From groscurt at mpiz-koeln.mpg.de Mon Dec 3 03:45:31 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 3 Dec 2007 09:45:31 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200711301223.07171.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <47267E18.4010509@ucalgary.ca> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> Message-ID: <200712030945.32685.groscurt@mpiz-koeln.mpg.de> Hi, I'm using CentralDigestCachedImpl for caching the datatypes and namespaces locally. CentralDigestCachedImpl cachedImpl = new CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl","http://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); This works fine and re-calls use the local cache. But when I create a new MobyDataObject, it starts again to fetch the datatypes Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects So how do I tell it, that its already has these information ? the MobyDataObject can also have a Registry Object - so i guess that can help - but how to I link my CachedCentral with a Registry object ? Or is this otherwise solveable ? thx andreas From ssoiland at cs.man.ac.uk Mon Dec 3 07:04:57 2007 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Mon, 3 Dec 2007 12:04:57 +0000 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: Message-ID: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> On 11/30/07, Mark Wilkinson wrote: > To migrate Taverna, edit the taverna/conf/mygrid.properties file to point > to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl Should we change the default in Taverna's shipped mygrid.properties to the ucalgary one? We have a Taverna 1.7 release going out in a few weeks and would of course like BioMoby to work by default.. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From edward.kawas at gmail.com Mon Dec 3 09:25:48 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 3 Dec 2007 06:25:48 -0800 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> Message-ID: Hi Stian, I just replaced all instances where mobycentral was used to ucalgary. I also had to update the biomoby plugins maven repository to be the new one at ucalgary. Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland Sent: December-03-07 4:05 AM To: Core developer announcements Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! On 11/30/07, Mark Wilkinson wrote: > To migrate Taverna, edit the taverna/conf/mygrid.properties file to point > to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl Should we change the default in Taverna's shipped mygrid.properties to the ucalgary one? We have a Taverna 1.7 release going out in a few weeks and would of course like BioMoby to work by default.. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From arnaud at ebi.ac.uk Wed Dec 5 04:28:18 2007 From: arnaud at ebi.ac.uk (Arnaud Kerhornou) Date: Wed, 05 Dec 2007 09:28:18 +0000 Subject: [MOBY-dev] biomoby.org down ? Message-ID: <47566F32.8050804@ebi.ac.uk> Hi, When I try to go to biomoby.org on my browser, I get to a WordPress error page, saying, "error establishing a database connection", so is biomoby site down ? Arnaud From Pieter.Neerincx at wur.nl Wed Dec 5 05:55:18 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 5 Dec 2007 11:55:18 +0100 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: <47566F32.8050804@ebi.ac.uk> References: <47566F32.8050804@ebi.ac.uk> Message-ID: <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: > Hi, > > When I try to go to biomoby.org on my browser, I get to a WordPress > error page, saying, "error establishing a database connection", > so is biomoby site down ? Yep, same overhere :(... > > Arnaud > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Wed Dec 5 09:48:04 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 Dec 2007 06:48:04 -0800 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> References: <47566F32.8050804@ebi.ac.uk> <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> Message-ID: It's working from Canada. Are you still having problems there? M On Wed, 05 Dec 2007 02:55:18 -0800, Pieter Neerincx wrote: > > On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: > >> Hi, >> >> When I try to go to biomoby.org on my browser, I get to a WordPress >> error page, saying, "error establishing a database connection", >> so is biomoby site down ? > > Yep, same overhere :(... > >> >> Arnaud >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Wed Dec 5 09:57:08 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 05 Dec 2007 15:57:08 +0100 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: References: <47566F32.8050804@ebi.ac.uk> <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> Message-ID: <4756BC44.2030908@toulouse.inra.fr> Bonjour, It's working now. Sebastien Mark Wilkinson wrote: > It's working from Canada. Are you still having problems there? > > M > > > On Wed, 05 Dec 2007 02:55:18 -0800, Pieter Neerincx > wrote: > > >> On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: >> >> >>> Hi, >>> >>> When I try to go to biomoby.org on my browser, I get to a WordPress >>> error page, saying, "error establishing a database connection", >>> so is biomoby site down ? >>> >> Yep, same overhere :(... >> >> >>> Arnaud >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20071205/b30e27ff/attachment.vcf From Pieter.Neerincx at wur.nl Wed Dec 5 10:01:32 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 5 Dec 2007 16:01:32 +0100 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: References: <47566F32.8050804@ebi.ac.uk> <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> Message-ID: Yep, site is back overhere as well :) On 5-dec-2007, at 15:48, Mark Wilkinson wrote: > It's working from Canada. Are you still having problems there? > > M > > > On Wed, 05 Dec 2007 02:55:18 -0800, Pieter Neerincx > wrote: > >> >> On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: >> >>> Hi, >>> >>> When I try to go to biomoby.org on my browser, I get to a WordPress >>> error page, saying, "error establishing a database connection", >>> so is biomoby site down ? >> >> Yep, same overhere :(... >> >>> >>> Arnaud >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From groscurt at mpiz-koeln.mpg.de Wed Dec 5 11:42:51 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 5 Dec 2007 17:42:51 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200712030945.32685.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> Message-ID: <200712051742.51315.groscurt@mpiz-koeln.mpg.de> Hi, sorry for reasking that - but has anyone an answer ? Thanks andreas On Monday 03 December 2007 09:45, Andreas Groscurth wrote: > Hi, > > I'm using CentralDigestCachedImpl for caching the datatypes and namespaces > locally. > > CentralDigestCachedImpl cachedImpl = new > CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl","htt >p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); > cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); > cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); > > This works fine and re-calls use the local cache. > > But when I create a new MobyDataObject, it starts again to fetch the > datatypes > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > > So how do I tell it, that its already has these information ? the > MobyDataObject can also have a Registry Object - so i guess that can help - > but how to I link my CachedCentral with a Registry object ? > > Or is this otherwise solveable ? > > thx > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gordonp at ucalgary.ca Wed Dec 5 12:21:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 05 Dec 2007 10:21:37 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200712051742.51315.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> Message-ID: <4756DE21.3000105@ucalgary.ca> Hi Andreas, The concluision we reached a few weeks ago is that CentralDigestCachedImpl and org.biomoby.shared.data.* use different catching schemes,which I will reconcile once Martin has set up some unit tests for the CentralImpls. Usually there is no compelling reason to use both caches...if you are using org.biomoby.shared.data.* to create and past data instances, CentralDigestCachedImpl.CACHE_PART_DATATYPES doesn't really do anything for you, and vice versa. If you are using org.biomoby.shared.data.*, drop the updateCache() calls you had, and use instead: Registry registry = new Registry("calgary", "http://moby.ucalgary.ca/moby/MOBY-Central.pl", "http://moby.ucalgary.ca/MOBY/Central"); RegistryCache.cacheOntologyFile(registry, Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis); MobyDataType.loadDataTypes(RegistryCache.getOntologyFile(registry, Central.DATA_TYPES_RESOURCE_NAME).toURI().toURL(), registry); I just added the allowedAgeMillis parameter for convenience. You'll want to do a CVS update. For MobyNamespace it's similar.. MobyNamespace.loadNamespaces(RegistryCache.getOntologyFile(registry, Central.NAMESPACES_RESOURCE_NAME).toURI().toURL(), registry); Hopefully, we can reconcile the Central calls cache and this code soon, so you don't need to pick. I could have also made a MobyNamespace.loadNamespaces(registry) method, but in keeping with the Law of Demeter, it's better for MobyNamespace and MobyDataType to not explicitly know about RegistryCache, hence the MobyNamespace.loadNamespaces(url, registry) signature. Regards, Paul Andreas Groscurth wrote: > Hi, > > sorry for reasking that - but has anyone an answer ? > > Thanks > andreas > > On Monday 03 December 2007 09:45, Andreas Groscurth wrote: > >> Hi, >> >> I'm using CentralDigestCachedImpl for caching the datatypes and namespaces >> locally. >> >> CentralDigestCachedImpl cachedImpl = new >> CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl","htt >> p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); >> >> This works fine and re-calls use the local cache. >> >> But when I create a new MobyDataObject, it starts again to fetch the >> datatypes >> >> Fetching data type ontology from >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >> >> So how do I tell it, that its already has these information ? the >> MobyDataObject can also have a Registry Object - so i guess that can help - >> but how to I link my CachedCentral with a Registry object ? >> >> Or is this otherwise solveable ? >> >> thx >> andreas >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From gordonp at ucalgary.ca Wed Dec 5 12:35:10 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 05 Dec 2007 10:35:10 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <4756DE21.3000105@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> Message-ID: <4756E14E.3030809@ucalgary.ca> Hi Andreas, I just simplified it a bit, so it's two lines (and should not be garbled in split lines the e-mail) > Registry registry = new Registry("calgary", "http://moby.ucalgary.ca/moby/MOBY-Central.pl", "http://moby.ucalgary.ca/MOBY/Central"); > MobyDataType.loadDataTypes(RegistryCache.cacheOntologyFile(registry, Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis).toURI().toURL(), registry); > From markw at illuminae.com Wed Dec 5 12:36:13 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 Dec 2007 09:36:13 -0800 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: Here is the (very rapid!) review from Briefings in Bioinformatics. LOL! Well, the reviewers couldn't differ more in their desires for the manuscript!! It's almost as if we should write TWO manuscipts... one for each audience. Actually, I did suggest this on-list a few weeks ago, but nobody was brave enough to take me up on the suggestion... are there any takers now? Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. I should still have time to do some editing if anyone has suggestions. Best wishes! Mark ------- Forwarded message ------- From: briefings at oxfordjournals.org To: markw at illuminae.com Cc: Subject: Briefings in Bioinformatics - Decision on BIB-07-0068 Date: Tue, 04 Dec 2007 08:04:55 -0800 04-Dec-2007 Dear Dr Wilkinson, I am writing to inform you that your manuscript entitled 'Interoperability with Moby 1.0 - It?s Better than Sharing Your Toothbrush!' (BIB-07-0068) has now been peer-reviewed. The comments of the reviewers follow at the end of this email. We should like to invite you to respond to the comments of the reviewers and revise your manuscript according to their suggestions. To revise your manuscript, log into http://mc.manuscriptcentral.com/bib and enter your Author Center, where you will find your manuscript listed under "Manuscripts with Decisions." Under "Actions," click on "Create a Revision." When creating your revision, you will be asked to provide a response to the reviewers' comments, point-by-point. Where possible, please provide this response in the text box provided, rather than uploading your response as a document. Please ensure that any changes made to your manuscript are highlighted in colour, bold or underlining. By doing this, you will help us to minimise the time needed to provide you with a decision. IMPORTANT: Your original files are available to you when you upload your revised manuscript. Please delete any redundant files before completing the submission. Because we are trying to facilitate timely publication of manuscripts submitted to Briefings in Bioinformatics, we request that you submit your revised manuscript within the next four weeks. Once again, thank you for submitting your manuscript to Briefings in Bioinformatics and I look forward to receiving your revised paper in due course. Yours sincerely, Sophie Gilmour On behalf of Dr Martin Bishop, Editor-in-Chief, Briefings in Bioinformatics Reviewers' Comments to Author: Reviewer: 1 Comments to the Author This manuscript presents BioMoby, a mature framework for data integration and interoperability between web services. BioMoby has been developed over the last 5 years by a world wide community. These developments have now reached an important point: the stable version 1.0 of BioMoby is being presented here. This manuscript gives a description of how the framework is organized technically, compares it to peer semantic and schema technologies and presents a use case how a ?Biologist? can use it to execute an analysis workflow. For a reader with technical background the paper is well written and gives a good overview of the framework. At the same time this issue is also our largest concern with this manuscript. Overall it feels rather technical and it seems to be addressing primarily bioinformatics developers. This manuscript has been submitted to Briefings in Bioinformatics which has a more user oriented target group. It would be nice to introduce BioMoby particularly to those end users, but we feel that the focus of this manuscript needs an adjustment for this. The example of pages 4 and 5 of the actual workflow of an analysis is interesting to read and demonstrates the power of BioMoby well. We suggest to support this with screenshots of how the user can actually perform the steps of this analysis. The comparison with other semantic web standards is fine for a technical audience, but in this case it might be going too much into detail. Reviewer: 2 Comments to the Author I believe it could be improved with additional discussion and assessment of the differences between its approach and W3C Semantic Web. As the author states, BioMoby developed independently from the W3C semantic web specifications yet is addressing at least in part, some of the same use-cases in bioinformatics. Granted this is more from a service perspective than a knowledge-model perspective. Nonetheless, the rather "independent" evolution of these two approaches, particularly in light of the more productionized current state of BioMoby, suggests a more extensive comparison of the two paths of development. I would like to see such an expanded discussion in the paper - even a few more paragraphs. Editor's Comments to Author: Editor: 1 Comments to the Author: The referees differ somewhat in the balance expected. It is true that Briefings is orientated to Biological users. However, it is also read by Bioinformatics developers. The editor leaves it to the author to decide how to deal with these different emphases. -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From edward.kawas at gmail.com Thu Dec 6 11:04:22 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 6 Dec 2007 08:04:22 -0800 Subject: [MOBY-dev] jmoby CentralImpl is updated Message-ID: Hi, CentralImpl has been updated to reflect the newest mobycentral endpoint/namespace. 2 methods were created: getDefaultURI/getDefaultURL that query http://biomoby.org/mobycentral iff the system property 'moby.check.default' exists and is set to true. ***IMPORTANT*** Also, note that a new dependency 'commons-codec' was needed so make sure to do an 'ant gather' | './build-dev.sh gather' before using the new code. Eddie From phillip.lord at newcastle.ac.uk Thu Dec 6 12:54:11 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Thu, 06 Dec 2007 17:54:11 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: (Mark Wilkinson's message of "Wed\, 05 Dec 2007 09\:36\:13 -0800") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: <878x47iu9o.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil From phillip.lord at newcastle.ac.uk Thu Dec 6 12:54:11 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Thu, 06 Dec 2007 17:54:11 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: (Mark Wilkinson's message of "Wed\, 05 Dec 2007 09\:36\:13 -0800") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: <878x47iu9o.