorPerResidue' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryBfactorPerResidue' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1124 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 19 08:30:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 12:30:11 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromAminoAcidSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1000 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 19 09:12:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 13:12:15 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryDCD' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryDCD' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1125 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 19 09:57:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 09:57:50 -0400 (EDT) Subject: [BioCatalogue-developers] [1717] branches/integration-jan10/app: REST Support work Message-ID: <20100319135750.EC9381598086@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Fri Mar 19 11:07:43 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 19 Mar 2010 15:07:43 +0000 Subject: [BioCatalogue-developers] important notes from the skype chat Message-ID: Hi guys, the main points from our skype chat early on. 1- We are aiming for a release on Monday next week which will include: -REST services support improvement -SOAP operations UI -REST APIs/documentation -Service ownership, at least on the test site -JIRA -New developer wiki 2-Actions: Eric to redirect contact at biocatalogue.org to the developer list Eric to create a branch for the service ownership work Franck send some ideas to Eric about the test script documentation 3-After the release, we'll tackle these issues : - Service changes monitoring - curation tools including write API - try it first Free to add anything missing Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From jits at cs.man.ac.uk Fri Mar 19 11:18:59 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 19 Mar 2010 15:18:59 +0000 Subject: [BioCatalogue-developers] important notes from the skype chat In-Reply-To: References: Message-ID: <4BA395E3.802@cs.man.ac.uk> Franck, thanks. One thing to point out - > Service ownership, at least on the test site This will only make it on to the *test* site AFTER the release, because it will be done in a branch and can only be deployed on test when it gets onto trunk (unless we deploy it on a sandbox environment instead). The test server has to essentially be a duplicate of the live server. Also to add your comprehensive list for 1 below... - New wiki homepage. - Better help texts for test scripts. For 2-Actions, add: - ALL: to clean up the development wiki pages ready for release. Cheers, Jits Franck Tanoh wrote: > Hi guys, > the main points from our skype chat early on. > > 1- We are aiming for a release on Monday next week which will include: > -REST services support improvement > -SOAP operations UI > -REST APIs/documentation > -Service ownership, at least on the test site > -JIRA > -New developer wiki > > 2-Actions: > Eric to redirect contact at biocatalogue.org to the developer list > Eric to create a branch for the service ownership work > Franck send some ideas to Eric about the test script documentation > > 3-After the release, we'll tackle these issues : > - Service changes monitoring > - curation tools including write API > - try it first > > Free to add anything missing > > Franck > From noreply at rubyforge.org Fri Mar 19 11:41:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 11:41:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1718] branches/integration-jan10/app: Initial work on the new SOAP Operations UI. Message-ID: <20100319154103.0BE9C1598096@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 19 11:49:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 11:49:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1719] trunk: Merged integration-jan10 revisions 1635:1718 into trunk. Message-ID: <20100319154935.8796C159809C@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Fri Mar 19 12:05:17 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 19 Mar 2010 16:05:17 +0000 Subject: [BioCatalogue-developers] test script notes Message-ID: Hi Eric, -For the test script,it important to point that most of the users who've never heard/used Embrace registry might not know what the test script is and what is it for. So a summary of what it is and what is it for will be useful: You get get some text from the Embrace documentation : http://www.embraceregistry.net/content/information-service-providers. then we can point to the wiki for more information and example. -Also the link to add test is quite hidden. We need to make it obvious for example add it at the service level (so called 'service overview'). or an icon or text at the service overview level that can redirecct user/member to submit test page. The summary i mentioned above can be added just under the test script tab and as a tooltip if we put a link to the test script on the service page. -Currently the monitoring history is displayed from old info to recent info. for example: 4 day ago 3 days ago 1 days ago 10 min ago Can you reverse it instead. I think the most recent history should be on top. Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Fri Mar 19 12:46:42 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 19 Mar 2010 16:46:42 +0000 Subject: [BioCatalogue-developers] test script notes In-Reply-To: References: Message-ID: <4BA3AA72.3010102@ebi.ac.uk> Thanks Frank, I will take care of these. Eric Franck Tanoh wrote: > Hi Eric, > > -For the test script,it important to point that most of the users > who've never heard/used Embrace registry might not know what the test > script is and what is it for. > So a summary of what it is and what is it for will be useful: You get > get some text from the Embrace documentation : > http://www.embraceregistry.net/content/information-service-providers. > then we can point to the wiki for more information and example. > > -Also the link to add test is quite hidden. We need to make it obvious > for example add it at the service level (so called 'service > overview'). or an icon or text at the service overview level that can > redirecct user/member to submit test page. > The summary i mentioned above can be added just under the test script > tab and as a tooltip if we put a link to the test script on the > service page. > > -Currently the monitoring history is displayed from old info to recent > info. for example: > 4 day ago > 3 days ago > 1 days ago > 10 min ago > Can you reverse it instead. I think the most recent history should be on top. > > Franck > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Fri Mar 19 12:54:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 12:54:18 -0400 (EDT) Subject: [BioCatalogue-developers] [1720] trunk: More work on the new UI for SOAP operations and REST endpoints, with a new vertical tabs system. Message-ID: <20100319165418.8356E18582FA@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Fri Mar 19 13:34:08 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 19 Mar 2010 17:34:08 +0000 Subject: [BioCatalogue-developers] auto complete not working Message-ID: Hi guys, The 'auto complete' during search doesn't work at the moment. Seems like the server is unable to generate the files needed for that process (Jits- thanks for the explanation) Eric- can you take a look please? Thanks Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Fri Mar 19 13:41:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 17:41:28 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getPrincipalComponentFromPCZ_Report' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getPrincipalComponentFromPCZ_Report' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1161 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 19 13:45:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 13:45:19 -0400 (EDT) Subject: [BioCatalogue-developers] [1721] trunk: More work on the new UI for SOAP operations and REST endpoints. Message-ID: <20100319174519.545B718582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 19 13:53:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 17:53:28 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getNucleotideSequence' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getNucleotideSequence' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/940 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 19 13:55:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 13:55:19 -0400 (EDT) Subject: [BioCatalogue-developers] [1722] trunk/app: More work on the new UI for SOAP operations and REST endpoints. Message-ID: <20100319175519.5A84518582DF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 19 14:11:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 14:11:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1723] trunk/app/helpers/application_helper.rb: Refactoring for a helper method. Message-ID: <20100319181158.B057E18582F7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 19 14:16:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 14:16:08 -0400 (EDT) Subject: [BioCatalogue-developers] [1724] trunk/app/views/rest_parameters/_input_parameters.html.erb: Missing html escapes!! Message-ID: <20100319181608.C011518582F5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Mar 19 14:41:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 19 Mar 2010 14:41:11 -0400 (EDT) Subject: [BioCatalogue-developers] [1725] trunk: More work on the new UI for SOAP operations and REST endpoints. Message-ID: <20100319184111.AEEBC18582F8@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 19 18:12:19 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 19 Mar 2010 22:12:19 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getPrositeAnnStructure' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getPrositeAnnStructure' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/892 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 20 00:58:17 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 20 Mar 2010 04:58:17 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLAST blastp protein similarity search (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'BLAST blastp protein similarity search (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/92 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 20 16:01:53 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 20 Mar 2010 20:01:53 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runMDFromAMBER_MD_Structure' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runMDFromAMBER_MD_Structure' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1140 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 20 19:15:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 20 Mar 2010 23:15:41 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getEntryFromOMIM' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getEntryFromOMIM' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1056 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 21 02:27:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 21 Mar 2010 06:27:06 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsPerResidueFromMD_Trajectory' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryRmsPerResidueFromMD_Trajectory' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1132 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 21 16:19:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 21 Mar 2010 20:19:16 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'ConsensusPathDB' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'ConsensusPathDB' has changed status from 'Warning' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/188 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Mar 22 07:14:23 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:14:23 -0400 (EDT) Subject: [BioCatalogue-developers] [1726] trunk/app/views: More work on the SOAP operations UI: Message-ID: <20100322111423.282FF1678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:18:49 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:18:49 -0400 (EDT) Subject: [BioCatalogue-developers] [1727] trunk/app/views/soap_services/_show_service_tabs.html.erb: Added some information text to the Operations tab of Services. Message-ID: <20100322111849.BAB7818582DD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:20:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:20:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1728] trunk/app/views/soap_operations/_listing.html.erb: Reduced the amount of text shown for each SOAP operation in it's listings, from 700 characters to 400. Message-ID: <20100322112047.B80BD18582D5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:33:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:33:20 -0400 (EDT) Subject: [BioCatalogue-developers] [1729] trunk: Added a "Quick Browse" box to the top of the Operations tab to make it easier to quickly click through to an individual operation . Message-ID: <20100322113321.088E618582E1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:37:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:37:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1730] trunk/public/stylesheets/styles.css: Minor style update to the quick browse box. Message-ID: <20100322113737.5F2BA18582DD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:38:42 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:38:42 -0400 (EDT) Subject: [BioCatalogue-developers] [1731] trunk/public/stylesheets/styles.css: Prevent text from