From issues at mygrid.org.uk Fri Oct 1 12:43:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Oct 2010 17:43:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-490) Need a mechanism for activating the first user in the system in new deployments Message-ID: <29633402.9917.1285951395303.JavaMail.jira@rosalind.cs.man.ac.uk> Need a mechanism for activating the first user in the system in new deployments ------------------------------------------------------------------------------- Key: BIOCAT-490 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490 Project: BioCatalogue Issue Type: Improvement Components: User Management Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor When someone sets up a fresh instance of the BioCatalogue software they usually create a new user and then run into the issue of how to activate that user (in cases where a mail server wasn't set up). Need a way of solving this issue. One potential solution is to always activate the first user in a system (and maybe automatically make them an admin too?) OR when the app is first run have a "set up" wizard in which one of the tasks is to create an admin user. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Oct 1 12:43:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 1 Oct 2010 17:43:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-490) Need a mechanism for activating the first user in the system in new deployments Message-ID: <29633402.9917.1285951395303.JavaMail.jira@rosalind.cs.man.ac.uk> Need a mechanism for activating the first user in the system in new deployments ------------------------------------------------------------------------------- Key: BIOCAT-490 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-490 Project: BioCatalogue Issue Type: Improvement Components: User Management Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Minor When someone sets up a fresh instance of the BioCatalogue software they usually create a new user and then run into the issue of how to activate that user (in cases where a mail server wasn't set up). Need a way of solving this issue. One potential solution is to always activate the first user in a system (and maybe automatically make them an admin too?) OR when the app is first run have a "set up" wizard in which one of the tasks is to create an admin user. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Fri Oct 1 13:20:02 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 01 Oct 2010 18:20:02 +0100 Subject: [BioCatalogue-developers] EdUnify differential requirements In-Reply-To: References: Message-ID: <4CA61842.30808@cs.man.ac.uk> Hi Tod, [cc'ing to the BioCatalogue internal developers mailing list. I hope this is okay?] So sorry for not replying sooner. Just been catching up with all the emails and trying to attend to some things here. Please see my comments below... Jackson, Tod wrote: > Hello Jits! > > I hope all is well with you and I?m not sure if you?ve been ?hitched? > yet but if so, I hope that all went well and I wish you the very best! Thanks very much! :-) Yeap, I got hitched on the 4th of Sept and then was on my honeymoon in Miami for the following 10 days (which unfortunately ended in me being very ill, but that's a story for another day). > > I know you are probably still be busy with the Taverna workbench > project and that pesky little marriage thing but I wanted to pass some > more information along just to keep you in the loop as to what we?re > doing and where we?re going with EdUnify. As I?ve mentioned in the > past, we?re working toward an October ?go-live? of the EdUnify beta > site. We?ll be launching the beta at Educause in October (12th ? 15th > I believe). We?re also giving a presentation at Educause in October > and another at the Internet 2 conference in November. VERY exciting stuff :-) :-) Good luck with this, hope it all goes smashingly well! Thanks very much for the updates. > > For the October launch, we?ve been working through a set of > ?differential requirements? that the EdUnify team thinks are important > for this particular use of the BioCatalogue product given the group of > folks we?re targeting (higher-ed organizations, higher-ed vendors etc.). > > So, we?ve got a list of these posted on the EdUnify wiki and I am > getting ready to start trying to implement the highest priority items > for the October launch. We thought it would be a good idea to run > these past you. We?d like to get your input on these from a couple > perspectives: > > 1. Are any of these things you think would be candidates for the > base product once we get the collaboration documents all worked > out etc.? > 2. Are any of these items things you?re already planning (or might > want to plan) for future releases of BioCatalogue? > > > One of the reasons we?re asking is because if you think any of our > highest priority items are things that might be coming in future > releases anyway, we?ll likely hold off on implementing them now (let > you do the work :-)). I also realize that some of these requirements > may be irrelevant to the BioCatalogue project itself. I think that?s > okay based on the fact that we really are targeting different > audiences and for the EdUnify audience, there are things that seem > important that I don?t think are relevant to BioCatalogue itself. > We?ll just have to make sure we come up with a plan to isolate the > differences appropriately. > > Again, I know you?re extremely busy but if you could somehow find the > time to take a look at: > https://wiki.service.emory.edu/display/edunity/EdUnify+Differential+Requirements > and provide any feedback you might have, we?d be extremely grateful. > I realize some of them might be a little vague so if you need any > clarification, just let me know and I?ll do my best to clarify. It > would actually be good for someone like you who understands the > product but hasn?t been involved in the lower-level conversations > we?ve had about these to vet them a bit anyway just to make sure they > make sense in general terms. > > If you follow that link above, you should see a bulleted list of items > under 5 high-level categories. The items in bold are the highest > priority items that we?re focusing on for the October launch. There > are six items all under the category of ?Service Registration and > Annotation? that we?re focusing on first. Please let me know what you > think and if you think you?ll have some time to take a look. That's a very interesting list and many of the things resonate well with our own roadmap (which we hope to update very soon). Many of these would be great candidates for integrating into the base product. Especially so in the Service Registration and Annotation section. In fact we have already started work on point 1. in that section. I'd be very glad to get involved here and discuss this further. Maybe we could go through each point in detail in a Skype chat? How about sometime on Wednesday next week? I agree totally about coming up with a plan to isolate differences and to try and keep things in sync. One thing to consider is: we are doing a big release in about 3 weeks time with loads of new features and fixes (especially for the API) and it would be great if you could possibly upgrade your installations. Some initial info on this upgrade is available here: http://www.biocatalogue.org/wiki/doku.php?id=development:release_notes:revision_oct_2010. Sorry for the late notice, unfortunately it's very hard for us to schedule these things here. We'd be glad to help out with these upgrades as much as we can. > > Again, I thank you for your time and look forward to hearing from you. The pleasure is ours. It's so great to see our software actively used and even further developed! Kind regards, Jits > > Best Regards, > Tod > ------------------------------------------------------------------------ > This e-mail message (including any attachments) is for the sole use of > the intended recipient(s) and may contain confidential and privileged > information. If the reader of this message is not the intended > recipient, you are hereby notified that any dissemination, distribution > or copying of this message (including any attachments) is strictly > prohibited. > > If you have received this message in error, please contact > the sender by reply e-mail message and destroy all copies of the > original message (including attachments). From utopia at cs.man.ac.uk Fri Oct 1 17:31:51 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 01 Oct 2010 22:31:51 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:addHydrogensFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:addHydrogensFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1143 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 Mon Oct 4 05:31:02 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 04 Oct 2010 10:31:02 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue-hackers] Addion Soaplab2 services] Message-ID: <4CA99ED6.5080806@cs.man.ac.uk> Hi Eric, Could you look into this please? Jits -------- Original Message -------- Subject: [BioCatalogue-hackers] Addion Soaplab2 services Date: Mon, 04 Oct 2010 10:45:42 +0200 From: Carsten Schnober Organisation: ELDA To: biocatalogue-hackers at rubyforge.org Hi list, I am opening a new thread with this issue because it's (probably) not related to my previous problems. I have set up a local Biocatalogue server and a Tomcat server providing Soaplab 2 on another machine in the local network. Now I am trying to add the Soaplab services to the Biocatalogue registry by selecting "Register a Service -> Soaplab Server". Then, I am pasting the URL "http://192.168.1.198:8080/soaplab2/services/list?wsdl" (which is perfectly reachable in the local network) into the form. A click on "Preview" gives me a complete list of the services provided by the Soaplab server. However, when I do "Submit", the host is registered as a service provider (named 192-168-1-198), but none of the services is. Any clues? Thanks, Carsten _______________________________________________ BioCatalogue-hackers mailing list BioCatalogue-hackers at rubyforge.org http://rubyforge.org/mailman/listinfo/biocatalogue-hackers From ericnzuo at ebi.ac.uk Mon Oct 4 05:46:06 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 04 Oct 2010 10:46:06 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue-hackers] Addion Soaplab2 services] In-Reply-To: <4CA99ED6.5080806@cs.man.ac.uk> References: <4CA99ED6.5080806@cs.man.ac.uk> Message-ID: <4CA9A25E.6060604@ebi.ac.uk> I was already replying to that. But basically what I think is the issue is that his job workers are not running. The submission of the individual services is done by the background process. I think every thing else works fine for him. However, I do not seem to have received the original mail, only the bounce from mailman! Eric On 04/10/2010 10:31, Jiten Bhagat wrote: > Hi Eric, > > Could you look into this please? > > Jits > > > -------- Original Message -------- > Subject: [BioCatalogue-hackers] Addion Soaplab2 services > Date: Mon, 04 Oct 2010 10:45:42 +0200 > From: Carsten Schnober > Organisation: ELDA > To: biocatalogue-hackers at rubyforge.org > > > > Hi list, > I am opening a new thread with this issue because it's (probably) not > related to my previous problems. > I have set up a local Biocatalogue server and a Tomcat server providing > Soaplab 2 on another machine in the local network. Now I am trying to > add the Soaplab services to the Biocatalogue registry by selecting > "Register a Service -> Soaplab Server". Then, I am pasting the URL > "http://192.168.1.198:8080/soaplab2/services/list?wsdl" (which is > perfectly reachable in the local network) into the form. A click on > "Preview" gives me a complete list of the services provided by the > Soaplab server. However, when I do "Submit", the host is registered as a > service provider (named 192-168-1-198), but none of the services is. > Any clues? Thanks, > Carsten > _______________________________________________ > BioCatalogue-hackers mailing list > BioCatalogue-hackers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-hackers -- 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 Oct 4 05:52:40 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 04 Oct 2010 10:52:40 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue-hackers] Addion Soaplab2 services] In-Reply-To: <4CA9A25E.6060604@ebi.ac.uk> References: <4CA99ED6.5080806@cs.man.ac.uk> <4CA9A25E.6060604@ebi.ac.uk> Message-ID: <4CA9A3E8.1080306@cs.man.ac.uk> Eric Nzuobontane wrote: > I was already replying to that. But basically what I think is the > issue is that his job workers are not running. The submission of the > individual services is done by the background process. I think every > thing else works fine for him. Ahh, okay, that makes sense. We need to document this some where. > > However, I do not seem to have received the original mail, only the > bounce from mailman! Oh. If you keep getting this behaviour let me know and I'll look into it. Cheers, Jits > > Eric > > On 04/10/2010 10:31, Jiten Bhagat wrote: >> Hi Eric, >> >> Could you look into this please? >> >> Jits >> >> >> -------- Original Message -------- >> Subject: [BioCatalogue-hackers] Addion Soaplab2 services >> Date: Mon, 04 Oct 2010 10:45:42 +0200 >> From: Carsten Schnober >> Organisation: ELDA >> To: biocatalogue-hackers at rubyforge.org >> >> >> >> Hi list, >> I am opening a new thread with this issue because it's (probably) not >> related to my previous problems. >> I have set up a local Biocatalogue server and a Tomcat server providing >> Soaplab 2 on another machine in the local network. Now I am trying to >> add the Soaplab services to the Biocatalogue registry by selecting >> "Register a Service -> Soaplab Server". Then, I am pasting the URL >> "http://192.168.1.198:8080/soaplab2/services/list?wsdl" (which is >> perfectly reachable in the local network) into the form. A click on >> "Preview" gives me a complete list of the services provided by the >> Soaplab server. However, when I do "Submit", the host is registered as a >> service provider (named 192-168-1-198), but none of the services is. >> Any clues? Thanks, >> Carsten >> _______________________________________________ >> BioCatalogue-hackers mailing list >> BioCatalogue-hackers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-hackers > > From ericnzuo at ebi.ac.uk Mon Oct 4 05:57:04 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 04 Oct 2010 10:57:04 +0100 Subject: [BioCatalogue-developers] [Fwd: [BioCatalogue-hackers] Addion Soaplab2 services] In-Reply-To: <4CA99ED6.5080806@cs.man.ac.uk> References: <4CA99ED6.5080806@cs.man.ac.uk> Message-ID: <4CA9A4F0.6050206@ebi.ac.uk> Hi Carsten, Thanks for using BioCatalogue. My first guess is that the job workers may not be running. Basically BioCatalogue does long running tasks like submitting services from a soaplab server in a background process. I assume you are running your application in production mode. What you need to do is go to your BioCatalogue root and type "script/worker start" . You can also check your database to see if the entries for registering the services were created. These will be in the "delayed_jobs" table. Basically anything in the delayed_jobs table is something to be run as a background process. Please get back to me if that does not solve your problem. regards, Eric > > -------- Original Message -------- > Subject: [BioCatalogue-hackers] Addion Soaplab2 services > Date: Mon, 04 Oct 2010 10:45:42 +0200 > From: Carsten Schnober > Organisation: ELDA > To: biocatalogue-hackers at rubyforge.org > > > > Hi list, > I am opening a new thread with this issue because it's (probably) not > related to my previous problems. > I have set up a local Biocatalogue server and a Tomcat server providing > Soaplab 2 on another machine in the local network. Now I am trying to > add the Soaplab services to the Biocatalogue registry by selecting > "Register a Service -> Soaplab Server". Then, I am pasting the URL > "http://192.168.1.198:8080/soaplab2/services/list?wsdl" (which is > perfectly reachable in the local network) into the form. A click on > "Preview" gives me a complete list of the services provided by the > Soaplab server. However, when I do "Submit", the host is registered as a > service provider (named 192-168-1-198), but none of the services is. > Any clues? Thanks, > Carsten > _______________________________________________ > BioCatalogue-hackers mailing list > BioCatalogue-hackers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-hackers -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Mon Oct 4 06:22:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Oct 2010 11:22:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-491) Register the BioCatalogue API into the BioCatalogue Message-ID: <18630607.9921.1286187735337.JavaMail.jira@rosalind.cs.man.ac.uk> Register the BioCatalogue API into the BioCatalogue --------------------------------------------------- Key: BIOCAT-491 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-491 Project: BioCatalogue Issue Type: New Feature Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Need to be able to find the BioCatalogue API in the BioCatalogue -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Oct 4 06:46:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Oct 2010 11:46:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-492) Implement support for DAS services Message-ID: <31286071.9922.1286189175303.JavaMail.jira@rosalind.cs.man.ac.uk> Implement support for DAS services ---------------------------------- Key: BIOCAT-492 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-492 Project: BioCatalogue Issue Type: New Feature Components: REST Services Support Reporter: Jiten Bhagat Assignee: Jiten Bhagat The current thinking is DAS services are just REST services but with the label "DAS" (much like how we do for Soaplab). -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Oct 4 06:55:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Oct 2010 11:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-493) Implement the ability to harvest DAS services from DAS registries Message-ID: <6791634.9923.1286189715307.JavaMail.jira@rosalind.cs.man.ac.uk> Implement the ability to harvest DAS services from DAS registries ----------------------------------------------------------------- Key: BIOCAT-493 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493 Project: BioCatalogue Issue Type: New Feature Components: REST Services Support, Service Submission Reporter: Jiten Bhagat Assignee: Jiten Bhagat We need the ability to harvest DAS services (and all annotations/metadata) from DAS registries, especially the central DAS registry. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Oct 4 06:57:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Oct 2010 11:57:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-494) Harvest DAS services and all metadata from the central DAS registry Message-ID: <9402951.9924.1286189835300.JavaMail.jira@rosalind.cs.man.ac.uk> Harvest DAS services and all metadata from the central DAS registry ------------------------------------------------------------------- Key: BIOCAT-494 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-494 Project: BioCatalogue Issue Type: Task Components: Content Acquisition Reporter: Jiten Bhagat Assignee: Jiten Bhagat Harvest all DAS services (together with their annotations/metadata) from the central DAS registry (http://www.dasregistry.org/) -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Oct 4 07:49:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 4 Oct 2010 12:49:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-493) Implement the ability to harvest DAS services from DAS registries In-Reply-To: <6791634.9923.1286189715307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <26371142.9925.1286192955333.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15999#action_15999 ] Eric Nzuobontane commented on BIOCAT-493: ----------------------------------------- Do we really need to do this? That would mean we need a sync mechanism for those annotations in the catalogue and the das server. Is that the way we want to go? > Implement the ability to harvest DAS services from DAS registries > ----------------------------------------------------------------- > > Key: BIOCAT-493 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493 > Project: BioCatalogue > Issue Type: New Feature > Components: REST Services Support, Service Submission > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > We need the ability to harvest DAS services (and all annotations/metadata) from DAS registries, especially the central DAS registry. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Oct 4 09:27:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Mon, 4 Oct 2010 14:27:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-493) Implement the ability to harvest DAS services from DAS registries In-Reply-To: <6791634.9923.1286189715307.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <7090014.9927.1286198835312.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16000#action_16000 ] Jiten Bhagat commented on BIOCAT-493: ------------------------------------- We may not go for a full sync, but at the very least we should provide the ability to do a one-time harvest (like we did for SeekDa) so we at least get the content into the catalogue. In the longer run (and resource permitting), a full sync would be the ideal feature. But, of course, we should be practical about this. > Implement the ability to harvest DAS services from DAS registries > ----------------------------------------------------------------- > > Key: BIOCAT-493 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-493 > Project: BioCatalogue > Issue Type: New Feature > Components: REST Services Support, Service Submission > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > > We need the ability to harvest DAS services (and all annotations/metadata) from DAS registries, especially the central DAS registry. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Mon Oct 4 10:37:36 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 04 Oct 2010 15:37:36 +0100 Subject: [BioCatalogue-developers] Adding Soaplab2 services In-Reply-To: <4CA9E56D.6040400@elda.org> References: <4CA99ED6.5080806@cs.man.ac.uk> <4CA9A4F0.6050206@ebi.ac.uk> <4CA9E56D.6040400@elda.org> Message-ID: <4CA9E6B0.3090309@ebi.ac.uk> On 04/10/2010 15:32, Carsten Schnober wrote: > On 04/10/2010 11:57, Eric Nzuobontane wrote: > > Hi, > >> I assume you are running your application in production mode. What you >> need to do is go to your BioCatalogue root and type >> "script/worker start" . You can also check your database to see if the >> entries for registering the services were created. These will be in the >> "delayed_jobs" table. Basically anything in the delayed_jobs table is >> something to be run as a background process. > This solved it, thanks a lot! The jobs got queued up in the delay_jobs > table, indeed. > BTW, I am not running in production mode, so I had to change the value > for RAILS_ENV to 'development' in the file script/worker. Great! I think we need to add this note to our installation process( or documentation in general ). Nice to know it is working now. 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 utopia at cs.man.ac.uk Tue Oct 5 02:47:13 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Tue, 05 Oct 2010 07:47:13 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'CLUSTAL W multiple alignment (CNRS IBCP)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'CLUSTAL W multiple alignment (CNRS IBCP)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/91 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 issues at mygrid.org.uk Tue Oct 5 04:23:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 5 Oct 2010 09:23:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-495) Implement similar searches feature - "people who searched for X searched for Y too" Message-ID: <9737834.9935.1286266995425.JavaMail.jira@rosalind.cs.man.ac.uk> Implement similar searches feature - "people who searched for X searched for Y too" ----------------------------------------------------------------------------------- Key: BIOCAT-495 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-495 Project: BioCatalogue Issue Type: New Feature Components: Search / Filtering / Browsing Reporter: Jiten Bhagat Assignee: Jiten Bhagat We can use the information stored in the activity logs to build similar searches (and even similar filters) functionality. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ytanoh at cs.man.ac.uk Tue Oct 5 12:47:57 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 5 Oct 2010 17:47:57 +0100 Subject: [BioCatalogue-developers] dead link in the biocatalogue Message-ID: hi guys, Do you know any software we could use the flag dead link in the catalogue? Eric can we reuse REST endpoint test you wrote? Cheers, 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 Oct 5 16:50:17 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 05 Oct 2010 21:50:17 +0100 Subject: [BioCatalogue-developers] dead link in the biocatalogue In-Reply-To: References: Message-ID: <4CAB8F89.3040707@cs.man.ac.uk> Hi Franck, Eric and I discussed last week a task to write a script that goes through all the content in the db and flags dead links. Should be a very simple thing! Eric - what's the progress of this? Jits Franck Tanoh wrote: > hi guys, > > Do you know any software we could use the flag dead link in the catalogue? > Eric can we reuse REST endpoint test you wrote? > > Cheers, > Franck > > From ericnzuo at ebi.ac.uk Wed Oct 6 06:25:15 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 06 Oct 2010 11:25:15 +0100 Subject: [BioCatalogue-developers] BioCatalogue in BioCatalogue In-Reply-To: References: <4CA8B452.8010801@manchester.ac.uk> <4CA8CEA7.5030800@ebi.ac.uk> <4CA9A449.6070201@cs.man.ac.uk> <4CA9AAD5.3030805@cs.man.ac.uk> <4CAA0106.9060802@manchester.ac.uk> <4CABA918.2080309@cs.man.ac.uk> <36242.213.106.89.217.1286319206.squirrel@webmail.ebi.ac.uk> <4CABADDC.90303@cs.man.ac.uk> <39844.213.106.89.217.1286319937.squirrel@webmail.ebi.ac.uk> Message-ID: <4CAC4E8B.3000406@ebi.ac.uk> I updated the monitoring status for the BioCatalogue entry as "unchecked" for our own registry did not sit well . Eric On 06/10/2010 10:15, Franck Tanoh wrote: > Hi Eric, > > I've been having problem deleting stuff as well... > > Franck > > On 6 October 2010 00:05, wrote: >> OK, it is possible that the load balancer times out if the application >> appears unresponsive( long running request). I will have a look at the >> logs tomorrow to see if there is anything in them anyway. >> >> Eric >> >> >>> Ah ha! I did try to set it to EBI but it failed with a timeout error >>> (this is because the merge providers process needs optimisations). When >>> I refreshed it wasn't showing as EBI, but looks like it is now! >>> >>> Jits >>> >>> >>> >>> ericnzuo at ebi.ac.uk wrote: >>>> Hi Jits, >>>> I see the provider listed as EBI already. I am not sure what needs to be >>>> done here. >>>> >>>> Eric >>>> >>>> >>>>> I figured I'd at least create the REST service entry for the >>>>> BioCatalogue API in the BioCatalogue. >>>>> >>>>> Here it is: http://www.biocatalogue.org/services/2738 >>>>> >>>>> I do need to change the service provider to EBI, which I will do with >>>>> Eric's help tomorrow. >>>>> >>>>> Jits >>>>> >>>>> >>>>> >>>>> Carole Goble wrote: >>>>> >>>>>> Jits >>>>>> >>>>>> I can smoke screen it I expect but some smartarse might spot it. >>>>>> >>>>>> Carole >>>>>> >>>>>> >>>>>>> I should also mention that I just haven't had the time to even think >>>>>>> about this... sorry :-( >>>>>>> >>>>>>> If it's urgent let me know, I can do this in the next couple of days. >>>>>>> >>>>>>> Jits >>>>>>> >>>>>>> >>>>>>> Jiten Bhagat wrote: >>>>>>> >>>>>>> >>>>>>>> Yeap, agreed, I will definitely do it :-) It's been in my task list >>>>>>>> to >>>>>>>> do so for a while now. I've just been waiting till after the next >>>>>>>> release as there is a lot of new API stuff coming out and I wanted >>>>>>>> to >>>>>>>> spend a bulk of time once to do it (instead of then spending more >>>>>>>> time >>>>>>>> updating the entry). >>>>>>>> >>>>>>>> Carole - if it's important for your talk I can register it right >>>>>>>> now? >>>>>>>> >>>>>>>> Cheers, >>>>>>>> Jits >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Rodrigo Lopez wrote: >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Jits is the main author of the paper and should submit the BC to >>>>>>>>> the BC >>>>>>>>> Just my two cents. >>>>>>>>> >>>>>>>>> R:) >>>>>>>>> >>>>>>>>> On 03/10/2010 17:50, Carole Goble wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> All >>>>>>>>>> >>>>>>>>>> given that the BioCatalogue is a REST service I tried to find it >>>>>>>>>> in the >>>>>>>>>> BioCatalogue (an obvious question that will be asked) >>>>>>>>>> search gave me 26 returns, none of them biocatalogue >>>>>>>>>> >>>>>>>>>> Have we registered biocatalogue? >>>>>>>>>> >>>>>>>>>> Carole >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Wed Oct 6 06:27:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 6 Oct 2010 11:27:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-496) Re-index the biocatalogue live site Message-ID: <34153.9936.1286360835407.JavaMail.jira@rosalind.cs.man.ac.uk> Re-index the biocatalogue live site ----------------------------------- Key: BIOCAT-496 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-496 Project: BioCatalogue Issue Type: Task Components: Server Management Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane reindex the application as queries are apparently taking long and timing out. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 6 06:29:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Wed, 6 Oct 2010 11:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-496) Re-index the biocatalogue live site In-Reply-To: <34153.9936.1286360835407.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16436638.9937.1286360955346.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-496?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane updated BIOCAT-496: ------------------------------------ Priority: Critical (was: Major) > Re-index the biocatalogue live site > ----------------------------------- > > Key: BIOCAT-496 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-496 > Project: BioCatalogue > Issue Type: Task > Components: Server Management > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Priority: Critical > > reindex the application as queries are apparently taking long and timing out. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Wed Oct 6 07:31:53 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Wed, 06 Oct 2010 12:31:53 +0100 Subject: [BioCatalogue-developers] dead link in the biocatalogue In-Reply-To: <4CAB8F89.3040707@cs.man.ac.uk> References: <4CAB8F89.3040707@cs.man.ac.uk> Message-ID: <4CAC5E29.2030507@ebi.ac.uk> Hi, I have not done any work on this unfortunately. I can try to get something in place by tomorrow if it is that urgent. But it will be rudimentary. Eric On 05/10/2010 21:50, Jiten Bhagat wrote: > Hi Franck, > > Eric and I discussed last week a task to write a script that goes > through all the content in the db and flags dead links. Should be a very > simple thing! > > Eric - what's the progress of this? > > Jits > > > Franck Tanoh wrote: >> hi guys, >> >> Do you know any software we could use the flag dead link in the catalogue? >> Eric can we reuse REST endpoint test you wrote? >> >> Cheers, >> Franck >> >> > _______________________________________________ > 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 Wed Oct 6 07:41:30 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 6 Oct 2010 12:41:30 +0100 Subject: [BioCatalogue-developers] BioCatalogue in BioCatalogue In-Reply-To: <4CAC4E8B.3000406@ebi.ac.uk> References: <4CA8B452.8010801@manchester.ac.uk> <4CA8CEA7.5030800@ebi.ac.uk> <4CA9A449.6070201@cs.man.ac.uk> <4CA9AAD5.3030805@cs.man.ac.uk> <4CAA0106.9060802@manchester.ac.uk> <4CABA918.2080309@cs.man.ac.uk> <36242.213.106.89.217.1286319206.squirrel@webmail.ebi.ac.uk> <4CABADDC.90303@cs.man.ac.uk> <39844.213.106.89.217.1286319937.squirrel@webmail.ebi.ac.uk> <4CAC4E8B.3000406@ebi.ac.uk> Message-ID: Hi Eric, Doesn't have to be the perfect solution ... something that can flag those dead links. Also should allow to query the database as well to list all dead links. Cheers Franck On 6 October 2010 11:25, Eric Nzuobontane wrote: > ?I updated the monitoring status for the BioCatalogue entry as "unchecked" > for our own registry did not sit well . > > Eric > > > On 06/10/2010 10:15, Franck Tanoh wrote: >> >> Hi Eric, >> >> I've been having problem deleting stuff as well... >> >> Franck >> >> On 6 October 2010 00:05, ?wrote: >>> >>> OK, it is possible that the load balancer times out if the application >>> appears unresponsive( long running request). I will have a look at the >>> logs tomorrow to see if there is anything in them ?anyway. >>> >>> Eric >>> >>> >>>> Ah ha! I did try to set it to EBI but it failed with a timeout error >>>> (this is because the merge providers process needs optimisations). When >>>> I refreshed it wasn't showing as EBI, but looks like it is now! >>>> >>>> Jits >>>> >>>> >>>> >>>> ericnzuo at ebi.ac.uk wrote: >>>>> >>>>> Hi Jits, >>>>> I see the provider listed as EBI already. I am not sure what needs to >>>>> be >>>>> done here. >>>>> >>>>> Eric >>>>> >>>>> >>>>>> I figured I'd at least create the REST service entry for the >>>>>> BioCatalogue API in the BioCatalogue. >>>>>> >>>>>> Here it is: http://www.biocatalogue.org/services/2738 >>>>>> >>>>>> I do need to change the service provider to EBI, which I will do with >>>>>> Eric's help tomorrow. >>>>>> >>>>>> Jits >>>>>> >>>>>> >>>>>> >>>>>> Carole Goble wrote: >>>>>> >>>>>>> Jits >>>>>>> >>>>>>> I can smoke screen it I expect but some smartarse might spot it. >>>>>>> >>>>>>> Carole >>>>>>> >>>>>>> >>>>>>>> I should also mention that I just haven't had the time to even think >>>>>>>> about this... sorry :-( >>>>>>>> >>>>>>>> If it's urgent let me know, I can do this in the next couple of >>>>>>>> days. >>>>>>>> >>>>>>>> Jits >>>>>>>> >>>>>>>> >>>>>>>> Jiten Bhagat wrote: >>>>>>>> >>>>>>>> >>>>>>>>> Yeap, agreed, I will definitely do it :-) It's been in my task list >>>>>>>>> to >>>>>>>>> do so for a while now. I've just been waiting till after the next >>>>>>>>> release as there is a lot of new API stuff coming out and I wanted >>>>>>>>> to >>>>>>>>> spend a bulk of time once to do it (instead of then spending more >>>>>>>>> time >>>>>>>>> updating the entry). >>>>>>>>> >>>>>>>>> Carole - if it's important for your talk I can register it right >>>>>>>>> now? >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> Jits >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> Rodrigo Lopez wrote: >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Jits is the main author of the paper and should submit the BC to >>>>>>>>>> the BC >>>>>>>>>> Just my two cents. >>>>>>>>>> >>>>>>>>>> R:) >>>>>>>>>> >>>>>>>>>> On 03/10/2010 17:50, Carole Goble wrote: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> All >>>>>>>>>>> >>>>>>>>>>> given that the BioCatalogue is a REST service I tried to find it >>>>>>>>>>> in the >>>>>>>>>>> BioCatalogue (an obvious question that will be asked) >>>>>>>>>>> search gave me 26 returns, none of them biocatalogue >>>>>>>>>>> >>>>>>>>>>> Have we registered biocatalogue? >>>>>>>>>>> >>>>>>>>>>> Carole >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >> >> > > > -- > 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 issues at mygrid.org.uk Wed Oct 6 11:31:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 6 Oct 2010 16:31:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-497) Look into using the change logs (generated from the service update checker) to calculate service API stability In-Reply-To: <14812729.9946.1286378955308.