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil From markw at illuminae.com Thu Dec 6 12:52:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Thu, 6 Dec 2007 17:52:35 +0000 GMT Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <878x47iu9o.fsf@dinley.ncl.ac.uk> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> Message-ID: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Is that a hint? -- Mark Wilkinson ...on the road! -----Original Message----- From: Phillip Lord Date: Thu, 06 Dec 2007 17:54:11 To:Core developer announcements Cc:Core developer announcements Subject: Re: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Dec 6 12:52:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Thu, 6 Dec 2007 17:52:35 +0000 GMT Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <878x47iu9o.fsf@dinley.ncl.ac.uk> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> Message-ID: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Is that a hint? -- Mark Wilkinson ...on the road! -----Original Message----- From: Phillip Lord Date: Thu, 06 Dec 2007 17:54:11 To:Core developer announcements Cc:Core developer announcements Subject: Re: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Thu Dec 6 13:04:24 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 06 Dec 2007 18:04:24 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: <878x47iu9o.fsf@dinley.ncl.ac.uk> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> Message-ID: <475839A8.8060106@cs.man.ac.uk> Phillip Lord wrote: > Well, you could write two papers, but the other approach would be to refer to > any other work which compared biomoby to current semantic web approaches. currently exists in phd form. http://www.cs.man.ac.uk/~hulld/phd/ robert wants to write it up as a paper, which we'll do next year I think the theory and the practice (myGrid, Taverna and BioMOBY) are poles apart, as you know, they are like chalk and cheese. Duncan -- Duncan Hull http://duncan.hull.name +44 (0) 161 306 5139 From Pieter.Neerincx at wur.nl Thu Dec 6 13:42:08 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 6 Dec 2007 19:42:08 +0100 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: <84AE6BA0-5EF2-4B60-B570-C4A6A389B36B@wur.nl> Hi Mark et al., On 5-dec-2007, at 18:36, Mark Wilkinson wrote: > Here is the (very rapid!) review from Briefings in Bioinformatics. > > LOL! Well, the reviewers couldn't differ more in their desires for > the > manuscript!! It's almost as if we should write TWO manuscipts... > one for > each audience. "The editor leaves it to the author to decide how to deal with these different emphases." Hmmm that sounds like what I sometimes do when I'm making a new tool and don't know how to solve a problem: make it a user configurable parameter and sell my lack of inspiration as a feature as in "it's completely customisable" :). Anyway, in the end it's the editors who decide what they want in their magazine, so in my opinion it's the editor who should tell us what he/she wants in BIB. We could adjust according to reviewer one or two or split up into two articles and adjust according to both, but it would be a shame if we adjust to reviewer 1 and then in the end BIB tells us they rejected the manuscript, because they were looking for something like suggested by reviewer two. Maybe we should just explicitly ask the editor to tell us what they want... My 0.02 ? Pi > Actually, I did suggest this on-list a few weeks ago, but > nobody was brave enough to take me up on the suggestion... are > there any > takers now? > > Comments are welcome. I'm leaving for Moby meetings/talks in Koln, > Wageningen, and Amsterdam tomorrow so I am away for the next 10 > days. I > should still have time to do some editing if anyone has suggestions. > Best wishes! > > Mark > > > > > ------- Forwarded message ------- > From: briefings at oxfordjournals.org > To: markw at illuminae.com > Cc: > Subject: Briefings in Bioinformatics - Decision on BIB-07-0068 > Date: Tue, 04 Dec 2007 08:04:55 -0800 > > 04-Dec-2007 > > Dear Dr Wilkinson, > > I am writing to inform you that your manuscript entitled > 'Interoperability > with Moby 1.0 - It?s Better than Sharing Your > Toothbrush!' (BIB-07-0068) > has now been peer-reviewed. The comments of the reviewers follow > at the > end of this email. > > We should like to invite you to respond to the comments of the > reviewers > and revise your manuscript according to their suggestions. > > To revise your manuscript, log into http://mc.manuscriptcentral.com/ > bib > and enter your Author Center, where you will find your manuscript > listed > under "Manuscripts with Decisions." Under "Actions," click on > "Create a > Revision." > > When creating your revision, you will be asked to provide a > response to > the reviewers' comments, point-by-point. Where possible, please > provide > this response in the text box provided, rather than uploading your > response as a document. Please ensure that any changes made to your > manuscript are highlighted in colour, bold or underlining. By > doing this, > you will help us to minimise the time needed to provide you with a > decision. > > IMPORTANT: Your original files are available to you when you > upload your > revised manuscript. Please delete any redundant files before > completing > the submission. > > Because we are trying to facilitate timely publication of manuscripts > submitted to Briefings in Bioinformatics, we request that you > submit your > revised manuscript within the next four weeks. > > Once again, thank you for submitting your manuscript to Briefings in > Bioinformatics and I look forward to receiving your revised paper > in due > course. > > Yours sincerely, > > > > Sophie Gilmour > On behalf of Dr Martin Bishop, > Editor-in-Chief, Briefings in Bioinformatics > > Reviewers' Comments to Author: > Reviewer: 1 > Comments to the Author > This manuscript presents BioMoby, a mature framework for data > integration > and interoperability between web services. BioMoby has been > developed over > the last 5 years by a world wide community. These developments have > now > reached an important point: the stable version 1.0 of BioMoby is being > presented here. This manuscript gives a description of how the > framework > is organized technically, compares it to peer semantic and schema > technologies and presents a use case how a ?Biologist? can use it to > execute an analysis workflow. > > For a reader with technical background the paper is well written > and gives > a good overview of the framework. At the same time this issue is > also > our largest concern with this manuscript. Overall it feels rather > technical and it seems to be addressing primarily bioinformatics > developers. This manuscript has been submitted to Briefings in > Bioinformatics which has a more user oriented target group. It > would be > nice to introduce BioMoby particularly to those end users, but we feel > that the focus of this manuscript needs an adjustment for this. > > The example of pages 4 and 5 of the actual workflow of an analysis is > interesting to read and demonstrates the power of BioMoby well. We > suggest > to support this with screenshots of how the user can actually > perform the > steps of this analysis. The comparison with other semantic web > standards > is fine for a technical audience, but in this case it might be > going too > much into detail. > > Reviewer: 2 > Comments to the Author > I believe it could be improved with additional discussion and > assessment > of the differences between its approach and W3C Semantic Web. > > As the author states, BioMoby developed independently from the W3C > semantic web specifications yet is addressing at least in part, > some of > the same use-cases in bioinformatics. Granted this is more from a > service > perspective than a knowledge-model perspective. Nonetheless, the > rather > "independent" evolution of these two approaches, particularly in > light of > the more productionized current state of BioMoby, suggests a more > extensive comparison of the two paths of development. > > I would like to see such an expanded discussion in the paper - even > a few > more paragraphs. > > Editor's Comments to Author: > Editor: 1 > Comments to the Author: > The referees differ somewhat in the balance expected. > It is true that Briefings is orientated to Biological users. > However, it is also read by Bioinformatics developers. > The editor leaves it to the author to decide how to deal with these > different emphases. > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Fri Dec 7 04:51:52 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 07 Dec 2007 10:51:52 +0100 Subject: [MOBY-dev] getDeadServices Message-ID: <475917B8.8060505@toulouse.inra.fr> Bonjour ? tous, Is there on the new server the list of dead services as returned by the old URL: http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService?getDeadServices It's very usefull to filter available and almost working services. Thanks, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20071207/020a9104/attachment.vcf From Pieter.Neerincx at wur.nl Fri Dec 7 06:01:45 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 7 Dec 2007 12:01:45 +0100 Subject: [MOBY-dev] getDeadServices In-Reply-To: <475917B8.8060505@toulouse.inra.fr> References: <475917B8.8060505@toulouse.inra.fr> Message-ID: <9986FF15-72DF-414A-A1AE-3A6402245638@wur.nl> Hi Sebastien, Yes, try : http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Cheers, Pi On 7-dec-2007, at 10:51, Sebastien Carrere wrote: > Bonjour ? tous, > > Is there on the new server the list of dead services as returned by > the old URL: > http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService? > getDeadServices > > > It's very usefull to filter available and almost working services. > > Thanks, > > Sebastien > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Fri Dec 7 06:51:56 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 07 Dec 2007 12:51:56 +0100 Subject: [MOBY-dev] getDeadServices In-Reply-To: <9986FF15-72DF-414A-A1AE-3A6402245638@wur.nl> References: <475917B8.8060505@toulouse.inra.fr> <9986FF15-72DF-414A-A1AE-3A6402245638@wur.nl> Message-ID: <475933DC.1020109@toulouse.inra.fr> Great ! Thanks Pieter. Sebastien. Pieter Neerincx wrote: > Hi Sebastien, > > Yes, try : http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers, > > Pi > > On 7-dec-2007, at 10:51, Sebastien Carrere wrote: > > >> Bonjour ? tous, >> >> Is there on the new server the list of dead services as returned by >> the old URL: >> http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService? >> getDeadServices >> >> >> It's very usefull to filter available and almost working services. >> >> Thanks, >> >> Sebastien >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20071207/99a3dd54/attachment.vcf From phillip.lord at newcastle.ac.uk Fri Dec 7 10:50:21 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Fri, 07 Dec 2007 15:50:21 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> (mark wilkinson's message of "Thu\, 6 Dec 2007 17\:52\:35 +0000 GMT") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Message-ID: <87y7c6v70i.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == mark wilkinson writes: Mark> Is that a hint? Just thought it might help. It's your paper. I leave it to the authors to decide how to deal....etc Phil From phillip.lord at newcastle.ac.uk Fri Dec 7 10:50:21 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Fri, 07 Dec 2007 15:50:21 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> (mark wilkinson's message of "Thu\, 6 Dec 2007 17\:52\:35 +0000 GMT") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Message-ID: <87y7c6v70i.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == mark wilkinson writes: Mark> Is that a hint? Just thought it might help. It's your paper. I leave it to the authors to decide how to deal....etc Phil From groscurt at mpiz-koeln.mpg.de Fri Dec 7 11:16:41 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 7 Dec 2007 17:16:41 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <4756DE21.3000105@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> Message-ID: <200712071716.41802.groscurt@mpiz-koeln.mpg.de> Hi Paul, thanks for the message... So do i understand it correctly ? I create such Registry object and then I pass that instance to any of the org.biomoby.shared.data.*. e.g. new MobyDataObject( "something", "anything", registry) ? thanks andreas On Wednesday 05 December 2007 18:21, Paul Gordon wrote: > Hi Andreas, > > The concluision we reached a few weeks ago is that > CentralDigestCachedImpl and org.biomoby.shared.data.* use different > catching schemes,which I will reconcile once Martin has set up some unit > tests for the CentralImpls. Usually there is no compelling reason to > use both caches...if you are using org.biomoby.shared.data.* to create > and past data instances, CentralDigestCachedImpl.CACHE_PART_DATATYPES > doesn't really do anything for you, and vice versa. If you are using > org.biomoby.shared.data.*, drop the updateCache() calls you had, and use > instead: > > Registry registry = new Registry("calgary", > "http://moby.ucalgary.ca/moby/MOBY-Central.pl", > "http://moby.ucalgary.ca/MOBY/Central"); > RegistryCache.cacheOntologyFile(registry, > Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis); > MobyDataType.loadDataTypes(RegistryCache.getOntologyFile(registry, > Central.DATA_TYPES_RESOURCE_NAME).toURI().toURL(), registry); > > I just added the allowedAgeMillis parameter for convenience. You'll want > to do a CVS update. For MobyNamespace it's similar.. > > MobyNamespace.loadNamespaces(RegistryCache.getOntologyFile(registry, > Central.NAMESPACES_RESOURCE_NAME).toURI().toURL(), registry); > > Hopefully, we can reconcile the Central calls cache and this code soon, > so you don't need to pick. I could have also made a > MobyNamespace.loadNamespaces(registry) method, but in keeping with the > Law of Demeter, it's better for MobyNamespace and MobyDataType to not > explicitly know about RegistryCache, hence the > MobyNamespace.loadNamespaces(url, registry) signature. > > Regards, > > Paul > > Andreas Groscurth wrote: > > Hi, > > > > sorry for reasking that - but has anyone an answer ? > > > > Thanks > > andreas > > > > On Monday 03 December 2007 09:45, Andreas Groscurth wrote: > >> Hi, > >> > >> I'm using CentralDigestCachedImpl for caching the datatypes and > >> namespaces locally. > >> > >> CentralDigestCachedImpl cachedImpl = new > >> CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl"," > >>htt p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); > >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); > >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); > >> > >> This works fine and re-calls use the local cache. > >> > >> But when I create a new MobyDataObject, it starts again to fetch the > >> datatypes > >> > >> Fetching data type ontology from > >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > >> > >> So how do I tell it, that its already has these information ? the > >> MobyDataObject can also have a Registry Object - so i guess that can > >> help - but how to I link my CachedCentral with a Registry object ? > >> > >> Or is this otherwise solveable ? > >> > >> thx > >> andreas > >> _______________________________________________ > >> MOBY-dev mailing list > >> MOBY-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gordonp at ucalgary.ca Fri Dec 7 11:26:52 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Dec 2007 09:26:52 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200712071716.41802.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> <200712071716.41802.groscurt@mpiz-koeln.mpg.de> Message-ID: <4759744C.5090608@ucalgary.ca> Yes. If you use the default c-tor for anything, e.g.: new MobyDataObject( "something", "anything") this is the same as setting the registry to null. Because the null registry uses the default registry from RegistriesList, and this still points to the defunct server in Vancouver, the default c-tors currently fail. It was actually a good opportunity for me to discover the parts of my jMOBY code that were not Registry-aware, because they would hang, trying to connect to UBC when they should be connecting to Calgary :-) That being said, if you want to use the default registry in Calgary, I will be switching the default action to connect to Calgary in the next day or so (as I've found all my multi-registry bugs, I think). You'll only need to use c-tors with a registry parameter if you want to use a specialized registry. Andreas Groscurth wrote: > Hi Paul, > > thanks for the message... > > So do i understand it correctly ? I create such Registry object and then I > pass that instance to any of the org.biomoby.shared.data.*. > > e.g. new MobyDataObject( "something", "anything", registry) > > ? > > thanks > andreas > > On Wednesday 05 December 2007 18:21, Paul Gordon wrote: > >> Hi Andreas, >> >> The concluision we reached a few weeks ago is that >> CentralDigestCachedImpl and org.biomoby.shared.data.* use different >> catching schemes,which I will reconcile once Martin has set up some unit >> tests for the CentralImpls. Usually there is no compelling reason to >> use both caches...if you are using org.biomoby.shared.data.* to create >> and past data instances, CentralDigestCachedImpl.CACHE_PART_DATATYPES >> doesn't really do anything for you, and vice versa. If you are using >> org.biomoby.shared.data.*, drop the updateCache() calls you had, and use >> instead: >> >> Registry registry = new Registry("calgary", >> "http://moby.ucalgary.ca/moby/MOBY-Central.pl", >> "http://moby.ucalgary.ca/MOBY/Central"); >> RegistryCache.cacheOntologyFile(registry, >> Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis); >> MobyDataType.loadDataTypes(RegistryCache.getOntologyFile(registry, >> Central.DATA_TYPES_RESOURCE_NAME).toURI().toURL(), registry); >> >> I just added the allowedAgeMillis parameter for convenience. You'll want >> to do a CVS update. For MobyNamespace it's similar.. >> >> MobyNamespace.loadNamespaces(RegistryCache.getOntologyFile(registry, >> Central.NAMESPACES_RESOURCE_NAME).toURI().toURL(), registry); >> >> Hopefully, we can reconcile the Central calls cache and this code soon, >> so you don't need to pick. I could have also made a >> MobyNamespace.loadNamespaces(registry) method, but in keeping with the >> Law of Demeter, it's better for MobyNamespace and MobyDataType to not >> explicitly know about RegistryCache, hence the >> MobyNamespace.loadNamespaces(url, registry) signature. >> >> Regards, >> >> Paul >> >> Andreas Groscurth wrote: >> >>> Hi, >>> >>> sorry for reasking that - but has anyone an answer ? >>> >>> Thanks >>> andreas >>> >>> On Monday 03 December 2007 09:45, Andreas Groscurth wrote: >>> >>>> Hi, >>>> >>>> I'm using CentralDigestCachedImpl for caching the datatypes and >>>> namespaces locally. >>>> >>>> CentralDigestCachedImpl cachedImpl = new >>>> CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl"," >>>> htt p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); >>>> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); >>>> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); >>>> >>>> This works fine and re-calls use the local cache. >>>> >>>> But when I create a new MobyDataObject, it starts again to fetch the >>>> datatypes >>>> >>>> Fetching data type ontology from >>>> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >>>> >>>> So how do I tell it, that its already has these information ? the >>>> MobyDataObject can also have a Registry Object - so i guess that can >>>> help - but how to I link my CachedCentral with a Registry object ? >>>> >>>> Or is this otherwise solveable ? >>>> >>>> thx >>>> andreas >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From jmfernandez at cnio.es Tue Dec 11 11:02:52 2007 From: jmfernandez at cnio.es (=?UTF-8?B?Sm9zw6kgTWFyw61hIEZlcm7DoW5kZXogR29uesOhbGV6?