oveflowing on vertical tabs. Message-ID: <20100322113842.B188518582DF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:40:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:40:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1732] trunk: REST support work Message-ID: <20100322114048.267B018582DD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 07:55:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 07:55:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1733] trunk: Further style and layout updates for the vertical tabs. Message-ID: <20100322115505.52D5D1678217@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 09:39:45 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 09:39:45 -0400 (EDT) Subject: [BioCatalogue-developers] [1734] trunk/app: REST support work Message-ID: <20100322133946.1505518582DE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 10:02:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 10:02:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1735] trunk/app: REST support work Message-ID: <20100322140222.6243C18582E7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 11:11:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 11:11:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1736] trunk: REST support work Message-ID: <20100322151109.6965A18582D6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 12:33:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 12:33:46 -0400 (EDT) Subject: [BioCatalogue-developers] [1737] trunk: REST support work Message-ID: <20100322163346.8C79D18582E1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 13:09:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 13:09:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1738] trunk/app/helpers/rest_services_helper.rb: REST support work Message-ID: <20100322170933.6E3EF18582DE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 13:19:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 13:19:10 -0400 (EDT) Subject: [BioCatalogue-developers] [1739] trunk/app/views/rest_parameters/_input_parameters.html.erb: minor UI change Message-ID: <20100322171910.ED46C18582D5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 22 14:40:55 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 22 Mar 2010 14:40:55 -0400 (EDT) Subject: [BioCatalogue-developers] [1740] trunk/script/biocatalogue/sanity_check.rb: Initial work on a " sanity_check" script which we can use to regularly check for data consistency issues etc , to help identify discrepancies in stats and generally ensure that the system is in a healthy state . Message-ID: <20100322184055.A1A6E18582BF@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Mon Mar 22 14:41:42 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 22 Mar 2010 18:41:42 +0000 Subject: [BioCatalogue-developers] Stats discrepancy due to orphaned data Message-ID: <4BA7B9E6.9070708@cs.man.ac.uk> Hi Eric, For when you get back - We've noticed a discrepancy in the stats for the total number of services vs total number of SOAP services + REST services. It seems like the numbers differ by 3. So I've begun work on a "sanity_check" script (here: script/biocatalogue/sanity_check.rb) which we can use to regularly check for data consistency issues etc, to help with discrepancies like the above. When I ran it on my data (which was from a backup in early Jan) I get: ERROR: SoapService 118 does not have an associated ServiceVersion ERROR: RestService 14 does not have an associated ServiceVersion ERROR: RestService 15 does not have an associated ServiceVersion Not sure how this has happened! Probably via one of the import scripts. Can we get these objects removed from the live database please (the best way is probably to do it in script/console)? Cheers, Jits From utopia at cs.man.ac.uk Mon Mar 22 22:24:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 23 Mar 2010 02:24:45 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1059 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 23 04:40:35 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 23 Mar 2010 08:40:35 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'engineDB_06_08' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'engineDB_06_08' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/214 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 23 04:40:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 23 Mar 2010 08:40:52 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'engineDB_06_08' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'engineDB_06_08' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/214 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 23 09:05:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 23 Mar 2010 13:05:10 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:pdg.cnb.uam.es:getInteractionsXML' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:pdg.cnb.uam.es:getInteractionsXML' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/766 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 23 09:47:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 23 Mar 2010 13:47:40 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getCDSSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getCDSSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/929 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Tue Mar 23 11:56:11 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 23 Mar 2010 15:56:11 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4B97704D.6040107@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B96E79D.4040206@cs.man.ac.uk> <4B976F68.7080600@ebi.ac.uk> <4B97704D.6040107@cs.man.ac.uk> Message-ID: <4BA8E49B.7090103@cs.man.ac.uk> All the tasks from RubyForge have been merged into JIRA (http://www.mygrid.org.uk/dev/issues/browse/BIOCAT). Thanks to Mannie and Alan for sorting it. So now we need to set aside some time to go through and clean up / reassign, etc. Eric: you need an account. Let me know when you want me to set one up for you. Jits Jiten Bhagat wrote: > Yeap, you can put *new* tasks in there, but I still need to migrate the > existing ones into there. > > Please can anyone who needs an account for JIRA let me know (giving me > their preferred email address). > > Cheers, > Jits > > > Eric Nzuobontane wrote: > >> OK. Does that mean we can start using Jira? >> >> Eric >> >> >> >> Jiten Bhagat wrote: >> >>> Hi guys, >>> >>> I've finally received the data dump for the tasks list from the >>> Rubyforge guys. So hopefully in the next week or so I'll have it >>> migrated. >>> >>> So from now on please don't add any new tasks to Rubyforge. These won't >>> make it to JIRA and will be lost when we (eventually) delete the >>> Rubyforge tasks list. >>> >>> Cheers, >>> Jits >>> >>> >>> Jiten Bhagat wrote: >>> >>> >>>> Hi guys, >>>> >>>> I'm going to migrate the Rubyforge task list to JIRA in the next few >>>> days. So please don't add any more new tasks on Rubyforge. >>>> >>>> Cheers, >>>> 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 noreply at rubyforge.org Tue Mar 23 12:57:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 23 Mar 2010 12:57:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1741] trunk: REST support work Message-ID: <20100323165728.3EA4518582CA@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Mar 23 21:59:47 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 24 Mar 2010 01:59:47 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4BA8E49B.7090103@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B96E79D.4040206@cs.man.ac.uk> <4B976F68.7080600@ebi.ac.uk> <4B97704D.6040107@cs.man.ac.uk> <4BA8E49B.7090103@cs.man.ac.uk> Message-ID: Good job. Will Thursday or Friday be a good time for you guys? Franck On 23 March 2010 15:56, Jiten Bhagat wrote: > All the tasks from RubyForge have been merged into JIRA > (http://www.mygrid.org.uk/dev/issues/browse/BIOCAT). Thanks to Mannie > and Alan for sorting it. > > So now we need to set aside some time to go through and clean up / > reassign, etc. > > Eric: you need an account. Let me know when you want me to set one up > for you. > > Jits > > > Jiten Bhagat wrote: >> Yeap, you can put *new* tasks in there, but I still need to migrate the >> existing ones into there. >> >> Please can anyone who needs an account for JIRA let me know (giving me >> their preferred email address). >> >> Cheers, >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> OK. Does that mean we can start using Jira? >>> >>> Eric >>> >>> >>> >>> Jiten Bhagat wrote: >>> >>>> Hi guys, >>>> >>>> I've finally received the data dump for the tasks list from the >>>> Rubyforge guys. So hopefully in the next week or so I'll have it >>>> migrated. >>>> >>>> So from now on please don't add any new tasks to Rubyforge. These won't >>>> make it to JIRA and will be lost when we (eventually) delete the >>>> Rubyforge tasks list. >>>> >>>> Cheers, >>>> Jits >>>> >>>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>>> Hi guys, >>>>> >>>>> I'm going to migrate the Rubyforge task list to JIRA in the next few >>>>> days. So please don't add any more new tasks on Rubyforge. >>>>> >>>>> Cheers, >>>>> 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 > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Tue Mar 23 22:10:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 24 Mar 2010 02:10:34 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:textQueryUniprot' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:textQueryUniprot' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1055 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 24 05:03:01 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 24 Mar 2010 09:03:01 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runSLR' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runSLR' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1096 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Wed Mar 24 05:54:01 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 24 Mar 2010 09:54:01 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B96E79D.4040206@cs.man.ac.uk> <4B976F68.7080600@ebi.ac.uk> <4B97704D.6040107@cs.man.ac.uk> <4BA8E49B.7090103@cs.man.ac.uk> Message-ID: <4BA9E139.50804@cs.man.ac.uk> Franck Tanoh wrote: > Good job. > > Will Thursday or Friday be a good time for you guys? > Probably not :-( We need to prepare for the release on Monday and also there might be NAR paper stuff to action. Lets aim for next week sometime. Jits > Franck > > On 23 March 2010 15:56, Jiten Bhagat wrote: > >> All the tasks from RubyForge have been merged into JIRA >> (http://www.mygrid.org.uk/dev/issues/browse/BIOCAT). Thanks to Mannie >> and Alan for sorting it. >> >> So now we need to set aside some time to go through and clean up / >> reassign, etc. >> >> Eric: you need an account. Let me know when you want me to set one up >> for you. >> >> Jits >> >> >> Jiten Bhagat wrote: >> >>> Yeap, you can put *new* tasks in there, but I still need to migrate the >>> existing ones into there. >>> >>> Please can anyone who needs an account for JIRA let me know (giving me >>> their preferred email address). >>> >>> Cheers, >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>> >>>> OK. Does that mean we can start using Jira? >>>> >>>> Eric >>>> >>>> >>>> >>>> Jiten Bhagat wrote: >>>> >>>> >>>>> Hi guys, >>>>> >>>>> I've finally received the data dump for the tasks list from the >>>>> Rubyforge guys. So hopefully in the next week or so I'll have it >>>>> migrated. >>>>> >>>>> So from now on please don't add any new tasks to Rubyforge. These won't >>>>> make it to JIRA and will be lost when we (eventually) delete the >>>>> Rubyforge tasks list. >>>>> >>>>> Cheers, >>>>> Jits >>>>> >>>>> >>>>> Jiten Bhagat wrote: >>>>> >>>>> >>>>> >>>>>> Hi guys, >>>>>> >>>>>> I'm going to migrate the Rubyforge task list to JIRA in the next few >>>>>> days. So please don't add any more new tasks on Rubyforge. >>>>>> >>>>>> Cheers, >>>>>> 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 utopia at cs.man.ac.uk Wed Mar 24 06:30:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 24 Mar 2010 10:30:34 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1840 The test was aborted because it did not complete within 1800 seconds. As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Wed Mar 24 06:33:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 24 Mar 2010 10:33:36 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Failed In-Reply-To: References: Message-ID: <4BA9EA80.8090803@cs.man.ac.uk> Eric, As you'll notice below, EMBRACE has the ability to abort and then report on scripts that take longer than a certain amount of time. Just wanted to check - is this the case with the Test Scripts execution work in the BioCatalogue? Cheers, Jits utopia at cs.man.ac.uk wrote: > This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: > http://embraceregistry.net/node/1840 > The test was aborted because it did not complete within 1800 seconds. > As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. > > If you have any questions, please reply to this email. > > Yours, > The EMBRACE Registry Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Wed Mar 24 06:45:43 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Mar 2010 06:45:43 -0400 (EDT) Subject: [BioCatalogue-developers] [1742] trunk/app: REST support work Message-ID: <20100324104543.5FCE518582E7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 24 07:43:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Mar 2010 07:43:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1743] trunk: REST support work Message-ID: <20100324114339.4FB0F18582E3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 24 08:21:31 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Mar 2010 08:21:31 -0400 (EDT) Subject: [BioCatalogue-developers] [1744] trunk: REST support work Message-ID: <20100324122132.1FC0E18582D4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 24 09:34:47 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Mar 2010 09:34:47 -0400 (EDT) Subject: [BioCatalogue-developers] [1745] trunk/app/models/rest_service.rb: REST support work Message-ID: <20100324133447.B2FFD18582F6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 24 11:44:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Mar 2010 11:44:04 -0400 (EDT) Subject: [BioCatalogue-developers] [1746] trunk: REST support work Message-ID: <20100324154404.B156D18582F6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 24 11:59:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 24 Mar 2010 11:59:20 -0400 (EDT) Subject: [BioCatalogue-developers] [1747] trunk/app/views/rest_methods/show.html.erb: missed out of last commit Message-ID: <20100324155920.C009B18582E7@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 24 13:58:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 24 Mar 2010 17:58:13 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'engineDB_06_08' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'engineDB_06_08' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/214 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 24 22:34:04 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 25 Mar 2010 02:34:04 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:searchBLOCKS' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:searchBLOCKS' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/898 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Mar 25 04:19:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 25 Mar 2010 08:19:34 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1840 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Thu Mar 25 06:19:17 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 25 Mar 2010 10:19:17 +0000 Subject: [BioCatalogue-developers] Stats discrepancy due to orphaned data In-Reply-To: <4BA7B9E6.9070708@cs.man.ac.uk> References: <4BA7B9E6.9070708@cs.man.ac.uk> Message-ID: <4BAB38A5.3080404@ebi.ac.uk> * - the orphaned soap service is http://www.ebi.ac.uk/soaplab/typed/services/edit.descseq?wsdl * - the orphaned rest service is LoCo (Low-Complexity) Web-Service (14 &15) The Service deployments are missing for the LoCo service so the endpoint is not available either! Eric Jiten Bhagat wrote: > Hi Eric, > > For when you get back - > > We've noticed a discrepancy in the stats for the total number of > services vs total number of SOAP services + REST services. It seems like > the numbers differ by 3. > > So I've begun work on a "sanity_check" script (here: > script/biocatalogue/sanity_check.rb) which we can use to regularly check > for data consistency issues etc, to help with discrepancies like the above. > > When I ran it on my data (which was from a backup in early Jan) I get: > > ERROR: SoapService 118 does not have an associated ServiceVersion > ERROR: RestService 14 does not have an associated ServiceVersion > ERROR: RestService 15 does not have an associated ServiceVersion > > Not sure how this has happened! Probably via one of the import scripts. > Can we get these objects removed from the live database please (the best > way is probably to do it in script/console)? > > Cheers, > Jits > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Thu Mar 25 07:30:55 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 25 Mar 2010 11:30:55 +0000 Subject: [BioCatalogue-developers] Tasks list In-Reply-To: <4BA9E139.50804@cs.man.ac.uk> References: <4B8CF4BD.1080706@cs.man.ac.uk> <4B96E79D.4040206@cs.man.ac.uk> <4B976F68.7080600@ebi.ac.uk> <4B97704D.6040107@cs.man.ac.uk> <4BA8E49B.7090103@cs.man.ac.uk> <4BA9E139.50804@cs.man.ac.uk> Message-ID: <4BAB496F.30405@ebi.ac.uk> Hi Guys, Nice one for the task list import. Jits, could you please remember to create an account for me? Thanks! Eric >> Good job. >> >> Will Thursday or Friday be a good time for you guys? >> >> > > Probably not :-( We need to prepare for the release on Monday and also > there might be NAR paper stuff to action. > > Lets aim for next week sometime. > > Jits > > >> Franck >> >> On 23 March 2010 15:56, Jiten Bhagat wrote: >> >> >>> All the tasks from RubyForge have been merged into JIRA >>> (http://www.mygrid.org.uk/dev/issues/browse/BIOCAT). Thanks to Mannie >>> and Alan for sorting it. >>> >>> So now we need to set aside some time to go through and clean up / >>> reassign, etc. >>> >>> Eric: you need an account. Let me know when you want me to set one up >>> for you. >>> >>> Jits >>> >>> >>> Jiten Bhagat wrote: >>> >>> >>>> Yeap, you can put *new* tasks in there, but I still need to migrate the >>>> existing ones into there. >>>> >>>> Please can anyone who needs an account for JIRA let me know (giving me >>>> their preferred email address). >>>> >>>> Cheers, >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>> >>>> >>>> >>>>> OK. Does that mean we can start using Jira? >>>>> >>>>> Eric >>>>> >>>>> >>>>> >>>>> Jiten Bhagat wrote: >>>>> >>>>> >>>>> >>>>>> Hi guys, >>>>>> >>>>>> I've finally received the data dump for the tasks list from the >>>>>> Rubyforge guys. So hopefully in the next week or so I'll have it >>>>>> migrated. >>>>>> >>>>>> So from now on please don't add any new tasks to Rubyforge. These won't >>>>>> make it to JIRA and will be lost when we (eventually) delete the >>>>>> Rubyforge tasks list. >>>>>> >>>>>> Cheers, >>>>>> Jits >>>>>> >>>>>> >>>>>> Jiten Bhagat wrote: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Hi guys, >>>>>>> >>>>>>> I'm going to migrate the Rubyforge task list to JIRA in the next few >>>>>>> days. So please don't add any more new tasks on Rubyforge. >>>>>>> >>>>>>> Cheers, >>>>>>> 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 >>> >>> >>> >> >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Mar 25 08:01:46 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Mar 2010 08:01:46 -0400 (EDT) Subject: [BioCatalogue-developers] [1748] trunk/app: REST support work Message-ID: <20100325120146.6AE8918582F1@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Mar 25 08:26:58 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 25 Mar 2010 12:26:58 +0000 Subject: [BioCatalogue-developers] NAR paper In-Reply-To: <4BA8902F.5050908@cs.man.ac.uk> References: <4BA6483A.1060003@manchester.ac.uk> <4BA8902F.5050908@cs.man.ac.uk> Message-ID: <4BAB5692.1090502@ebi.ac.uk> Hi Jits, From the comments I read from the reviewers of the paper, there seemed to be a suggestion that there would be both the read and write API at the time of publication. Or maybe I did not understand that? On another point, there seem to be some suggestion that there are (REST) services in EMBRACE that are not in BioCatalogue, though looking at the last import log, I did not seem to see any reported failure of REST services from embrace. I presume that they checked the site before the last import. Any time stamps of when the reviewers checked the site? Eric Jiten Bhagat wrote: > Hi Franck, > > I believe the actions boiled down to: > > - Carole to contact the editor. > - Carole to do an initial "rewrite" (mainly simplification and > reorganising, with spaces for new sections on API/features and > alternative systems). > - Katy to take care of fixing references, making terms consistent, etc. > - Jits/Rodrigo to do the section on API/features (I will send something > to Rodrigo by end of today or tomorrow morning). > - Rodrigo/Steve/Carole to oversee the whole paper to ensure it hits the > sweet spot. > > Please do add anything else I have missed. > > Jits > > > Franck Tanoh wrote: > >> Sorry couldn't join the meeting and just managed to get online. >> what are the actions that came up from the discussion about the paper >> at the meeting? >> >> Franck >> >> On 21 March 2010 16:24, Carole Goble wrote: >> >> >>> 3-4pm would like to dedicate to the NAR revisions >>> my office for the Manchester people >>> >>> carole >>> >>> >>> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur >> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Thu Mar 25 09:16:35 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 25 Mar 2010 13:16:35 +0000 Subject: [BioCatalogue-developers] How the NCRI folks will be using the BioCatalogue API In-Reply-To: <4BAA3BCA.5030600@cs.man.ac.uk> References: <4B9D42BD.2000801@cs.man.ac.uk> <4BAA3BCA.5030600@cs.man.ac.uk> Message-ID: Hi guys, while using ONIX to find biocat services I 've noticed that the URL for services in the ONIX are different from the URL you get using the biocat website for the same service. To be clearer here is an example: the ddbj blast service in ONIX has the following URL: http://www.biocatalogue.org/services/8 but using the biocat website i get the following url: http://www.biocatalogue.org/services/8-blast_920841 both links work but I think it's better to have just one unique URL for a service. The ONIX one which i guess is from the APIs will be my choice. cheers, Franck On 24 March 2010 16:20, Jiten Bhagat wrote: > More info from the NCRI folks (re: BioCat integration into ONIX): > > >From Alan Hogg... > > " > We actually released our new version of ONIX late last week just before > See Wah went. You can reach it on: > > http://www.ncri-onix.org.uk/portal/#S1 > > The resource catalogue now includes the BioCatalogue material so it is > probably easiest for you to capture what screen shots you need directly. > If to select Resource Catalogue from the main menu you will find > BioCatalogue as one of the listed catalogues. > " > > Jits > > > Jiten Bhagat wrote: >> Below is an explanation from one of the devs at NCRI on how they will be >> harvesting BioCatalogue data from the API (into ONIX): >> >> "At the moment, we are just periodically downloading your service >> metadata (once a week) to include in our "resource catalogue", which is >> effectively a meta-catalogue of cancer research-related catalogues. >> Users can search directly in the "resource catalogue," but the results >> will contain links to link back to the sources, e.g. yourself." >> >> Jits >> > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Thu Mar 25 10:45:03 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 25 Mar 2010 14:45:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getSequencesFromENSEMBLHomology' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getSequencesFromENSEMBLHomology' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/903 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From jits at cs.man.ac.uk Thu Mar 25 11:33:07 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 25 Mar 2010 15:33:07 +0000 Subject: [BioCatalogue-developers] NAR paper In-Reply-To: <4BAB5692.1090502@ebi.ac.uk> References: <4BA6483A.1060003@manchester.ac.uk> <4BA8902F.5050908@cs.man.ac.uk> <4BAB5692.1090502@ebi.ac.uk> Message-ID: <4BAB8233.7040409@cs.man.ac.uk> Hi Eric, Eric Nzuobontane wrote: > Hi Jits, > From the comments I read from the reviewers of the paper, there seemed > to be a suggestion that there would be both the read and write API at > the time of publication. Or maybe I did not understand that? I don't think that's necessarily the case - I think a read only API for now is fine. And that's what we'll talk about in the paper. > On another point, there seem to be some suggestion that there are > (REST) services in EMBRACE that are not in BioCatalogue, though > looking at the last import log, I did not seem to see any reported > failure of REST services from embrace. I presume that they checked the > site before the last import. Any time stamps of when the reviewers > checked the site? Yes, this was clearly before the EMBRACE import. I don't think we can know when the reviewers checked the site. Hopefully they will revisit and see that now the services are in. Jits > > Eric > > > > Jiten Bhagat wrote: >> Hi Franck, >> >> I believe the actions boiled down to: >> >> - Carole to contact the editor. >> - Carole to do an initial "rewrite" (mainly simplification and >> reorganising, with spaces for new sections on API/features and >> alternative systems). >> - Katy to take care of fixing references, making terms consistent, etc. >> - Jits/Rodrigo to do the section on API/features (I will send something >> to Rodrigo by end of today or tomorrow morning). >> - Rodrigo/Steve/Carole to oversee the whole paper to ensure it hits the >> sweet spot. >> >> Please do add anything else I have missed. >> >> Jits >> >> >> Franck Tanoh wrote: >> >>> Sorry couldn't join the meeting and just managed to get online. >>> what are the actions that came up from the discussion about the paper >>> at the meeting? >>> >>> Franck >>> >>> On 21 March 2010 16:24, Carole Goble >>> wrote: >>> >>> >>>> 3-4pm would like to dedicate to the NAR revisions >>>> my office for the Manchester people >>>> >>>> carole >>>> >>>> >>>> >>> >>> -- >>> "Science knows no country, because knowledge belongs to humanity, and >>> is the torch which illuminates the world." - Louis Pasteur >>> >>> > > From jits at cs.man.ac.uk Thu Mar 25 11:35:00 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 25 Mar 2010 15:35:00 +0000 Subject: [BioCatalogue-developers] How the NCRI folks will be using the BioCatalogue API In-Reply-To: References: <4B9D42BD.2000801@cs.man.ac.uk> <4BAA3BCA.5030600@cs.man.ac.uk> Message-ID: <4BAB82A4.5050501@cs.man.ac.uk> Hi Franck, Yes, good point. The idea behind URLs like "http://www.biocatalogue.org/services/8-blast_920841" is to be a bit more "human readable". But actually this turns out to be not do great so I'll change this behaviour. The next release should only show URLs like "http://www.biocatalogue.org/services/8" Cheers, Jits Franck Tanoh wrote: > Hi guys, > > while using ONIX to find biocat services I 've noticed that the URL > for services in the ONIX are different from the URL you get using the > biocat website for the same service. To be clearer here is an example: > the ddbj blast service in ONIX has the following URL: > http://www.biocatalogue.org/services/8 > but using the biocat website i get the following url: > http://www.biocatalogue.org/services/8-blast_920841 > both links work but I think it's better to have just one unique URL > for a service. The ONIX one which i guess is from the APIs will be my > choice. > > cheers, > Franck > > On 24 March 2010 16:20, Jiten Bhagat wrote: > >> More info from the NCRI folks (re: BioCat integration into ONIX): >> >> >From Alan Hogg... >> >> " >> We actually released our new version of ONIX late last week just before >> See Wah went. You can reach it on: >> >> http://www.ncri-onix.org.uk/portal/#S1 >> >> The resource catalogue now includes the BioCatalogue material so it is >> probably easiest for you to capture what screen shots you need directly. >> If to select Resource Catalogue from the main menu you will find >> BioCatalogue as one of the listed catalogues. >> " >> >> Jits >> >> >> Jiten Bhagat wrote: >> >>> Below is an explanation from one of the devs at NCRI on how they will be >>> harvesting BioCatalogue data from the API (into ONIX): >>> >>> "At the moment, we are just periodically downloading your service >>> metadata (once a week) to include in our "resource catalogue", which is >>> effectively a meta-catalogue of cancer research-related catalogues. >>> Users can search directly in the "resource catalogue," but the results >>> will contain links to link back to the sources, e.g. yourself." >>> >>> Jits >>> >>> > > > > From ericnzuo at ebi.ac.uk Thu Mar 25 11:50:35 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 25 Mar 2010 15:50:35 +0000 Subject: [BioCatalogue-developers] How the NCRI folks will be using the BioCatalogue API In-Reply-To: <4BAB82A4.5050501@cs.man.ac.uk> References: <4B9D42BD.2000801@cs.man.ac.uk> <4BAA3BCA.5030600@cs.man.ac.uk> <4BAB82A4.5050501@cs.man.ac.uk> Message-ID: <4BAB864B.6070108@ebi.ac.uk> Jiten Bhagat wrote: > Hi Franck, > > Yes, good point. > > The idea behind URLs like > "http://www.biocatalogue.org/services/8-blast_920841" is to be a bit > more "human readable". But actually this turns out to be not do great so > I'll change this behaviour. > > The next release should only show URLs like > "http://www.biocatalogue.org/services/8" > So will any bookmarks of the readable urls break? > Franck Tanoh wrote: > >> Hi guys, >> >> while using ONIX to find biocat services I 've noticed that the URL >> for services in the ONIX are different from the URL you get using the >> biocat website for the same service. To be clearer here is an example: >> the ddbj blast service in ONIX has the following URL: >> http://www.biocatalogue.org/services/8 >> but using the biocat website i get the following url: >> http://www.biocatalogue.org/services/8-blast_920841 >> both links work but I think it's better to have just one unique URL >> for a service. The ONIX one which i guess is from the APIs will be my >> choice. >> >> cheers, >> Franck >> >> On 24 March 2010 16:20, Jiten Bhagat wrote: >> >> >>> More info from the NCRI folks (re: BioCat integration into ONIX): >>> >>> >From Alan Hogg... >>> >>> " >>> We actually released our new version of ONIX late last week just before >>> See Wah went. You can reach it on: >>> >>> http://www.ncri-onix.org.uk/portal/#S1 >>> >>> The resource catalogue now includes the BioCatalogue material so it is >>> probably easiest for you to capture what screen shots you need directly. >>> If to select Resource Catalogue from the main menu you will find >>> BioCatalogue as one of the listed catalogues. >>> " >>> >>> Jits >>> >>> >>> Jiten Bhagat wrote: >>> >>> >>>> Below is an explanation from one of the devs at NCRI on how they will be >>>> harvesting BioCatalogue data from the API (into ONIX): >>>> >>>> "At the moment, we are just periodically downloading your service >>>> metadata (once a week) to include in our "resource catalogue", which is >>>> effectively a meta-catalogue of cancer research-related catalogues. >>>> Users can search directly in the "resource catalogue," but the results >>>> will contain links to link back to the sources, e.g. yourself." >>>> >>>> Jits >>>> >>>> >>>> >> >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu Mar 25 11:54:07 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 25 Mar 2010 15:54:07 +0000 Subject: [BioCatalogue-developers] How the NCRI folks will be using the BioCatalogue API In-Reply-To: <4BAB864B.6070108@ebi.ac.uk> References: <4B9D42BD.2000801@cs.man.ac.uk> <4BAA3BCA.5030600@cs.man.ac.uk> <4BAB82A4.5050501@cs.man.ac.uk> <4BAB864B.6070108@ebi.ac.uk> Message-ID: <4BAB871F.5020706@cs.man.ac.uk> Eric Nzuobontane wrote: > Jiten Bhagat wrote: >> Hi Franck, >> >> Yes, good point. >> >> The idea behind URLs like >> "http://www.biocatalogue.org/services/8-blast_920841" is to be a bit >> more "human readable". But actually this turns out to be not do great so >> I'll change this behaviour. >> >> The next release should only show URLs like >> "http://www.biocatalogue.org/services/8" >> > So will any bookmarks of the readable urls break? No, they will continue working. Both forms of the URL are handled in exactly the same way by the system. Jits > >> Franck Tanoh wrote: >> >>> Hi guys, >>> >>> while using ONIX to find biocat services I 've noticed that the URL >>> for services in the ONIX are different from the URL you get using the >>> biocat website for the same service. To be clearer here is an example: >>> the ddbj blast service in ONIX has the following URL: >>> http://www.biocatalogue.org/services/8 >>> but using the biocat website i get the following url: >>> http://www.biocatalogue.org/services/8-blast_920841 >>> both links work but I think it's better to have just one unique URL >>> for a service. The ONIX one which i guess is from the APIs will be my >>> choice. >>> >>> cheers, >>> Franck >>> >>> On 24 March 2010 16:20, Jiten Bhagat wrote: >>> >>>> More info from the NCRI folks (re: BioCat integration into ONIX): >>>> >>>> >From Alan Hogg... >>>> >>>> " >>>> We actually released our new version of ONIX late last week just >>>> before >>>> See Wah went. You can reach it on: >>>> >>>> http://www.ncri-onix.org.uk/portal/#S1 >>>> >>>> The resource catalogue now includes the BioCatalogue material so it is >>>> probably easiest for you to capture what screen shots you need >>>> directly. >>>> If to select Resource Catalogue from the main menu you will find >>>> BioCatalogue as one of the listed catalogues. >>>> " >>>> >>>> Jits >>>> >>>> >>>> Jiten Bhagat wrote: >>>> >>>>> Below is an explanation from one of the devs at NCRI on how they >>>>> will be >>>>> harvesting BioCatalogue data from the API (into ONIX): >>>>> >>>>> "At the moment, we are just periodically downloading your service >>>>> metadata (once a week) to include in our "resource catalogue", >>>>> which is >>>>> effectively a meta-catalogue of cancer research-related catalogues. >>>>> Users can search directly in the "resource catalogue," but the >>>>> results >>>>> will contain links to link back to the sources, e.g. yourself." >>>>> >>>>> Jits >>>>> >>>>> >>> >>> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > From noreply at rubyforge.org Thu Mar 25 11:56:25 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Mar 2010 11:56:25 -0400 (EDT) Subject: [BioCatalogue-developers] [1749] trunk/app/models/service.rb: Consolidated the URL format for services. Message-ID: <20100325155625.9973018582CE@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Mar 25 12:16:59 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 25 Mar 2010 16:16:59 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' changed to Failed In-Reply-To: References: Message-ID: Hi Eric, Anytime I look at those notifications, i get confused. Please, take a look at those 2 services and see why... the service in Embrace :http://embraceregistry.net/test/inb-devinbbscesfromxydatatexttoarrayfloat1 the service in BioCatalogue: http://www.biocatalogue.org/services/2355-fromxydatatexttoarrayfloatservice_930784 Maybe still the synchronisation problem but can't get my head around. Franck On 23 March 2010 02:24, wrote: > This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: > ? ?http://embraceregistry.net/node/1059 > > As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. > > If you have any questions, please reply to this email. > > Yours, > The EMBRACE Registry Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Thu Mar 25 12:52:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Mar 2010 12:52:24 -0400 (EDT) Subject: [BioCatalogue-developers] [1750] trunk/app/views/soap_operations/show.html.erb: More additions to the SOAP operations UI based on feedback from Franck. Message-ID: <20100325165224.B201A1858302@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Mar 25 13:00:20 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Mar 2010 13:00:20 -0400 (EDT) Subject: [BioCatalogue-developers] [1751] trunk/app/views/soap_operations/show.html.erb: More changes to the SOAP operations UI based on feedback. Message-ID: <20100325170021.651251858302@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Mar 25 13:15:03 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 25 Mar 2010 17:15:03 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' changed to Failed In-Reply-To: References: Message-ID: <4BAB9A17.9020702@ebi.ac.uk> Hi Franck > Hi Eric, > > Anytime I look at those notifications, i get confused. Please, take a > look at those 2 services and see why... > the service in Embrace > :http://embraceregistry.net/test/inb-devinbbscesfromxydatatexttoarrayfloat1 > As far as I can see, that failed 3 days ago in the embrace registry. BioCatalogue also indicates a failure 3 days ago. However, there has been no embrace test result ever since. BioCatalogue runs start at 10:15 pm, everyday. The embrace guys said they run at 10:00 am & pm. > the service in BioCatalogue: > http://www.biocatalogue.org/services/2355-fromxydatatexttoarrayfloatservice_930784 > This failed 3 days ago but passes ever since & there is no embrace data to compare with for recent runs. At least not that I can see. Even if they are not exactly synchonized, they should be in the order of hours of each other. Not order of days or sometimes months. But you can see the regularity of the biocatalogue runs. > Maybe still the synchronisation problem but can't get my head around. > > Franck > > > On 23 March 2010 02:24, wrote: > >> This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:fromXYDataTextToArrayFloat' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: >> http://embraceregistry.net/node/1059 >> >> As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. >> >> If you have any questions, please reply to this email. >> >> Yours, >> The EMBRACE Registry Team >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From noreply at rubyforge.org Thu Mar 25 13:58:08 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 25 Mar 2010 13:58:08 -0400 (EDT) Subject: [BioCatalogue-developers] [1752] trunk/: Ignore .rvmrc file Message-ID: <20100325175808.5901418582E7@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 26 00:13:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 04:13:56 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:textQueryOMIM' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:textQueryOMIM' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1061 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 26 00:33:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 04:33:29 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getPersistentFile' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getPersistentFile' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/868 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 26 05:23:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Mar 2010 05:23:10 -0400 (EDT) Subject: [BioCatalogue-developers] [1753] branches/service-ownership/: branch for initial work on service ownership/responsibility Message-ID: <20100326092310.BD6EC18582EC@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 26 06:00:00 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 10:00:00 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runTargetPDAS' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runTargetPDAS' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1093 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 26 06:12:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 10:12:33 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getSequenceByRegionFromENSEMBL' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getSequenceByRegionFromENSEMBL' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/906 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 26 06:29:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Mar 2010 06:29:57 -0400 (EDT) Subject: [BioCatalogue-developers] [1754] branches/service-ownership/: deleting badly created branch Message-ID: <20100326102957.6070118582CB@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 26 06:36:12 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 10:36:12 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runStructurePhysicalProperties' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runStructurePhysicalProperties' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1016 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Mar 26 07:18:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 11:18:28 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:multiplotArrayXYData' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:multiplotArrayXYData' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/899 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Fri Mar 26 08:07:10 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 26 Mar 2010 12:07:10 +0000 Subject: [BioCatalogue-developers] pathway common service status Message-ID: Hi Guys, The provider of pathway common service (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has asked me why their REST service status is amber while it seem to be working fine? If the endpoint changes from 'http://www.pathwaycommons.org/pc' to 'http://www.pathwaycommons.org' will it change the status in the biocat? Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Fri Mar 26 08:57:02 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 12:57:02 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromProsite' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromProsite' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/877 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Fri Mar 26 09:34:50 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 26 Mar 2010 13:34:50 +0000 Subject: [BioCatalogue-developers] pathway common service status In-Reply-To: References: Message-ID: <4BACB7FA.90802@ebi.ac.uk> Hi Franck > The provider of pathway common service > (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has > asked me why their REST service status is amber while it seem to be > working fine? > The reason is that the endpoint does not necessarily resolve to a valid url and since we do not have any parameters, this gives us 'failure' status code. If and when users are able to give us parameters as well as their base url, we should be able to solve this problem > If the endpoint changes from 'http://www.pathwaycommons.org/pc' to > 'http://www.pathwaycommons.org' will it change the status in the > No, but 'http://www.pathwaycommons.org/pc/' will change it to green. Notice the trailing forward slash... Eric > biocat? > > Cheers, > Franck > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Fri Mar 26 09:42:55 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 26 Mar 2010 13:42:55 +0000 Subject: [BioCatalogue-developers] pathway common service status In-Reply-To: <4BACB7FA.90802@ebi.ac.uk> References: <4BACB7FA.90802@ebi.ac.uk> Message-ID: <4BACB9DF.7020809@cs.man.ac.uk> Sounds like in this particular case changing the base endpoint (aka base URL) will solve this particular problem. With Mannie's new work the user will be able to do this directly. For now this might need to be a db manual change (unless user is willing to wait a week or so?) Jits Eric Nzuobontane wrote: > Hi Franck >> The provider of pathway common service >> (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has >> asked me why their REST service status is amber while it seem to be >> working fine? >> > The reason is that the endpoint does not necessarily resolve to a > valid url and since we do not have any parameters, this gives us > 'failure' status code. If and when users are able to give us > parameters as well as their base url, we should be able to solve this > problem >> If the endpoint changes from 'http://www.pathwaycommons.org/pc' to >> 'http://www.pathwaycommons.org' will it change the status in the >> > No, but 'http://www.pathwaycommons.org/pc/' will change it to green. > > Notice the trailing forward slash... > > Eric > >> biocat? >> >> Cheers, >> Franck >> >> >> >> > > From utopia at cs.man.ac.uk Fri Mar 26 09:43:57 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 13:43:57 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossPepinfoFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossPepinfoFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/823 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 26 09:49:16 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Mar 2010 09:49:16 -0400 (EDT) Subject: [BioCatalogue-developers] [1755] trunk/app/views/home/index.html.erb: Change text on the homepage to say that the EMBRACE registry and the BioCatalogue have now been merged . Message-ID: <20100326134916.B7BE618582BF@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Fri Mar 26 10:24:19 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 26 Mar 2010 14:24:19 +0000 Subject: [BioCatalogue-developers] pathway common service status In-Reply-To: <4BACB9DF.7020809@cs.man.ac.uk> References: <4BACB7FA.90802@ebi.ac.uk> <4BACB9DF.7020809@cs.man.ac.uk> Message-ID: >> No, but 'http://www.pathwaycommons.org/pc/' will change it to green. If that solves the problem can you correct it in the database please? Thanks, Franck On 26 March 2010 13:42, Jiten Bhagat wrote: > Sounds like in this particular case changing the base endpoint (aka base > URL) will solve this particular problem. > > With Mannie's new work the user will be able to do this directly. For > now this might need to be a db manual change (unless user is willing to > wait a week or so?) > > Jits > > > Eric Nzuobontane wrote: >> Hi Franck >>> The provider of pathway common service >>> (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has >>> asked me why their REST service status is amber while it seem to be >>> working fine? >>> >> The reason is that the endpoint does not necessarily resolve to a >> valid url and since we do not have any parameters, this gives us >> 'failure' status code. If and when users are able to give us >> parameters as well as their base url, we should be able to solve this >> problem >>> If the endpoint changes from 'http://www.pathwaycommons.org/pc' ?to >>> 'http://www.pathwaycommons.org' will it change the status in the >>> >> No, ?but 'http://www.pathwaycommons.org/pc/' ?will change it to green. >> >> Notice the trailing forward slash... >> >> Eric >> >>> biocat? >>> >>> Cheers, >>> Franck >>> >>> >>> >>> >> >> > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Fri Mar 26 10:27:12 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 14:27:12 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromPDB' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromPDB' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/941 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Fri Mar 26 10:51:50 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 26 Mar 2010 14:51:50 +0000 Subject: [BioCatalogue-developers] pathway common service status In-Reply-To: References: <4BACB7FA.90802@ebi.ac.uk> <4BACB9DF.7020809@cs.man.ac.uk> Message-ID: <4BACCA06.1030506@ebi.ac.uk> will do. Eric Franck Tanoh wrote: >>> No, but 'http://www.pathwaycommons.org/pc/' will change it to green. >>> > If that solves the problem can you correct it in the database please? > > Thanks, > Franck > > On 26 March 2010 13:42, Jiten Bhagat wrote: > >> Sounds like in this particular case changing the base endpoint (aka base >> URL) will solve this particular problem. >> >> With Mannie's new work the user will be able to do this directly. For >> now this might need to be a db manual change (unless user is willing to >> wait a week or so?) >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> Hi Franck >>> >>>> The provider of pathway common service >>>> (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has >>>> asked me why their REST service status is amber while it seem to be >>>> working fine? >>>> >>>> >>> The reason is that the endpoint does not necessarily resolve to a >>> valid url and since we do not have any parameters, this gives us >>> 'failure' status code. If and when users are able to give us >>> parameters as well as their base url, we should be able to solve this >>> problem >>> >>>> If the endpoint changes from 'http://www.pathwaycommons.org/pc' to >>>> 'http://www.pathwaycommons.org' will it change the status in the >>>> >>>> >>> No, but 'http://www.pathwaycommons.org/pc/' will change it to green. >>> >>> Notice the trailing forward slash... >>> >>> Eric >>> >>> >>>> biocat? >>>> >>>> Cheers, >>>> Franck >>>> >>>> >>>> >>>> >>>> >>> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Fri Mar 26 10:53:20 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 26 Mar 2010 14:53:20 +0000 Subject: [BioCatalogue-developers] auto complete not working In-Reply-To: References: Message-ID: <4BACCA60.3050209@ebi.ac.uk> Query suggestions should be working now. Eric Franck Tanoh wrote: > Hi guys, > > The 'auto complete' during search doesn't work at the moment. > Seems like the server is unable to generate the files needed for that > process (Jits- thanks for the explanation) > Eric- can you take a look please? > > Thanks > Franck > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Fri Mar 26 11:08:23 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 26 Mar 2010 15:08:23 +0000 Subject: [BioCatalogue-developers] auto complete not working In-Reply-To: <4BACCA60.3050209@ebi.ac.uk> References: <4BACCA60.3050209@ebi.ac.uk> Message-ID: <4BACCDE7.5070606@cs.man.ac.uk> Excellent, thanks Eric. For future reference, what was the issue? Jits Eric Nzuobontane wrote: > Query suggestions should be working now. > > Eric > > > > Franck Tanoh wrote: >> Hi guys, >> >> The 'auto complete' during search doesn't work at the moment. >> Seems like the server is unable to generate the files needed for that >> process (Jits- thanks for the explanation) >> Eric- can you take a look please? >> >> Thanks >> Franck >> > > From noreply at rubyforge.org Fri Mar 26 11:21:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Mar 2010 11:21:40 -0400 (EDT) Subject: [BioCatalogue-developers] [1756] trunk/app/controllers/lookup_controller.rb: REST API work: fix for / lookup to respect the content type requested Message-ID: <20100326152140.BE6BF18582E3@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Fri Mar 26 11:21:11 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 26 Mar 2010 15:21:11 +0000 Subject: [BioCatalogue-developers] auto complete not working In-Reply-To: <4BACCDE7.5070606@cs.man.ac.uk> References: <4BACCA60.3050209@ebi.ac.uk> <4BACCDE7.5070606@cs.man.ac.uk> Message-ID: <4BACD0E7.5010305@ebi.ac.uk> permissions. The user that runs the application and the user that owns the files were not in the same group. Only group & owner have execute permission on files. Eric Jiten Bhagat wrote: > Excellent, thanks Eric. > > For future reference, what was the issue? > > Jits > > > Eric Nzuobontane wrote: > >> Query suggestions should be working now. >> >> Eric >> >> >> >> Franck Tanoh wrote: >> >>> Hi guys, >>> >>> The 'auto complete' during search doesn't work at the moment. >>> Seems like the server is unable to generate the files needed for that >>> process (Jits- thanks for the explanation) >>> Eric- can you take a look please? >>> >>> Thanks >>> Franck >>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Fri Mar 26 11:22:26 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 26 Mar 2010 15:22:26 +0000 Subject: [BioCatalogue-developers] auto complete not working In-Reply-To: <4BACCA60.3050209@ebi.ac.uk> References: <4BACCA60.3050209@ebi.ac.uk> Message-ID: Yep, working fine. Thanks, Franck On 26 March 2010 14:53, Eric Nzuobontane wrote: > Query suggestions should be working now. > > Eric > > > > Franck Tanoh wrote: >> >> Hi guys, >> >> The 'auto complete' during search doesn't work at the moment. >> Seems like the server is unable to generate the files needed for that >> process (Jits- thanks for the explanation) >> Eric- can you take a look please? >> >> Thanks >> Franck >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Fri Mar 26 11:22:01 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 26 Mar 2010 15:22:01 +0000 Subject: [BioCatalogue-developers] pathway common service status In-Reply-To: References: <4BACB7FA.90802@ebi.ac.uk> <4BACB9DF.7020809@cs.man.ac.uk> Message-ID: <4BACD119.2030208@ebi.ac.uk> Franck Tanoh wrote: >>> No, but 'http://www.pathwaycommons.org/pc/' will change it to green. >>> > If that solves the problem can you correct it in the database please? > Done > Thanks, > Franck > > On 26 March 2010 13:42, Jiten Bhagat wrote: > >> Sounds like in this particular case changing the base endpoint (aka base >> URL) will solve this particular problem. >> >> With Mannie's new work the user will be able to do this directly. For >> now this might need to be a db manual change (unless user is willing to >> wait a week or so?) >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> Hi Franck >>> >>>> The provider of pathway common service >>>> (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has >>>> asked me why their REST service status is amber while it seem to be >>>> working fine? >>>> >>>> >>> The reason is that the endpoint does not necessarily resolve to a >>> valid url and since we do not have any parameters, this gives us >>> 'failure' status code. If and when users are able to give us >>> parameters as well as their base url, we should be able to solve this >>> problem >>> >>>> If the endpoint changes from 'http://www.pathwaycommons.org/pc' to >>>> 'http://www.pathwaycommons.org' will it change the status in the >>>> >>>> >>> No, but 'http://www.pathwaycommons.org/pc/' will change it to green. >>> >>> Notice the trailing forward slash... >>> >>> Eric >>> >>> >>>> biocat? >>>> >>>> Cheers, >>>> Franck >>>> >>>> >>>> >>>> >>>> >>> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Fri Mar 26 11:25:33 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 26 Mar 2010 15:25:33 +0000 Subject: [BioCatalogue-developers] pathway common service status In-Reply-To: <4BACCA06.1030506@ebi.ac.uk> References: <4BACB7FA.90802@ebi.ac.uk> <4BACB9DF.7020809@cs.man.ac.uk> <4BACCA06.1030506@ebi.ac.uk> Message-ID: Cool, I've noticed you've done it already... Thanks, Franck On 26 March 2010 14:51, Eric Nzuobontane wrote: > will do. > > Eric > > Franck Tanoh wrote: >>>> >>>> No, ?but 'http://www.pathwaycommons.org/pc/' ?will change it to green. >>>> >> >> If that solves the problem can you correct it in the database please? >> >> Thanks, >> Franck >> >> On 26 March 2010 13:42, Jiten Bhagat wrote: >> >>> >>> Sounds like in this particular case changing the base endpoint (aka base >>> URL) will solve this particular problem. >>> >>> With Mannie's new work the user will be able to do this directly. For >>> now this might need to be a db manual change (unless user is willing to >>> wait a week or so?) >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> >>>> Hi Franck >>>> >>>>> >>>>> The provider of pathway common service >>>>> (http://www.biocatalogue.org/services/2621-pathway-commons_185566) has >>>>> asked me why their REST service status is amber while it seem to be >>>>> working fine? >>>>> >>>>> >>>> >>>> The reason is that the endpoint does not necessarily resolve to a >>>> valid url and since we do not have any parameters, this gives us >>>> 'failure' status code. If and when users are able to give us >>>> parameters as well as their base url, we should be able to solve this >>>> problem >>>> >>>>> >>>>> If the endpoint changes from 'http://www.pathwaycommons.org/pc' ?to >>>>> 'http://www.pathwaycommons.org' will it change the status in the >>>>> >>>>> >>>> >>>> No, ?but 'http://www.pathwaycommons.org/pc/' ?will change it to green. >>>> >>>> Notice the trailing forward slash... >>>> >>>> Eric >>>> >>>> >>>>> >>>>> biocat? >>>>> >>>>> Cheers, >>>>> Franck >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> >> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ytanoh at cs.man.ac.uk Fri Mar 26 11:45:50 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 26 Mar 2010 15:45:50 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromPDB' changed to Failed In-Reply-To: References: Message-ID: The test script in the BioCatalogue seems to be working fine ... The Embrace test for this service (http://embraceregistry.net/node/941) failed a hour ago and BioCatalogue confirmed it when the same service (http://www.biocatalogue.org/services/2479-getentryfrompdbservice_370361) was tested 45 min later. Cheers, Franck On 26 March 2010 14:27, wrote: > This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromPDB' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: > ? ?http://embraceregistry.net/node/941 > > As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. > > If you have any questions, please reply to this email. > > Yours, > The EMBRACE Registry Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Fri Mar 26 13:51:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 26 Mar 2010 17:51:11 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromBLASTText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPMUTHotSpotFromBLASTText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1002 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Fri Mar 26 14:31:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 26 Mar 2010 14:31:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1757] trunk/app/controllers/application_controller.rb: Bugfix: remove " limit" when generating filter links. Message-ID: <20100326183133.19FAC18582EF@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Fri Mar 26 22:37:31 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 27 Mar 2010 02:37:31 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'Genome Atlas' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'Genome Atlas' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1694 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 27 06:38:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 27 Mar 2010 10:38:34 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getActiveSiteInterfaceFromPDBId' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getActiveSiteInterfaceFromPDBId' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1109 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 27 07:08:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 27 Mar 2010 11:08:28 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getStructureFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1165 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 27 10:48:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 27 Mar 2010 14:48:25 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:loadPersistentFile' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:loadPersistentFile' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/869 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 27 15:27:18 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 27 Mar 2010 19:27:18 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:parseMotifMatricesFromMEME' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:parseMotifMatricesFromMEME' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/775 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sat Mar 27 22:42:43 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 03:42:43 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLASTatlas' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'BLASTatlas' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1690 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 01:52:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 06:52:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runS3det' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runS3det' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1100 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 08:36:59 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 13:36:59 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getCodonTableFromEmboss' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getCodonTableFromEmboss' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/889 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 09:55:54 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 14:55:54 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getCollectivityIndexesFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1155 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 10:07:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 15:07:34 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runNucleosomePotential' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runNucleosomePotential' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1112 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 11:50:06 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 16:50:06 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:displayDomainsFromAnnStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:displayDomainsFromAnnStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/888 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 16:22:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 28 Mar 2010 21:22:23 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMemeText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMemeText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/774 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Sun Mar 28 23:25:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 04:25:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetCTL - Prediction of CTL epitopes in protein sequences' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'NetCTL - Prediction of CTL epitopes in protein sequences' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1625 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 01:59:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 06:59:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runFirestar' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runFirestar' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1099 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Mar 29 04:23:06 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 29 Mar 2010 04:23:06 -0400 (EDT) Subject: [BioCatalogue-developers] [1758] branches/service-ownership/: initial work on service ownership Message-ID: <20100329082306.82D9C18582CB@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Mar 29 05:05:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 10:05:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:unzipTrajectory' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:unzipTrajectory' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1172 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 05:07:29 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 10:07:29 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runPPSearchAgainstProsite' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runPPSearchAgainstProsite' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/884 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Mon Mar 29 05:13:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 29 Mar 2010 05:13:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1759] branches: branch of web service ownership from working copy Message-ID: <20100329091329.1DBB518582D6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 29 05:47:30 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 29 Mar 2010 05:47:30 -0400 (EDT) Subject: [BioCatalogue-developers] [1760] branches/service-ownership/: remove redundant branch Message-ID: <20100329094730.A947F18582D6@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Mar 29 07:07:48 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 29 Mar 2010 07:07:48 -0400 (EDT) Subject: [BioCatalogue-developers] [1761] branches/web-service-ownership: completing commit of initial service-responsibility work Message-ID: <20100329110748.7D0C61D799A3@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Mon Mar 29 08:18:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 13:18:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossRestrictFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossRestrictFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/827 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 08:52:53 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 13:52:53 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parsePropertySequenceFromFSOLVText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parsePropertySequenceFromFSOLVText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/992 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 08:56:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 13:56:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromSCOPPath' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromSCOPPath' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/803 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Mon Mar 29 09:13:38 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 29 Mar 2010 14:13:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetCTL - Prediction of CTL epitopes in protein sequences' changed to Warning In-Reply-To: References: Message-ID: Hi Eric, I couldn't find the service below in the biocatalogue: (http://embraceregistry.net/service/netctl-prediction-ctl-epitopes-protein-sequences). I found the version imported from seekda: http://www.biocatalogue.org/services/1757-wsnetctl_1_1_86199. The reason why i was looking for it was to see how we handle 'WARNING' from Embrace. Franck On 29 March 2010 04:25, wrote: > This is an automatic notification to let you know that your service 'NetCTL - Prediction of CTL epitopes in protein sequences' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: > ? ?http://embraceregistry.net/node/1625 > > As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. > > If you have any questions, please reply to this email. > > Yours, > The EMBRACE Registry Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Mon Mar 29 09:23:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 14:23:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromCATH' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromCATH' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/902 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 10:20:30 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 15:20:30 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:fromFASTAToAminoAcidSequenceCollection' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:fromFASTAToAminoAcidSequenceCollection' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/787 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 11:23:10 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 16:23:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:getProdomDomainsFromUniProt' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:getProdomDomainsFromUniProt' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1060 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 11:24:39 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 16:24:39 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:parseRulesFromMotif' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:parseRulesFromMotif' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/922 