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <12896890.9947.1286379075306.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-497?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-497: -------------------------------- Priority: Minor (was: Major) > Look into using the change logs (generated from the service update checker) to calculate service API stability > -------------------------------------------------------------------------------------------------------------- > > Key: BIOCAT-497 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-497 > Project: BioCatalogue > Issue Type: New Feature > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Minor > > Original query from Richard Adams: > {quote} > Hi Katy, > I've just been having a browse around Biocatalogue - it's really > useful! - as we're trying to enhance our support for webservices > within our SBSI project, by providing UI plugins to access some of the > SysBio services. > I was wondering if Biocatalogue would provide stats on API stability > of webservices (e.g., breaking API changes such as removal of a > method, for example)? > Clearly some services will be more experimental than others, for app > developers developing UI to access the plugins then stability of the > API ( as well as the % availability) is influential in deciding which > webservices to offer/support. > Perhaps I've missed something in the Help files, but couldn't see > anything directly related to API changes. > Cheers > Richard > {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 6 11:29:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 6 Oct 2010 16:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-497) Look into using the change logs (generated from the service update checker) to calculate service API stability Message-ID: <14812729.9946.1286378955308.JavaMail.jira@rosalind.cs.man.ac.uk> Look into using the change logs (generated from the service update checker) to calculate service API stability -------------------------------------------------------------------------------------------------------------- Key: BIOCAT-497 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-497 Project: BioCatalogue Issue Type: New Feature Reporter: Jiten Bhagat Assignee: Jiten Bhagat Original query from Richard Adams: {quote} Hi Katy, I've just been having a browse around Biocatalogue - it's really useful! - as we're trying to enhance our support for webservices within our SBSI project, by providing UI plugins to access some of the SysBio services. I was wondering if Biocatalogue would provide stats on API stability of webservices (e.g., breaking API changes such as removal of a method, for example)? Clearly some services will be more experimental than others, for app developers developing UI to access the plugins then stability of the API ( as well as the % availability) is influential in deciding which webservices to offer/support. Perhaps I've missed something in the Help files, but couldn't see anything directly related to API changes. Cheers Richard {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Wed Oct 6 11:29:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Wed, 6 Oct 2010 16:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-497) Look into using the change logs (generated from the service update checker) to calculate service API stability Message-ID: <14812729.9946.1286378955308.JavaMail.jira@rosalind.cs.man.ac.uk> Look into using the change logs (generated from the service update checker) to calculate service API stability -------------------------------------------------------------------------------------------------------------- Key: BIOCAT-497 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-497 Project: BioCatalogue Issue Type: New Feature Reporter: Jiten Bhagat Assignee: Jiten Bhagat Original query from Richard Adams: {quote} Hi Katy, I've just been having a browse around Biocatalogue - it's really useful! - as we're trying to enhance our support for webservices within our SBSI project, by providing UI plugins to access some of the SysBio services. I was wondering if Biocatalogue would provide stats on API stability of webservices (e.g., breaking API changes such as removal of a method, for example)? Clearly some services will be more experimental than others, for app developers developing UI to access the plugins then stability of the API ( as well as the % availability) is influential in deciding which webservices to offer/support. Perhaps I've missed something in the Help files, but couldn't see anything directly related to API changes. Cheers Richard {quote} -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 7 04:42:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 7 Oct 2010 09:42:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-477) Parse the biocatalogue content to flag any dead links In-Reply-To: <16018195.9859.1285599555309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <16504715.9953.1286440935441.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-477: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Parse the biocatalogue content to flag any dead links > ----------------------------------------------------- > > Key: BIOCAT-477 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Links within the biocatalogue will become inaccessible from time to time. The object of this task is to flag such links thereby generating a curation event which should be followed up by a human curator. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 7 04:50:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 7 Oct 2010 09:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-498) Create a listing(index) page for all service tests Message-ID: <7834499.9954.1286441415341.JavaMail.jira@rosalind.cs.man.ac.uk> Create a listing(index) page for all service tests -------------------------------------------------- Key: BIOCAT-498 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498 Project: BioCatalogue Issue Type: Task Components: Web Interface Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane The listing of service test will enable an easy navigation for monitoring purposes. At the moment, it is hard going through the service to get to the service test especially when one has to look at a number of tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 7 10:51:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Oct 2010 15:51:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-499) Create a new VM for the BioCatalogue system Message-ID: <13641006.9964.1286463075344.JavaMail.jira@rosalind.cs.man.ac.uk> Create a new VM for the BioCatalogue system ------------------------------------------- Key: BIOCAT-499 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-499 Project: BioCatalogue Issue Type: New Feature Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Critical There is an old Fedora 11 VM that was used previously to allow people to easily set up their own BioCatalogue instance. This is now badly out of date. So create a new VM (preferably Ubuntu based) with all the latest stuff. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 7 10:53:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 7 Oct 2010 15:53:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-500) Document how to use and update the VM Message-ID: <16227861.9965.1286463195301.JavaMail.jira@rosalind.cs.man.ac.uk> Document how to use and update the VM ------------------------------------- Key: BIOCAT-500 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-500 Project: BioCatalogue Issue Type: Sub-task Reporter: Jiten Bhagat Assignee: Jiten Bhagat Document how to set up, use and update the BioCatalogue VM. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Oct 7 12:28:01 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 7 Oct 2010 12:28:01 -0400 (EDT) Subject: [BioCatalogue-developers] [2271] trunk/script/biocatalogue/links_checker.rb: - Initial work on " links_checker" script. Message-ID: <20101007162801.1F624185836B@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Oct 7 13:35:36 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 07 Oct 2010 18:35:36 +0100 Subject: [BioCatalogue-developers] [2271] trunk/script/biocatalogue/links_checker.rb: - Initial work on " links_checker" script. In-Reply-To: <20101007162801.1F624185836B@rubyforge.org> References: <20101007162801.1F624185836B@rubyforge.org> Message-ID: <4CAE04E8.5030005@cs.man.ac.uk> Hi Eric, What's the "bug with the rest service models"? Cheers, Jits noreply at rubyforge.org wrote: > > Revision > 2271 > Author > ebontane > Date > 2010-10-07 12:28:00 -0400 (Thu, 07 Oct 2010) > > > Log Message > > - Initial work on "links_checker" script. Script will flag the links that are inaccessible in service descriptions and other annotations. > > > Added Paths > > * trunk/script/biocatalogue/links_checker.rb > <#trunkscriptbiocataloguelinks_checkerrb> > > > Diff > > > Added: trunk/script/biocatalogue/links_checker.rb (0 => 2271) > > > --- trunk/script/biocatalogue/links_checker.rb (rev 0) > +++ trunk/script/biocatalogue/links_checker.rb 2010-10-07 16:28:00 UTC (rev 2271) > @@ -0,0 +1,194 @@ > +#!/usr/bin/env ruby > + > +# Generate a list of links found in descriptions and other annotations > +# and check the status of the links > +# > +# NOTE : This is meant to only flag links that might need to be checked > +# by a human curator > +# > +# -e, --environment=name Specifies the environment to run this script under (test|development|production). > +# Default: development > +# > +# -h, --help Show this help message. > +# > +# Depedencies: > +# - Rails (v2.3.2) > +# > +# TODO : add documentation URLs to the list of links > +# TODO : parse URLs before check > +# TODO : Extend to Rest services. These are failing bec of a bug with the rest service models! > + > +require 'optparse' > +require 'benchmark' > +require 'pp' > + > +class LinksChecker > + > + attr_accessor :options > + > + def initialize(args) > + @options = { > + :environment => (ENV['RAILS_ENV'] || "production").dup, > + } > + > + args.options do |opts| > + opts.on("-e", "--environment=name", String, > + "Specifies the environment to run this script under (test|development|production).", > + "Default: development") { |v| @options[:environment] = v } > + > + opts.separator "" > + > + opts.on("-h", "--help", "Show this help message.") { puts opts; exit } > + > + opts.parse! > + end > + > + # Start the Rails app > + > + ENV["RAILS_ENV"] = @options[:environment] > + RAILS_ENV.replace(@options[:environment]) if defined?(RAILS_ENV) > + > + require File.join(File.dirname(__FILE__), '..', '..', 'config', 'environment') > + end > + > + > + > + #puts "Redirecting output of $stdout to log file: '{RAILS_ROOT}/log/link_checker_{current_time}.log' ..." > + #$stdout = File.new(File.join(File.dirname(__FILE__), '..', '..', 'log', "links_checker_#{Time.now.strftime('%Y%m%d-%H%M')}.log"), "w") > + #$stdout.sync = true > + > + def run > + all_links = [] > + Service.all.each do |service| > + unless service.latest_version.service_versionified.is_a?(RestService) > + puts "Getting links in descriptions for service : #{service.name}" > + #pp self.check_all(links_for_service(service)) > + all_links << links_for_service_h(service) unless links_for_service_h(service).empty? > + end > + end > + pp all_links > + end > + > + protected > + > + def service_annotatables(service) > + annotatables = [] > + service_instance = service.latest_version.service_versionified > + annotatables.concat(service.service_deployments) > + annotatables << service_instance > + if service_instance.respond_to?(:soap_operations) > + annotatables.concat(service_instance.soap_operations) > + service_instance.soap_operations.each do |op| > + annotatables.concat(op.soap_inputs) > + annotatables.concat(op.soap_outputs) > + end > + end > + if service_instance.respond_to?(:rest_resources) > + annotatables.concat(service_instance.rest_resources) > + end > + return annotatables > + end > + > + def non_provider_annotations(parent, attr='description') > + if parent.respond_to?(:annotations) > + return parent.annotations.collect{|a| a.value if a.attribute.name.downcase == attr}.compact > + end > + return [] > + end > + > + def get_links_from_text(text) > + pieces = text.split > + pieces.collect!{ |p| p if p.match('http|www')}.compact > + end > + > + #TODO : parse the urls before running check > + def parse_link(link) > + > + end > + > + def links_for_annotatable(annotatable) > + links = [] > + if annotatable.respond_to?(:description) > + if annotatable.description > + links.concat(self.get_links_from_text(annotatable.description)) > + end > + self.non_provider_annotations(annotatable).each do |ann| > + links.concat(self.get_links_from_text(ann)) > + end > + end > + return links > + end > + > + def links_for_annotatable_h(annotatable) > + links = {} > + unless self.links_for_annotatable(annotatable).empty? > + links[annotatable.class.name+(annotatable.id.to_s)] = self.links_for_annotatable(annotatable) > + end > + return links > + end > + > + def links_for_service(service) > + links = [] > + self.service_annotatables(service).each do |ann| > + links.concat(self.links_for_annotatable(ann)) > + end > + return links > + end > + > + # Returns a hash of services and the links of links > + # found in the service components like soap > + # operations and inputs & outputs. > + # Has structure: > + # { service_name+id => [ { component_class+id => [ list of urls]}, > + # { component_class+id => [ list of urls]} ]} > + # > + # Example: > + # {"WSDBFetchServerService2701"=> > + # [{"SoapOperation19687"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#fetchbatch_db_ids_format_style)."]}, > + # {"SoapOperation19686"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#fetchdata_query_format_style)."]}, > + # {"SoapOperation19685"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#getdbformats_db)."]}, > + # {"SoapOperation19690"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#getformatstyles_db_format)."]}, > + # {"SoapOperation19688"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#getsupporteddbs)."]}, > + # {"SoapOperation19689"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#getsupportedformats)."]}, > + # {"SoapOperation19691"=> > + # ["http://www.ebi.ac.uk/Tools/webservices/services/dbfetch#fetchdata_query_format_style)."]} > + # ] > + # } > + # > + # > + > + def links_for_service_h(service) > + links = [] > + s_links = {} > + self.service_annotatables(service).each do |ann| > + unless links_for_annotatable_h(ann).empty? > + links << links_for_annotatable_h(ann) > + end > + end > + s_links[service.name+(service.id.to_s)] = links unless links.empty? > + return s_links > + end > + > + #check the accessibility of a url. Follows up to 3 redirects > + def accessible?(url) > + return BioCatalogue::AvailabilityCheck::URLCheck.new(url).available? > + end > + > + def check_all(links=[]) > + checked = {} > + links.each do |link| > + checked[link] = self.accessible?