=) Date: Tue, 11 Dec 2007 17:02:52 +0100 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> Message-ID: <475EB4AC.2060409@cnio.es> Hi Eddie, so, which is the URL of the new maven repository for biomoby? Best Regards, Jos?? Mar??a Edward Kawas wrote: > Hi Stian, > > I just replaced all instances where mobycentral was used to ucalgary. I also > had to update the biomoby plugins maven repository to be the new one at > ucalgary. > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland > Sent: December-03-07 4:05 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! > > On 11/30/07, Mark Wilkinson wrote: >> To migrate Taverna, edit the taverna/conf/mygrid.properties file to point >> to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl > > Should we change the default in Taverna's shipped mygrid.properties to > the ucalgary one? We have a Taverna 1.7 release going out in a few > weeks and would of course like BioMoby to work by default.. > -- "Premature optimization is the root of all evil." - Donald Knuth Jos?? Mar??a Fern??ndez Gonz??lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog??a Estructural y Bioinform??tica Structural Biology and Bioinformatics Centro Nacional de Investigaciones Oncol??gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern??ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Tue Dec 11 11:10:37 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 11 Dec 2007 08:10:37 -0800 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: <475EB4AC.2060409@cnio.es> References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> <475EB4AC.2060409@cnio.es> Message-ID: http://moby.ucalgary.ca/moby_maven/ Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a Fern?ndez Gonz?lez Sent: December-11-07 8:03 AM To: Core developer announcements Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! Hi Eddie, so, which is the URL of the new maven repository for biomoby? Best Regards, Jos? Mar?a Edward Kawas wrote: > Hi Stian, > > I just replaced all instances where mobycentral was used to ucalgary. I also > had to update the biomoby plugins maven repository to be the new one at > ucalgary. > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland > Sent: December-03-07 4:05 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! > > On 11/30/07, Mark Wilkinson wrote: >> To migrate Taverna, edit the taverna/conf/mygrid.properties file to point >> to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl > > Should we change the default in Taverna's shipped mygrid.properties to > the ucalgary one? We have a Taverna 1.7 release going out in a few > weeks and would of course like BioMoby to work by default.. > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog?a Estructural y Bioinform?tica Structural Biology and Bioinformatics Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From jmfernandez at cnio.es Tue Dec 11 11:20:28 2007 From: jmfernandez at cnio.es (=?UTF-8?B?Sm9zw6kgTWFyw61hIEZlcm7DoW5kZXogR29uesOhbGV6?=) Date: Tue, 11 Dec 2007 17:20:28 +0100 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> <475EB4AC.2060409@cnio.es> Message-ID: <475EB8CC.4090101@cnio.es> Thanks! Edward Kawas wrote: > http://moby.ucalgary.ca/moby_maven/ > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos?? Mar??a Fern??ndez Gonz??lez > Sent: December-11-07 8:03 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! > > Hi Eddie, > so, which is the URL of the new maven repository for biomoby? > > Best Regards, > Jos?? Mar??a > > Edward Kawas wrote: >> Hi Stian, >> >> I just replaced all instances where mobycentral was used to ucalgary. I also >> had to update the biomoby plugins maven repository to be the new one at >> ucalgary. >> >> Thanks, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland >> Sent: December-03-07 4:05 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! >> >> On 11/30/07, Mark Wilkinson wrote: >>> To migrate Taverna, edit the taverna/conf/mygrid.properties file to point >>> to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl >> Should we change the default in Taverna's shipped mygrid.properties to >> the ucalgary one? We have a Taverna 1.7 release going out in a few >> weeks and would of course like BioMoby to work by default.. >> > -- "Premature optimization is the root of all evil." - Donald Knuth Jos?? Mar??a Fern??ndez Gonz??lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog??a Estructural y Bioinform??tica Structural Biology and Bioinformatics Centro Nacional de Investigaciones Oncol??gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern??ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From martin.senger at gmail.com Tue Dec 11 11:35:14 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Dec 2007 08:35:14 -0800 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> <475EB4AC.2060409@cnio.es> Message-ID: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> > http://moby.ucalgary.ca/moby_maven/ It may be true now. But in the longer term (I mean February 2008 when the Biohackathon happens in Japan - and where the new jMoby development is expected to happen, as well) jMoby will be using the open-bio maven repository (http://biomoby.org/m2repo/) and will be fully mavenized not only for the Taverna purposes but for all jMoby development. This is my plan, at least. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Dec 13 06:38:57 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Dec 2007 12:38:57 +0100 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> Message-ID: <200712131238.58226.groscurt@mpiz-koeln.mpg.de> Hi everyone, we have some problems with our application server and Moby - we havent figured out where the problem is, but I do have some questions. The problem is that our application server (jboss) kind of breaks down every morning and does not take any more request until we restart it. In the Jboss log we find zig of requests from moby central K 48735392 ms ? ? 136.159.169.80 ? ? K 59662027 ms ? ? 136.159.169.80 ? ? K 59482196 ms ? ? 136.159.169.80 ? ? K 37045625 ms ? ? 136.159.169.80 ? ? K 37797970 ms ? ? 136.159.169.80 ? ? K 37605298 ms ? ? 136.159.169.80 ? ? K 48353212 ms ? ? 136.159.169.80 ? ? K 74660526 ms ? ? 10.0.0.128 ? ? K 59448187 ms ? ? 136.159.169.80 ? ? K 37331868 ms ? ? 136.159.169.80 ? ? K 68473066 ms ? ? 136.159.169.80 ? ? K 22891987 ms ? ? 136.159.169.80 ? ? K 23234088 ms ? ? 136.159.169.80 ? ? K = Keepalive (this is just a short version of the whole log).... In the web server log we have the following entries 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/1.1" 200 771 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 739 "-" "SOAP::Lite/Perl/0.69" (again a short version) So, over the night MobyCentral calls our services frequently and this results in the 'sleeping' of the jboss.. to figure out what happens - what exactly happens during these calls ? what are these calls ? - and why are they marked as 'keep alive' ? Any suggestions on that ? Thanks Andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From schoof at mpiz-koeln.mpg.de Thu Dec 13 07:20:40 2007 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Thu, 13 Dec 2007 13:20:40 +0100 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <200712131238.58226.groscurt@mpiz-koeln.mpg.de> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> <200712131238.58226.groscurt@mpiz-koeln.mpg.de> Message-ID: <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> Okay we figured out the keepalive bit, still for tracking purposes it would be great to know who or what is calling these services and what the calls are. Best, Heiko On 13.12.2007, at 12:38, Andreas Groscurth wrote: > Hi everyone, > > we have some problems with our application server and Moby - we > havent figured > out where the problem is, but I do have some questions. > > The problem is that our application server (jboss) kind of breaks > down every > morning and does not take any more request until we restart it. > > In the Jboss log we find zig of requests from moby central > > K 48735392 ms ? ? 136.159.169.80 ? ? > K 59662027 ms ? ? 136.159.169.80 ? ? > K 59482196 ms ? ? 136.159.169.80 ? ? > K 37045625 ms ? ? 136.159.169.80 ? ? > K 37797970 ms ? ? 136.159.169.80 ? ? > K 37605298 ms ? ? 136.159.169.80 ? ? > K 48353212 ms ? ? 136.159.169.80 ? ? > K 74660526 ms ? ? 10.0.0.128 ? ? > K 59448187 ms ? ? 136.159.169.80 ? ? > K 37331868 ms ? ? 136.159.169.80 ? ? > K 68473066 ms ? ? 136.159.169.80 ? ? > K 22891987 ms ? ? 136.159.169.80 ? ? > K 23234088 ms ? ? 136.159.169.80 ? ? > > K = Keepalive > > (this is just a short version of the whole log).... > > In the web server log we have the following entries > > 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] > "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" > "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] > "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/ > 1.1" 200 > 771 "-" "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] > "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" > "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] > "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" > "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] > "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 > 739 "-" > "SOAP::Lite/Perl/0.69" > > (again a short version) > > So, over the night MobyCentral calls our services frequently and > this results > in the 'sleeping' of the jboss.. > > to figure out what happens - what exactly happens during these > calls ? what > are these calls ? - and why are they marked as 'keep alive' ? > > Any suggestions on that ? > > Thanks > Andreas > > > > -- > Andreas Groscurth > Bioinformatics Developer > Max Planck Institute for Plant Breeding Research > Carl-von-Linn?-Weg 10 > 50829 Cologne > Germany > E-mail: groscurt at mpiz-koeln.mpg.de > Phone: +49(0)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Dec 13 07:53:59 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 Dec 2007 04:53:59 -0800 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> <200712131238.58226.groscurt@mpiz-koeln.mpg.de> <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> Message-ID: Almost certainly it is the "isAlive" script, which sends an empty message and looks for an empty response. M On Thu, 13 Dec 2007 04:20:40 -0800, Heiko Schoof wrote: > Okay we figured out the keepalive bit, still for tracking purposes it > would be great to know who or what is calling these services and what > the calls are. > > Best, Heiko > > On 13.12.2007, at 12:38, Andreas Groscurth wrote: > >> Hi everyone, >> >> we have some problems with our application server and Moby - we havent >> figured >> out where the problem is, but I do have some questions. >> >> The problem is that our application server (jboss) kind of breaks down >> every >> morning and does not take any more request until we restart it. >> >> In the Jboss log we find zig of requests from moby central >> >> K 48735392 ms ? ? 136.159.169.80 ? ? >> K 59662027 ms ? ? 136.159.169.80 ? ? >> K 59482196 ms ? ? 136.159.169.80 ? ? >> K 37045625 ms ? ? 136.159.169.80 ? ? >> K 37797970 ms ? ? 136.159.169.80 ? ? >> K 37605298 ms ? ? 136.159.169.80 ? ? >> K 48353212 ms ? ? 136.159.169.80 ? ? >> K 74660526 ms ? ? 10.0.0.128 ? ? >> K 59448187 ms ? ? 136.159.169.80 ? ? >> K 37331868 ms ? ? 136.159.169.80 ? ? >> K 68473066 ms ? ? 136.159.169.80 ? ? >> K 22891987 ms ? ? 136.159.169.80 ? ? >> K 23234088 ms ? ? 136.159.169.80 ? ? >> >> K = Keepalive >> >> (this is just a short version of the whole log).... >> >> In the web server log we have the following entries >> >> 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] >> "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] >> "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/1.1" >> 200 >> 771 "-" "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] >> "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] >> "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] >> "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 739 >> "-" >> "SOAP::Lite/Perl/0.69" >> >> (again a short version) >> >> So, over the night MobyCentral calls our services frequently and this >> results >> in the 'sleeping' of the jboss.. >> >> to figure out what happens - what exactly happens during these calls ? >> what >> are these calls ? - and why are they marked as 'keep alive' ? >> >> Any suggestions on that ? >> >> Thanks >> Andreas >> >> >> >> --Andreas Groscurth >> Bioinformatics Developer >> Max Planck Institute for Plant Breeding Research >> Carl-von-Linn?-Weg 10 >> 50829 Cologne >> Germany >> E-mail: groscurt at mpiz-koeln.mpg.de >> Phone: +49(0)221-5062-449 >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Dec 13 07:54:57 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 Dec 2007 04:54:57 -0800 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> <200712131238.58226.groscurt@mpiz-koeln.mpg.de> <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> Message-ID: Would you like me to set the "agent" property in the code so that it reports itself as "isAlive script" in your logfiles? Greetings from Wageningen! Mark On Thu, 13 Dec 2007 04:20:40 -0800, Heiko Schoof wrote: > Okay we figured out the keepalive bit, still for tracking purposes it > would be great to know who or what is calling these services and what > the calls are. > > Best, Heiko > > On 13.12.2007, at 12:38, Andreas Groscurth wrote: > >> Hi everyone, >> >> we have some problems with our application server and Moby - we havent >> figured >> out where the problem is, but I do have some questions. >> >> The problem is that our application server (jboss) kind of breaks down >> every >> morning and does not take any more request until we restart it. >> >> In the Jboss log we find zig of requests from moby central >> >> K 48735392 ms ? ? 136.159.169.80 ? ? >> K 59662027 ms ? ? 136.159.169.80 ? ? >> K 59482196 ms ? ? 136.159.169.80 ? ? >> K 37045625 ms ? ? 136.159.169.80 ? ? >> K 37797970 ms ? ? 136.159.169.80 ? ? >> K 37605298 ms ? ? 136.159.169.80 ? ? >> K 48353212 ms ? ? 136.159.169.80 ? ? >> K 74660526 ms ? ? 10.0.0.128 ? ? >> K 59448187 ms ? ? 136.159.169.80 ? ? >> K 37331868 ms ? ? 136.159.169.80 ? ? >> K 68473066 ms ? ? 136.159.169.80 ? ? >> K 22891987 ms ? ? 136.159.169.80 ? ? >> K 23234088 ms ? ? 136.159.169.80 ? ? >> >> K = Keepalive >> >> (this is just a short version of the whole log).... >> >> In the web server log we have the following entries >> >> 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] >> "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] >> "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/1.1" >> 200 >> 771 "-" "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] >> "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] >> "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] >> "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 739 >> "-" >> "SOAP::Lite/Perl/0.69" >> >> (again a short version) >> >> So, over the night MobyCentral calls our services frequently and this >> results >> in the 'sleeping' of the jboss.. >> >> to figure out what happens - what exactly happens during these calls ? >> what >> are these calls ? - and why are they marked as 'keep alive' ? >> >> Any suggestions on that ? >> >> Thanks >> Andreas >> >> >> >> --Andreas Groscurth >> Bioinformatics Developer >> Max Planck Institute for Plant Breeding Research >> Carl-von-Linn?-Weg 10 >> 50829 Cologne >> Germany >> E-mail: groscurt at mpiz-koeln.mpg.de >> Phone: +49(0)221-5062-449 >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Mon Dec 17 16:50:42 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 17 Dec 2007 13:50:42 -0800 Subject: [MOBY-dev] Fixing local RDF metadata Message-ID: Hi all, I noticed a little while ago that Moby Central is including the isAlive tag in the metadata that it presents to the service provider when they register their service. This is bad! The service provider is not supposed to know if their service is alive or not (from the perspective of the Registry) so they shouldn't have that tag in their metadata. Eddie has just fixed the Moby Central code so that it doesn't do this anymore, but in order to fix your metadata you would need to remove the isAlive tag from each of your service instances. I did that using a perl in-place edit as follows: perl -pi.bak -e "s/\w+<\/mygrid:isAlive>//g" *.rdf It's probably worth doing, so that your local metadata doesn't over-rule what the registry says the alive/dead state of your service is. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Sebastien.Carrere at toulouse.inra.fr Tue Dec 18 03:31:47 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Tue, 18 Dec 2007 09:31:47 +0100 Subject: [MOBY-dev] Fixing local RDF metadata In-Reply-To: References: Message-ID: <47678573.9020806@toulouse.inra.fr> Bonjour Mark, Do you talking about the "" tag ? Because my RDF files do not contain any "mygrid:" namespaced tags: http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/iant/rdf/dna/iANTblastxSwissProt.rdf Are my rdf files not correct ? Sebastien Mark Wilkinson wrote: > Hi all, > > I noticed a little while ago that Moby Central is including the > isAlive tag in the metadata that it presents to the service provider > when they register their service. This is bad! The service provider > is not supposed to know if their service is alive or not (from the > perspective of the Registry) so they shouldn't have that tag in their > metadata. > > Eddie has just fixed the Moby Central code so that it doesn't do this > anymore, but in order to fix your metadata you would need to remove > the isAlive tag from each of your service instances. > > I did that using a perl in-place edit as follows: > > perl -pi.bak -e "s/\w+<\/mygrid:isAlive>//g" *.rdf > > It's probably worth doing, so that your local metadata doesn't > over-rule what the registry says the alive/dead state of your service is. > > Cheers! > > M > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee > and may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received > this communication in error, please notify the sender immediately by > reply e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From markw at illuminae.com Tue Dec 18 05:00:25 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 18 Dec 2007 02:00:25 -0800 Subject: [MOBY-dev] Fixing local RDF metadata In-Reply-To: <47678573.9020806@toulouse.inra.fr> References: <47678573.9020806@toulouse.inra.fr> Message-ID: Yes. The namespace is just a token... whatever "a" is should map to a mygrid ontology, so it will need to be modified to whatever namespace you have. M On Tue, 18 Dec 2007 00:31:47 -0800, Sebastien Carrere wrote: > Bonjour Mark, > > Do you talking about the "" tag ? > Because my RDF files do not contain any "mygrid:" namespaced tags: > http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/iant/rdf/dna/iANTblastxSwissProt.rdf > > Are my rdf files not correct ? > > Sebastien > > > > Mark Wilkinson wrote: >> Hi all, >> >> I noticed a little while ago that Moby Central is including the >> isAlive tag in the metadata that it presents to the service provider >> when they register their service. This is bad! The service provider >> is not supposed to know if their service is alive or not (from the >> perspective of the Registry) so they shouldn't have that tag in their >> metadata. >> >> Eddie has just fixed the Moby Central code so that it doesn't do this >> anymore, but in order to fix your metadata you would need to remove >> the isAlive tag from each of your service instances. >> >> I did that using a perl in-place edit as follows: >> >> perl -pi.bak -e "s/\w+<\/mygrid:isAlive>//g" *.rdf >> >> It's probably worth doing, so that your local metadata doesn't >> over-rule what the registry says the alive/dead state of your service >> is. >> >> Cheers! >> >> M >> >> >> ---- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > From groscurt at mpiz-koeln.mpg.de Tue Dec 18 08:30:56 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 18 Dec 2007 14:30:56 +0100 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: References: Message-ID: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Hi, since the movement of Moby we have severe problems with Taverna and Moby. When taverna tries to retrieve information about a dataobject (e.g. in the 'Brief search' for matching services), we always run into a NullPointerException with the message "Cannot parse MOBY Object Ontology" in org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF My guess is, that there is somehow the 'old' pre-movement code and because of that its not working. If so - I would be more than glad and thankfull if one can repair these asap... we are working currently a lot with taverna and like to present it (and moby) to our students... but in this state its not really presentable :-( Hope this can be fixed soon. Thanks andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From edward.kawas at gmail.com Tue Dec 18 08:33:47 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 18 Dec 2007 05:33:47 -0800 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: <36A6C2801FB34C988F481FBDC8A1C4B1@OfficePC> Hi Andreas, In the next day or two there will be a new release of taverna. This should fix all of the problems that you are encountering. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: December-18-07 5:31 AM To: Core developer announcements Subject: [MOBY-dev] Taverna Moby Problems Hi, since the movement of Moby we have severe problems with Taverna and Moby. When taverna tries to retrieve information about a dataobject (e.g. in the 'Brief search' for matching services), we always run into a NullPointerException with the message "Cannot parse MOBY Object Ontology" in org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF My guess is, that there is somehow the 'old' pre-movement code and because of that its not working. If so - I would be more than glad and thankfull if one can repair these asap... we are working currently a lot with taverna and like to present it (and moby) to our students... but in this state its not really presentable :-( Hope this can be fixed soon. Thanks andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Dec 18 08:45:30 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 18 Dec 2007 14:45:30 +0100 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: <200712181445.30753.groscurt@mpiz-koeln.mpg.de> awesome... thanks On Tuesday 18 December 2007 14:30, Andreas Groscurth wrote: > Hi, > > since the movement of Moby we have severe problems with Taverna and Moby. > > When taverna tries to retrieve information about a dataobject (e.g. in the > 'Brief search' for matching services), we always run into a > NullPointerException with the message "Cannot parse MOBY Object Ontology" > in > > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF > > > My guess is, that there is somehow the 'old' pre-movement code and because > of that its not working. > > If so - I would be more than glad and thankfull if one can repair these > asap... we are working currently a lot with taverna and like to present it > (and moby) to our students... but in this state its not really > presentable :-( > > Hope this can be fixed soon. > > Thanks > andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From Pieter.Neerincx at wur.nl Tue Dec 18 08:56:09 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 18 Dec 2007 14:56:09 +0100 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: Hi Andreas, I know Eddie is working on this. There is also the issue that fetching the data to do a semantic search can be extremely slow right now. Eddie told me he will implement some caching for the data types similar to how the services are cached. A new Taverna 1.7 that contains fixes for these issues was announced for monday December 17 (yesterday). Apparently it's delayed a bit, but you'll probably see it very soon. In case soon is not soon enough: we had a course last week with a Taverna and BioMOBY workshop. Fortunately Eddie was there :) and I have a patched Taverna 1.6.2 we used for that course. It has the speed issue described above, bu apart from that it's fully functional. Let me know if you need copy... Cheers, Pi On 18-dec-2007, at 14:30, Andreas Groscurth wrote: > Hi, > > since the movement of Moby we have severe problems with Taverna and > Moby. > > When taverna tries to retrieve information about a dataobject (e.g. > in the > 'Brief search' for matching services), we always run into a > NullPointerException with the message "Cannot parse MOBY Object > Ontology" in > > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF > > > My guess is, that there is somehow the 'old' pre-movement code and > because of > that its not working. > > If so - I would be more than glad and thankfull if one can repair > these > asap... we are working currently a lot with taverna and like to > present it > (and moby) to our students... but in this state its not really > presentable :-( > > Hope this can be fixed soon. > > Thanks > andreas > > -- > Andreas Groscurth > Bioinformatics Developer > Max Planck Institute for Plant Breeding Research > Carl-von-Linn?-Weg 10 > 50829 Cologne > Germany > E-mail: groscurt at mpiz-koeln.mpg.de > Phone: +49(0)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From ssoiland at cs.man.ac.uk Tue Dec 18 09:42:19 2007 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Tue, 18 Dec 2007 14:42:19 +0000 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: <43abb4040712180642m6402e12dl7a2f319738a55d70@mail.gmail.com> On 12/18/07, Pieter Neerincx wrote: > A new Taverna 1.7 that > contains fixes for these issues was announced for monday December 17 > (yesterday). Apparently it's delayed a bit, but you'll probably see > it very soon. It should be out in a few hours. :-) -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From gordonp at ucalgary.ca Tue Dec 18 13:08:44 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 18 Dec 2007 11:08:44 -0700 Subject: [MOBY-dev] Commits mailing list awry? Message-ID: <47680CAC.1080202@ucalgary.ca> Hi all, Am I the only one no longer receiving commits e-mails? I'm not sure if my mail server is trashing them, or if the open-bio server just isn't sending them. I've committed several file in the last week, and have received bupkis From markw at illuminae.com Tue Dec 18 13:59:28 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 18 Dec 2007 18:59:28 +0000 GMT Subject: [MOBY-dev] Commits mailing list awry? In-Reply-To: <47680CAC.1080202@ucalgary.ca> References: <47680CAC.1080202@ucalgary.ca> Message-ID: <1476491191-1198004368-cardhu_blackberry.rim.net-11822-@engine27-cell01> I still receive them, and haven't touched the mailing system... -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Tue, 18 Dec 2007 11:08:44 To:Core developer announcements Subject: [MOBY-dev] Commits mailing list awry? Hi all, Am I the only one no longer receiving commits e-mails? I'm not sure if my mail server is trashing them, or if the open-bio server just isn't sending them. I've committed several file in the last week, and have received bupkis _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Wed Dec 19 11:13:25 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 19 Dec 2007 17:13:25 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <4756E14E.3030809@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> <4756E14E.3030809@ucalgary.ca> Message-ID: <96A0EC82-DD5C-43C8-9528-FA4B1266C2EC@farmbio.uu.se> Hi, What is the status of the CentralDigestCachedImpl? What does it cache now and what is cached using the RegistryCache? If I use MobyServiceType.loadServiceTypes(serviceTypesDefURL, mobyRegistry); to cache service types, how does this relate to the CentralDigestCachedImpl? There were talks of simplifying this process and I'm sorry if I have missed something on the list regarding this. Thanks, .../Ola On Dec 5, 2007, at 18:35 , Paul Gordon wrote: > Hi Andreas, > > I just simplified it a bit, so it's two lines (and should not be > garbled > in split lines the e-mail) >> Registry registry = new Registry("calgary", "http:// >> moby.ucalgary.ca/moby/MOBY-Central.pl", "http://moby.ucalgary.ca/ >> MOBY/Central"); >> MobyDataType.loadDataTypes(RegistryCache.cacheOntologyFile >> (registry, Central.DATA_TYPES_RESOURCE_NAME, >> allowedAgeMillis).toURI().toURL(), registry); >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Dec 19 12:04:28 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 19 Dec 2007 10:04:28 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <96A0EC82-DD5C-43C8-9528-FA4B1266C2EC@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> <4756E14E.3030809@ucalgary.ca> <96A0EC82-DD5C-43C8-9528-FA4B1266C2EC@farmbio.uu.se> Message-ID: <47694F1C.7010300@ucalgary.ca> Hi Ola, This is still on the "to do" list, as we don't yet have unit tests to make sure the integration is backward compatible. We'll let you know as soon as its done. Once again, if you are using org.biomoby.shared.data, this is primarily for elegance, not performance, as CentralImpls and the MobyDataType/MobyNamespace/MobyServiceType classes are caching different kinds of information generally. Regards, Paul Ola Spjuth wrote: > Hi, > > What is the status of the CentralDigestCachedImpl? What does it cache > now and what is cached using the RegistryCache? If I use > MobyServiceType.loadServiceTypes(serviceTypesDefURL, mobyRegistry); to > cache service types, how does this relate to the > CentralDigestCachedImpl? There were talks of simplifying this process > and I'm sorry if I have missed something on the list regarding this. > > Thanks, > > .../Ola > > > > On Dec 5, 2007, at 18:35 , Paul Gordon wrote: > >> Hi Andreas, >> >> I just simplified it a bit, so it's two lines (and should not be garbled >> in split lines the e-mail) >>> Registry registry = new Registry("calgary", >>> "http://moby.ucalgary.ca/moby/MOBY-Central.pl", >>> "http://moby.ucalgary.ca/MOBY/Central"); >>> MobyDataType.loadDataTypes(RegistryCache.cacheOntologyFile(registry, >>> Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis).toURI().toURL(), >>> registry); >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From edward.kawas at gmail.com Wed Dec 19 14:14:41 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Dec 2007 11:14:41 -0800 Subject: [MOBY-dev] generating rdf for services that have already been registered Message-ID: <0A564BBA2CD74E3DAA6296216FAA22B9@OfficePC> Hi, I have been getting requests from people to produce a web form that produces RDF for services that have already been registered (similar to a form that once existed). This cgi script is also located in the cvs @ moby-live/Perl/scripts/GenerateRDF.cgi I have done so and the form for the default mobycentral registry is located at: http://moby.ucalgary.ca/cgi-bin/GenerateRDF.cgi Unfortunately, unlike the previous form, you cannot use this form to modify signatureURLs. If people want this functionality, please let me know and I might add it at a later date. If you have any questions, comments or concerns, please let me know! Eddie From sylvie.huchet at enst-bretagne.fr Thu Dec 20 10:43:41 2007 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Thu, 20 Dec 2007 16:43:41 +0100 Subject: [MOBY-dev] Calling moby-async category services Message-ID: <476A8DAD.1060208@enst-bretagne.fr> Hi, I'd like to know how asynchronous services (category moby-async) can be called using the java API : the CentralImpl.findService method returns only synchronous services (category moby). Besides, is it possible to see asynchronous services with the Dashborad client ? By default they are not visible. Some services have been their category changed from moby to moby-async... Thanks a lot, Sylvie. -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From martin.senger at gmail.com Thu Dec 20 12:17:51 2007 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 20 Dec 2007 09:17:51 -0800 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <476A8DAD.1060208@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> Message-ID: <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> > I'd like to know how asynchronous services (category moby-async) can be > called > using the java API It is on the to-do list. A good opportunity to implement it will be the second week of February where several BioMoby developers meet at the Biohackaton in Japan. I hope to use this event to remove most of the items from my long-standing moby-to-do list. I am sorry for the delay. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Thu Dec 20 14:54:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 20 Dec 2007 12:54:26 -0700 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> Message-ID: <476AC872.70408@ucalgary.ca> Hi Sylvie, The current class that implements asynchronous service calls is MobyRequest (via AsyncClient). You can find both synchronous and asynchronous services by setting the Service category to the empty string ("") before calling CentralImpl. As Martin mentions below, the mechanism currently used to run asynchronous services will change next year (so there will probably be other ways to call async services introduced), but the MobyRequest API will not need to change. MobyRequest handles both synchronous and asynchronous calls transparently. Regards, Paul Martin Senger wrote: >> I'd like to know how asynchronous services (category moby-async) can be >> called >> using the java API >> > > > It is on the to-do list. A good opportunity to implement it will be the > second week of February where several BioMoby developers meet at the > Biohackaton in Japan. I hope to use this event to remove most of the items > from my long-standing moby-to-do list. I am sorry for the delay. > > Martin > > From sylvie.huchet at enst-bretagne.fr Thu Dec 20 16:49:18 2007 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Thu, 20 Dec 2007 22:49:18 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <476AC872.70408@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> Message-ID: <476AE35E.1080607@enst-bretagne.fr> Thank you for the information of how finding both synchronous and asynchronous services. No possibilities to view asynchronous services with the Dashboard client ? Regards, Sylvie. Paul Gordon a ?crit : > Hi Sylvie, > > The current class that implements asynchronous service calls is > MobyRequest (via AsyncClient). You can find both synchronous and > asynchronous services by setting the Service category to the empty > string ("") before calling CentralImpl. As Martin mentions below, the > mechanism currently used to run asynchronous services will change next > year (so there will probably be other ways to call async services > introduced), but the MobyRequest API will not need to change. > MobyRequest handles both synchronous and asynchronous calls transparently. > > Regards, > > Paul > > Martin Senger wrote: > >>> I'd like to know how asynchronous services (category moby-async) can be >>> called >>> using the java API >>> >> >> >> >> It is on the to-do list. A good opportunity to implement it will be the >> second week of February where several BioMoby developers meet at the >> Biohackaton in Japan. I hope to use this event to remove most of the >> items >> from my long-standing moby-to-do list. I am sorry for the delay. >> >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From groscurt at mpiz-koeln.mpg.de Mon Dec 3 08:45:31 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 3 Dec 2007 09:45:31 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200711301223.07171.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <47267E18.4010509@ucalgary.ca> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> Message-ID: <200712030945.32685.groscurt@mpiz-koeln.mpg.de> Hi, I'm using CentralDigestCachedImpl for caching the datatypes and namespaces locally. CentralDigestCachedImpl cachedImpl = new CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl","http://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); This works fine and re-calls use the local cache. But when I create a new MobyDataObject, it starts again to fetch the datatypes Fetching data type ontology from http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects So how do I tell it, that its already has these information ? the MobyDataObject can also have a Registry Object - so i guess that can help - but how to I link my CachedCentral with a Registry object ? Or is this otherwise solveable ? thx andreas From ssoiland at cs.man.ac.uk Mon Dec 3 12:04:57 2007 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Mon, 3 Dec 2007 12:04:57 +0000 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: Message-ID: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> On 11/30/07, Mark Wilkinson wrote: > To migrate Taverna, edit the taverna/conf/mygrid.properties file to point > to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl Should we change the default in Taverna's shipped mygrid.properties to the ucalgary one? We have a Taverna 1.7 release going out in a few weeks and would of course like BioMoby to work by default.. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From edward.kawas at gmail.com Mon Dec 3 14:25:48 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 3 Dec 2007 06:25:48 -0800 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> Message-ID: Hi Stian, I just replaced all instances where mobycentral was used to ucalgary. I also had to update the biomoby plugins maven repository to be the new one at ucalgary. Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland Sent: December-03-07 4:05 AM To: Core developer announcements Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! On 11/30/07, Mark Wilkinson wrote: > To migrate Taverna, edit the taverna/conf/mygrid.properties file to point > to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl Should we change the default in Taverna's shipped mygrid.properties to the ucalgary one? We have a Taverna 1.7 release going out in a few weeks and would of course like BioMoby to work by default.. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From arnaud at ebi.ac.uk Wed Dec 5 09:28:18 2007 From: arnaud at ebi.ac.uk (Arnaud Kerhornou) Date: Wed, 05 Dec 2007 09:28:18 +0000 Subject: [MOBY-dev] biomoby.org down ? Message-ID: <47566F32.8050804@ebi.ac.uk> Hi, When I try to go to biomoby.org on my browser, I get to a WordPress error page, saying, "error establishing a database connection", so is biomoby site down ? Arnaud From Pieter.Neerincx at wur.nl Wed Dec 5 10:55:18 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 5 Dec 2007 11:55:18 +0100 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: <47566F32.8050804@ebi.ac.uk> References: <47566F32.8050804@ebi.ac.uk> Message-ID: <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: > Hi, > > When I try to go to biomoby.org on my browser, I get to a WordPress > error page, saying, "error establishing a database connection", > so is biomoby site down ? Yep, same overhere :(... > > Arnaud > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Wed Dec 5 14:48:04 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 Dec 2007 06:48:04 -0800 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> References: <47566F32.8050804@ebi.ac.uk> <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> Message-ID: It's working from Canada. Are you still having problems there? M On Wed, 05 Dec 2007 02:55:18 -0800, Pieter Neerincx wrote: > > On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: > >> Hi, >> >> When I try to go to biomoby.org on my browser, I get to a WordPress >> error page, saying, "error establishing a database connection", >> so is biomoby site down ? > > Yep, same overhere :(... > >> >> Arnaud >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Wed Dec 5 14:57:08 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 05 Dec 2007 15:57:08 +0100 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: References: <47566F32.8050804@ebi.ac.uk> <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> Message-ID: <4756BC44.2030908@toulouse.inra.fr> Bonjour, It's working now. Sebastien Mark Wilkinson wrote: > It's working from Canada. Are you still having problems there? > > M > > > On Wed, 05 Dec 2007 02:55:18 -0800, Pieter Neerincx > wrote: > > >> On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: >> >> >>> Hi, >>> >>> When I try to go to biomoby.org on my browser, I get to a WordPress >>> error page, saying, "error establishing a database connection", >>> so is biomoby site down ? >>> >> Yep, same overhere :(... >> >> >>> Arnaud >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From Pieter.Neerincx at wur.nl Wed Dec 5 15:01:32 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 5 Dec 2007 16:01:32 +0100 Subject: [MOBY-dev] biomoby.org down ? In-Reply-To: References: <47566F32.8050804@ebi.ac.uk> <87222CA4-B89C-45B0-BEED-4AD2E6E93056@wur.nl> Message-ID: Yep, site is back overhere as well :) On 5-dec-2007, at 15:48, Mark Wilkinson wrote: > It's working from Canada. Are you still having problems there? > > M > > > On Wed, 05 Dec 2007 02:55:18 -0800, Pieter Neerincx > wrote: > >> >> On 5-dec-2007, at 10:28, Arnaud Kerhornou wrote: >> >>> Hi, >>> >>> When I try to go to biomoby.org on my browser, I get to a WordPress >>> error page, saying, "error establishing a database connection", >>> so is biomoby site down ? >> >> Yep, same overhere :(... >> >>> >>> Arnaud >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From groscurt at mpiz-koeln.mpg.de Wed Dec 5 16:42:51 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 5 Dec 2007 17:42:51 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200712030945.32685.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> Message-ID: <200712051742.51315.groscurt@mpiz-koeln.mpg.de> Hi, sorry for reasking that - but has anyone an answer ? Thanks andreas On Monday 03 December 2007 09:45, Andreas Groscurth wrote: > Hi, > > I'm using CentralDigestCachedImpl for caching the datatypes and namespaces > locally. > > CentralDigestCachedImpl cachedImpl = new > CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl","htt >p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); > cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); > cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); > > This works fine and re-calls use the local cache. > > But when I create a new MobyDataObject, it starts again to fetch the > datatypes > > Fetching data type ontology from > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > > So how do I tell it, that its already has these information ? the > MobyDataObject can also have a Registry Object - so i guess that can help - > but how to I link my CachedCentral with a Registry object ? > > Or is this otherwise solveable ? > > thx > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gordonp at ucalgary.ca Wed Dec 5 17:21:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 05 Dec 2007 10:21:37 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200712051742.51315.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> Message-ID: <4756DE21.3000105@ucalgary.ca> Hi Andreas, The concluision we reached a few weeks ago is that CentralDigestCachedImpl and org.biomoby.shared.data.* use different catching schemes,which I will reconcile once Martin has set up some unit tests for the CentralImpls. Usually there is no compelling reason to use both caches...if you are using org.biomoby.shared.data.* to create and past data instances, CentralDigestCachedImpl.CACHE_PART_DATATYPES doesn't really do anything for you, and vice versa. If you are using org.biomoby.shared.data.*, drop the updateCache() calls you had, and use instead: Registry registry = new Registry("calgary", "http://moby.ucalgary.ca/moby/MOBY-Central.pl", "http://moby.ucalgary.ca/MOBY/Central"); RegistryCache.cacheOntologyFile(registry, Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis); MobyDataType.loadDataTypes(RegistryCache.getOntologyFile(registry, Central.DATA_TYPES_RESOURCE_NAME).toURI().toURL(), registry); I just added the allowedAgeMillis parameter for convenience. You'll want to do a CVS update. For MobyNamespace it's similar.. MobyNamespace.loadNamespaces(RegistryCache.getOntologyFile(registry, Central.NAMESPACES_RESOURCE_NAME).toURI().toURL(), registry); Hopefully, we can reconcile the Central calls cache and this code soon, so you don't need to pick. I could have also made a MobyNamespace.loadNamespaces(registry) method, but in keeping with the Law of Demeter, it's better for MobyNamespace and MobyDataType to not explicitly know about RegistryCache, hence the MobyNamespace.loadNamespaces(url, registry) signature. Regards, Paul Andreas Groscurth wrote: > Hi, > > sorry for reasking that - but has anyone an answer ? > > Thanks > andreas > > On Monday 03 December 2007 09:45, Andreas Groscurth wrote: > >> Hi, >> >> I'm using CentralDigestCachedImpl for caching the datatypes and namespaces >> locally. >> >> CentralDigestCachedImpl cachedImpl = new >> CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl","htt >> p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); >> >> This works fine and re-calls use the local cache. >> >> But when I create a new MobyDataObject, it starts again to fetch the >> datatypes >> >> Fetching data type ontology from >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >> >> So how do I tell it, that its already has these information ? the >> MobyDataObject can also have a Registry Object - so i guess that can help - >> but how to I link my CachedCentral with a Registry object ? >> >> Or is this otherwise solveable ? >> >> thx >> andreas >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From gordonp at ucalgary.ca Wed Dec 5 17:35:10 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 05 Dec 2007 10:35:10 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <4756DE21.3000105@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> Message-ID: <4756E14E.3030809@ucalgary.ca> Hi Andreas, I just simplified it a bit, so it's two lines (and should not be garbled in split lines the e-mail) > Registry registry = new Registry("calgary", "http://moby.ucalgary.ca/moby/MOBY-Central.pl", "http://moby.ucalgary.ca/MOBY/Central"); > MobyDataType.loadDataTypes(RegistryCache.cacheOntologyFile(registry, Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis).toURI().toURL(), registry); > From markw at illuminae.com Wed Dec 5 17:36:13 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 05 Dec 2007 09:36:13 -0800 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: Here is the (very rapid!) review from Briefings in Bioinformatics. LOL! Well, the reviewers couldn't differ more in their desires for the manuscript!! It's almost as if we should write TWO manuscipts... one for each audience. Actually, I did suggest this on-list a few weeks ago, but nobody was brave enough to take me up on the suggestion... are there any takers now? Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. I should still have time to do some editing if anyone has suggestions. Best wishes! Mark ------- Forwarded message ------- From: briefings at oxfordjournals.org To: markw at illuminae.com Cc: Subject: Briefings in Bioinformatics - Decision on BIB-07-0068 Date: Tue, 04 Dec 2007 08:04:55 -0800 04-Dec-2007 Dear Dr Wilkinson, I am writing to inform you that your manuscript entitled 'Interoperability with Moby 1.0 - It?s Better than Sharing Your Toothbrush!' (BIB-07-0068) has now been peer-reviewed. The comments of the reviewers follow at the end of this email. We should like to invite you to respond to the comments of the reviewers and revise your manuscript according to their suggestions. To revise your manuscript, log into http://mc.manuscriptcentral.com/bib and enter your Author Center, where you will find your manuscript listed under "Manuscripts with Decisions." Under "Actions," click on "Create a Revision." When creating your revision, you will be asked to provide a response to the reviewers' comments, point-by-point. Where possible, please provide this response in the text box provided, rather than uploading your response as a document. Please ensure that any changes made to your manuscript are highlighted in colour, bold or underlining. By doing this, you will help us to minimise the time needed to provide you with a decision. IMPORTANT: Your original files are available to you when you upload your revised manuscript. Please delete any redundant files before completing the submission. Because we are trying to facilitate timely publication of manuscripts submitted to Briefings in Bioinformatics, we request that you submit your revised manuscript within the next four weeks. Once again, thank you for submitting your manuscript to Briefings in Bioinformatics and I look forward to receiving your revised paper in due course. Yours sincerely, Sophie Gilmour On behalf of Dr Martin Bishop, Editor-in-Chief, Briefings in Bioinformatics Reviewers' Comments to Author: Reviewer: 1 Comments to the Author This manuscript presents BioMoby, a mature framework for data integration and interoperability between web services. BioMoby has been developed over the last 5 years by a world wide community. These developments have now reached an important point: the stable version 1.0 of BioMoby is being presented here. This manuscript gives a description of how the framework is organized technically, compares it to peer semantic and schema technologies and presents a use case how a ?Biologist? can use it to execute an analysis workflow. For a reader with technical background the paper is well written and gives a good overview of the framework. At the same time this issue is also our largest concern with this manuscript. Overall it feels rather technical and it seems to be addressing primarily bioinformatics developers. This manuscript has been submitted to Briefings in Bioinformatics which has a more user oriented target group. It would be nice to introduce BioMoby particularly to those end users, but we feel that the focus of this manuscript needs an adjustment for this. The example of pages 4 and 5 of the actual workflow of an analysis is interesting to read and demonstrates the power of BioMoby well. We suggest to support this with screenshots of how the user can actually perform the steps of this analysis. The comparison with other semantic web standards is fine for a technical audience, but in this case it might be going too much into detail. Reviewer: 2 Comments to the Author I believe it could be improved with additional discussion and assessment of the differences between its approach and W3C Semantic Web. As the author states, BioMoby developed independently from the W3C semantic web specifications yet is addressing at least in part, some of the same use-cases in bioinformatics. Granted this is more from a service perspective than a knowledge-model perspective. Nonetheless, the rather "independent" evolution of these two approaches, particularly in light of the more productionized current state of BioMoby, suggests a more extensive comparison of the two paths of development. I would like to see such an expanded discussion in the paper - even a few more paragraphs. Editor's Comments to Author: Editor: 1 Comments to the Author: The referees differ somewhat in the balance expected. It is true that Briefings is orientated to Biological users. However, it is also read by Bioinformatics developers. The editor leaves it to the author to decide how to deal with these different emphases. -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From edward.kawas at gmail.com Thu Dec 6 16:04:22 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 6 Dec 2007 08:04:22 -0800 Subject: [MOBY-dev] jmoby CentralImpl is updated Message-ID: Hi, CentralImpl has been updated to reflect the newest mobycentral endpoint/namespace. 2 methods were created: getDefaultURI/getDefaultURL that query http://biomoby.org/mobycentral iff the system property 'moby.check.default' exists and is set to true. ***IMPORTANT*** Also, note that a new dependency 'commons-codec' was needed so make sure to do an 'ant gather' | './build-dev.sh gather' before using the new code. Eddie From phillip.lord at newcastle.ac.uk Thu Dec 6 17:54:11 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Thu, 06 Dec 2007 17:54:11 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: (Mark Wilkinson's message of "Wed\, 05 Dec 2007 09\:36\:13 -0800") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: <878x47iu9o.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil From phillip.lord at newcastle.ac.uk Thu Dec 6 17:54:11 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Thu, 06 Dec 2007 17:54:11 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: (Mark Wilkinson's message of "Wed\, 05 Dec 2007 09\:36\:13 -0800") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: <878x47iu9o.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil From markw at illuminae.com Thu Dec 6 17:52:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Thu, 6 Dec 2007 17:52:35 +0000 GMT Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <878x47iu9o.fsf@dinley.ncl.ac.uk> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> Message-ID: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Is that a hint? -- Mark Wilkinson ...on the road! -----Original Message----- From: Phillip Lord Date: Thu, 06 Dec 2007 17:54:11 To:Core developer announcements Cc:Core developer announcements Subject: Re: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Dec 6 17:52:35 2007 From: markw at illuminae.com (mark wilkinson) Date: Thu, 6 Dec 2007 17:52:35 +0000 GMT Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <878x47iu9o.fsf@dinley.ncl.ac.uk> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> Message-ID: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Is that a hint? -- Mark Wilkinson ...on the road! -----Original Message----- From: Phillip Lord Date: Thu, 06 Dec 2007 17:54:11 To:Core developer announcements Cc:Core developer announcements Subject: Re: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 >>>>> "Mark" == Mark Wilkinson writes: Mark> Here is the (very rapid!) review from Briefings in Bioinformatics. Mark> LOL! Well, the reviewers couldn't differ more in their desires for the Mark> manuscript!! It's almost as if we should write TWO manuscipts... one Mark> for each audience. Actually, I did suggest this on-list a few weeks Mark> ago, but nobody was brave enough to take me up on the suggestion... Mark> are there any takers now? Mark> Comments are welcome. I'm leaving for Moby meetings/talks in Koln, Mark> Wageningen, and Amsterdam tomorrow so I am away for the next 10 days. Mark> I should still have time to do some editing if anyone has suggestions. Entertaining. Mark> Reviewer: 2 Comments to the Author I believe it could be improved with Mark> additional discussion and assessment of the differences between its Mark> approach and W3C Semantic Web. Mark> As the author states, BioMoby developed independently from the W3C Mark> semantic web specifications yet is addressing at least in part, some Mark> of the same use-cases in bioinformatics. Granted this is more from a Mark> service perspective than a knowledge-model perspective. Nonetheless, Mark> the rather "independent" evolution of these two approaches, Mark> particularly in light of the more productionized current state of Mark> BioMoby, suggests a more extensive comparison of the two paths of Mark> development. Mark> I would like to see such an expanded discussion in the paper - even a Mark> few more paragraphs. Mark> Editor's Comments to Author: Editor: 1 Comments to the Author: The Mark> referees differ somewhat in the balance expected. It is true that Mark> Briefings is orientated to Biological users. However, it is also read Mark> by Bioinformatics developers. The editor leaves it to the author to Mark> decide how to deal with these different emphases. Well, you could write two papers, but the other approach would be to refer to any other