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Mon Mar 29 12:27:47 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 29 Mar 2010 17:27:47 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetCTL - Prediction of CTL epitopes in protein sequences' changed to Warning In-Reply-To: References: Message-ID: <4BB0D503.70003@ebi.ac.uk> On how warnings are handled, see http://www.biocatalogue.org/services/144-wsblastatlas_1_0_ws2_990748#testscripts http://embraceregistry.net/node/1690 On why the service is not in BioCatalogue, I will have a look at the import log. Which is also available in dropbox. Eric Franck Tanoh wrote: > Hi Eric, > > I couldn't find the service below in the biocatalogue: > (http://embraceregistry.net/service/netctl-prediction-ctl-epitopes-protein-sequences). > I found the version imported from seekda: > http://www.biocatalogue.org/services/1757-wsnetctl_1_1_86199. The > reason why i was looking for it was to see how we handle 'WARNING' > from Embrace. > > Franck > > On 29 March 2010 04:25, wrote: > >> This is an automatic notification to let you know that your service 'NetCTL - Prediction of CTL epitopes in protein sequences' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: >> http://embraceregistry.net/node/1625 >> >> As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. >> >> If you have any questions, please reply to this email. >> >> Yours, >> The EMBRACE Registry Team >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> > > > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ytanoh at cs.man.ac.uk Mon Mar 29 12:45:10 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 29 Mar 2010 17:45:10 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetCTL - Prediction of CTL epitopes in protein sequences' changed to Warning In-Reply-To: <4BB0D503.70003@ebi.ac.uk> References: <4BB0D503.70003@ebi.ac.uk> Message-ID: Thanks for the infos, I found the service in the import log: ... It must be in the biocat then but where? I've unsuccessfully used all possible options in hand to find it. Franck On 29 March 2010 17:27, Eric Nzuobontane wrote: > On how warnings are handled, see > http://www.biocatalogue.org/services/144-wsblastatlas_1_0_ws2_990748#testscripts > http://embraceregistry.net/node/1690 > > On why the service is not in BioCatalogue, I will have a look at the import > log. Which is also available in dropbox. > > Eric > > > Franck Tanoh wrote: >> >> Hi Eric, >> >> I couldn't find the service below in the biocatalogue: >> >> (http://embraceregistry.net/service/netctl-prediction-ctl-epitopes-protein-sequences). >> I found the version imported from seekda: >> http://www.biocatalogue.org/services/1757-wsnetctl_1_1_86199. ?The >> reason why i was looking for it was to see how we handle 'WARNING' >> from Embrace. >> >> Franck >> >> On 29 March 2010 04:25, ? wrote: >> >>> >>> This is an automatic notification to let you know that your service >>> 'NetCTL - Prediction of CTL epitopes in protein sequences' has changed >>> status from 'Passed' to 'Warning'. Follow the link to investigate: >>> ? http://embraceregistry.net/node/1625 >>> >>> As this service has entered an erroneous state, it might be worthwhile >>> leaving a comment on the above page to let people know how long it might >>> take to resolve. >>> >>> If you have any questions, please reply to this email. >>> >>> Yours, >>> The EMBRACE Registry Team >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >>> >> >> >> >> > > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From utopia at cs.man.ac.uk Mon Mar 29 15:01:35 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 20:01:35 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:pdg.cnb.uam.es:getInteractingMethods' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:pdg.cnb.uam.es:getInteractingMethods' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/765 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 15:40:08 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 29 Mar 2010 20:40:08 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPSIBlastpFromAminoAcidSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPSIBlastpFromAminoAcidSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1006 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Mar 29 21:56:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 30 Mar 2010 02:56:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getFlexAnalysisFromPCZ' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getFlexAnalysisFromPCZ' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1164 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 30 01:04:53 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 30 Mar 2010 06:04:53 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMatScanGFFCollectionVsInputMatrices' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMatScanGFFCollectionVsInputMatrices' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/780 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 30 01:34:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 30 Mar 2010 06:34:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runCExonic' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runCExonic' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1098 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 30 03:46:20 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 30 Mar 2010 08:46:20 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getGOTerm' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getGOTerm' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/879 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 30 03:50:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 30 Mar 2010 08:50:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossTmapFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossTmapFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/829 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Mar 30 07:19:29 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 07:19:29 -0400 (EDT) Subject: [BioCatalogue-developers] [1762] trunk/app/views: Add API docs links to the header and footer. Message-ID: <20100330111929.2D9AD18582D7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 07:19:52 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 07:19:52 -0400 (EDT) Subject: [BioCatalogue-developers] [1763] trunk/app/views/soap_operations/show.html.erb: Add more descriptive page title to SOAP operation pages. Message-ID: <20100330111952.DC8F618582D7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 07:28:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 07:28:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1764] trunk/app/views/soap_operations/_breadcrumbs.html.erb: Added breadcrumbs for the show SOAP operation page. Message-ID: <20100330112802.B2B2318582F3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 07:51:18 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 07:51:18 -0400 (EDT) Subject: [BioCatalogue-developers] [1765] trunk: Style improvements to the operations/enpoints UI. Message-ID: <20100330115118.854771D799AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:00:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:00:10 -0400 (EDT) Subject: [BioCatalogue-developers] [1766] trunk/app/models/service_test.rb: put most recent test result(status ) at top Message-ID: <20100330120010.37A7518582D7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:09:11 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:09:11 -0400 (EDT) Subject: [BioCatalogue-developers] [1767] trunk: REST support work Message-ID: <20100330120911.375B21D799AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:30:04 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:30:04 -0400 (EDT) Subject: [BioCatalogue-developers] [1768] trunk/public: Potential new tab colour. Message-ID: <20100330123004.7C0631D799AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:40:28 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:40:28 -0400 (EDT) Subject: [BioCatalogue-developers] [1769] trunk: Added an anchor to each SOAP operation listing so that previous URLs like: http://www.biocatalogue.org/services/4#soap_operation_678 still work. Message-ID: <20100330124029.0406D1D799AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:44:58 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:44:58 -0400 (EDT) Subject: [BioCatalogue-developers] [1770] trunk/public: New H1 and tab background styles Message-ID: <20100330124459.07A251858289@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:49:38 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:49:38 -0400 (EDT) Subject: [BioCatalogue-developers] [1771] trunk/app/views/rest_methods/_breadcrumbs.html.erb: Bugfix for REST methods show page breadcrumbs Message-ID: <20100330124938.76E5218582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 08:54:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 08:54:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1772] trunk: Better styles for the "Quick Browse" box. Message-ID: <20100330125422.9CC7D18582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Mar 30 09:03:45 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 30 Mar 2010 14:03:45 +0100 Subject: [BioCatalogue-developers] Am I okay to go ahead and... Message-ID: <4BB1F6B1.5050701@cs.man.ac.uk> ... announce the release of the API tomorrow, assuming the release goes as planned? By "announce" I mean: - Send an email to the biocatalogue-friends list - Make a site announcement on http://www.biocatalogue.org We can maybe leave wider announcements (myExperiment, taverna-hackers, taverna-users, etc) till later? Jits From jits at cs.man.ac.uk Tue Mar 30 09:20:58 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 30 Mar 2010 14:20:58 +0100 Subject: [BioCatalogue-developers] Am I okay to go ahead and... In-Reply-To: <4BB1F6B1.5050701@cs.man.ac.uk> References: <4BB1F6B1.5050701@cs.man.ac.uk> Message-ID: <4BB1FABA.5020801@cs.man.ac.uk> Oops, ignore that... that was meant to go to the main list. Jits Jiten Bhagat wrote: > ... announce the release of the API tomorrow, assuming the release goes > as planned? > > By "announce" I mean: > - Send an email to the biocatalogue-friends list > - Make a site announcement on http://www.biocatalogue.org > > We can maybe leave wider announcements (myExperiment, taverna-hackers, > taverna-users, etc) till later? > > Jits > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Tue Mar 30 09:36:40 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 09:36:40 -0400 (EDT) Subject: [BioCatalogue-developers] [1773] trunk/public/stylesheets/styles.css: Various style tweaks, including changing the H1 style to a more basic title style. Message-ID: <20100330133640.79B8D1858289@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 09:41:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 09:41:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1774] trunk/public/stylesheets/styles.css: Actions menu now has a background colour Message-ID: <20100330134139.967C11D799AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 11:10:55 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 11:10:55 -0400 (EDT) Subject: [BioCatalogue-developers] [1775] trunk: Various style and layout fixes. Message-ID: <20100330151055.C0CF518582E1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 11:18:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 11:18:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1776] trunk/app/views/soap_operations/show.html.erb: Removed " Soap Operation:" from title in SOAP operation show page Message-ID: <20100330151836.0684B18582FD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 11:24:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 11:24:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1777] trunk/app/views: minor UI updates Message-ID: <20100330152402.1CDF21858304@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 11:29:10 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 11:29:10 -0400 (EDT) Subject: [BioCatalogue-developers] [1778] trunk/app/views/rest_methods: typo fix Message-ID: <20100330152910.93DA71D799AA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 12:32:00 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 12:32:00 -0400 (EDT) Subject: [BioCatalogue-developers] [1779] trunk: Added a snippet for description to the collapsed SOAP inputs and outputs boxes . Message-ID: <20100330163200.C915E18582D0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 12:35:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 12:35:09 -0400 (EDT) Subject: [BioCatalogue-developers] [1780] trunk/app/helpers/application_helper.rb: Documentation update Message-ID: <20100330163509.44BB218582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 12:52:12 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 12:52:12 -0400 (EDT) Subject: [BioCatalogue-developers] [1781] trunk/app/views/search: Bugfix for badly floated button on search Message-ID: <20100330165214.28FF53C8033@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 13:25:39 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 13:25:39 -0400 (EDT) Subject: [BioCatalogue-developers] [1782] trunk/app/views/soap_operations/show.html.erb: Added help text for Parameter Order field on SOAP operation show page. Message-ID: <20100330172539.A41191D799AD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 13:26:44 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 13:26:44 -0400 (EDT) Subject: [BioCatalogue-developers] [1783] trunk/app/views/soap_operations/show.html.erb: Removed orange box around input and output names. Message-ID: <20100330172644.D38063C8033@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 13:33:51 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 13:33:51 -0400 (EDT) Subject: [BioCatalogue-developers] [1784] trunk: When collapsed inputs and outputs boxes links are hovered over then highlight to emphasise that it is clickable . Message-ID: <20100330173352.0791618582E1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 13:43:34 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 13:43:34 -0400 (EDT) Subject: [BioCatalogue-developers] [1785] trunk: In the Quick Browse box on the show SOAP operation page, the selected operation is now highlighted. Message-ID: <20100330174334.18B9C18582EC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 13:54:02 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 13:54:02 -0400 (EDT) Subject: [BioCatalogue-developers] [1786] trunk/app/views/soap_operations/show.html.erb: Do a proper truncate on the operation names on the vertical tabs. Message-ID: <20100330175402.6B6DE185827F@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Mar 30 14:02:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 30 Mar 2010 19:02:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:genome.imim.es:runMetaAlignment' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:genome.imim.es:runMetaAlignment' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/778 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Tue Mar 30 14:14:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:14:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1787] trunk: Better tabs styles to make it more obvious what the current selected tab is . Message-ID: <20100330181417.CBE711D798FC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 14:19:24 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:19:24 -0400 (EDT) Subject: [BioCatalogue-developers] [1788] trunk/public/stylesheets/styles.css: Dropped down a notch the darkness of the borders of the different tabs styles . Message-ID: <20100330181924.C356818582DC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 14:22:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:22:50 -0400 (EDT) Subject: [BioCatalogue-developers] [1789] trunk/public/stylesheets/styles.css: Small style tweaks Message-ID: <20100330182250.C535818582E1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 14:25:00 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:25:00 -0400 (EDT) Subject: [BioCatalogue-developers] [1790] trunk/public/stylesheets/styles.css: Small style tweaks Message-ID: <20100330182501.014243C8036@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 14:26:56 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:26:56 -0400 (EDT) Subject: [BioCatalogue-developers] [1791] trunk/app/views/annotations/_tags_flat.html.erb: typo fix Message-ID: <20100330182656.CB8413C8036@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 14:35:33 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:35:33 -0400 (EDT) Subject: [BioCatalogue-developers] [1792] trunk: Added a shadow style and applied it to categories. Message-ID: <20100330183533.F3BFB18582E3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Mar 30 14:37:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 30 Mar 2010 14:37:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1793] trunk/public/stylesheets/styles.css: Added shadow styles to the tabbed boxes Message-ID: <20100330183735.7CD161D799AD@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Tue Mar 30 20:36:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 01:36:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getPrositeAnnStructureFromPDBID' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getPrositeAnnStructureFromPDBID' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/915 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 30 21:32:52 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 02:32:52 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getNucleotideSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getNucleotideSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/940 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Tue Mar 30 23:23:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 04:23:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossPatmatdb' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossPatmatdb' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/819 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 31 00:49:24 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 05:49:24 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getHomologiesFromEnsembl' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getHomologiesFromEnsembl' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/893 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 31 01:29:34 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 06:29:34 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:frommmCifToPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:frommmCifToPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/935 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 31 01:42:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 06:42:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getPrositeAnnStructure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getPrositeAnnStructure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/892 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Mar 31 05:02:37 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 05:02:37 -0400 (EDT) Subject: [BioCatalogue-developers] [1794] trunk/app/views: - made changes to the REST UI elements to match the SOAP UI Message-ID: <20100331090237.D1D9F18582EF@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 05:39:21 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 05:39:21 -0400 (EDT) Subject: [BioCatalogue-developers] [1795] trunk/app: bug fix for create_expand_collapse_link() in ApplicationHelper Message-ID: <20100331093921.D3DCF18582D8@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 31 05:45:40 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 10:45:40 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossIepFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossIepFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/873 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Mar 31 05:56:05 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 05:56:05 -0400 (EDT) Subject: [BioCatalogue-developers] [1796] trunk/app/views/rest_methods/show.html.erb: minor UI tweak to stop help text in the tag box from wrapping. Message-ID: <20100331095605.A288418582DC@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 31 06:33:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 11:33:14 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'NetChop - Prediction of proteasomal cleavages (MHC ligands)' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'NetChop - Prediction of proteasomal cleavages (MHC ligands)' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1626 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ytanoh at cs.man.ac.uk Wed Mar 31 07:28:32 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 31 Mar 2010 12:28:32 +0100 Subject: [BioCatalogue-developers] endpoint help text Message-ID: Hi Mannie, I've tried to write some help text for the REST service based on the existing text and my views after registering couple of REST services. We can discuss that and see how it can be improved. Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- A non-text attachment was scrubbed... Name: endpoint help.doc Type: application/msword Size: 36352 bytes Desc: not available URL: From noreply at rubyforge.org Wed Mar 31 07:41:50 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 07:41:50 -0400 (EDT) Subject: [BioCatalogue-developers] [1797] trunk/app/views/rest_methods/show.html.erb: added tooltip to the tabs in the REST UI Message-ID: <20100331114151.0B5EF18582F4@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 31 08:06:42 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 13:06:42 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:inb.bsc.es:refineTextQueryOMIM' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:inb.bsc.es:refineTextQueryOMIM' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1053 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Mar 31 09:03:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 09:03:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1798] trunk/app/views: REST support work Message-ID: <20100331130317.7466418582FA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 09:24:19 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 09:24:19 -0400 (EDT) Subject: [BioCatalogue-developers] [1799] trunk/app/views/rest_methods: REST support work Message-ID: <20100331132419.DB7F518582F8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 09:24:32 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 09:24:32 -0400 (EDT) Subject: [BioCatalogue-developers] [1800] trunk/app/views/annotations/_categories.html.erb: Removed shadow from categories as it made them stand out too much. Message-ID: <20100331132432.937ED18582FA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 09:25:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 09:25:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1801] trunk/public/2009/xml/rest/schema-v1.xsd: REST API work: fixed the schema for cases where Annotations have "RestMethod", " RestParameter" or "RestRepresentation" as the annotatable. Message-ID: <20100331132522.D4F1518582FA@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Wed Mar 31 09:11:29 2010 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 31 Mar 2010 14:11:29 +0100 Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <201003311311.o2VDBTRH028698@spike.ebi.ac.uk> The original message was received at Wed, 31 Mar 2010 14:10:28 +0100 from pweb-3a.ebi.ac.uk [172.18.1.107] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] fail#index (NoMethodError) "undefined method `hello_world' for nil:NilClass" Date: Wed, 31 Mar 2010 14:10:28 +0100 Size: 11824 URL: From noreply at rubyforge.org Wed Mar 31 10:09:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 10:09:27 -0400 (EDT) Subject: [BioCatalogue-developers] [1802] trunk/app/views: update REST support help text Message-ID: <20100331140927.37B9518582FD@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 10:40:22 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 10:40:22 -0400 (EDT) Subject: [BioCatalogue-developers] [1803] trunk/app/views/layouts/_footer.html.erb: Added link to " Registry Stats" in footer. Message-ID: <20100331144022.63D9718582F8@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 10:45:35 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 10:45:35 -0400 (EDT) Subject: [BioCatalogue-developers] [1804] trunk/app/views: Fixes to links Message-ID: <20100331144535.C124818582D0@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Mar 31 10:46:17 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 10:46:17 -0400 (EDT) Subject: [BioCatalogue-developers] [1805] trunk/app/views/widgets/_breadcrumbs_bar.html.erb: Moved last search notice to the left hand side based on feedback from Carole . Message-ID: <20100331144617.42A3618582F3@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 31 11:56:58 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 16:56:58 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:parseAminoAcidSequenceFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:parseAminoAcidSequenceFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/990 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From noreply at rubyforge.org Wed Mar 31 12:43:59 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 31 Mar 2010 12:43:59 -0400 (EDT) Subject: [BioCatalogue-developers] [1806] trunk: Funkier UI for the last search notice box - moved from the right hand side of the breadcrumbs bar to a box that slides down at the very top of the page (Carole asked for it to be more noticeable, and the developer has giveth). Message-ID: <20100331164359.8702E185830E@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Mar 31 13:51:17 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 18:51:17 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:mmb.pcb.ub.es:runPSIBlastpFromFASTA' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:mmb.pcb.ub.es:runPSIBlastpFromFASTA' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1005 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 31 15:07:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 20:07:56 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:runEmbossAntigenicFromSequence' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:runEmbossAntigenicFromSequence' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/808 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 31 16:05:28 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 21:05:28 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB:inb.bsc.es:getEntryFromDSSP' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB:inb.bsc.es:getEntryFromDSSP' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/789 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Wed Mar 31 18:14:19 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 31 Mar 2010 23:14:19 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:fromPrankToSLR' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:fromPrankToSLR' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/1094 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team