(link) > + end > + return checked > + end > + > +end > + > +LinksChecker.new(ARGV.clone).run > + > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From utopia at cs.man.ac.uk Fri Oct 8 06:32:44 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 08 Oct 2010 11:32:44 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:solvateStructureWithLigandsFromAMBER_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:solvateStructureWithLigandsFromAMBER_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1179 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 Oct 8 07:04:54 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 8 Oct 2010 07:04:54 -0400 (EDT) Subject: [BioCatalogue-developers] [2272] trunk/script/biocatalogue/similar_searches_report.rb: Implemented a similar searches report. Message-ID: <20101008110454.DAD4D1858385@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Oct 8 13:03:07 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 8 Oct 2010 13:03:07 -0400 (EDT) Subject: [BioCatalogue-developers] [2273] trunk/script/biocatalogue/links_checker.rb: futher work on script to flag 'dead' links Message-ID: <20101008170307.AFFE619782D4@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Sat Oct 9 14:15:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 09 Oct 2010 19:15:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'CLUSTAL W multiple alignment (CNRS IBCP)' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'CLUSTAL W multiple alignment (CNRS IBCP)' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/91 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Mon Oct 11 11:55:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 11 Oct 2010 16:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-498) Create a listing(index) page for all service tests In-Reply-To: <7834499.9954.1286441415341.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9727789.9966.1286812515412.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-498 started by Eric Nzuobontane. > Create a listing(index) page for all service tests > -------------------------------------------------- > > Key: BIOCAT-498 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > The listing of service test will enable an easy navigation for monitoring purposes. At the moment, it is hard going through the service to get to the service test especially when one has to look at a number of tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Mon Oct 11 11:57:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 11 Oct 2010 16:57:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-498) Create a listing(index) page for all service tests In-Reply-To: <7834499.9954.1286441415341.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22712868.9967.1286812635344.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16003#action_16003 ] Eric Nzuobontane commented on BIOCAT-498: ----------------------------------------- I have created an index of the service tests and made it sortable by creation date and success rate. This allows one to navigate from the test to the services as otherwise it is quite hard to see which services have been failing. > Create a listing(index) page for all service tests > -------------------------------------------------- > > Key: BIOCAT-498 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > The listing of service test will enable an easy navigation for monitoring purposes. At the moment, it is hard going through the service to get to the service test especially when one has to look at a number of tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Mon Oct 11 12:15:53 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 11 Oct 2010 12:15:53 -0400 (EDT) Subject: [BioCatalogue-developers] [2274] trunk: add index to service tests. Message-ID: <20101011161553.9125519783CA@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Tue Oct 12 04:41:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 12 Oct 2010 09:41:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-498) Create a listing(index) page for all service tests In-Reply-To: <7834499.9954.1286441415341.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <24641926.9968.1286872875459.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-498. ------------------------------------- Resolution: Implemented > Create a listing(index) page for all service tests > -------------------------------------------------- > > Key: BIOCAT-498 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > The listing of service test will enable an easy navigation for monitoring purposes. At the moment, it is hard going through the service to get to the service test especially when one has to look at a number of tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Oct 12 04:41:18 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 12 Oct 2010 09:41:18 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-408) Write addiction endpoint checking tests where basic test fails In-Reply-To: <23193000.6462.1277195355409.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5033783.9969.1286872878408.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-408. ------------------------------------- Resolution: Implemented > Write addiction endpoint checking tests where basic test fails > -------------------------------------------------------------- > > Key: BIOCAT-408 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Add supplementary tests for the service where basic checks fails. For the endpoint of soap services, try connecting to the service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Tue Oct 12 04:53:15 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 12 Oct 2010 09:53:15 +0100 Subject: [BioCatalogue-developers] updated the test site Message-ID: <4CB421FB.8090506@ebi.ac.uk> Hi Guys, I have updated the test site with the latest codebase. One thing I have added is the listing of service tests http://test.biocatalogue.org/service_tests/ I find it much easier to go from the test to the service when checking for failing services. Let me know what you think. Eric -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Tue Oct 12 05:07:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Tue, 12 Oct 2010 10:07:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-408) Write addiction endpoint checking tests where basic test fails In-Reply-To: <23193000.6462.1277195355409.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <30189020.9970.1286874435329.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16004#action_16004 ] Jiten Bhagat commented on BIOCAT-408: ------------------------------------- {quote} Write addiction endpoint checking tests where basic test fails {quote} addiction? ;-) > Write addiction endpoint checking tests where basic test fails > -------------------------------------------------------------- > > Key: BIOCAT-408 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408 > Project: BioCatalogue > Issue Type: Task > Components: Service Monitoring > Environment: RoR > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Add supplementary tests for the service where basic checks fails. For the endpoint of soap services, try connecting to the service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From jits at cs.man.ac.uk Tue Oct 12 05:10:22 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 12 Oct 2010 10:10:22 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB421FB.8090506@ebi.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> Message-ID: <4CB425FE.40304@cs.man.ac.uk> Eric Nzuobontane wrote: > Hi Guys, > > I have updated the test site with the latest codebase. One thing I > have added is the listing of service tests > http://test.biocatalogue.org/service_tests/ > > I find it much easier to go from the test to the service when checking > for failing services. Let me know what you think. Looks good! :-) Could you re do the sorting stuff to follow how it's done on all the other indexes please? Mainly, look at the services index as that also has UI bits. Jits > > Eric > From ytanoh at cs.man.ac.uk Tue Oct 12 07:27:47 2010 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 12 Oct 2010 12:27:47 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB421FB.8090506@ebi.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> Message-ID: Hi Eric, That's really useful. Thanks Maybe you can add more items in the 'sort by' . e.g possibility to find disable endpoint/test script/ wsdl testing. Do you count 'warning' status as failure when you're deriving the overall success rate? I would also like to sort by warning status too. How are you getting on the the dead links? We had a discussion today in our meeting about that. We thought that it's probably not a good idea to delete them but that depends on how many there are in the catalogue. For example a link might be down for a while because a server is down or under maintenance...need a policy in that....let see how many we got first. Cheers Franck On 12 October 2010 09:53, Eric Nzuobontane wrote: > ?Hi Guys, > > I have updated the test site with the latest codebase. One thing I have > added is the listing of service tests > http://test.biocatalogue.org/service_tests/ > > I find it much easier to go from the test to the service when checking for > failing services. ?Let me know what you think. > > Eric > > -- > Eric Nzuobontane > ================================== > European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge > CB10 1SD > United Kingdom > > Tel ? : +44 1223 492654 > email : ericnzuo at ebi.ac.uk > ================================== > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- ?"Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From ericnzuo at ebi.ac.uk Tue Oct 12 07:43:04 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 12 Oct 2010 12:43:04 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: References: <4CB421FB.8090506@ebi.ac.uk> Message-ID: <4CB449C8.7060003@ebi.ac.uk> Hi Frank, On 12/10/2010 12:27, Franck Tanoh wrote: > Hi Eric, > > That's really useful. Thanks > Maybe you can add more items in the 'sort by' . e.g possibility to > find disable endpoint/test script/ wsdl testing. Well, I did not want to add disabled stuff here except this is meant to be seen my only admins. That I was not exactly sure about because I would imagine Rodrigo & Hamish wanting to see that list. For now, only active tests are included in the index > Do you count 'warning' status as failure when you're deriving the > overall success rate? I would also like to sort by warning status too. yes, warning are considered as failure when calculating success rate > How are you getting on the the dead links? We had a discussion today > in our meeting about that. We thought that it's probably not a good > idea to delete them but that depends on how many there are in the > catalogue. For example a link might be down for a while because a > server is down or under maintenance...need a policy in that....let see > how many we got first. I already wrote a first pass of the script which is also available on the test site. I will run it on the test data now and send you the link. Eric > Cheers > Franck > > > On 12 October 2010 09:53, Eric Nzuobontane wrote: >> Hi Guys, >> >> I have updated the test site with the latest codebase. One thing I have >> added is the listing of service tests >> http://test.biocatalogue.org/service_tests/ >> >> I find it much easier to go from the test to the service when checking for >> failing services. Let me know what you think. >> >> Eric >> >> -- >> Eric Nzuobontane >> ================================== >> European Bioinformatics Institute >> Wellcome Trust Genome Campus >> Hinxton, Cambridge >> CB10 1SD >> United Kingdom >> >> Tel : +44 1223 492654 >> email : ericnzuo at ebi.ac.uk >> ================================== >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From ericnzuo at ebi.ac.uk Tue Oct 12 07:46:21 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 12 Oct 2010 12:46:21 +0100 Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-408) Write addiction endpoint checking tests where basic test fails In-Reply-To: <30189020.9970.1286874435329.JavaMail.jira@rosalind.cs.man.ac.uk> References: <30189020.9970.1286874435329.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4CB44A8D.2050902@ebi.ac.uk> Addiction!!! :) That is what happens when reading over your stuff is a problem!! Eric On 12/10/2010 10:07, Jiten Bhagat (JIRA) wrote: > [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16004#action_16004 ] > > Jiten Bhagat commented on BIOCAT-408: > ------------------------------------- > > {quote} > Write addiction endpoint checking tests where basic test fails > {quote} > > addiction? ;-) > >> Write addiction endpoint checking tests where basic test fails >> -------------------------------------------------------------- >> >> Key: BIOCAT-408 >> URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-408 >> Project: BioCatalogue >> Issue Type: Task >> Components: Service Monitoring >> Environment: RoR >> Reporter: Eric Nzuobontane >> Assignee: Eric Nzuobontane >> Original Estimate: 1 day >> Remaining Estimate: 1 day >> >> Add supplementary tests for the service where basic checks fails. For the endpoint of soap services, try connecting to the service. -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Tue Oct 12 08:15:16 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 12 Oct 2010 13:15:16 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-501) Allow people to opt out of receiving notifications about a service In-Reply-To: <16386281.9973.1286885715336.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3850292.9974.1286885716534.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-501?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-501: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Allow people to opt out of receiving notifications about a service > ------------------------------------------------------------------ > > Key: BIOCAT-501 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-501 > Project: BioCatalogue > Issue Type: Task > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > The motivation : Rodrigo submited the citeXplore service to BioCatalogue. As he does not maintain the service, he would not like to receive notifications( monitoring ) about the service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Oct 12 08:15:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 12 Oct 2010 13:15:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-501) Allow people to opt out of receiving notifications about a service Message-ID: <16386281.9973.1286885715336.JavaMail.jira@rosalind.cs.man.ac.uk> Allow people to opt out of receiving notifications about a service ------------------------------------------------------------------ Key: BIOCAT-501 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-501 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Jiten Bhagat The motivation : Rodrigo submited the citeXplore service to BioCatalogue. As he does not maintain the service, he would not like to receive notifications( monitoring ) about the service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Tue Oct 12 08:20:36 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 12 Oct 2010 13:20:36 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB449C8.7060003@ebi.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> <4CB449C8.7060003@ebi.ac.uk> Message-ID: <4CB45294.6000603@ebi.ac.uk> Hi Franck, Please have a look at this http://test.biocatalogue.org/links_checker_20101012-1308.html Note that this is for alert purposes only. And we should actually make sure that we are trying to access the right link. A rough attempt has been made to parse the links programmatically but that is not full proof! Have fun! Eric On 12/10/2010 12:43, Eric Nzuobontane wrote: > Hi Frank, > > On 12/10/2010 12:27, Franck Tanoh wrote: >> Hi Eric, >> >> That's really useful. Thanks >> Maybe you can add more items in the 'sort by' . e.g possibility to >> find disable endpoint/test script/ wsdl testing. > Well, I did not want to add disabled stuff here except this is meant > to be seen my only admins. That I was not exactly sure about because I > would imagine Rodrigo & Hamish wanting to see that list. For now, only > active tests are included in the index >> Do you count 'warning' status as failure when you're deriving the >> overall success rate? I would also like to sort by warning status too. > yes, warning are considered as failure when calculating success rate >> How are you getting on the the dead links? We had a discussion today >> in our meeting about that. We thought that it's probably not a good >> idea to delete them but that depends on how many there are in the >> catalogue. For example a link might be down for a while because a >> server is down or under maintenance...need a policy in that....let see >> how many we got first. > > I already wrote a first pass of the script which is also available on > the test site. I will run it on the test data now and send you the link. > > Eric > >> Cheers >> Franck >> >> >> On 12 October 2010 09:53, Eric Nzuobontane wrote: >>> Hi Guys, >>> >>> I have updated the test site with the latest codebase. One thing I have >>> added is the listing of service tests >>> http://test.biocatalogue.org/service_tests/ >>> >>> I find it much easier to go from the test to the service when >>> checking for >>> failing services. Let me know what you think. >>> >>> Eric >>> >>> -- >>> Eric Nzuobontane >>> ================================== >>> European Bioinformatics Institute >>> Wellcome Trust Genome Campus >>> Hinxton, Cambridge >>> CB10 1SD >>> United Kingdom >>> >>> Tel : +44 1223 492654 >>> email : ericnzuo at ebi.ac.uk >>> ================================== >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> >> >> > > -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Tue Oct 12 09:05:57 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 12 Oct 2010 14:05:57 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB45294.6000603@ebi.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> <4CB449C8.7060003@ebi.ac.uk> <4CB45294.6000603@ebi.ac.uk> Message-ID: <4CB45D35.8070709@cs.man.ac.uk> Hi Eric, Would be good if the report contained links to the actual page in which the link resides. Tip 1: try (somehow) to use the helper method 'url_for_web_interface' which is in the application controller. Tip 2: make the links in the report always open up in a new window, by adding: target="_blank" ... to the tag for the link. Jits Eric Nzuobontane wrote: > Hi Franck, > > Please have a look at this > http://test.biocatalogue.org/links_checker_20101012-1308.html > > Note that this is for alert purposes only. And we should actually make > sure that we are trying to access the right link. > A rough attempt has been made to parse the links programmatically but > that is not full proof! > > Have fun! > > Eric > > > On 12/10/2010 12:43, Eric Nzuobontane wrote: >> Hi Frank, >> >> On 12/10/2010 12:27, Franck Tanoh wrote: >>> Hi Eric, >>> >>> That's really useful. Thanks >>> Maybe you can add more items in the 'sort by' . e.g possibility to >>> find disable endpoint/test script/ wsdl testing. >> Well, I did not want to add disabled stuff here except this is meant >> to be seen my only admins. That I was not exactly sure about because >> I would imagine Rodrigo & Hamish wanting to see that list. For now, >> only active tests are included in the index >>> Do you count 'warning' status as failure when you're deriving the >>> overall success rate? I would also like to sort by warning status too. >> yes, warning are considered as failure when calculating success rate >>> How are you getting on the the dead links? We had a discussion today >>> in our meeting about that. We thought that it's probably not a good >>> idea to delete them but that depends on how many there are in the >>> catalogue. For example a link might be down for a while because a >>> server is down or under maintenance...need a policy in that....let see >>> how many we got first. >> >> I already wrote a first pass of the script which is also available on >> the test site. I will run it on the test data now and send you the link. >> >> Eric >> >>> Cheers >>> Franck >>> >>> >>> On 12 October 2010 09:53, Eric Nzuobontane wrote: >>>> Hi Guys, >>>> >>>> I have updated the test site with the latest codebase. One thing I >>>> have >>>> added is the listing of service tests >>>> http://test.biocatalogue.org/service_tests/ >>>> >>>> I find it much easier to go from the test to the service when >>>> checking for >>>> failing services. Let me know what you think. >>>> >>>> Eric >>>> >>>> -- >>>> Eric Nzuobontane >>>> ================================== >>>> European Bioinformatics Institute >>>> Wellcome Trust Genome Campus >>>> Hinxton, Cambridge >>>> CB10 1SD >>>> United Kingdom >>>> >>>> Tel : +44 1223 492654 >>>> email : ericnzuo at ebi.ac.uk >>>> ================================== >>>> >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >>> >>> >> >> > > From issues at mygrid.org.uk Tue Oct 12 09:18:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 12 Oct 2010 14:18:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-477) Parse the biocatalogue content to flag any dead links In-Reply-To: <16018195.9859.1285599555309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <28323162.9977.1286889495328.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16005#action_16005 ] Eric Nzuobontane commented on BIOCAT-477: ----------------------------------------- Hi Eric, Would be good if the report contained links to the actual page in which the link resides. Tip 1: try (somehow) to use the helper method 'url_for_web_interface' which is in the application controller. Tip 2: make the links in the report always open up in a new window, by adding: target="_blank" ... to the tag for the link. Jits > Parse the biocatalogue content to flag any dead links > ----------------------------------------------------- > > Key: BIOCAT-477 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Links within the biocatalogue will become inaccessible from time to time. The object of this task is to flag such links thereby generating a curation event which should be followed up by a human curator. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Tue Oct 12 22:46:41 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 13 Oct 2010 03:46:41 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2810 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Thu Oct 14 05:26:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Thu, 14 Oct 2010 10:26:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-502) Update the fail controller to only allow it to process when an admin user hits it Message-ID: <14642526.9979.1287048375608.JavaMail.jira@rosalind.cs.man.ac.uk> Update the fail controller to only allow it to process when an admin user hits it --------------------------------------------------------------------------------- Key: BIOCAT-502 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-502 Project: BioCatalogue Issue Type: Bug Components: Misc Codebase Reporter: Jiten Bhagat Assignee: Eric Nzuobontane ... this is to prevent someone spamming us through our own error emails! The solution is to add a before_filter in the fail controller to check that a user is logged in and that they are an admin. Only then should it actually go ahead with the failure and send out the error email. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 14 08:50:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 14 Oct 2010 13:50:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-503) Check the that services have the appropriate contacts, especially the ones that were registered by BioCatalogue team members Message-ID: <31281353.9991.1287060615323.JavaMail.jira@rosalind.cs.man.ac.uk> Check the that services have the appropriate contacts, especially the ones that were registered by BioCatalogue team members ---------------------------------------------------------------------------------------------------------------------------- Key: BIOCAT-503 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-503 Project: BioCatalogue Issue Type: Task Reporter: Eric Nzuobontane Assignee: Franck Tanoh Many services were registered by BioCatalogue team members and other people that do not maintain the services. This means that notifications about the services may be sent to those people instead of the appropriate responsible persons. It is important to review the content and make sure we have appropriate contacts for the services. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Oct 14 11:03:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 14 Oct 2010 11:03:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2275] trunk/script/biocatalogue/links_checker.rb: link to the services that might have dead links in the report Message-ID: <20101014150327.197BC1678310@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Oct 14 11:12:09 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 14 Oct 2010 11:12:09 -0400 (EDT) Subject: [BioCatalogue-developers] [2276] trunk/script/biocatalogue/links_checker.rb: fix minor bug Message-ID: <20101014151210.096351858379@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Oct 14 11:44:42 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 14 Oct 2010 16:44:42 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB45D35.8070709@cs.man.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> <4CB449C8.7060003@ebi.ac.uk> <4CB45294.6000603@ebi.ac.uk> <4CB45D35.8070709@cs.man.ac.uk> Message-ID: <4CB7256A.30703@ebi.ac.uk> OK, I have added links to the services on which the links are found. Also where possible, links to the sub-objects of the service. That means some links do not work! Those for soap services for example. A new report is available on the test site... http://test.biocatalogue.org/links_checker_20101014-1632.html Eric On 12/10/2010 14:05, Jiten Bhagat wrote: > Hi Eric, > > Would be good if the report contained links to the actual page in which > the link resides. > > Tip 1: try (somehow) to use the helper method 'url_for_web_interface' > which is in the application controller. > Tip 2: make the links in the report always open up in a new window, by > adding: > > target="_blank" > > ... to the tag for the link. > > Jits > > > Eric Nzuobontane wrote: >> Hi Franck, >> >> Please have a look at this >> http://test.biocatalogue.org/links_checker_20101012-1308.html >> >> Note that this is for alert purposes only. And we should actually make >> sure that we are trying to access the right link. >> A rough attempt has been made to parse the links programmatically but >> that is not full proof! >> >> Have fun! >> >> Eric >> >> >> On 12/10/2010 12:43, Eric Nzuobontane wrote: >>> Hi Frank, >>> >>> On 12/10/2010 12:27, Franck Tanoh wrote: >>>> Hi Eric, >>>> >>>> That's really useful. Thanks >>>> Maybe you can add more items in the 'sort by' . e.g possibility to >>>> find disable endpoint/test script/ wsdl testing. >>> Well, I did not want to add disabled stuff here except this is meant >>> to be seen my only admins. That I was not exactly sure about because >>> I would imagine Rodrigo& Hamish wanting to see that list. For now, >>> only active tests are included in the index >>>> Do you count 'warning' status as failure when you're deriving the >>>> overall success rate? I would also like to sort by warning status too. >>> yes, warning are considered as failure when calculating success rate >>>> How are you getting on the the dead links? We had a discussion today >>>> in our meeting about that. We thought that it's probably not a good >>>> idea to delete them but that depends on how many there are in the >>>> catalogue. For example a link might be down for a while because a >>>> server is down or under maintenance...need a policy in that....let see >>>> how many we got first. >>> I already wrote a first pass of the script which is also available on >>> the test site. I will run it on the test data now and send you the link. >>> >>> Eric >>> >>>> Cheers >>>> Franck >>>> >>>> >>>> On 12 October 2010 09:53, Eric Nzuobontane wrote: >>>>> Hi Guys, >>>>> >>>>> I have updated the test site with the latest codebase. One thing I >>>>> have >>>>> added is the listing of service tests >>>>> http://test.biocatalogue.org/service_tests/ >>>>> >>>>> I find it much easier to go from the test to the service when >>>>> checking for >>>>> failing services. Let me know what you think. >>>>> >>>>> Eric >>>>> >>>>> -- >>>>> Eric Nzuobontane >>>>> ================================== >>>>> European Bioinformatics Institute >>>>> Wellcome Trust Genome Campus >>>>> Hinxton, Cambridge >>>>> CB10 1SD >>>>> United Kingdom >>>>> >>>>> Tel : +44 1223 492654 >>>>> email : ericnzuo at ebi.ac.uk >>>>> ================================== >>>>> >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>> >>>> >>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From jits at cs.man.ac.uk Thu Oct 14 11:49:00 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Thu, 14 Oct 2010 16:49:00 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB7256A.30703@ebi.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> <4CB449C8.7060003@ebi.ac.uk> <4CB45294.6000603@ebi.ac.uk> <4CB45D35.8070709@cs.man.ac.uk> <4CB7256A.30703@ebi.ac.uk> Message-ID: <4CB7266C.90300@cs.man.ac.uk> Eric Nzuobontane wrote: > OK, I have added links to the services on which the links are found. > Also where possible, links to the sub-objects of the service. Ace! > That means some links do not work! Those for soap services for example. Link to the parent service in this case. As all info on the SoapService / RestService is shown on the Service show page. > > A new report is available on the test site... > > http://test.biocatalogue.org/links_checker_20101014-1632.html What do the different colours mean? Jits > > Eric > > > On 12/10/2010 14:05, Jiten Bhagat wrote: >> Hi Eric, >> >> Would be good if the report contained links to the actual page in which >> the link resides. >> >> Tip 1: try (somehow) to use the helper method 'url_for_web_interface' >> which is in the application controller. > > >> Tip 2: make the links in the report always open up in a new window, by >> adding: >> >> target="_blank" >> >> ... to the tag for the link. >> >> Jits >> >> >> Eric Nzuobontane wrote: >>> Hi Franck, >>> >>> Please have a look at this >>> http://test.biocatalogue.org/links_checker_20101012-1308.html >>> >>> Note that this is for alert purposes only. And we should actually make >>> sure that we are trying to access the right link. >>> A rough attempt has been made to parse the links programmatically but >>> that is not full proof! >>> >>> Have fun! >>> >>> Eric >>> >>> >>> On 12/10/2010 12:43, Eric Nzuobontane wrote: >>>> Hi Frank, >>>> >>>> On 12/10/2010 12:27, Franck Tanoh wrote: >>>>> Hi Eric, >>>>> >>>>> That's really useful. Thanks >>>>> Maybe you can add more items in the 'sort by' . e.g possibility to >>>>> find disable endpoint/test script/ wsdl testing. >>>> Well, I did not want to add disabled stuff here except this is meant >>>> to be seen my only admins. That I was not exactly sure about because >>>> I would imagine Rodrigo& Hamish wanting to see that list. For now, >>>> only active tests are included in the index >>>>> Do you count 'warning' status as failure when you're deriving the >>>>> overall success rate? I would also like to sort by warning status >>>>> too. >>>> yes, warning are considered as failure when calculating success rate >>>>> How are you getting on the the dead links? We had a discussion today >>>>> in our meeting about that. We thought that it's probably not a good >>>>> idea to delete them but that depends on how many there are in the >>>>> catalogue. For example a link might be down for a while because a >>>>> server is down or under maintenance...need a policy in that....let >>>>> see >>>>> how many we got first. >>>> I already wrote a first pass of the script which is also available on >>>> the test site. I will run it on the test data now and send you the >>>> link. >>>> >>>> Eric >>>> >>>>> Cheers >>>>> Franck >>>>> >>>>> >>>>> On 12 October 2010 09:53, Eric Nzuobontane >>>>> wrote: >>>>>> Hi Guys, >>>>>> >>>>>> I have updated the test site with the latest codebase. One thing I >>>>>> have >>>>>> added is the listing of service tests >>>>>> http://test.biocatalogue.org/service_tests/ >>>>>> >>>>>> I find it much easier to go from the test to the service when >>>>>> checking for >>>>>> failing services. Let me know what you think. >>>>>> >>>>>> Eric >>>>>> >>>>>> -- >>>>>> Eric Nzuobontane >>>>>> ================================== >>>>>> European Bioinformatics Institute >>>>>> Wellcome Trust Genome Campus >>>>>> Hinxton, Cambridge >>>>>> CB10 1SD >>>>>> United Kingdom >>>>>> >>>>>> Tel : +44 1223 492654 >>>>>> email : ericnzuo at ebi.ac.uk >>>>>> ================================== >>>>>> >>>>>> _______________________________________________ >>>>>> BioCatalogue-developers mailing list >>>>>> BioCatalogue-developers at rubyforge.org >>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>> >>>>> >>>> >>> > > From issues at mygrid.org.uk Thu Oct 14 11:48:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 14 Oct 2010 16:48:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-477) Parse the biocatalogue content to flag any dead links In-Reply-To: <16018195.9859.1285599555309.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <22771963.9993.1287071295330.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16007#action_16007 ] Eric Nzuobontane commented on BIOCAT-477: ----------------------------------------- Links to the services and components added to the report. > Parse the biocatalogue content to flag any dead links > ----------------------------------------------------- > > Key: BIOCAT-477 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-477 > Project: BioCatalogue > Issue Type: Task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Links within the biocatalogue will become inaccessible from time to time. The object of this task is to flag such links thereby generating a curation event which should be followed up by a human curator. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From ericnzuo at ebi.ac.uk Thu Oct 14 12:00:02 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 14 Oct 2010 17:00:02 +0100 Subject: [BioCatalogue-developers] updated the test site In-Reply-To: <4CB7266C.90300@cs.man.ac.uk> References: <4CB421FB.8090506@ebi.ac.uk> <4CB449C8.7060003@ebi.ac.uk> <4CB45294.6000603@ebi.ac.uk> <4CB45D35.8070709@cs.man.ac.uk> <4CB7256A.30703@ebi.ac.uk> <4CB7266C.90300@cs.man.ac.uk> Message-ID: <4CB72902.20305@ebi.ac.uk> The colors are just for visual ease to my eye. So I can see that I am looking at different things. Distinction is services with odd or even ids. So nothing functional. Eric On 14/10/2010 16:49, Jiten Bhagat wrote: > Eric Nzuobontane wrote: >> OK, I have added links to the services on which the links are found. >> Also where possible, links to the sub-objects of the service. > Ace! > >> That means some links do not work! Those for soap services for example. > Link to the parent service in this case. As all info on the SoapService > / RestService is shown on the Service show page. > >> A new report is available on the test site... >> >> http://test.biocatalogue.org/links_checker_20101014-1632.html > What do the different colours mean? > > Jits > >> Eric >> >> >> On 12/10/2010 14:05, Jiten Bhagat wrote: >>> Hi Eric, >>> >>> Would be good if the report contained links to the actual page in which >>> the link resides. >>> >>> Tip 1: try (somehow) to use the helper method 'url_for_web_interface' >>> which is in the application controller. >> >>> Tip 2: make the links in the report always open up in a new window, by >>> adding: >>> >>> target="_blank" >>> >>> ... to the tag for the link. >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>>> Hi Franck, >>>> >>>> Please have a look at this >>>> http://test.biocatalogue.org/links_checker_20101012-1308.html >>>> >>>> Note that this is for alert purposes only. And we should actually make >>>> sure that we are trying to access the right link. >>>> A rough attempt has been made to parse the links programmatically but >>>> that is not full proof! >>>> >>>> Have fun! >>>> >>>> Eric >>>> >>>> >>>> On 12/10/2010 12:43, Eric Nzuobontane wrote: >>>>> Hi Frank, >>>>> >>>>> On 12/10/2010 12:27, Franck Tanoh wrote: >>>>>> Hi Eric, >>>>>> >>>>>> That's really useful. Thanks >>>>>> Maybe you can add more items in the 'sort by' . e.g possibility to >>>>>> find disable endpoint/test script/ wsdl testing. >>>>> Well, I did not want to add disabled stuff here except this is meant >>>>> to be seen my only admins. That I was not exactly sure about because >>>>> I would imagine Rodrigo& Hamish wanting to see that list. For now, >>>>> only active tests are included in the index >>>>>> Do you count 'warning' status as failure when you're deriving the >>>>>> overall success rate? I would also like to sort by warning status >>>>>> too. >>>>> yes, warning are considered as failure when calculating success rate >>>>>> How are you getting on the the dead links? We had a discussion today >>>>>> in our meeting about that. We thought that it's probably not a good >>>>>> idea to delete them but that depends on how many there are in the >>>>>> catalogue. For example a link might be down for a while because a >>>>>> server is down or under maintenance...need a policy in that....let >>>>>> see >>>>>> how many we got first. >>>>> I already wrote a first pass of the script which is also available on >>>>> the test site. I will run it on the test data now and send you the >>>>> link. >>>>> >>>>> Eric >>>>> >>>>>> Cheers >>>>>> Franck >>>>>> >>>>>> >>>>>> On 12 October 2010 09:53, Eric Nzuobontane >>>>>> wrote: >>>>>>> Hi Guys, >>>>>>> >>>>>>> I have updated the test site with the latest codebase. One thing I >>>>>>> have >>>>>>> added is the listing of service tests >>>>>>> http://test.biocatalogue.org/service_tests/ >>>>>>> >>>>>>> I find it much easier to go from the test to the service when >>>>>>> checking for >>>>>>> failing services. Let me know what you think. >>>>>>> >>>>>>> Eric >>>>>>> >>>>>>> -- >>>>>>> Eric Nzuobontane >>>>>>> ================================== >>>>>>> European Bioinformatics Institute >>>>>>> Wellcome Trust Genome Campus >>>>>>> Hinxton, Cambridge >>>>>>> CB10 1SD >>>>>>> United Kingdom >>>>>>> >>>>>>> Tel : +44 1223 492654 >>>>>>> email : ericnzuo at ebi.ac.uk >>>>>>> ================================== >>>>>>> >>>>>>> _______________________________________________ >>>>>>> BioCatalogue-developers mailing list >>>>>>> BioCatalogue-developers at rubyforge.org >>>>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>>>> >> -- Eric Nzuobontane ================================== European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Tel : +44 1223 492654 email : ericnzuo at ebi.ac.uk ================================== From issues at mygrid.org.uk Thu Oct 14 12:16:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 14 Oct 2010 17:16:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-504) Do not check links on archived services! Message-ID: <26229424.9994.1287072975305.JavaMail.jira@rosalind.cs.man.ac.uk> Do not check links on archived services! ---------------------------------------- Key: BIOCAT-504 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-504 Project: BioCatalogue Issue Type: Sub-task Components: Data Reporter: Eric Nzuobontane Assignee: Jiten Bhagat There is no need to check links on archived services as no action is supposed to be taken given the services are already archived! -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 14 12:16:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 14 Oct 2010 17:16:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-504) Do not check links on archived services! Message-ID: <26229424.9994.1287072975305.JavaMail.jira@rosalind.cs.man.ac.uk> Do not check links on archived services! ---------------------------------------- Key: BIOCAT-504 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-504 Project: BioCatalogue Issue Type: Sub-task Components: Data Reporter: Eric Nzuobontane Assignee: Jiten Bhagat There is no need to check links on archived services as no action is supposed to be taken given the services are already archived! -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 14 12:24:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 14 Oct 2010 17:24:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Assigned: (BIOCAT-504) Do not check links on archived services! In-Reply-To: <26229424.9994.1287072975305.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <11901895.9995.1287073455329.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-504?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reassigned BIOCAT-504: --------------------------------------- Assignee: Eric Nzuobontane (was: Jiten Bhagat) > Do not check links on archived services! > ---------------------------------------- > > Key: BIOCAT-504 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-504 > Project: BioCatalogue > Issue Type: Sub-task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > There is no need to check links on archived services as no action is supposed to be taken given the services are already archived! -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 14 12:27:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 14 Oct 2010 17:27:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-505) Add links checker report link to the curation dashboard Message-ID: <8685878.9996.1287073635327.JavaMail.jira@rosalind.cs.man.ac.uk> Add links checker report link to the curation dashboard ------------------------------------------------------- Key: BIOCAT-505 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-505 Project: BioCatalogue Issue Type: Sub-task Components: Curation Dashboard Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Thu Oct 14 18:55:45 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 14 Oct 2010 23:55:45 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathwayinference' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'pathwayinference' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2812 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Thu Oct 14 18:59:25 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 14 Oct 2010 23:59:25 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathfinding' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathfinding' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2810 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Oct 18 05:59:56 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 18 Oct 2010 10:59:56 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runTTSFinder' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runTTSFinder' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1104 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Mon Oct 18 06:24:22 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 18 Oct 2010 11:24:22 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getPubMed' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getPubMed' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1090 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 Oct 18 07:44:27 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 18 Oct 2010 07:44:27 -0400 (EDT) Subject: [BioCatalogue-developers] [2277] trunk/app/models: REST API work: fix for differentiating between ' self' and 'resource' in the JSON outputs of ServiceTest resources. Message-ID: <20101018114427.3EB7B1978401@rubyforge.org> An HTML attachment was scrubbed... URL: From utopia at cs.man.ac.uk Wed Oct 20 14:38:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Wed, 20 Oct 2010 19:38:09 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'pathwayinference' changed to Passed Message-ID: This is an automatic notification to let you know that your service 'pathwayinference' has changed status from 'Failed' to 'Passed'. Follow the link to investigate: http://embraceregistry.net/node/2812 If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From ericnzuo at ebi.ac.uk Thu Oct 21 08:44:02 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 21 Oct 2010 13:44:02 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Fwd: [BioCatalogue-hackers] Monitoring] Message-ID: <4CC03592.2080903@ebi.ac.uk> -------- Original Message -------- Subject: Re: [Fwd: [BioCatalogue-hackers] Monitoring] Date: Tue, 19 Oct 2010 17:49:45 +0200 From: Carsten Schnober Organization: ELDA To: ericnzuo at ebi.ac.uk On 19/10/2010 13:17, ericnzuo at ebi.ac.uk wrote: Hi Eric, thanks for your help! > Monitoring in BioCatalogue is done at two levels. What the call the > availability monitoring which is done with the application and functional > monitoring which is done via external scripts. The availability monitoring is all I need for now and it is now working fine, thanks to your instructions. It has been fairly easy though, if you know what to do... Regards, Carsten -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Oct 21 08:48:43 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 21 Oct 2010 13:48:43 +0100 Subject: [BioCatalogue-developers] preparation for the SAB In-Reply-To: <4CBEFB49.5000408@cs.man.ac.uk> References: <4CBC6E9B.2040800@manchester.ac.uk> <54157.145.64.35.45.1287483245.squirrel@webmail.ebi.ac.uk> <4CBEFB49.5000408@cs.man.ac.uk> Message-ID: <4CC036AB.7030400@ebi.ac.uk> Hi Jits, I am aware of the Emory instance(s) of BioCatalogue and the http://www.elda.org/ one managed by Carsten. Are there any other instances around that you are aware of? Eric On 20/10/2010 15:23, Jiten Bhagat wrote: > Franck, > > Our alliance with Emory actually goes much deeper - they have further > developed the software and deployed TWO instances for their projects. > Eg, check out: http://news.tradingcharts.com/futures/3/2/146984423.html > (it's a shame though that that article doesn't mention the BioCatalogue). > > Jits > > > Franck Tanoh wrote: >> Some slides about our activities attached. >> Feel free to add anything missing. >> >> Franck >> >> On 19 October 2010 12:52, Franck Tanoh> > wrote: >> >> All, >> Actions from last SAB meeting summarised in the slides attached. >> >> Franck >> >> >> On 19 October 2010 11:14,> > wrote: >> >> > All >> > >> > For the SAB we need to prepare the following, with slides - >> can people >> > begin to gather data. >> > the slides I produced for BioITworld are here: >> > >> http://dl.dropbox.com/u/617206/BioIT10-BioCatalogue-final-clean.ppt >> > >> > we need at least 1 person from the EBI to attend. >> >> >> I will be attending the SAB meeting. >> For the tasks that needs to be done, it is necessary to assign >> people to >> be responsible for them. Of course they can ask for >> information from >> people if it so requires >> >> > >> > 1. review of actions of last SAB >> > >> > we need to go through each of these in turn - they are on >> the wiki >> > http://www.biocatalogue.org/wiki/doku.php?id=meetings >> >> This might be something which Franck might start doing. >> > >> > 2. update of biocatalogue activity >> > >> > for this we need >> > >> > - content: facts and figures and analytics. The analytics >> from Google >> > and those from the EBI don't seem to match up >> OK, I am not exactly sure what does not match up. But the >> level of detail >> provided from the two sources is different. But I will be >> looking at the >> stats and generating some graph on trends. >> > - detailed analytics for curation -- how many providers have >> been in >> > touch? how many refresh their entries? >> >> It may be more relevant to see which providers have been >> annotating their >> entries and whether there are any patterns that emerge from that. >> >> > - technical features updates, releases and roadmap against >> resources >> > - dissemination and promotion - papers, presentations, meetings >> > - collaborations - e.g. EdUnify, NCRI >> > - places we think need more work to be concentrated on: >> > content community building >> > software community building >> > provider community building >> > >> > 3. outlook and sustainability >> > >> > - follow on funds ? >> > - possible takeups ? >> > - post January running of catalogue >> > - registry rot prevention. hosting at EBI vs curation at EBI and >> > platform refresh procedure? a VM? how to prepare for the end? >> > responsibility without authority. >> > >> > >> > 4. project management meeting face to face >> > >> > - tackle the project end >> > - meeting immediately post SAB at 16.00 for 1 hour to make major >> > end-project decisions. >> >> I will be available for this as well >> >> > >> > >> > >> > 4. AOB >> > >> >> Eric >> >> >> >> >> -- >> "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 ================================== From ericnzuo at ebi.ac.uk Thu Oct 21 10:53:52 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 21 Oct 2010 15:53:52 +0100 Subject: [BioCatalogue-developers] Hashie gem Message-ID: <4CC05400.6030800@ebi.ac.uk> Hi Jits, Is there a reason why the hashie gem is not in vendor/gems? At the moment, this breaks the service_annotation_report script! 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 utopia at cs.man.ac.uk Fri Oct 22 14:46:33 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 22 Oct 2010 19:46:33 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getTrajectoryRadiusOfGyrationFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getTrajectoryRadiusOfGyrationFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1127 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 Oct 23 06:45:09 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 23 Oct 2010 11:45:09 +0100 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 jits at cs.man.ac.uk Sat Oct 23 08:59:38 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sat, 23 Oct 2010 13:59:38 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Fwd: [BioCatalogue-hackers] Monitoring] In-Reply-To: <4CC03592.2080903@ebi.ac.uk> References: <4CC03592.2080903@ebi.ac.uk> Message-ID: <4CC2DC3A.9040104@cs.man.ac.uk> Eric, It would have been very useful if the instructions you had sent to Carsten were sent to the biocatalogue-hackers list too. That way if someone asks the same kind of question the could find the answer beforehand or we could point them to the email in the archive (or even used that to put together a wiki page). Jits Eric Nzuobontane wrote: > > > -------- Original Message -------- > Subject: Re: [Fwd: [BioCatalogue-hackers] Monitoring] > Date: Tue, 19 Oct 2010 17:49:45 +0200 > From: Carsten Schnober > Organization: ELDA > To: ericnzuo at ebi.ac.uk > > > > On 19/10/2010 13:17, ericnzuo at ebi.ac.uk wrote: > > Hi Eric, > thanks for your help! > > > Monitoring in BioCatalogue is done at two levels. What the call the > > availability monitoring which is done with the application and functional > > monitoring which is done via external scripts. > > The availability monitoring is all I need for now and it is now working > fine, thanks to your instructions. It has been fairly easy though, if > you know what to do... > Regards, > Carsten > > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From jits at cs.man.ac.uk Sat Oct 23 09:01:29 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Sat, 23 Oct 2010 14:01:29 +0100 Subject: [BioCatalogue-developers] Hashie gem In-Reply-To: <4CC05400.6030800@ebi.ac.uk> References: <4CC05400.6030800@ebi.ac.uk> Message-ID: <4CC2DCA9.3070602@cs.man.ac.uk> Reasons for this at the moment: - It's only required for the service_annotation_script. - It extends the core Ruby Hash class so I didn't want this to be used in production until we had fully verified that it doesn't affect anything else. ... so I kept it as something that should be installed in the dev environment only, for now. Jits Eric Nzuobontane wrote: > Hi Jits, > > Is there a reason why the hashie gem is not in vendor/gems? At the > moment, this breaks the service_annotation_report script! > > Eric > From utopia at cs.man.ac.uk Sat Oct 23 21:02:21 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 24 Oct 2010 02:02:21 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromPDB_CollectionToMD_TrajectoryNetCDF' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromPDB_CollectionToMD_TrajectoryNetCDF' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1130 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 Oct 24 19:39:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Mon, 25 Oct 2010 00:39:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'metabolicgraphconstruction' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'metabolicgraphconstruction' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/2814 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 Oct 25 05:14:54 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 25 Oct 2010 10:14:54 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Fwd: [BioCatalogue-hackers] Monitoring] In-Reply-To: <4CC2DC3A.9040104@cs.man.ac.uk> References: <4CC03592.2080903@ebi.ac.uk> <4CC2DC3A.9040104@cs.man.ac.uk> Message-ID: <4CC54A8E.5070202@ebi.ac.uk> On 23/10/2010 13:59, Jiten Bhagat wrote: > Eric, > > It would have been very useful if the instructions you had sent to > Carsten were sent to the biocatalogue-hackers list too. That way if > someone asks the same kind of question the could find the answer > beforehand or we could point them to the email in the archive (or even > used that to put together a wiki page). I believe I did send the response to the hackers list. Unfortunately, it seems my post did not get through to the list. Again, I do not understand why I do not get the mails from the BioCatalogue hackers list! I will try and re-send the response to the list if I can find it in my sent folder... Eric > Jits > > > Eric Nzuobontane wrote: >> >> -------- Original Message -------- >> Subject: Re: [Fwd: [BioCatalogue-hackers] Monitoring] >> Date: Tue, 19 Oct 2010 17:49:45 +0200 >> From: Carsten Schnober >> Organization: ELDA >> To: ericnzuo at ebi.ac.uk >> >> >> >> On 19/10/2010 13:17, ericnzuo at ebi.ac.uk wrote: >> >> Hi Eric, >> thanks for your help! >> >>> Monitoring in BioCatalogue is done at two levels. What the call the >>> availability monitoring which is done with the application and functional >>> monitoring which is done via external scripts. >> The availability monitoring is all I need for now and it is now working >> fine, thanks to your instructions. It has been fairly easy though, if >> you know what to do... >> Regards, >> Carsten >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 Oct 25 05:23:49 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 25 Oct 2010 10:23:49 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Fwd: [BioCatalogue-hackers] Monitoring] In-Reply-To: <4CC54A8E.5070202@ebi.ac.uk> References: <4CC03592.2080903@ebi.ac.uk> <4CC2DC3A.9040104@cs.man.ac.uk> <4CC54A8E.5070202@ebi.ac.uk> Message-ID: <4CC54CA5.8020300@cs.man.ac.uk> It's because you weren't subscribed. I've subscribed you now. You'll get an email with a link to a page where you will need to confirm. Jits Eric Nzuobontane wrote: > > > On 23/10/2010 13:59, Jiten Bhagat wrote: >> Eric, >> >> It would have been very useful if the instructions you had sent to >> Carsten were sent to the biocatalogue-hackers list too. That way if >> someone asks the same kind of question the could find the answer >> beforehand or we could point them to the email in the archive (or even >> used that to put together a wiki page). > I believe I did send the response to the hackers list. Unfortunately, > it seems my post did not get through to the list. Again, I do not > understand why I do not get the mails from the BioCatalogue hackers > list! I will try and re-send the response to the list if I can find it > in my sent folder... > > Eric > > >> Jits >> >> >> Eric Nzuobontane wrote: >>> >>> -------- Original Message -------- >>> Subject: Re: [Fwd: [BioCatalogue-hackers] Monitoring] >>> Date: Tue, 19 Oct 2010 17:49:45 +0200 >>> From: Carsten Schnober >>> Organization: ELDA >>> To: ericnzuo at ebi.ac.uk >>> >>> >>> >>> On 19/10/2010 13:17, ericnzuo at ebi.ac.uk wrote: >>> >>> Hi Eric, >>> thanks for your help! >>> >>>> Monitoring in BioCatalogue is done at two levels. What the call the >>>> availability monitoring which is done with the application and >>>> functional >>>> monitoring which is done via external scripts. >>> The availability monitoring is all I need for now and it is now working >>> fine, thanks to your instructions. It has been fairly easy though, if >>> you know what to do... >>> Regards, >>> Carsten >>> >>> ------------------------------------------------------------------------ >>> >>> >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > > From ericnzuo at ebi.ac.uk Mon Oct 25 05:24:11 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 25 Oct 2010 10:24:11 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Fwd: [BioCatalogue-hackers] Monitoring] In-Reply-To: <4CC54CA5.8020300@cs.man.ac.uk> References: <4CC03592.2080903@ebi.ac.uk> <4CC2DC3A.9040104@cs.man.ac.uk> <4CC54A8E.5070202@ebi.ac.uk> <4CC54CA5.8020300@cs.man.ac.uk> Message-ID: <4CC54CBB.3000204@ebi.ac.uk> OK, thanks! Eric On 25/10/2010 10:23, Jiten Bhagat wrote: > It's because you weren't subscribed. I've subscribed you now. You'll get > an email with a link to a page where you will need to confirm. > > Jits > > > Eric Nzuobontane wrote: >> >> On 23/10/2010 13:59, Jiten Bhagat wrote: >>> Eric, >>> >>> It would have been very useful if the instructions you had sent to >>> Carsten were sent to the biocatalogue-hackers list too. That way if >>> someone asks the same kind of question the could find the answer >>> beforehand or we could point them to the email in the archive (or even >>> used that to put together a wiki page). >> I believe I did send the response to the hackers list. Unfortunately, >> it seems my post did not get through to the list. Again, I do not >> understand why I do not get the mails from the BioCatalogue hackers >> list! I will try and re-send the response to the list if I can find it >> in my sent folder... > > >> Eric >> >> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>>> -------- Original Message -------- >>>> Subject: Re: [Fwd: [BioCatalogue-hackers] Monitoring] >>>> Date: Tue, 19 Oct 2010 17:49:45 +0200 >>>> From: Carsten Schnober >>>> Organization: ELDA >>>> To: ericnzuo at ebi.ac.uk >>>> >>>> >>>> >>>> On 19/10/2010 13:17, ericnzuo at ebi.ac.uk wrote: >>>> >>>> Hi Eric, >>>> thanks for your help! >>>> >>>>> Monitoring in BioCatalogue is done at two levels. What the call the >>>>> availability monitoring which is done with the application and >>>>> functional >>>>> monitoring which is done via external scripts. >>>> The availability monitoring is all I need for now and it is now working >>>> fine, thanks to your instructions. It has been fairly easy though, if >>>> you know what to do... >>>> Regards, >>>> Carsten >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> >>>> _______________________________________________ >>>> 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 Oct 25 05:28:24 2010 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 25 Oct 2010 10:28:24 +0100 Subject: [BioCatalogue-developers] Fwd: Re: [Fwd: [BioCatalogue-hackers] Monitoring] In-Reply-To: <4CC54CBB.3000204@ebi.ac.uk> References: <4CC03592.2080903@ebi.ac.uk> <4CC2DC3A.9040104@cs.man.ac.uk> <4CC54A8E.5070202@ebi.ac.uk> <4CC54CA5.8020300@cs.man.ac.uk> <4CC54CBB.3000204@ebi.ac.uk> Message-ID: <4CC54DB8.1020104@cs.man.ac.uk> No problem. Note, there has been a fair bit of activity on there lately. You may want to follow up on the archives - http://rubyforge.org/pipermail/biocatalogue-hackers/ Jits Eric Nzuobontane wrote: > OK, thanks! > > Eric > > > On 25/10/2010 10:23, Jiten Bhagat wrote: >> It's because you weren't subscribed. I've subscribed you now. You'll get >> an email with a link to a page where you will need to confirm. >> >> Jits >> >> >> Eric Nzuobontane wrote: >>> >>> On 23/10/2010 13:59, Jiten Bhagat wrote: >>>> Eric, >>>> >>>> It would have been very useful if the instructions you had sent to >>>> Carsten were sent to the biocatalogue-hackers list too. That way if >>>> someone asks the same kind of question the could find the answer >>>> beforehand or we could point them to the email in the archive (or even >>>> used that to put together a wiki page). >>> I believe I did send the response to the hackers list. Unfortunately, >>> it seems my post did not get through to the list. Again, I do not >>> understand why I do not get the mails from the BioCatalogue hackers >>> list! I will try and re-send the response to the list if I can find it >>> in my sent folder... >> >> >>> Eric >>> >>> >>>> Jits >>>> >>>> >>>> Eric Nzuobontane wrote: >>>>> -------- Original Message -------- >>>>> Subject: Re: [Fwd: [BioCatalogue-hackers] Monitoring] >>>>> Date: Tue, 19 Oct 2010 17:49:45 +0200 >>>>> From: Carsten Schnober >>>>> Organization: ELDA >>>>> To: ericnzuo at ebi.ac.uk >>>>> >>>>> >>>>> >>>>> On 19/10/2010 13:17, ericnzuo at ebi.ac.uk wrote: >>>>> >>>>> Hi Eric, >>>>> thanks for your help! >>>>> >>>>>> Monitoring in BioCatalogue is done at two levels. What the call the >>>>>> availability monitoring which is done with the application and >>>>>> functional >>>>>> monitoring which is done via external scripts. >>>>> The availability monitoring is all I need for now and it is now >>>>> working >>>>> fine, thanks to your instructions. It has been fairly easy though, if >>>>> you know what to do... >>>>> Regards, >>>>> Carsten >>>>> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> BioCatalogue-developers mailing list >>>>> BioCatalogue-developers at rubyforge.org >>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>>> >>> > > From noreply at rubyforge.org Mon Oct 25 09:26:57 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 25 Oct 2010 09:26:57 -0400 (EDT) Subject: [BioCatalogue-developers] [2278] trunk/app: use similar pattern as with services to sort service tests by availability and creation date Message-ID: <20101025132657.CF9971678317@rubyforge.org> An HTML attachment was scrubbed... URL: From issues at mygrid.org.uk Mon Oct 25 09:34:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Mon, 25 Oct 2010 14:34:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Reopened: (BIOCAT-498) Create a listing(index) page for all service tests In-Reply-To: <7834499.9954.1286441415341.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <23735653.10313.1288013655346.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane reopened BIOCAT-498: ------------------------------------- Use the same pattern for sorting services in the service test index to sort by creation & availability > Create a listing(index) page for all service tests > -------------------------------------------------- > > Key: BIOCAT-498 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-498 > Project: BioCatalogue > Issue Type: Task > Components: Web Interface > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > The listing of service test will enable an easy navigation for monitoring purposes. At the moment, it is hard going through the service to get to the service test especially when one has to look at a number of tests -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Tue Oct 26 09:19:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Tue, 26 Oct 2010 14:19:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-505) Add links checker report link to the curation dashboard In-Reply-To: <8685878.9996.1287073635327.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <9935545.10327.1288099155330.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-505?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-505 started by Eric Nzuobontane. > Add links checker report link to the curation dashboard > ------------------------------------------------------- > > Key: BIOCAT-505 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-505 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 28 04:55:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 28 Oct 2010 09:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-506) Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) Message-ID: <12444050.10333.1288256115454.JavaMail.jira@rosalind.cs.man.ac.uk> Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) ---------------------------------------------------------------------------------------- Key: BIOCAT-506 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506 Project: BioCatalogue Issue Type: Task Components: Wiki Environment: wiki Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Complete the BioCatalogue installation process by adding the monitoring setup instructions. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 28 07:23:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 28 Oct 2010 12:23:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-507) Soap service show(hmtl format) should redirect to the parent service Message-ID: <28972168.10334.1288264995363.JavaMail.jira@rosalind.cs.man.ac.uk> Soap service show(hmtl format) should redirect to the parent service -------------------------------------------------------------------- Key: BIOCAT-507 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-507 Project: BioCatalogue Issue Type: Refinement Components: Web Interface Environment: RoR, UI Reporter: Eric Nzuobontane Assignee: Eric Nzuobontane Rather than return an error page, soap service show should redirect to the parent service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Thu Oct 28 07:30:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Thu, 28 Oct 2010 12:30:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-507) Soap service show(hmtl format) should redirect to the parent service In-Reply-To: <28972168.10334.1288264995363.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <10814897.10335.1288265415362.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-507?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16041#action_16041 ] Eric Nzuobontane commented on BIOCAT-507: ----------------------------------------- Comments from Jits & Eric: yeah i think thats a good point [28/10/2010 11:21:57] Jiten Bhagat: and is relevant to the new soap_services and rest_services indexes in the API [28/10/2010 11:22:12] Jiten Bhagat: one thing we have to be very careful about is what kind of redirect we do [28/10/2010 11:22:22] Jiten Bhagat: i think 303 means that the resource has permanently moved [28/10/2010 11:22:30] Jiten Bhagat: which is what we dont want [28/10/2010 11:23:01] Jiten Bhagat: in any case, have a look at the way we've done the url_for_web_interface helper method(s), there might already be some code in there that can be used [28/10/2010 11:24:02] Eric Nzuobontane: ok. But I was thinking that redirect would only be for the html format [28/10/2010 11:24:42] Jiten Bhagat: oh yeah, definitely [28/10/2010 11:24:52] Jiten Bhagat: this only applies for the html interface, not the API [28/10/2010 11:25:10] Jiten Bhagat: but it's still an HTTP redirect and we have to make sure we use the correct HTTP status code when redirecting [28/10/2010 11:25:19] Eric Nzuobontane: right [28/10/2010 11:25:41] Jiten Bhagat: note that this goes against the linked data and REST idealogies... [28/10/2010 11:26:16] Eric Nzuobontane: I see [28/10/2010 11:26:35] Jiten Bhagat: because if you have a resource: http://.../soap_services/3 ... that should have respresentations like: http://.../soap_services/3.html http://.../soap_services/3.xml http://.../soap_services/3.json http://.../soap_services/3.atom etc [28/10/2010 11:26:44] Jiten Bhagat: and if one of those doesnt exist then you should show a 404 [28/10/2010 11:27:05] Jiten Bhagat: but then again REST and linked data arent practical for web interfaces for human users! [28/10/2010 11:27:28] Jiten Bhagat: so i'm happy with what you're proposing :) [28/10/2010 11:27:43] Jiten Bhagat: and we need to look into what http status code to use when doing the redirect [28/10/2010 11:28:00] Jiten Bhagat: have a look here: http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html [28/10/2010 11:28:10] Jiten Bhagat: it will be one of the 3xx ones [28/10/2010 11:28:24] Jiten Bhagat: ah, 301 is "moved permanently" [28/10/2010 11:28:33] Jiten Bhagat: 303 "see other" would make sense actually [28/10/2010 11:28:35] Jiten Bhagat: for the HTML calls [28/10/2010 11:29:13] Jiten Bhagat: OR 307 "temporary redirect" [28/10/2010 11:29:35] Jiten Bhagat: but not sure how browsers would treat that [28/10/2010 11:31:10] Eric Nzuobontane: note also says pre-http user agents would not understand 303 [28/10/2010 11:31:22] Eric Nzuobontane: Not sure how many of them are still around! [28/10/2010 11:31:54] Eric Nzuobontane: pre-http:/1.1 [28/10/2010 11:32:20] Jiten Bhagat: i would think none that are relevant! [28/10/2010 11:32:31] Eric Nzuobontane: I actually think 303 is more appropriate then 307 [28/10/2010 11:33:53] Eric Nzuobontane: bec the resource itself does not reside under a different uri [28/10/2010 11:37:05] Jiten Bhagat: yeap [28/10/2010 11:37:14] Jiten Bhagat: and 303 is heavily used in Linked Data [28/10/2010 11:38:02] Jiten Bhagat: have a read of this section... http://www.biocatalogue.org/wiki/doku.php?id=public:api#uris_linked_data_and_content_negotiation > Soap service show(hmtl format) should redirect to the parent service > -------------------------------------------------------------------- > > Key: BIOCAT-507 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-507 > Project: BioCatalogue > Issue Type: Refinement > Components: Web Interface > Environment: RoR, UI > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > Rather than return an error page, soap service show should redirect to the parent service. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From noreply at rubyforge.org Thu Oct 28 09:09:59 2010 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 28 Oct 2010 09:09:59 -0400 (EDT) Subject: [BioCatalogue-developers] [2279] trunk: - added link from the curation dashboard to the link checker report Message-ID: <20101028131000.1D0931678316@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Oct 28 09:49:59 2010 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 28 Oct 2010 14:49:59 +0100 Subject: [BioCatalogue-developers] Links checker report button on curation dashboard Message-ID: <4CC97F87.3070103@ebi.ac.uk> Hi Frank, I have added a button linking to the url checker report on the curation dash board. See test site http://test.biocatalogue.org/curation -- 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 Oct 28 10:17:23 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Thu, 28 Oct 2010 15:17:23 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:optimizeStructureFromNAMD_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:optimizeStructureFromNAMD_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1176 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 Oct 28 23:40:14 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 04:40:14 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryBINPOS' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:fromMD_TrajectoryToMD_TrajectoryBINPOS' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1129 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Fri Oct 29 06:55:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 29 Oct 2010 11:55:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Work started: (BIOCAT-506) Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) In-Reply-To: <12444050.10333.1288256115454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <33169025.10438.1288349715341.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Work on BIOCAT-506 started by Eric Nzuobontane. > Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-506 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Environment: wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Complete the BioCatalogue installation process by adding the monitoring setup instructions. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Oct 29 06:59:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 29 Oct 2010 11:59:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-506) Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) In-Reply-To: <12444050.10333.1288256115454.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <3770437.10439.1288349955335.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16065#action_16065 ] Eric Nzuobontane commented on BIOCAT-506: ----------------------------------------- Added this section http://www.biocatalogue.org/wiki/doku.php?id=development:installation#running_the_biocatalogue_monitoring on the installation page > Add documentation on how to setup the monitoring on the wiki (BioCatalogue installation) > ---------------------------------------------------------------------------------------- > > Key: BIOCAT-506 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-506 > Project: BioCatalogue > Issue Type: Task > Components: Wiki > Environment: wiki > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > Original Estimate: 1 day > Remaining Estimate: 1 day > > Complete the BioCatalogue installation process by adding the monitoring setup instructions. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Oct 29 07:18:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 29 Oct 2010 12:18:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-505) Add links checker report link to the curation dashboard In-Reply-To: <8685878.9996.1287073635327.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <21312649.10440.1288351095351.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-505?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-505. ------------------------------------- Resolution: Implemented Now available on the test site > Add links checker report link to the curation dashboard > ------------------------------------------------------- > > Key: BIOCAT-505 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-505 > Project: BioCatalogue > Issue Type: Sub-task > Components: Curation Dashboard > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Oct 29 09:06:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 29 Oct 2010 14:06:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-200) Need to import the Soaplab services metadata from Feta Message-ID: <17840624.10441.1288357575360.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16067#action_16067 ] Eric Nzuobontane commented on BIOCAT-200: ----------------------------------------- Is this task still relevant? > Need to import the Soaplab services metadata from Feta > ------------------------------------------------------ > > Key: BIOCAT-200 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > ... as these could not be imported in the first instance. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Oct 29 09:29:15 2010 From: issues at mygrid.org.uk (Eric Nzuobontane (JIRA)) Date: Fri, 29 Oct 2010 14:29:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Resolved: (BIOCAT-504) Do not check links on archived services! In-Reply-To: <26229424.9994.1287072975305.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <4577887.10444.1288358955320.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-504?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Eric Nzuobontane resolved BIOCAT-504. ------------------------------------- Resolution: Implemented > Do not check links on archived services! > ---------------------------------------- > > Key: BIOCAT-504 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-504 > Project: BioCatalogue > Issue Type: Sub-task > Components: Data > Reporter: Eric Nzuobontane > Assignee: Eric Nzuobontane > > There is no need to check links on archived services as no action is supposed to be taken given the services are already archived! -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Fri Oct 29 10:13:15 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Fri, 29 Oct 2010 15:13:15 +0100 (BST) Subject: [BioCatalogue-developers] [JIRA] Commented: (BIOCAT-200) Need to import the Soaplab services metadata from Feta Message-ID: <212078.10445.1288361595758.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16068#action_16068 ] Jiten Bhagat commented on BIOCAT-200: ------------------------------------- Yes, I think it is still relevant; the FETA registry contained a lot of annotations to do with Soaplab services which hasn't been imported into the BioCatalogue yet. > Need to import the Soaplab services metadata from Feta > ------------------------------------------------------ > > Key: BIOCAT-200 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-200 > Project: BioCatalogue > Issue Type: Task > Components: Content Acquisition, Misc Codebase > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Critical > > ... as these could not be imported in the first instance. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From utopia at cs.man.ac.uk Fri Oct 29 11:58:11 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 16:58:11 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:getSymbolInteractions' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:getSymbolInteractions' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1088 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Oct 29 12:01:47 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:01:47 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:cnio.es:runFirestar' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:cnio.es:runFirestar' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1099 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 Oct 29 12:16:37 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:16:37 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runLeapFromAMBER_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runLeapFromAMBER_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1182 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From utopia at cs.man.ac.uk Fri Oct 29 12:20:55 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:20:55 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:solvateStructureFromAMBER_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:solvateStructureFromAMBER_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1178 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 Oct 29 12:21:44 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:21:44 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:runMDFromNAMD_MD_Structure' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:runMDFromNAMD_MD_Structure' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1138 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 Oct 29 12:33:16 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:33:16 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getSliceFromMD_Trajectory' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getSliceFromMD_Trajectory' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1147 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 Oct 29 12:35:15 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:35:15 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getSecondaryStructureFromPDBText' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getSecondaryStructureFromPDBText' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1169 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 Oct 29 12:38:49 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:38:49 +0100 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 Fri Oct 29 12:39:48 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:39:48 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getHingePointsWithSCMethodFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getHingePointsWithSCMethodFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1160 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 Oct 29 12:40:26 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Fri, 29 Oct 2010 17:40:26 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'INB-dev:mmb.pcb.ub.es:getHingePointsWithDDMethodFromPCZ_Report' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'INB-dev:mmb.pcb.ub.es:getHingePointsWithDDMethodFromPCZ_Report' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/1158 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 Oct 30 04:12:38 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sat, 30 Oct 2010 09:12:38 +0100 Subject: [BioCatalogue-developers] EMBRACE Registry: 'GeneWiz' changed to Warning Message-ID: This is an automatic notification to let you know that your service 'GeneWiz' has changed status from 'Passed' to 'Warning'. Follow the link to investigate: http://embraceregistry.net/node/1840 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 Oct 31 14:29:17 2010 From: utopia at cs.man.ac.uk (utopia at cs.man.ac.uk) Date: Sun, 31 Oct 2010 18:29:17 +0000 Subject: [BioCatalogue-developers] EMBRACE Registry: 'BLAST (DDBJ)' changed to Failed Message-ID: This is an automatic notification to let you know that your service 'BLAST (DDBJ)' has changed status from 'Passed' to 'Failed'. Follow the link to investigate: http://embraceregistry.net/node/169 As this service has entered an erroneous state, it might be worthwhile leaving a comment on the above page to let people know how long it might take to resolve. If you have any questions, please reply to this email. Yours, The EMBRACE Registry Team From issues at mygrid.org.uk Sun Oct 31 17:20:09 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Sun, 31 Oct 2010 21:20:09 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Updated: (BIOCAT-508) Look to changing the style of field names in ALL JSON outputs in the REST API In-Reply-To: <18306186.10446.1288560005033.JavaMail.jira@rosalind.cs.man.ac.uk> Message-ID: <5226214.10447.1288560009648.JavaMail.jira@rosalind.cs.man.ac.uk> [ http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Jiten Bhagat updated BIOCAT-508: -------------------------------- Original Estimate: 6 hours (was: 6 minutes) Remaining Estimate: 6 hours (was: 6 minutes) > Look to changing the style of field names in ALL JSON outputs in the REST API > ----------------------------------------------------------------------------- > > Key: BIOCAT-508 > URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508 > Project: BioCatalogue > Issue Type: Task > Components: REST API > Reporter: Jiten Bhagat > Assignee: Jiten Bhagat > Priority: Blocker > Original Estimate: 6 hours > Remaining Estimate: 6 hours > > Currently field names in the JSON outputs use Ruby naming conventions (eg: "service_type"), but the XML outputs of the API uses camel casing (eg: "serviceType"). Need to standardise on one if possible. So the proposal is to change all the JSON outputs to use camel case. > Need to take into consideration how this affects Sergey's BioCatalogue plugin (which is being polished up by Alex now) AND Mannie's BioCatalogue Mass Curator app. It might be that it's not worth changing the current outputs because they will have too much of an impact. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira From issues at mygrid.org.uk Sun Oct 31 17:20:05 2010 From: issues at mygrid.org.uk (Jiten Bhagat (JIRA)) Date: Sun, 31 Oct 2010 21:20:05 +0000 (GMT) Subject: [BioCatalogue-developers] [JIRA] Created: (BIOCAT-508) Look to changing the style of field names in ALL JSON outputs in the REST API Message-ID: <18306186.10446.1288560005033.JavaMail.jira@rosalind.cs.man.ac.uk> Look to changing the style of field names in ALL JSON outputs in the REST API ----------------------------------------------------------------------------- Key: BIOCAT-508 URL: http://www.mygrid.org.uk/dev/issues/browse/BIOCAT-508 Project: BioCatalogue Issue Type: Task Components: REST API Reporter: Jiten Bhagat Assignee: Jiten Bhagat Priority: Blocker Currently field names in the JSON outputs use Ruby naming conventions (eg: "service_type"), but the XML outputs of the API uses camel casing (eg: "serviceType"). Need to standardise on one if possible. So the proposal is to change all the JSON outputs to use camel case. Need to take into consideration how this affects Sergey's BioCatalogue plugin (which is being polished up by Alex now) AND Mannie's BioCatalogue Mass Curator app. It might be that it's not worth changing the current outputs because they will have too much of an impact. -- This message is automatically generated by JIRA. - If you think it was sent incorrectly contact one of the administrators: http://www.mygrid.org.uk/dev/issues/secure/Administrators.jspa - For more information on JIRA, see: http://www.atlassian.com/software/jira