work which compared biomoby to current semantic web approaches. I'm not sure that such a paper exists, but you might be able to find one with google... Phil _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Thu Dec 6 18:04:24 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Thu, 06 Dec 2007 18:04:24 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: <878x47iu9o.fsf@dinley.ncl.ac.uk> References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> Message-ID: <475839A8.8060106@cs.man.ac.uk> Phillip Lord wrote: > Well, you could write two papers, but the other approach would be to refer to > any other work which compared biomoby to current semantic web approaches. currently exists in phd form. http://www.cs.man.ac.uk/~hulld/phd/ robert wants to write it up as a paper, which we'll do next year I think the theory and the practice (myGrid, Taverna and BioMOBY) are poles apart, as you know, they are like chalk and cheese. Duncan -- Duncan Hull http://duncan.hull.name +44 (0) 161 306 5139 From Pieter.Neerincx at wur.nl Thu Dec 6 18:42:08 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 6 Dec 2007 19:42:08 +0100 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision on BIB-07-0068 In-Reply-To: References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> Message-ID: <84AE6BA0-5EF2-4B60-B570-C4A6A389B36B@wur.nl> Hi Mark et al., On 5-dec-2007, at 18:36, Mark Wilkinson wrote: > Here is the (very rapid!) review from Briefings in Bioinformatics. > > LOL! Well, the reviewers couldn't differ more in their desires for > the > manuscript!! It's almost as if we should write TWO manuscipts... > one for > each audience. "The editor leaves it to the author to decide how to deal with these different emphases." Hmmm that sounds like what I sometimes do when I'm making a new tool and don't know how to solve a problem: make it a user configurable parameter and sell my lack of inspiration as a feature as in "it's completely customisable" :). Anyway, in the end it's the editors who decide what they want in their magazine, so in my opinion it's the editor who should tell us what he/she wants in BIB. We could adjust according to reviewer one or two or split up into two articles and adjust according to both, but it would be a shame if we adjust to reviewer 1 and then in the end BIB tells us they rejected the manuscript, because they were looking for something like suggested by reviewer two. Maybe we should just explicitly ask the editor to tell us what they want... My 0.02 ? Pi > Actually, I did suggest this on-list a few weeks ago, but > nobody was brave enough to take me up on the suggestion... are > there any > takers now? > > Comments are welcome. I'm leaving for Moby meetings/talks in Koln, > Wageningen, and Amsterdam tomorrow so I am away for the next 10 > days. I > should still have time to do some editing if anyone has suggestions. > Best wishes! > > Mark > > > > > ------- Forwarded message ------- > From: briefings at oxfordjournals.org > To: markw at illuminae.com > Cc: > Subject: Briefings in Bioinformatics - Decision on BIB-07-0068 > Date: Tue, 04 Dec 2007 08:04:55 -0800 > > 04-Dec-2007 > > Dear Dr Wilkinson, > > I am writing to inform you that your manuscript entitled > 'Interoperability > with Moby 1.0 - It?s Better than Sharing Your > Toothbrush!' (BIB-07-0068) > has now been peer-reviewed. The comments of the reviewers follow > at the > end of this email. > > We should like to invite you to respond to the comments of the > reviewers > and revise your manuscript according to their suggestions. > > To revise your manuscript, log into http://mc.manuscriptcentral.com/ > bib > and enter your Author Center, where you will find your manuscript > listed > under "Manuscripts with Decisions." Under "Actions," click on > "Create a > Revision." > > When creating your revision, you will be asked to provide a > response to > the reviewers' comments, point-by-point. Where possible, please > provide > this response in the text box provided, rather than uploading your > response as a document. Please ensure that any changes made to your > manuscript are highlighted in colour, bold or underlining. By > doing this, > you will help us to minimise the time needed to provide you with a > decision. > > IMPORTANT: Your original files are available to you when you > upload your > revised manuscript. Please delete any redundant files before > completing > the submission. > > Because we are trying to facilitate timely publication of manuscripts > submitted to Briefings in Bioinformatics, we request that you > submit your > revised manuscript within the next four weeks. > > Once again, thank you for submitting your manuscript to Briefings in > Bioinformatics and I look forward to receiving your revised paper > in due > course. > > Yours sincerely, > > > > Sophie Gilmour > On behalf of Dr Martin Bishop, > Editor-in-Chief, Briefings in Bioinformatics > > Reviewers' Comments to Author: > Reviewer: 1 > Comments to the Author > This manuscript presents BioMoby, a mature framework for data > integration > and interoperability between web services. BioMoby has been > developed over > the last 5 years by a world wide community. These developments have > now > reached an important point: the stable version 1.0 of BioMoby is being > presented here. This manuscript gives a description of how the > framework > is organized technically, compares it to peer semantic and schema > technologies and presents a use case how a ?Biologist? can use it to > execute an analysis workflow. > > For a reader with technical background the paper is well written > and gives > a good overview of the framework. At the same time this issue is > also > our largest concern with this manuscript. Overall it feels rather > technical and it seems to be addressing primarily bioinformatics > developers. This manuscript has been submitted to Briefings in > Bioinformatics which has a more user oriented target group. It > would be > nice to introduce BioMoby particularly to those end users, but we feel > that the focus of this manuscript needs an adjustment for this. > > The example of pages 4 and 5 of the actual workflow of an analysis is > interesting to read and demonstrates the power of BioMoby well. We > suggest > to support this with screenshots of how the user can actually > perform the > steps of this analysis. The comparison with other semantic web > standards > is fine for a technical audience, but in this case it might be > going too > much into detail. > > Reviewer: 2 > Comments to the Author > I believe it could be improved with additional discussion and > assessment > of the differences between its approach and W3C Semantic Web. > > As the author states, BioMoby developed independently from the W3C > semantic web specifications yet is addressing at least in part, > some of > the same use-cases in bioinformatics. Granted this is more from a > service > perspective than a knowledge-model perspective. Nonetheless, the > rather > "independent" evolution of these two approaches, particularly in > light of > the more productionized current state of BioMoby, suggests a more > extensive comparison of the two paths of development. > > I would like to see such an expanded discussion in the paper - even > a few > more paragraphs. > > Editor's Comments to Author: > Editor: 1 > Comments to the Author: > The referees differ somewhat in the balance expected. > It is true that Briefings is orientated to Biological users. > However, it is also read by Bioinformatics developers. > The editor leaves it to the author to decide how to deal with these > different emphases. > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have > received this > communication in error, please notify the sender immediately by reply > e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Fri Dec 7 09:51:52 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 07 Dec 2007 10:51:52 +0100 Subject: [MOBY-dev] getDeadServices Message-ID: <475917B8.8060505@toulouse.inra.fr> Bonjour ? tous, Is there on the new server the list of dead services as returned by the old URL: http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService?getDeadServices It's very usefull to filter available and almost working services. Thanks, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From Pieter.Neerincx at wur.nl Fri Dec 7 11:01:45 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 7 Dec 2007 12:01:45 +0100 Subject: [MOBY-dev] getDeadServices In-Reply-To: <475917B8.8060505@toulouse.inra.fr> References: <475917B8.8060505@toulouse.inra.fr> Message-ID: <9986FF15-72DF-414A-A1AE-3A6402245638@wur.nl> Hi Sebastien, Yes, try : http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Cheers, Pi On 7-dec-2007, at 10:51, Sebastien Carrere wrote: > Bonjour ? tous, > > Is there on the new server the list of dead services as returned by > the old URL: > http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService? > getDeadServices > > > It's very usefull to filter available and almost working services. > > Thanks, > > Sebastien > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Fri Dec 7 11:51:56 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Fri, 07 Dec 2007 12:51:56 +0100 Subject: [MOBY-dev] getDeadServices In-Reply-To: <9986FF15-72DF-414A-A1AE-3A6402245638@wur.nl> References: <475917B8.8060505@toulouse.inra.fr> <9986FF15-72DF-414A-A1AE-3A6402245638@wur.nl> Message-ID: <475933DC.1020109@toulouse.inra.fr> Great ! Thanks Pieter. Sebastien. Pieter Neerincx wrote: > Hi Sebastien, > > Yes, try : http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers, > > Pi > > On 7-dec-2007, at 10:51, Sebastien Carrere wrote: > > >> Bonjour ? tous, >> >> Is there on the new server the list of dead services as returned by >> the old URL: >> http://mobycentral.icapture.ubc.ca:8090/authority/ValidateService? >> getDeadServices >> >> >> It's very usefull to filter available and almost working services. >> >> Thanks, >> >> Sebastien >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From phillip.lord at newcastle.ac.uk Fri Dec 7 15:50:21 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Fri, 07 Dec 2007 15:50:21 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> (mark wilkinson's message of "Thu\, 6 Dec 2007 17\:52\:35 +0000 GMT") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Message-ID: <87y7c6v70i.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == mark wilkinson writes: Mark> Is that a hint? Just thought it might help. It's your paper. I leave it to the authors to decide how to deal....etc Phil From phillip.lord at newcastle.ac.uk Fri Dec 7 15:50:21 2007 From: phillip.lord at newcastle.ac.uk (Phillip Lord) Date: Fri, 07 Dec 2007 15:50:21 +0000 Subject: [MOBY-dev] Fwd: Briefings in Bioinformatics - Decision onBIB-07-0068 In-Reply-To: <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> (mark wilkinson's message of "Thu\, 6 Dec 2007 17\:52\:35 +0000 GMT") References: <380684995.1196784295870.JavaMail.wladmin@mcv3-wl17> <878x47iu9o.fsf@dinley.ncl.ac.uk> <1872088192-1196963792-cardhu_blackberry.rim.net-15473-@engine24-cell01> Message-ID: <87y7c6v70i.fsf@dinley.ncl.ac.uk> >>>>> "Mark" == mark wilkinson writes: Mark> Is that a hint? Just thought it might help. It's your paper. I leave it to the authors to decide how to deal....etc Phil From groscurt at mpiz-koeln.mpg.de Fri Dec 7 16:16:41 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 7 Dec 2007 17:16:41 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <4756DE21.3000105@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> Message-ID: <200712071716.41802.groscurt@mpiz-koeln.mpg.de> Hi Paul, thanks for the message... So do i understand it correctly ? I create such Registry object and then I pass that instance to any of the org.biomoby.shared.data.*. e.g. new MobyDataObject( "something", "anything", registry) ? thanks andreas On Wednesday 05 December 2007 18:21, Paul Gordon wrote: > Hi Andreas, > > The concluision we reached a few weeks ago is that > CentralDigestCachedImpl and org.biomoby.shared.data.* use different > catching schemes,which I will reconcile once Martin has set up some unit > tests for the CentralImpls. Usually there is no compelling reason to > use both caches...if you are using org.biomoby.shared.data.* to create > and past data instances, CentralDigestCachedImpl.CACHE_PART_DATATYPES > doesn't really do anything for you, and vice versa. If you are using > org.biomoby.shared.data.*, drop the updateCache() calls you had, and use > instead: > > Registry registry = new Registry("calgary", > "http://moby.ucalgary.ca/moby/MOBY-Central.pl", > "http://moby.ucalgary.ca/MOBY/Central"); > RegistryCache.cacheOntologyFile(registry, > Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis); > MobyDataType.loadDataTypes(RegistryCache.getOntologyFile(registry, > Central.DATA_TYPES_RESOURCE_NAME).toURI().toURL(), registry); > > I just added the allowedAgeMillis parameter for convenience. You'll want > to do a CVS update. For MobyNamespace it's similar.. > > MobyNamespace.loadNamespaces(RegistryCache.getOntologyFile(registry, > Central.NAMESPACES_RESOURCE_NAME).toURI().toURL(), registry); > > Hopefully, we can reconcile the Central calls cache and this code soon, > so you don't need to pick. I could have also made a > MobyNamespace.loadNamespaces(registry) method, but in keeping with the > Law of Demeter, it's better for MobyNamespace and MobyDataType to not > explicitly know about RegistryCache, hence the > MobyNamespace.loadNamespaces(url, registry) signature. > > Regards, > > Paul > > Andreas Groscurth wrote: > > Hi, > > > > sorry for reasking that - but has anyone an answer ? > > > > Thanks > > andreas > > > > On Monday 03 December 2007 09:45, Andreas Groscurth wrote: > >> Hi, > >> > >> I'm using CentralDigestCachedImpl for caching the datatypes and > >> namespaces locally. > >> > >> CentralDigestCachedImpl cachedImpl = new > >> CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl"," > >>htt p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); > >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); > >> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); > >> > >> This works fine and re-calls use the local cache. > >> > >> But when I create a new MobyDataObject, it starts again to fetch the > >> datatypes > >> > >> Fetching data type ontology from > >> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects > >> > >> So how do I tell it, that its already has these information ? the > >> MobyDataObject can also have a Registry Object - so i guess that can > >> help - but how to I link my CachedCentral with a Registry object ? > >> > >> Or is this otherwise solveable ? > >> > >> thx > >> andreas > >> _______________________________________________ > >> MOBY-dev mailing list > >> MOBY-dev at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From gordonp at ucalgary.ca Fri Dec 7 16:26:52 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 07 Dec 2007 09:26:52 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <200712071716.41802.groscurt@mpiz-koeln.mpg.de> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> <200712071716.41802.groscurt@mpiz-koeln.mpg.de> Message-ID: <4759744C.5090608@ucalgary.ca> Yes. If you use the default c-tor for anything, e.g.: new MobyDataObject( "something", "anything") this is the same as setting the registry to null. Because the null registry uses the default registry from RegistriesList, and this still points to the defunct server in Vancouver, the default c-tors currently fail. It was actually a good opportunity for me to discover the parts of my jMOBY code that were not Registry-aware, because they would hang, trying to connect to UBC when they should be connecting to Calgary :-) That being said, if you want to use the default registry in Calgary, I will be switching the default action to connect to Calgary in the next day or so (as I've found all my multi-registry bugs, I think). You'll only need to use c-tors with a registry parameter if you want to use a specialized registry. Andreas Groscurth wrote: > Hi Paul, > > thanks for the message... > > So do i understand it correctly ? I create such Registry object and then I > pass that instance to any of the org.biomoby.shared.data.*. > > e.g. new MobyDataObject( "something", "anything", registry) > > ? > > thanks > andreas > > On Wednesday 05 December 2007 18:21, Paul Gordon wrote: > >> Hi Andreas, >> >> The concluision we reached a few weeks ago is that >> CentralDigestCachedImpl and org.biomoby.shared.data.* use different >> catching schemes,which I will reconcile once Martin has set up some unit >> tests for the CentralImpls. Usually there is no compelling reason to >> use both caches...if you are using org.biomoby.shared.data.* to create >> and past data instances, CentralDigestCachedImpl.CACHE_PART_DATATYPES >> doesn't really do anything for you, and vice versa. If you are using >> org.biomoby.shared.data.*, drop the updateCache() calls you had, and use >> instead: >> >> Registry registry = new Registry("calgary", >> "http://moby.ucalgary.ca/moby/MOBY-Central.pl", >> "http://moby.ucalgary.ca/MOBY/Central"); >> RegistryCache.cacheOntologyFile(registry, >> Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis); >> MobyDataType.loadDataTypes(RegistryCache.getOntologyFile(registry, >> Central.DATA_TYPES_RESOURCE_NAME).toURI().toURL(), registry); >> >> I just added the allowedAgeMillis parameter for convenience. You'll want >> to do a CVS update. For MobyNamespace it's similar.. >> >> MobyNamespace.loadNamespaces(RegistryCache.getOntologyFile(registry, >> Central.NAMESPACES_RESOURCE_NAME).toURI().toURL(), registry); >> >> Hopefully, we can reconcile the Central calls cache and this code soon, >> so you don't need to pick. I could have also made a >> MobyNamespace.loadNamespaces(registry) method, but in keeping with the >> Law of Demeter, it's better for MobyNamespace and MobyDataType to not >> explicitly know about RegistryCache, hence the >> MobyNamespace.loadNamespaces(url, registry) signature. >> >> Regards, >> >> Paul >> >> Andreas Groscurth wrote: >> >>> Hi, >>> >>> sorry for reasking that - but has anyone an answer ? >>> >>> Thanks >>> andreas >>> >>> On Monday 03 December 2007 09:45, Andreas Groscurth wrote: >>> >>>> Hi, >>>> >>>> I'm using CentralDigestCachedImpl for caching the datatypes and >>>> namespaces locally. >>>> >>>> CentralDigestCachedImpl cachedImpl = new >>>> CentralDigestCachedImpl("http://moby.ucalgary.ca/moby/MOBY-Central.pl"," >>>> htt p://moby.ucalgary.ca/MOBY/Central", file.getAbsolutePath() ); >>>> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_DATATYPES ); >>>> cachedImpl.updateCache( CentralDigestCachedImpl.CACHE_PART_NAMESPACES ); >>>> >>>> This works fine and re-calls use the local cache. >>>> >>>> But when I create a new MobyDataObject, it starts again to fetch the >>>> datatypes >>>> >>>> Fetching data type ontology from >>>> http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects >>>> >>>> So how do I tell it, that its already has these information ? the >>>> MobyDataObject can also have a Registry Object - so i guess that can >>>> help - but how to I link my CachedCentral with a Registry object ? >>>> >>>> Or is this otherwise solveable ? >>>> >>>> thx >>>> andreas >>>> _______________________________________________ >>>> MOBY-dev mailing list >>>> MOBY-dev at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > From jmfernandez at cnio.es Tue Dec 11 16:02:52 2007 From: jmfernandez at cnio.es (=?UTF-8?B?Sm9zw6kgTWFyw61hIEZlcm7DoW5kZXogR29uesOhbGV6?=) Date: Tue, 11 Dec 2007 17:02:52 +0100 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> Message-ID: <475EB4AC.2060409@cnio.es> Hi Eddie, so, which is the URL of the new maven repository for biomoby? Best Regards, Jos?? Mar??a Edward Kawas wrote: > Hi Stian, > > I just replaced all instances where mobycentral was used to ucalgary. I also > had to update the biomoby plugins maven repository to be the new one at > ucalgary. > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland > Sent: December-03-07 4:05 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! > > On 11/30/07, Mark Wilkinson wrote: >> To migrate Taverna, edit the taverna/conf/mygrid.properties file to point >> to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl > > Should we change the default in Taverna's shipped mygrid.properties to > the ucalgary one? We have a Taverna 1.7 release going out in a few > weeks and would of course like BioMoby to work by default.. > -- "Premature optimization is the root of all evil." - Donald Knuth Jos?? Mar??a Fern??ndez Gonz??lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog??a Estructural y Bioinform??tica Structural Biology and Bioinformatics Centro Nacional de Investigaciones Oncol??gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern??ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Tue Dec 11 16:10:37 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 11 Dec 2007 08:10:37 -0800 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: <475EB4AC.2060409@cnio.es> References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> <475EB4AC.2060409@cnio.es> Message-ID: http://moby.ucalgary.ca/moby_maven/ Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos? Mar?a Fern?ndez Gonz?lez Sent: December-11-07 8:03 AM To: Core developer announcements Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! Hi Eddie, so, which is the URL of the new maven repository for biomoby? Best Regards, Jos? Mar?a Edward Kawas wrote: > Hi Stian, > > I just replaced all instances where mobycentral was used to ucalgary. I also > had to update the biomoby plugins maven repository to be the new one at > ucalgary. > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland > Sent: December-03-07 4:05 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! > > On 11/30/07, Mark Wilkinson wrote: >> To migrate Taverna, edit the taverna/conf/mygrid.properties file to point >> to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl > > Should we change the default in Taverna's shipped mygrid.properties to > the ucalgary one? We have a Taverna 1.7 release going out in a few > weeks and would of course like BioMoby to work by default.. > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog?a Estructural y Bioinform?tica Structural Biology and Bioinformatics Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From jmfernandez at cnio.es Tue Dec 11 16:20:28 2007 From: jmfernandez at cnio.es (=?UTF-8?B?Sm9zw6kgTWFyw61hIEZlcm7DoW5kZXogR29uesOhbGV6?=) Date: Tue, 11 Dec 2007 17:20:28 +0100 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> <475EB4AC.2060409@cnio.es> Message-ID: <475EB8CC.4090101@cnio.es> Thanks! Edward Kawas wrote: > http://moby.ucalgary.ca/moby_maven/ > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jos?? Mar??a Fern??ndez Gonz??lez > Sent: December-11-07 8:03 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! > > Hi Eddie, > so, which is the URL of the new maven repository for biomoby? > > Best Regards, > Jos?? Mar??a > > Edward Kawas wrote: >> Hi Stian, >> >> I just replaced all instances where mobycentral was used to ucalgary. I also >> had to update the biomoby plugins maven repository to be the new one at >> ucalgary. >> >> Thanks, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland >> Sent: December-03-07 4:05 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] It's worse than that... she's dead, Jim! >> >> On 11/30/07, Mark Wilkinson wrote: >>> To migrate Taverna, edit the taverna/conf/mygrid.properties file to point >>> to the new MOBY Central: http://moby.ucalgary.ca/moby/MOBY-Central.pl >> Should we change the default in Taverna's shipped mygrid.properties to >> the ucalgary one? We have a Taverna 1.7 release going out in a few >> weeks and would of course like BioMoby to work by default.. >> > -- "Premature optimization is the root of all evil." - Donald Knuth Jos?? Mar??a Fern??ndez Gonz??lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Biolog??a Estructural y Bioinform??tica Structural Biology and Bioinformatics Centro Nacional de Investigaciones Oncol??gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern??ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From martin.senger at gmail.com Tue Dec 11 16:35:14 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 11 Dec 2007 08:35:14 -0800 Subject: [MOBY-dev] It's worse than that... she's dead, Jim! In-Reply-To: References: <43abb4040712030404y7aceecf2v81897c804b2f0d25@mail.gmail.com> <475EB4AC.2060409@cnio.es> Message-ID: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> > http://moby.ucalgary.ca/moby_maven/ It may be true now. But in the longer term (I mean February 2008 when the Biohackathon happens in Japan - and where the new jMoby development is expected to happen, as well) jMoby will be using the open-bio maven repository (http://biomoby.org/m2repo/) and will be fully mavenized not only for the Taverna purposes but for all jMoby development. This is my plan, at least. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Thu Dec 13 11:38:57 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 13 Dec 2007 12:38:57 +0100 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> Message-ID: <200712131238.58226.groscurt@mpiz-koeln.mpg.de> Hi everyone, we have some problems with our application server and Moby - we havent figured out where the problem is, but I do have some questions. The problem is that our application server (jboss) kind of breaks down every morning and does not take any more request until we restart it. In the Jboss log we find zig of requests from moby central K 48735392 ms ? ? 136.159.169.80 ? ? K 59662027 ms ? ? 136.159.169.80 ? ? K 59482196 ms ? ? 136.159.169.80 ? ? K 37045625 ms ? ? 136.159.169.80 ? ? K 37797970 ms ? ? 136.159.169.80 ? ? K 37605298 ms ? ? 136.159.169.80 ? ? K 48353212 ms ? ? 136.159.169.80 ? ? K 74660526 ms ? ? 10.0.0.128 ? ? K 59448187 ms ? ? 136.159.169.80 ? ? K 37331868 ms ? ? 136.159.169.80 ? ? K 68473066 ms ? ? 136.159.169.80 ? ? K 22891987 ms ? ? 136.159.169.80 ? ? K 23234088 ms ? ? 136.159.169.80 ? ? K = Keepalive (this is just a short version of the whole log).... In the web server log we have the following entries 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/1.1" 200 771 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" "SOAP::Lite/Perl/0.69" 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 739 "-" "SOAP::Lite/Perl/0.69" (again a short version) So, over the night MobyCentral calls our services frequently and this results in the 'sleeping' of the jboss.. to figure out what happens - what exactly happens during these calls ? what are these calls ? - and why are they marked as 'keep alive' ? Any suggestions on that ? Thanks Andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From schoof at mpiz-koeln.mpg.de Thu Dec 13 12:20:40 2007 From: schoof at mpiz-koeln.mpg.de (Heiko Schoof) Date: Thu, 13 Dec 2007 13:20:40 +0100 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <200712131238.58226.groscurt@mpiz-koeln.mpg.de> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> <200712131238.58226.groscurt@mpiz-koeln.mpg.de> Message-ID: <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> Okay we figured out the keepalive bit, still for tracking purposes it would be great to know who or what is calling these services and what the calls are. Best, Heiko On 13.12.2007, at 12:38, Andreas Groscurth wrote: > Hi everyone, > > we have some problems with our application server and Moby - we > havent figured > out where the problem is, but I do have some questions. > > The problem is that our application server (jboss) kind of breaks > down every > morning and does not take any more request until we restart it. > > In the Jboss log we find zig of requests from moby central > > K 48735392 ms ? ? 136.159.169.80 ? ? > K 59662027 ms ? ? 136.159.169.80 ? ? > K 59482196 ms ? ? 136.159.169.80 ? ? > K 37045625 ms ? ? 136.159.169.80 ? ? > K 37797970 ms ? ? 136.159.169.80 ? ? > K 37605298 ms ? ? 136.159.169.80 ? ? > K 48353212 ms ? ? 136.159.169.80 ? ? > K 74660526 ms ? ? 10.0.0.128 ? ? > K 59448187 ms ? ? 136.159.169.80 ? ? > K 37331868 ms ? ? 136.159.169.80 ? ? > K 68473066 ms ? ? 136.159.169.80 ? ? > K 22891987 ms ? ? 136.159.169.80 ? ? > K 23234088 ms ? ? 136.159.169.80 ? ? > > K = Keepalive > > (this is just a short version of the whole log).... > > In the web server log we have the following entries > > 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] > "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" > "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] > "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/ > 1.1" 200 > 771 "-" "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] > "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" > "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] > "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" > "SOAP::Lite/Perl/0.69" > 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] > "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 > 739 "-" > "SOAP::Lite/Perl/0.69" > > (again a short version) > > So, over the night MobyCentral calls our services frequently and > this results > in the 'sleeping' of the jboss.. > > to figure out what happens - what exactly happens during these > calls ? what > are these calls ? - and why are they marked as 'keep alive' ? > > Any suggestions on that ? > > Thanks > Andreas > > > > -- > Andreas Groscurth > Bioinformatics Developer > Max Planck Institute for Plant Breeding Research > Carl-von-Linn?-Weg 10 > 50829 Cologne > Germany > E-mail: groscurt at mpiz-koeln.mpg.de > Phone: +49(0)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Dec 13 12:53:59 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 Dec 2007 04:53:59 -0800 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> <200712131238.58226.groscurt@mpiz-koeln.mpg.de> <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> Message-ID: Almost certainly it is the "isAlive" script, which sends an empty message and looks for an empty response. M On Thu, 13 Dec 2007 04:20:40 -0800, Heiko Schoof wrote: > Okay we figured out the keepalive bit, still for tracking purposes it > would be great to know who or what is calling these services and what > the calls are. > > Best, Heiko > > On 13.12.2007, at 12:38, Andreas Groscurth wrote: > >> Hi everyone, >> >> we have some problems with our application server and Moby - we havent >> figured >> out where the problem is, but I do have some questions. >> >> The problem is that our application server (jboss) kind of breaks down >> every >> morning and does not take any more request until we restart it. >> >> In the Jboss log we find zig of requests from moby central >> >> K 48735392 ms ? ? 136.159.169.80 ? ? >> K 59662027 ms ? ? 136.159.169.80 ? ? >> K 59482196 ms ? ? 136.159.169.80 ? ? >> K 37045625 ms ? ? 136.159.169.80 ? ? >> K 37797970 ms ? ? 136.159.169.80 ? ? >> K 37605298 ms ? ? 136.159.169.80 ? ? >> K 48353212 ms ? ? 136.159.169.80 ? ? >> K 74660526 ms ? ? 10.0.0.128 ? ? >> K 59448187 ms ? ? 136.159.169.80 ? ? >> K 37331868 ms ? ? 136.159.169.80 ? ? >> K 68473066 ms ? ? 136.159.169.80 ? ? >> K 22891987 ms ? ? 136.159.169.80 ? ? >> K 23234088 ms ? ? 136.159.169.80 ? ? >> >> K = Keepalive >> >> (this is just a short version of the whole log).... >> >> In the web server log we have the following entries >> >> 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] >> "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] >> "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/1.1" >> 200 >> 771 "-" "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] >> "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] >> "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] >> "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 739 >> "-" >> "SOAP::Lite/Perl/0.69" >> >> (again a short version) >> >> So, over the night MobyCentral calls our services frequently and this >> results >> in the 'sleeping' of the jboss.. >> >> to figure out what happens - what exactly happens during these calls ? >> what >> are these calls ? - and why are they marked as 'keep alive' ? >> >> Any suggestions on that ? >> >> Thanks >> Andreas >> >> >> >> --Andreas Groscurth >> Bioinformatics Developer >> Max Planck Institute for Plant Breeding Research >> Carl-von-Linn?-Weg 10 >> 50829 Cologne >> Germany >> E-mail: groscurt at mpiz-koeln.mpg.de >> Phone: +49(0)221-5062-449 >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Dec 13 12:54:57 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 13 Dec 2007 04:54:57 -0800 Subject: [MOBY-dev] Your killing us.... In-Reply-To: <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> References: <4d93f07c0712110835n2e17b1e4o92b514f9982a8d49@mail.gmail.com> <200712131238.58226.groscurt@mpiz-koeln.mpg.de> <68246AA5-D7AF-4F12-A10D-C08189CD15FF@mpiz-koeln.mpg.de> Message-ID: Would you like me to set the "agent" property in the code so that it reports itself as "isAlive script" in your logfiles? Greetings from Wageningen! Mark On Thu, 13 Dec 2007 04:20:40 -0800, Heiko Schoof wrote: > Okay we figured out the keepalive bit, still for tracking purposes it > would be great to know who or what is calling these services and what > the calls are. > > Best, Heiko > > On 13.12.2007, at 12:38, Andreas Groscurth wrote: > >> Hi everyone, >> >> we have some problems with our application server and Moby - we havent >> figured >> out where the problem is, but I do have some questions. >> >> The problem is that our application server (jboss) kind of breaks down >> every >> morning and does not take any more request until we restart it. >> >> In the Jboss log we find zig of requests from moby central >> >> K 48735392 ms ? ? 136.159.169.80 ? ? >> K 59662027 ms ? ? 136.159.169.80 ? ? >> K 59482196 ms ? ? 136.159.169.80 ? ? >> K 37045625 ms ? ? 136.159.169.80 ? ? >> K 37797970 ms ? ? 136.159.169.80 ? ? >> K 37605298 ms ? ? 136.159.169.80 ? ? >> K 48353212 ms ? ? 136.159.169.80 ? ? >> K 74660526 ms ? ? 10.0.0.128 ? ? >> K 59448187 ms ? ? 136.159.169.80 ? ? >> K 37331868 ms ? ? 136.159.169.80 ? ? >> K 68473066 ms ? ? 136.159.169.80 ? ? >> K 22891987 ms ? ? 136.159.169.80 ? ? >> K 23234088 ms ? ? 136.159.169.80 ? ? >> >> K = Keepalive >> >> (this is just a short version of the whole log).... >> >> In the web server log we have the following entries >> >> 136.159.169.80 - - [12/Dec/2007:22:44:55 +0100] >> "POST /axis/services/get_GO_Term_by_Database_ID HTTP/1.1" 200 719 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:45:37 +0100] >> "POST /axis/services/BuildPhylogeneticTreeFromFastaAlignment HTTP/1.1" >> 200 >> 771 "-" "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:47:47 +0100] >> "POST /axis/services/get_agi_code_by_keyword HTTP/1.1" 200 707 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:20 +0100] >> "POST /axis/services/GetInAndOrthologsFromRefSeq HTTP/1.1" 200 723 "-" >> "SOAP::Lite/Perl/0.69" >> 136.159.169.80 - - [12/Dec/2007:22:48:22 +0100] >> "POST /axis/services/buildMultipleAlignmentWithMAFFT HTTP/1.1" 200 739 >> "-" >> "SOAP::Lite/Perl/0.69" >> >> (again a short version) >> >> So, over the night MobyCentral calls our services frequently and this >> results >> in the 'sleeping' of the jboss.. >> >> to figure out what happens - what exactly happens during these calls ? >> what >> are these calls ? - and why are they marked as 'keep alive' ? >> >> Any suggestions on that ? >> >> Thanks >> Andreas >> >> >> >> --Andreas Groscurth >> Bioinformatics Developer >> Max Planck Institute for Plant Breeding Research >> Carl-von-Linn?-Weg 10 >> 50829 Cologne >> Germany >> E-mail: groscurt at mpiz-koeln.mpg.de >> Phone: +49(0)221-5062-449 >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Mon Dec 17 21:50:42 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 17 Dec 2007 13:50:42 -0800 Subject: [MOBY-dev] Fixing local RDF metadata Message-ID: Hi all, I noticed a little while ago that Moby Central is including the isAlive tag in the metadata that it presents to the service provider when they register their service. This is bad! The service provider is not supposed to know if their service is alive or not (from the perspective of the Registry) so they shouldn't have that tag in their metadata. Eddie has just fixed the Moby Central code so that it doesn't do this anymore, but in order to fix your metadata you would need to remove the isAlive tag from each of your service instances. I did that using a perl in-place edit as follows: perl -pi.bak -e "s/\w+<\/mygrid:isAlive>//g" *.rdf It's probably worth doing, so that your local metadata doesn't over-rule what the registry says the alive/dead state of your service is. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From Sebastien.Carrere at toulouse.inra.fr Tue Dec 18 08:31:47 2007 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Tue, 18 Dec 2007 09:31:47 +0100 Subject: [MOBY-dev] Fixing local RDF metadata In-Reply-To: References: Message-ID: <47678573.9020806@toulouse.inra.fr> Bonjour Mark, Do you talking about the "" tag ? Because my RDF files do not contain any "mygrid:" namespaced tags: http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/iant/rdf/dna/iANTblastxSwissProt.rdf Are my rdf files not correct ? Sebastien Mark Wilkinson wrote: > Hi all, > > I noticed a little while ago that Moby Central is including the > isAlive tag in the metadata that it presents to the service provider > when they register their service. This is bad! The service provider > is not supposed to know if their service is alive or not (from the > perspective of the Registry) so they shouldn't have that tag in their > metadata. > > Eddie has just fixed the Moby Central code so that it doesn't do this > anymore, but in order to fix your metadata you would need to remove > the isAlive tag from each of your service instances. > > I did that using a perl in-place edit as follows: > > perl -pi.bak -e "s/\w+<\/mygrid:isAlive>//g" *.rdf > > It's probably worth doing, so that your local metadata doesn't > over-rule what the registry says the alive/dead state of your service is. > > Cheers! > > M > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee > and may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received > this communication in error, please notify the sender immediately by > reply e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien.Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From markw at illuminae.com Tue Dec 18 10:00:25 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 18 Dec 2007 02:00:25 -0800 Subject: [MOBY-dev] Fixing local RDF metadata In-Reply-To: <47678573.9020806@toulouse.inra.fr> References: <47678573.9020806@toulouse.inra.fr> Message-ID: Yes. The namespace is just a token... whatever "a" is should map to a mygrid ontology, so it will need to be modified to whatever namespace you have. M On Tue, 18 Dec 2007 00:31:47 -0800, Sebastien Carrere wrote: > Bonjour Mark, > > Do you talking about the "" tag ? > Because my RDF files do not contain any "mygrid:" namespaced tags: > http://lipm-bioinfo.toulouse.inra.fr/biomoby/analysis/iant/rdf/dna/iANTblastxSwissProt.rdf > > Are my rdf files not correct ? > > Sebastien > > > > Mark Wilkinson wrote: >> Hi all, >> >> I noticed a little while ago that Moby Central is including the >> isAlive tag in the metadata that it presents to the service provider >> when they register their service. This is bad! The service provider >> is not supposed to know if their service is alive or not (from the >> perspective of the Registry) so they shouldn't have that tag in their >> metadata. >> >> Eddie has just fixed the Moby Central code so that it doesn't do this >> anymore, but in order to fix your metadata you would need to remove >> the isAlive tag from each of your service instances. >> >> I did that using a perl in-place edit as follows: >> >> perl -pi.bak -e "s/\w+<\/mygrid:isAlive>//g" *.rdf >> >> It's probably worth doing, so that your local metadata doesn't >> over-rule what the registry says the alive/dead state of your service >> is. >> >> Cheers! >> >> M >> >> >> ---- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > From groscurt at mpiz-koeln.mpg.de Tue Dec 18 13:30:56 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 18 Dec 2007 14:30:56 +0100 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: References: Message-ID: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Hi, since the movement of Moby we have severe problems with Taverna and Moby. When taverna tries to retrieve information about a dataobject (e.g. in the 'Brief search' for matching services), we always run into a NullPointerException with the message "Cannot parse MOBY Object Ontology" in org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF My guess is, that there is somehow the 'old' pre-movement code and because of that its not working. If so - I would be more than glad and thankfull if one can repair these asap... we are working currently a lot with taverna and like to present it (and moby) to our students... but in this state its not really presentable :-( Hope this can be fixed soon. Thanks andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From edward.kawas at gmail.com Tue Dec 18 13:33:47 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 18 Dec 2007 05:33:47 -0800 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: <36A6C2801FB34C988F481FBDC8A1C4B1@OfficePC> Hi Andreas, In the next day or two there will be a new release of taverna. This should fix all of the problems that you are encountering. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth Sent: December-18-07 5:31 AM To: Core developer announcements Subject: [MOBY-dev] Taverna Moby Problems Hi, since the movement of Moby we have severe problems with Taverna and Moby. When taverna tries to retrieve information about a dataobject (e.g. in the 'Brief search' for matching services), we always run into a NullPointerException with the message "Cannot parse MOBY Object Ontology" in org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF My guess is, that there is somehow the 'old' pre-movement code and because of that its not working. If so - I would be more than glad and thankfull if one can repair these asap... we are working currently a lot with taverna and like to present it (and moby) to our students... but in this state its not really presentable :-( Hope this can be fixed soon. Thanks andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Dec 18 13:45:30 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 18 Dec 2007 14:45:30 +0100 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: <200712181445.30753.groscurt@mpiz-koeln.mpg.de> awesome... thanks On Tuesday 18 December 2007 14:30, Andreas Groscurth wrote: > Hi, > > since the movement of Moby we have severe problems with Taverna and Moby. > > When taverna tries to retrieve information about a dataobject (e.g. in the > 'Brief search' for matching services), we always run into a > NullPointerException with the message "Cannot parse MOBY Object Ontology" > in > > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF > > > My guess is, that there is somehow the 'old' pre-movement code and because > of that its not working. > > If so - I would be more than glad and thankfull if one can repair these > asap... we are working currently a lot with taverna and like to present it > (and moby) to our students... but in this state its not really > presentable :-( > > Hope this can be fixed soon. > > Thanks > andreas -- Andreas Groscurth Bioinformatics Developer Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-449 From Pieter.Neerincx at wur.nl Tue Dec 18 13:56:09 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 18 Dec 2007 14:56:09 +0100 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: Hi Andreas, I know Eddie is working on this. There is also the issue that fetching the data to do a semantic search can be extremely slow right now. Eddie told me he will implement some caching for the data types similar to how the services are cached. A new Taverna 1.7 that contains fixes for these issues was announced for monday December 17 (yesterday). Apparently it's delayed a bit, but you'll probably see it very soon. In case soon is not soon enough: we had a course last week with a Taverna and BioMOBY workshop. Fortunately Eddie was there :) and I have a patched Taverna 1.6.2 we used for that course. It has the speed issue described above, bu apart from that it's fully functional. Let me know if you need copy... Cheers, Pi On 18-dec-2007, at 14:30, Andreas Groscurth wrote: > Hi, > > since the movement of Moby we have severe problems with Taverna and > Moby. > > When taverna tries to retrieve information about a dataobject (e.g. > in the > 'Brief search' for matching services), we always run into a > NullPointerException with the message "Cannot parse MOBY Object > Ontology" in > > org.biomoby.shared.extended.DataTypeParser.getMobyDataTypesFromRDF > > > My guess is, that there is somehow the 'old' pre-movement code and > because of > that its not working. > > If so - I would be more than glad and thankfull if one can repair > these > asap... we are working currently a lot with taverna and like to > present it > (and moby) to our students... but in this state its not really > presentable :-( > > Hope this can be fixed soon. > > Thanks > andreas > > -- > Andreas Groscurth > Bioinformatics Developer > Max Planck Institute for Plant Breeding Research > Carl-von-Linn?-Weg 10 > 50829 Cologne > Germany > E-mail: groscurt at mpiz-koeln.mpg.de > Phone: +49(0)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From ssoiland at cs.man.ac.uk Tue Dec 18 14:42:19 2007 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Tue, 18 Dec 2007 14:42:19 +0000 Subject: [MOBY-dev] Taverna Moby Problems In-Reply-To: References: <200712181430.56369.groscurt@mpiz-koeln.mpg.de> Message-ID: <43abb4040712180642m6402e12dl7a2f319738a55d70@mail.gmail.com> On 12/18/07, Pieter Neerincx wrote: > A new Taverna 1.7 that > contains fixes for these issues was announced for monday December 17 > (yesterday). Apparently it's delayed a bit, but you'll probably see > it very soon. It should be out in a few hours. :-) -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From gordonp at ucalgary.ca Tue Dec 18 18:08:44 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 18 Dec 2007 11:08:44 -0700 Subject: [MOBY-dev] Commits mailing list awry? Message-ID: <47680CAC.1080202@ucalgary.ca> Hi all, Am I the only one no longer receiving commits e-mails? I'm not sure if my mail server is trashing them, or if the open-bio server just isn't sending them. I've committed several file in the last week, and have received bupkis From markw at illuminae.com Tue Dec 18 18:59:28 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 18 Dec 2007 18:59:28 +0000 GMT Subject: [MOBY-dev] Commits mailing list awry? In-Reply-To: <47680CAC.1080202@ucalgary.ca> References: <47680CAC.1080202@ucalgary.ca> Message-ID: <1476491191-1198004368-cardhu_blackberry.rim.net-11822-@engine27-cell01> I still receive them, and haven't touched the mailing system... -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Tue, 18 Dec 2007 11:08:44 To:Core developer announcements Subject: [MOBY-dev] Commits mailing list awry? Hi all, Am I the only one no longer receiving commits e-mails? I'm not sure if my mail server is trashing them, or if the open-bio server just isn't sending them. I've committed several file in the last week, and have received bupkis _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From ola.spjuth at farmbio.uu.se Wed Dec 19 16:13:25 2007 From: ola.spjuth at farmbio.uu.se (Ola Spjuth) Date: Wed, 19 Dec 2007 17:13:25 +0100 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <4756E14E.3030809@ucalgary.ca> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> <4756E14E.3030809@ucalgary.ca> Message-ID: <96A0EC82-DD5C-43C8-9528-FA4B1266C2EC@farmbio.uu.se> Hi, What is the status of the CentralDigestCachedImpl? What does it cache now and what is cached using the RegistryCache? If I use MobyServiceType.loadServiceTypes(serviceTypesDefURL, mobyRegistry); to cache service types, how does this relate to the CentralDigestCachedImpl? There were talks of simplifying this process and I'm sorry if I have missed something on the list regarding this. Thanks, .../Ola On Dec 5, 2007, at 18:35 , Paul Gordon wrote: > Hi Andreas, > > I just simplified it a bit, so it's two lines (and should not be > garbled > in split lines the e-mail) >> Registry registry = new Registry("calgary", "http:// >> moby.ucalgary.ca/moby/MOBY-Central.pl", "http://moby.ucalgary.ca/ >> MOBY/Central"); >> MobyDataType.loadDataTypes(RegistryCache.cacheOntologyFile >> (registry, Central.DATA_TYPES_RESOURCE_NAME, >> allowedAgeMillis).toURI().toURL(), registry); >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Dec 19 17:04:28 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 19 Dec 2007 10:04:28 -0700 Subject: [MOBY-dev] Using CentralDigestCachedImpl.... In-Reply-To: <96A0EC82-DD5C-43C8-9528-FA4B1266C2EC@farmbio.uu.se> References: <91C40642-83C2-4ECC-92C7-BB150BD700CA@farmbio.uu.se> <200711301223.07171.groscurt@mpiz-koeln.mpg.de> <200712030945.32685.groscurt@mpiz-koeln.mpg.de> <200712051742.51315.groscurt@mpiz-koeln.mpg.de> <4756DE21.3000105@ucalgary.ca> <4756E14E.3030809@ucalgary.ca> <96A0EC82-DD5C-43C8-9528-FA4B1266C2EC@farmbio.uu.se> Message-ID: <47694F1C.7010300@ucalgary.ca> Hi Ola, This is still on the "to do" list, as we don't yet have unit tests to make sure the integration is backward compatible. We'll let you know as soon as its done. Once again, if you are using org.biomoby.shared.data, this is primarily for elegance, not performance, as CentralImpls and the MobyDataType/MobyNamespace/MobyServiceType classes are caching different kinds of information generally. Regards, Paul Ola Spjuth wrote: > Hi, > > What is the status of the CentralDigestCachedImpl? What does it cache > now and what is cached using the RegistryCache? If I use > MobyServiceType.loadServiceTypes(serviceTypesDefURL, mobyRegistry); to > cache service types, how does this relate to the > CentralDigestCachedImpl? There were talks of simplifying this process > and I'm sorry if I have missed something on the list regarding this. > > Thanks, > > .../Ola > > > > On Dec 5, 2007, at 18:35 , Paul Gordon wrote: > >> Hi Andreas, >> >> I just simplified it a bit, so it's two lines (and should not be garbled >> in split lines the e-mail) >>> Registry registry = new Registry("calgary", >>> "http://moby.ucalgary.ca/moby/MOBY-Central.pl", >>> "http://moby.ucalgary.ca/MOBY/Central"); >>> MobyDataType.loadDataTypes(RegistryCache.cacheOntologyFile(registry, >>> Central.DATA_TYPES_RESOURCE_NAME, allowedAgeMillis).toURI().toURL(), >>> registry); >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From edward.kawas at gmail.com Wed Dec 19 19:14:41 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Dec 2007 11:14:41 -0800 Subject: [MOBY-dev] generating rdf for services that have already been registered Message-ID: <0A564BBA2CD74E3DAA6296216FAA22B9@OfficePC> Hi, I have been getting requests from people to produce a web form that produces RDF for services that have already been registered (similar to a form that once existed). This cgi script is also located in the cvs @ moby-live/Perl/scripts/GenerateRDF.cgi I have done so and the form for the default mobycentral registry is located at: http://moby.ucalgary.ca/cgi-bin/GenerateRDF.cgi Unfortunately, unlike the previous form, you cannot use this form to modify signatureURLs. If people want this functionality, please let me know and I might add it at a later date. If you have any questions, comments or concerns, please let me know! Eddie From sylvie.huchet at enst-bretagne.fr Thu Dec 20 15:43:41 2007 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Thu, 20 Dec 2007 16:43:41 +0100 Subject: [MOBY-dev] Calling moby-async category services Message-ID: <476A8DAD.1060208@enst-bretagne.fr> Hi, I'd like to know how asynchronous services (category moby-async) can be called using the java API : the CentralImpl.findService method returns only synchronous services (category moby). Besides, is it possible to see asynchronous services with the Dashborad client ? By default they are not visible. Some services have been their category changed from moby to moby-async... Thanks a lot, Sylvie. -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From martin.senger at gmail.com Thu Dec 20 17:17:51 2007 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 20 Dec 2007 09:17:51 -0800 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <476A8DAD.1060208@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> Message-ID: <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> > I'd like to know how asynchronous services (category moby-async) can be > called > using the java API It is on the to-do list. A good opportunity to implement it will be the second week of February where several BioMoby developers meet at the Biohackaton in Japan. I hope to use this event to remove most of the items from my long-standing moby-to-do list. I am sorry for the delay. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Thu Dec 20 19:54:26 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 20 Dec 2007 12:54:26 -0700 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> Message-ID: <476AC872.70408@ucalgary.ca> Hi Sylvie, The current class that implements asynchronous service calls is MobyRequest (via AsyncClient). You can find both synchronous and asynchronous services by setting the Service category to the empty string ("") before calling CentralImpl. As Martin mentions below, the mechanism currently used to run asynchronous services will change next year (so there will probably be other ways to call async services introduced), but the MobyRequest API will not need to change. MobyRequest handles both synchronous and asynchronous calls transparently. Regards, Paul Martin Senger wrote: >> I'd like to know how asynchronous services (category moby-async) can be >> called >> using the java API >> > > > It is on the to-do list. A good opportunity to implement it will be the > second week of February where several BioMoby developers meet at the > Biohackaton in Japan. I hope to use this event to remove most of the items > from my long-standing moby-to-do list. I am sorry for the delay. > > Martin > > From sylvie.huchet at enst-bretagne.fr Thu Dec 20 21:49:18 2007 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Thu, 20 Dec 2007 22:49:18 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <476AC872.70408@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> Message-ID: <476AE35E.1080607@enst-bretagne.fr> Thank you for the information of how finding both synchronous and asynchronous services. No possibilities to view asynchronous services with the Dashboard client ? Regards, Sylvie. Paul Gordon a ?crit : > Hi Sylvie, > > The current class that implements asynchronous service calls is > MobyRequest (via AsyncClient). You can find both synchronous and > asynchronous services by setting the Service category to the empty > string ("") before calling CentralImpl. As Martin mentions below, the > mechanism currently used to run asynchronous services will change next > year (so there will probably be other ways to call async services > introduced), but the MobyRequest API will not need to change. > MobyRequest handles both synchronous and asynchronous calls transparently. > > Regards, > > Paul > > Martin Senger wrote: > >>> I'd like to know how asynchronous services (category moby-async) can be >>> called >>> using the java API >>> >> >> >> >> It is on the to-do list. A good opportunity to implement it will be the >> second week of February where several BioMoby developers meet at the >> Biohackaton in Japan. I hope to use this event to remove most of the >> items >> from my long-standing moby-to-do list. I am sorry for the delay. >> >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: