From groscurt at mpiz-koeln.mpg.de Fri Jan 2 05:17:24 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 02 Jan 2009 11:17:24 +0100 Subject: [MOBY-dev] my fault Message-ID: <495DE9B4.6030409@mpiz-koeln.mpg.de> ok... o didnt see the context menu in the tree... there is a unregister option there. but still this is not intuitiv i think... anyone has any objection if i add a button as it is with the services ? thanks andreas -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Fri Jan 2 05:06:26 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 02 Jan 2009 11:06:26 +0100 Subject: [MOBY-dev] Unregister datatypes / namespaces in dashboard? Message-ID: <495DE722.9060007@mpiz-koeln.mpg.de> Hi, is there any reason why there is no button for unregistering a datatype or namespace or service type in dashboard as it is for service ? thanks Andreas oh.. and happy new year :) -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From andreas.groscurth at googlemail.com Mon Jan 5 05:17:38 2009 From: andreas.groscurth at googlemail.com (Andreas Groscurth) Date: Mon, 05 Jan 2009 11:17:38 +0100 Subject: [MOBY-dev] Minor changes in JMoby Message-ID: <4961DE42.1080203@googlemail.com> Hi all, during the winter break I made some changes in jmoby and committed them today (without any formatting... no guarantee though). 1. DEPLOYMENT Deployment via dashboard was only possible for Tomcat. I changed this that it is now also possible for JBoss (and probably other servers, but i couldnt test this). For the user the only difference is now that he/she has to enter the complete path to axis on the server. Before that it was sufficient to enter 'axis' in the field 'Axis relative path in Tomcat', now you have to enter e.g. 'webapps/axis' for tomcat or e.g. 'server/default/deploy/axis.war' for JBoss. I also replaced all 'Tomcat' entries in the labels of the fields in the MoSeS generator tab to 'Server' to reflect this generalization and I changed the corresponding build files and the documentation. The major difference is that now all 'tomcat' properties are renamed to 'server' (e.g. tomcat.host = server.host) to reflect the generalization. I'm still not happy that now there is the tomcat.xml file which is used for the deployment - but honestly i dont trust currently the renaming in the cvs via Eclipse (as i would love to rename it to server.xml or so) and so i kept it as it is. 2. SERVICE IMPLEMENTATION If a service returns a collection of datatypes, the skeleton will now also have a method which accepts a collection and not only an array. To be consistent with the existing jmoby API I kept the method which accepts the array. So now there are always two methods which the service provider can choose, based on the service implementation. If a datatype has any other primitives as relationship than String/Boolean it is now possible to pass the Java primitive and not only the moby primitive. E.g. AminoAcidSequence has the SequenceString which is a String and Length which is an Integer. Before there was the method setSequenceString(String sequence) and setSequenceString(MobyString sequence), but for Length there was only setLength(MobyInteger length). I added the templates for float and integer, so that now every datatype which has children of these primitives also have the methods for the Java corresponding primitives.. 3. DASHBOARD I added an unregistration button at the bar at the bottom (with the other buttons) to the registration panel of Namespaces, Data Types and Service Types in Dashboard, to be consistent with the unregistration button of the service regisration panel. The changes are tested and are compilable - if you find any errors or problems or have any objections let me know. Thanks and a happy new year. Andreas From andreas.groscurth at googlemail.com Tue Jan 6 04:29:05 2009 From: andreas.groscurth at googlemail.com (Andreas Groscurth) Date: Tue, 06 Jan 2009 10:29:05 +0100 Subject: [MOBY-dev] Cleaning the registry ? Message-ID: <49632461.7030201@googlemail.com> Hi all, I wrote a short script which basically fetches all namespaces and all datatypes registered at the Moby central in Canada. Both are then compared to all datatypes and namespaces of all registered services used for the input and the output definition. Assuming the retrieval methods in jmoby work correctly and my script does it also we have the following numbers: Registered Data Types: 721 Unused Data Types: 388 Registered Namespaces: 459 Unused Namespaces: 232 This means 53% of all registered datatypes are not used - and 50% of all Namespaces !!! How do you think about cleaning the registry once in a while and erase unsused datatypes and namespaces ? Of course they might be useable for a service provider someday, but for the sake of clarity I would suggest to do that. Cleaning both would reduce the number of entries by more than the half, which would result in smaller, more compact, better understandable and better browsable ontologies. What do you think ? Cheers Andreas From groscurt at mpiz-koeln.mpg.de Tue Jan 6 04:31:12 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 10:31:12 +0100 Subject: [MOBY-dev] Cleaning the registry Message-ID: <496324E0.9010509@mpiz-koeln.mpg.de> Hi all, I wrote a short script which basically fetches all namespaces and all datatypes registered at the Moby central in Canada. Both are then compared to all datatypes and namespaces of all registered services used for the input and the output definition. Assuming the retrieval methods in jmoby work correctly and my script does it also we have the following numbers: Registered Data Types: 721 Unused Data Types: 388 Registered Namespaces: 459 Unused Namespaces: 232 This means 53% of all registered datatypes are not used - and 50% of all Namespaces !!! How do you think about cleaning the registry once in a while and erase unsused datatypes and namespaces ? Of course they might be useable for a service provider someday, but for the sake of clarity I would suggest to do that. Cleaning both would reduce the number of entries by more than the half, which would result in smaller, more compact, better understandable and better browsable ontologies. What do you think ? Cheers Andreas PS: Sorry if you receive this email twice now... I (again) wrote the first mail from another, not registered, email account.... -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From py at pingoured.fr Tue Jan 6 04:37:26 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 06 Jan 2009 10:37:26 +0100 Subject: [MOBY-dev] Cleaning the registry In-Reply-To: <496324E0.9010509@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> Message-ID: <49632656.3060901@pingoured.fr> Andreas Groscurth wrote: > This means 53% of all registered datatypes are not used - and 50% of all > Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but for > the sake of clarity I would suggest to do that. Cleaning both would > reduce the number of entries by more than the half, which would result > in smaller, more compact, better understandable and better browsable > ontologies. > > What do you think ? For the theory, I think this is good idea but why not start by mailing the owner of the datatypes/namespaces to tell them that their creation is not used. I think that would be the first step before removing anything :) Could you provide the list of the datatypes and namespace you found somewhere ? Thanks and regards , Pierre From Sebastien.Carrere at toulouse.inra.fr Tue Jan 6 04:37:07 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Tue, 06 Jan 2009 10:37:07 +0100 Subject: [MOBY-dev] Cleaning the registry ? In-Reply-To: <49632461.7030201@googlemail.com> References: <49632461.7030201@googlemail.com> Message-ID: <49632643.9000700@toulouse.inra.fr> Hi all and Bonne Annee ! I totally agree with Andreas. This is what I do in Remora: I propose only used Datatypes and Namespaces in the starting page. The large amount of datatypes is a real (and old) problem for biologists (and bioinformaticians !) endusers. Sebastien Andreas Groscurth wrote: > Hi all, > > I wrote a short script which basically fetches all namespaces and all > datatypes registered at the Moby central in Canada. Both are then > compared to all datatypes and namespaces of all registered services > used for the input and the output definition. > > Assuming the retrieval methods in jmoby work correctly and my script > does it also we have the following numbers: > > Registered Data Types: 721 > Unused Data Types: 388 > > Registered Namespaces: 459 > Unused Namespaces: 232 > > This means 53% of all registered datatypes are not used - and 50% of > all Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but > for the sake of clarity I would suggest to do that. Cleaning both > would reduce the number of entries by more than the half, which would > result in smaller, more compact, better understandable and better > browsable ontologies. > > What do you think ? > > Cheers > Andreas > _______________________________________________ > 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 groscurt at mpiz-koeln.mpg.de Tue Jan 6 06:10:21 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 12:10:21 +0100 Subject: [MOBY-dev] Cleaning the registry In-Reply-To: <49632656.3060901@pingoured.fr> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49632656.3060901@pingoured.fr> Message-ID: <49633C1D.5010209@mpiz-koeln.mpg.de> Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: > >> This means 53% of all registered datatypes are not used - and 50% of >> all Namespaces !!! >> >> How do you think about cleaning the registry once in a while and >> erase unsused datatypes and namespaces ? >> >> Of course they might be useable for a service provider someday, but >> for the sake of clarity I would suggest to do that. Cleaning both >> would reduce the number of entries by more than the half, which would >> result in smaller, more compact, better understandable and better >> browsable ontologies. >> >> What do you think ? > > For the theory, I think this is good idea but why not start by mailing > the owner of the datatypes/namespaces to tell them that their creation > is not used. I think that would be the first step before removing > anything :) > > Could you provide the list of the datatypes and namespace you found > somewhere ? > > Thanks and regards > , Of course it would be nice to ask the owner to remove it, but honestly - the question is a) is the owner still reachable via this email, b) does he/she respond to it and c) does she/he unregister it ? The automatic way is more reliable ... BUT - I have found an error in my numbers... I count datatypes which are children of an used datatype as unused.... As soon as I correct this i will post the list with the unsused types and numbers on a web page. Cheers Andreas -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 6 08:32:28 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 14:32:28 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <496324E0.9010509@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> Message-ID: <49635D6C.3040608@mpiz-koeln.mpg.de> Hi, I uploaded to html files showing the unsused elements: http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html The corrected number for the datatypes is 331 / 721 (45%). I assume that people register their namespaces / datatypes in advance to their service. So of course their mightbe elements which will be used in the near future - I'm not talking about cleaning it every week or so. But thinking about a monthly basis is fair to me and via the LSID it can be checked how old the entry is. As you can see on the page - there are entries unused which are registered in 2001 etc... Cheers Andreas Andreas Groscurth wrote: > Hi all, > > I wrote a short script which basically fetches all namespaces and all > datatypes registered at the Moby central in Canada. Both are then > compared to all datatypes and namespaces of all registered services > used for the input and the output definition. > > Assuming the retrieval methods in jmoby work correctly and my script > does it also we have the following numbers: > > Registered Data Types: 721 > Unused Data Types: 388 > > Registered Namespaces: 459 > Unused Namespaces: 232 > > This means 53% of all registered datatypes are not used - and 50% of > all Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but > for the sake of clarity I would suggest to do that. Cleaning both > would reduce the number of entries by more than the half, which would > result in smaller, more compact, better understandable and better > browsable ontologies. > > What do you think ? > > Cheers > Andreas > > PS: Sorry if you receive this email twice now... I (again) wrote the > first mail from another, not registered, email account.... > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From py at pingoured.fr Tue Jan 6 08:43:15 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 06 Jan 2009 14:43:15 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49635D6C.3040608@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> Message-ID: <49635FF3.4040100@pingoured.fr> Andreas Groscurth wrote: > Hi, > > I uploaded to html files showing the unsused elements: > > http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html > http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html > > The corrected number for the datatypes is 331 / 721 (45%). I think there is still a bug, I see: OSE_object avilin05.avignon.inra.fr 2008-08-20 and I know this object (I created it), it has a bunch of children (OSE_author, OSE_experiment...) that are used by webservices :) We can not remove object that have children that are used. Thanks for the lists, Regards, Pierre From groscurt at mpiz-koeln.mpg.de Tue Jan 6 08:56:39 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 14:56:39 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49635FF3.4040100@pingoured.fr> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> Message-ID: <49636317.8070808@mpiz-koeln.mpg.de> If a datatype has children that are used by a webservice than they dont have anything to do with that datatype - so we can delete it. E.g. AminoAcidSequence has a String... String is a widely used datatype. Assuming AminoAcidSequence is not used at all it can be deregistered although it has a child String. Of course you can deregister a parent type which children are in use, but you cant deregister a child type which parent is in use.... Cheers Andreas Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> >> I uploaded to html files showing the unsused elements: >> >> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >> >> The corrected number for the datatypes is 331 / 721 (45%). > > I think there is still a bug, I see: > OSE_object avilin05.avignon.inra.fr 2008-08-20 > and I know this object (I created it), it has a bunch of children > (OSE_author, OSE_experiment...) that are used by webservices :) > > We can not remove object that have children that are used. > > Thanks for the lists, > > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 6 09:03:59 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 15:03:59 +0100 Subject: [MOBY-dev] test registry not working In-Reply-To: References: <494A3961.2060605@mpiz-koeln.mpg.de> Message-ID: <496364CF.5020601@mpiz-koeln.mpg.de> Hi Mark, any new information on the test exchange process ? Cheers Andreas Mark wrote: > We're having LOTS of problems with that machine at the moment. I'm in > the process of setting up a new server (two, actually) that will > replace the bioinfo machine. The address will, unfortunately, change > for the test registry but I'll try to convince our IT team to set-up > auto-forwarding. > > Thanks for your patience, > > M > > > > On Thu, 18 Dec 2008 03:52:01 -0800, Andreas Groscurth > wrote: > >> Hi, >> >> when i try to register anything at the test repository i receive >> >> ===ERROR=== >> Fault details: >> [stackTrace: null] >> [hostname: null] >> Fault string: DBI >> connect('moby_central:bioinfo.icapture.ubc.ca:3306','moby',...) >> failed: Can't connect to MySQL server on 'bioinfo.icapture.ubc.ca' >> (111) at >> /usr/lib/perl5/site_perl/5.8.5/MOBY/Adaptor/moby/queryapi/mysql.pm >> line 93 >> >> Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server >> Fault actor: null >> When calling: >> http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl >> =========== >> >> Cheers >> Andreas >> > > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From edward.kawas at gmail.com Tue Jan 6 09:27:36 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Jan 2009 06:27:36 -0800 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49636317.8070808@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> <49636317.8070808@mpiz-koeln.mpg.de> Message-ID: <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> Hey Andreas, I think that he meant something like ... you can't remove the datatype Object because it has a child DNASequence that is being used. 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: January-06-09 5:57 AM To: Core developer announcements Subject: Re: [MOBY-dev] [MOBY-l] Cleaning the registry If a datatype has children that are used by a webservice than they dont have anything to do with that datatype - so we can delete it. E.g. AminoAcidSequence has a String... String is a widely used datatype. Assuming AminoAcidSequence is not used at all it can be deregistered although it has a child String. Of course you can deregister a parent type which children are in use, but you cant deregister a child type which parent is in use.... Cheers Andreas Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> >> I uploaded to html files showing the unsused elements: >> >> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >> >> The corrected number for the datatypes is 331 / 721 (45%). > > I think there is still a bug, I see: > OSE_object avilin05.avignon.inra.fr 2008-08-20 > and I know this object (I created it), it has a bunch of children > (OSE_author, OSE_experiment...) that are used by webservices :) > > We can not remove object that have children that are used. > > Thanks for the lists, > > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ _______________________________________________ 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 Jan 6 09:42:14 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 15:42:14 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> <49636317.8070808@mpiz-koeln.mpg.de> <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> Message-ID: <49636DC6.7030203@mpiz-koeln.mpg.de> Ah... in the sense of the hierarchy... not the children (attributes / relationship or however this should be called). Then of course you are right... Edward Kawas wrote: > Hey Andreas, > > I think that he meant something like ... you can't remove the datatype > Object because it has a child DNASequence that is being used. > > 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: January-06-09 5:57 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [MOBY-l] Cleaning the registry > > If a datatype has children that are used by a webservice than they dont > have anything to do with that datatype - so we can delete it. > > E.g. > > AminoAcidSequence has a String... String is a widely used datatype. > Assuming AminoAcidSequence is not used at all it can be deregistered > although it has a child String. > > Of course you can deregister a parent type which children are in use, > but you cant deregister a child type which parent is in use.... > > Cheers > Andreas > > Pierre-Yves Chibon wrote: > >> Andreas Groscurth wrote: >> >>> Hi, >>> >>> I uploaded to html files showing the unsused elements: >>> >>> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >>> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >>> >>> The corrected number for the datatypes is 331 / 721 (45%). >>> >> I think there is still a bug, I see: >> OSE_object avilin05.avignon.inra.fr 2008-08-20 >> and I know this object (I created it), it has a bunch of children >> (OSE_author, OSE_experiment...) that are used by webservices :) >> >> We can not remove object that have children that are used. >> >> Thanks for the lists, >> >> Regards, >> >> Pierre >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From py at pingoured.fr Tue Jan 6 10:29:15 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 06 Jan 2009 16:29:15 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49636DC6.7030203@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> <49636317.8070808@mpiz-koeln.mpg.de> <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> <49636DC6.7030203@mpiz-koeln.mpg.de> Message-ID: <496378CB.4070208@pingoured.fr> Andreas Groscurth wrote: > Ah... in the sense of the hierarchy... not the children (attributes / > relationship or however this should be called). > > Then of course you are right... > > > Edward Kawas wrote: > >> Hey Andreas, >> >> I think that he meant something like ... you can't remove the datatype >> Object because it has a child DNASequence that is being used. >> Thanks for clarifying that's what I meant :) Regards, Pierre From pieter.neerincx at gmail.com Tue Jan 6 10:29:28 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Tue, 6 Jan 2009 16:29:28 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49635FF3.4040100@pingoured.fr> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> Message-ID: <4C2DC0E2-DA21-4334-82CE-84EA92A1B8FC@gmail.com> Hi, On 06 Jan 2009, at 14:43, Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> I uploaded to html files showing the unsused elements: >> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >> The corrected number for the datatypes is 331 / 721 (45%). > > I think there is still a bug, I see: > OSE_object avilin05.avignon.inra.fr 2008-08-20 > and I know this object (I created it), it has a bunch of children > (OSE_author, OSE_experiment...) that are used by webservices :) > > We can not remove object that have children that are used. Check, same here. I've registered a more generic object which I don't use directly in any service, but I do use a more specialized object that inherits from this one (ISA relationship). For all the other object and namespace "orphans" registered by www.bioinformatics.nl : they are actually used, but you can't figure that out using the ontologies (yet). Long time ago I ran into scalability issues. After trying several different solutions to the problem I started to use "pass-by-reference". Hence when I expect large inputs or outputs I replace them with a URL object. This URL points to a file somewhere on a server, which contains the actual data in BioMoby format. If one day pass-by-reference will become standardised as part of the official BioMoby specs, I expect to be able to take advantage of it with only minor tweaks as all the data I send around is already BioMoby compliant :). Registering those objects and namespace made sense to me because: 1. It allows me to use BioMoby tools to explore the registry + structure of the objects when designing/maintaining my own services. 2. Others might recycle these objects preventing the registration of objects/namespace which are virtually the same, but just with a slightly different name creating yet another alias. 3. It prevents others from registering objects/namespace with the same name, but a for a different purpose or with a different meaning. That would require me to rename lots of objects/namespace once pass-by- reference makes it into the BioMoby specs. Hence it makes my current services more potentially forward compatible... On a side note: Martin, any news on an official pass-by-reference RFC? I remember some time ago we had lengthy discussion on the mailinglist... I do realise that right now a BioMoby "enduser" can not see the difference between depreciated orphan objects/namespaces catching dust and the ones I registered with the future of a standardised pass-by- reference machanism for BioMoby in mind... Cheers, Pi > Thanks for the lists, > > Regards, > > Pierre > _______________________________________________ > 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: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Tue Jan 6 18:42:02 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 6 Jan 2009 23:42:02 +0000 Subject: [MOBY-dev] Cleaning the registry ? In-Reply-To: <49632643.9000700@toulouse.inra.fr> References: <49632461.7030201@googlemail.com> <49632643.9000700@toulouse.inra.fr> Message-ID: <4d93f07c0901061542y6db34503gcd84597a3dfec2fa@mail.gmail.com> > I totally agree with Andreas. Actually, I don't. Or: I agree only partially. The data types can be part of a domain model (as they are for the GCP project) - even without existing services, the model is still useful (and, for example, with Moses generated data types can be at once used in various Java programs). I may agree with namespaces - but because I am still not sure (and never been) what exactly namespaces in BioMoby mean, I cannot be even here sure :-) Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From jason at bioteam.net Tue Jan 6 19:11:42 2009 From: jason at bioteam.net (jason) Date: Tue, 06 Jan 2009 16:11:42 -0800 Subject: [MOBY-dev] Cleaning the registry Message-ID: <4963F33E.5070105@bioteam.net> Hi, all I think some manual clean is needed, too. For example, there are two text plain data type: text_plain and text-plain. I guess there are no difference between these two types. Another example is FASTA nucleotide sequence. What type is FASTA nucleotide sequence ? It can be FASTA_NA or NucleotideSequence. Here a piece of data can be represented by two types and there is no connection between these two types. If the user thinks his data as FASTA_NA and searches for service, he will miss the service for NucleotideSequence. Service producing FASTA_NA can not be chained to service accepting NucleotideSequence as input. This brings up another question: whether uncurated data type management works in reality or not. My understanding is that data type is the heart of biomoby. If the data type is not carefully managed, the beauty of biomoby only works in theory. -jason Andreas Groscurth wrote: > Hi all, > > I wrote a short script which basically fetches all namespaces and all > datatypes registered at the Moby central in Canada. Both are then > compared to all datatypes and namespaces of all registered services > used for the input and the output definition. > > Assuming the retrieval methods in jmoby work correctly and my script > does it also we have the following numbers: > > Registered Data Types: 721 > Unused Data Types: 388 > > Registered Namespaces: 459 > Unused Namespaces: 232 > > This means 53% of all registered datatypes are not used - and 50% of > all Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but > for the sake of clarity I would suggest to do that. Cleaning both > would reduce the number of entries by more than the half, which would > result in smaller, more compact, better understandable and better > browsable ontologies. > > What do you think ? > > Cheers > Andreas > _______________________________________________ > 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 Wed Jan 7 02:03:24 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 07 Jan 2009 08:03:24 +0100 Subject: [MOBY-dev] Cleaning the registry In-Reply-To: <4963F33E.5070105@bioteam.net> References: <4963F33E.5070105@bioteam.net> Message-ID: <496453BC.9030907@mpiz-koeln.mpg.de> > My understanding is that data type is the heart of biomoby. If the data type is not carefully managed, the beauty of biomoby only works in theory. Thats of course a way more broader topic you are talking about - this is not only cleaning unused datatypes but curating existing ones. Although I agree with you this comes with some problems. The main problem would be who to decide which datatype is the correct one or what is the truth in general... And of course what to do with the numerous datatypes which might be the children of a "wrong" datatype - and with all the services which use them.... and so on. > Actually, I don't. Or: I agree only partially. The data types can be part of > a domain model (as they are for the GCP project) - even without existing > services, the model is still useful (and, for example, with Moses generated > data types can be at once used in various Java programs). mhm sorry I dont get that point. Why are datatypes registered at the official production central of BioMoby if they are not used in BioMoby ? Just because they might be relevant for various Java programs ? Is the central then a collection of all domain models which are relevant for everything ? This sounds like abuse to me... I guess I dont get that one, but still for me the central repository of BioMoby should only contain elements which are useable and relevant for the BioMoby world (This excludes those datatypes and services which are not reachable for the public) Cheers Andreas jason wrote: > Hi, all > > I think some manual clean is needed, too. > For example, there are two text plain data type: text_plain and > text-plain. I guess there are no difference between these two types. > Another example is FASTA nucleotide sequence. What type is FASTA > nucleotide sequence ? It can be FASTA_NA or NucleotideSequence. Here > a piece of data can be represented by two types and there is no > connection between these two types. If the user thinks his data as > FASTA_NA and searches for service, he will miss the service for > NucleotideSequence. Service producing FASTA_NA can not be chained to > service accepting NucleotideSequence as input. > This brings up another question: whether uncurated data type > management works in reality or not. > > > -jason > > Andreas Groscurth wrote: >> Hi all, >> >> I wrote a short script which basically fetches all namespaces and all >> datatypes registered at the Moby central in Canada. Both are then >> compared to all datatypes and namespaces of all registered services >> used for the input and the output definition. >> >> Assuming the retrieval methods in jmoby work correctly and my script >> does it also we have the following numbers: >> >> Registered Data Types: 721 >> Unused Data Types: 388 >> >> Registered Namespaces: 459 >> Unused Namespaces: 232 >> >> This means 53% of all registered datatypes are not used - and 50% of >> all Namespaces !!! >> >> How do you think about cleaning the registry once in a while and >> erase unsused datatypes and namespaces ? >> >> Of course they might be useable for a service provider someday, but >> for the sake of clarity I would suggest to do that. Cleaning both >> would reduce the number of entries by more than the half, which would >> result in smaller, more compact, better understandable and better >> browsable ontologies. >> >> What do you think ? >> >> Cheers >> 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 -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Wed Jan 21 17:10:15 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Jan 2009 23:10:15 +0100 Subject: [MOBY-dev] Unregister datatypes / namespaces in dashboard? In-Reply-To: <495DE722.9060007@mpiz-koeln.mpg.de> References: <495DE722.9060007@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901211410l1ec689b6n42e61e70d1c9bc59@mail.gmail.com> > is there any reason why there is no button for unregistering a datatype or > namespace or service type in dashboard as it is for service ? I cannot start Dashboard now (on this computer) to check all answers but I definitely remember that most entities can be unregistered from the Dashboard. However, some (from various technical and UI aspects) entities can be unregistered by right-click on their names in the tree (and not by a button). Have you tried and still some are not covered? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Jan 21 17:14:32 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Jan 2009 23:14:32 +0100 Subject: [MOBY-dev] my fault In-Reply-To: <495DE9B4.6030409@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> > but still this is not intuitiv i think... anyone has any objection if i add > a button as it is with the services ? Please wait until I can check it (see my previous email) - [which will be on Monday 26th when I am back in the office at IRRI]. When I see it I will remember why it is this way and not the other one :-) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From andreas.groscurth at googlemail.com Thu Jan 22 03:41:13 2009 From: andreas.groscurth at googlemail.com (Andreas Groscurth) Date: Thu, 22 Jan 2009 09:41:13 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> Message-ID: <49783129.6010309@googlemail.com> Hi all, I was wondering if there is an easy and fast way to change the description of an ontology entry (such as datatype for example). Or do you have to follow the whole procedure of unregister it and then register it again ? This would be very problematic as you can unregister it as long as services are using it... So is there a way to change the description of an entity without going the long, stony way ? Thanks Andreas From martin.senger at gmail.com Thu Jan 22 06:16:03 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 22 Jan 2009 12:16:03 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <49783129.6010309@googlemail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> Message-ID: <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> > So is there a way to change the description of an entity without going the > long, stony way ? No, there is no such way in the BioMOBY API. I agree with you that it is paintful as it is now. The only thing we (you :-) ) can do is to write a Java method that does the whole long procedure for you, hidden from the end-users. But the quetsion is how safe such procedure can be (because during its run, the repository state is changed). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From pieter.neerincx at gmail.com Thu Jan 22 08:17:36 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Thu, 22 Jan 2009 14:17:36 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <49783129.6010309@googlemail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> Message-ID: <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> Hi, On 22 Jan 2009, at 09:41, Andreas Groscurth wrote: > Hi all, > > I was wondering if there is an easy and fast way to change the > description of an ontology entry (such as datatype for example). Or > do you have to follow the whole procedure of unregister it and then > register it again ? This would be very problematic as you can > unregister it as long as services are using it... > > So is there a way to change the description of an entity without > going the long, stony way ? No and for good reasons. If I designed a service for which I recycled one of the objects you designed and you change how this object is supposed to be used by changing the description, I have a problem. Hence it might brake any of the other entries in the ontologies that depend on it. Basically for BioMoby this means you have to de- and re- registering the object "the long way" to make sure all dependancies will be updated and all their LSIDs will change so everyone can easily determine these things have changed. I'd have to admit though it can be complicated procedure if all you want to is correct a typo for example, but for BioMoby it's very difficult to determine whether you just corrected a typo or changed the whole meaning of the object. Cheers, Pi > > > Thanks > Andreas > _______________________________________________ > 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: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Thu Jan 22 16:16:07 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 22 Jan 2009 21:16:07 +0000 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> Message-ID: <4d93f07c0901221316l5928bfbfyecd5619f31a50353@mail.gmail.com> > No and for good reasons. IMHO, well no, not really a good reason. In BioMoby, descriptions are just descriptions, they have nothing to do with ontology (like data types, namespaces, etc.). If I change its description, a service still has the same behaviour. I agree with you in one point, however. *Any* change, even a change in typos, should be reflected in the LSID revision, and, consequently, in all dependent LSID revisions (in the same way as it would be done by the long procedure of de- and re-registering). But because such change does not change behaviour of services and, therefore, does not jeopardize any clients, the all revision changes could be done hiddenly, by the registry code - which would guarantee the "atomicity" of such operation (which we cannot achieve easily from the clients). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Jan 26 03:25:07 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 26 Jan 2009 09:25:07 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> Message-ID: <497D7363.5090605@mpiz-koeln.mpg.de> I agree here with Martin ... i dont want to change anything which will change the LSID and therefore which might change any dependencies - in my case its ONLY the description. Still I dont see how this method should be easily written... Because if I do the whole procedure in the background I still need to unregister the datatype, meaning unregister all services which uses this datatype - and how to do that ? If the services provide a rdf, I would need to delete that rdf to unregister the services successfully - and this I cant do for all services. So if there isnt any other way - I dont see a possibility to have such all-in-once method ?! Andreas Martin Senger wrote: >> So is there a way to change the description of an entity without going the >> long, stony way ? >> > > > No, there is no such way in the BioMOBY API. I agree with you that it is > paintful as it is now. The only thing we (you :-) ) can do is to write a > Java method that does the whole long procedure for you, hidden from the > end-users. But the quetsion is how safe such procedure can be (because > during its run, the repository state is changed). > > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Mon Jan 26 04:16:53 2009 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 26 Jan 2009 17:16:53 +0800 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497D7363.5090605@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901260116g1ad7513apeac886459464d7fa@mail.gmail.com> > Still I dont see how this method should be easily written... If the > services provide a rdf For services with the RDF, I also do not see a way how to automate it. This is yet another argument why such change should be done completely on the registry site (but it would need a new method - or methods - in the Moby API). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Mon Jan 26 11:01:51 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 26 Jan 2009 09:01:51 -0700 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497D7363.5090605@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> Message-ID: <497DDE6F.7000906@ucalgary.ca> > I agree here with Martin ... i dont want to change anything which will > change the LSID and therefore which might change any dependencies - in > my case its ONLY the description. I respectfully disagree: the description is the *essence* of the data type. Otherwise the data type is just a random assortment of fields with no implied meaning in the real world, and therefore useless. If you change the description, you change the version, even if you think its minor, others may not. I agree that you should be able to change it without deregistering though, that's a major flaw... From martin.senger at gmail.com Mon Jan 26 19:50:26 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Jan 2009 08:50:26 +0800 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> Message-ID: <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> > Please wait until I can check it (see my previous email) - [which will be > on Monday 26th when I am back in the office at IRRI]. When I see it I will > remember why it is this way and not the other one :-) > The "normal" way to unregister an entity is by using the right-click popup menu. It is used consistently anywhere where there is a list of entities. Which is not the case for services (there is no list of all services in this panel) - and, therefore, the service panel has a separate "Unregister" button. I am not in favour to add the "Unregister" button to other subpanels. If we do that, we should remove it from the popup menu (otherwise it would be confusing to have two alternatives to do the same thing). But removing it from the popup menu will change the current functionality without a really good cause. People may be used to use this way and when it suddenly disappears, they may be confused. I do not see this, perhaps inconsistent, look&feel a big issue, therefore, I suggest to keep it as it is. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Mon Jan 26 22:00:42 2009 From: markw at illuminae.com (Mark) Date: Mon, 26 Jan 2009 19:00:42 -0800 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> Message-ID: I know that I am going to be crucified for this, but... Martin, I disagree with you :-) If we look at widely-used software like MS Word, the right-click context-menu contains all of the same options as you would get if you clicked on the main menu-bar and navigated to the appropriate place! Context-menu's are important (critical!). It isn't "a different way", it is THE SAME WAY, only presented in-context... M On Mon, 26 Jan 2009 16:50:26 -0800, Martin Senger wrote: >> Please wait until I can check it (see my previous email) - [which will >> be >> on Monday 26th when I am back in the office at IRRI]. When I see it I >> will >> remember why it is this way and not the other one :-) >> > > The "normal" way to unregister an entity is by using the right-click > popup > menu. It is used consistently anywhere where there is a list of entities. > Which is not the case for services (there is no list of all services in > this > panel) - and, therefore, the service panel has a separate "Unregister" > button. > > I am not in favour to add the "Unregister" button to other subpanels. If > we > do that, we should remove it from the popup menu (otherwise it would be > confusing to have two alternatives to do the same thing). But removing it > from the popup menu will change the current functionality without a > really > good cause. People may be used to use this way and when it suddenly > disappears, they may be confused. > > I do not see this, perhaps inconsistent, look&feel a big issue, > therefore, I > suggest to keep it as it is. > > Cheers, > Martin > From martin.senger at gmail.com Mon Jan 26 22:30:17 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Jan 2009 11:30:17 +0800 Subject: [MOBY-dev] my fault In-Reply-To: References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> Message-ID: <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> Then go ahead and implement the buttons.... [but make sure that the button is disabled when nothing is displayed in the subpanel, or, preferable, when what is displayed really exists in the registry (in the tree)]. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Mon Jan 26 22:51:02 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Jan 2009 11:51:02 +0800 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> Message-ID: <4d93f07c0901261951u6476f990i31039fe6adb21700@mail.gmail.com> > Then go ahead and implement the buttons.... Sorry, I thought that I was talking to Andreas who expressed the wish to implement these buttons. Andreas, please go ahead and implement it, it's fine with me. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Jan 27 02:32:08 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 27 Jan 2009 08:32:08 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497DDE6F.7000906@ucalgary.ca> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> Message-ID: <497EB878.8070402@mpiz-koeln.mpg.de> Of course the description is important for the understanding and the use of the datatype - but as its free text where everybody can add any information (and therefore also less information) i wouldnt count this as the *essence* of the datatype. If we would talk about a description ontology or other controlled vocabulary... I would agree. You could also say that random characters do not give an implied meaning - thats basically what the description is. Just as an example what i mean (actually this shows it for the description of a service) - if you have a service called "runBlast"... the description about is "Runs a Blast". Does this give you any implied meaning ? what version of blast, against what database, what blast program etc etc... Sorry - this is a general issue ... a random user based text should not be seen as the essence of any element in the ontology..... And my suggestion in the way i want to change them is basically add new information, being more specific or erazing typos... I know that allow this would also enable people to completly change the description of a datatype... but as we allow people already being that much I wouldnt dare to give this opportunity. Cheers Andreas Paul Gordon wrote: > >> I agree here with Martin ... i dont want to change anything which >> will change the LSID and therefore which might change any >> dependencies - in my case its ONLY the description. > I respectfully disagree: the description is the *essence* of the data > type. Otherwise the data type is just a random assortment of fields > with no implied meaning in the real world, and therefore useless. If > you change the description, you change the version, even if you think > its minor, others may not. > > I agree that you should be able to change it without deregistering > though, that's a major flaw... > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 27 02:35:21 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 27 Jan 2009 08:35:21 +0100 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901261951u6476f990i31039fe6adb21700@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> <4d93f07c0901261951u6476f990i31039fe6adb21700@mail.gmail.com> Message-ID: <497EB939.4040800@mpiz-koeln.mpg.de> Basically I already did - they are currently just commented out ;-) I will uncomment them and take care that if nothing is selected they will be disabled etc Cheers Andreas Martin Senger wrote: >> Then go ahead and implement the buttons.... >> > > > Sorry, I thought that I was talking to Andreas who expressed the wish to > implement these buttons. Andreas, please go ahead and implement it, it's > fine with me. > > Cheers, > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 27 02:40:19 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 27 Jan 2009 08:40:19 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497EB878.8070402@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> <497EB878.8070402@mpiz-koeln.mpg.de> Message-ID: <497EBA63.8050200@mpiz-koeln.mpg.de> *ups* sorry for some mistakes in my email.... too early here :( > but as we allow people already being that much I wouldnt dare to give this opportunity. i meant "I would dare...." of course... i should sleep longer... Andreas Groscurth wrote: > Of course the description is important for the understanding and the > use of the datatype - but as its free text where everybody can add any > information (and therefore also less information) i wouldnt count this > as the *essence* of the datatype. If we would talk about a description > ontology or other controlled vocabulary... I would agree. You could > also say that random characters do not give an implied meaning - thats > basically what the description is. > > Just as an example what i mean (actually this shows it for the > description of a service) - if you have a service called "runBlast"... > the description about is "Runs a Blast". > Does this give you any implied meaning ? what version of blast, > against what database, what blast program etc etc... > > Sorry - this is a general issue ... a random user based text should > not be seen as the essence of any element in the ontology..... > > And my suggestion in the way i want to change them is basically add > new information, being more specific or erazing typos... I know that > allow this would also enable people to completly change the > description of a datatype... but as we allow people already being that > much I wouldnt dare to give this opportunity. > > Cheers > Andreas > > Paul Gordon wrote: >> >>> I agree here with Martin ... i dont want to change anything which >>> will change the LSID and therefore which might change any >>> dependencies - in my case its ONLY the description. >> I respectfully disagree: the description is the *essence* of the data >> type. Otherwise the data type is just a random assortment of fields >> with no implied meaning in the real world, and therefore useless. If >> you change the description, you change the version, even if you think >> its minor, others may not. >> >> I agree that you should be able to change it without deregistering >> though, that's a major flaw... >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From gordonp at ucalgary.ca Tue Jan 27 10:07:05 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 27 Jan 2009 08:07:05 -0700 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497EB878.8070402@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> <497EB878.8070402@mpiz-koeln.mpg.de> Message-ID: <497F2319.9020704@ucalgary.ca> But in Moby, the description is what tells you the meaning. The user will infer the appropriateness of using a term based on that free text. Whether that inference is reasonable or not depends on the user and the person who created the term. I didn't say that the description is necessarily *correct* or precise, but that it *is* the usage contract in Moby. Andreas Groscurth wrote: > Of course the description is important for the understanding and the > use of the datatype - but as its free text where everybody can add any > information (and therefore also less information) i wouldnt count this > as the *essence* of the datatype. If we would talk about a description > ontology or other controlled vocabulary... I would agree. You could > also say that random characters do not give an implied meaning - thats > basically what the description is. > > Just as an example what i mean (actually this shows it for the > description of a service) - if you have a service called "runBlast"... > the description about is "Runs a Blast". > Does this give you any implied meaning ? what version of blast, > against what database, what blast program etc etc... > > Sorry - this is a general issue ... a random user based text should > not be seen as the essence of any element in the ontology..... > > And my suggestion in the way i want to change them is basically add > new information, being more specific or erazing typos... I know that > allow this would also enable people to completly change the > description of a datatype... but as we allow people already being that > much I wouldnt dare to give this opportunity. > > Cheers > Andreas > > Paul Gordon wrote: >> >>> I agree here with Martin ... i dont want to change anything which >>> will change the LSID and therefore which might change any >>> dependencies - in my case its ONLY the description. >> I respectfully disagree: the description is the *essence* of the data >> type. Otherwise the data type is just a random assortment of fields >> with no implied meaning in the real world, and therefore useless. If >> you change the description, you change the version, even if you think >> its minor, others may not. >> >> I agree that you should be able to change it without deregistering >> though, that's a major flaw... >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > From pieter.neerincx at gmail.com Tue Jan 27 17:47:45 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Tue, 27 Jan 2009 23:47:45 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497F2319.9020704@ucalgary.ca> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> <497EB878.8070402@mpiz-koeln.mpg.de> <497F2319.9020704@ucalgary.ca> Message-ID: <19477C3C-7825-46B9-918C-5120ADACEB13@gmail.com> On 27 Jan 2009, at 16:07, Paul Gordon wrote: > But in Moby, the description is what tells you the meaning. The > user will infer the appropriateness of using a term based on that > free text. Whether that inference is reasonable or not depends on > the user and the person who created the term. I didn't say that the > description is necessarily *correct* or precise, but that it *is* > the usage contract in Moby. Yep, I totally agree. The description is what gives you the meaning, especially for the primitives: String, DateTime, Float, Integer and Boolean. The fact that something is a string is not extremely informative. So we add an articleName attribute. Let's say I use a String primitive to store the name of a species. So now we have ... . That still doesn't tell me if I should use the systematical Latin name like for example Homo sapiens or the common name like human and in the case of a common name it doesn't have to be in English anyway, there could be case sensitivity issues, etc.... So there are a million ways to use this object. If this object was designed properly the description will take any confusion away and make it 100% clear what grammar to use for the species names. If the description doesn't specify it you'll end up trying to find out how the service works by painstaking trial and error. Note that the namespaces are not helping here as they cover only the context of the id attributes, but not the CDATA content of primitives nor the context of the element names. It's virtually impossible for BioMoby Central to figure out if you are only trying to correct a typo / add a more meaningful description or whether you are changing the meaning. The only way to make a shortcut as compared to taking "the long way" to update an object with many dependencies is if it's changed/hacked by someone with "raw" access to the SQL database, which basically means we got back to whether or not to curate Moby Central... > Andreas Groscurth wrote: >> Of course the description is important for the understanding and >> the use of the datatype - but as its free text where everybody can >> add any information (and therefore also less information) i wouldnt >> count this as the *essence* of the datatype. If we would talk about >> a description ontology or other controlled vocabulary... I would >> agree. You could also say that random characters do not give an >> implied meaning - thats basically what the description is. >> >> Just as an example what i mean (actually this shows it for the >> description of a service) - if you have a service called >> "runBlast"... the description about is "Runs a Blast". >> Does this give you any implied meaning ? what version of blast, >> against what database, what blast program etc etc... >> >> Sorry - this is a general issue ... a random user based text should >> not be seen as the essence of any element in the ontology..... >> >> And my suggestion in the way i want to change them is basically add >> new information, being more specific or erazing typos... I know >> that allow this would also enable people to completly change the >> description of a datatype... but as we allow people already being >> that much I wouldnt dare to give this opportunity. >> >> Cheers >> Andreas >> >> Paul Gordon wrote: >>> >>>> I agree here with Martin ... i dont want to change anything which >>>> will change the LSID and therefore which might change any >>>> dependencies - in my case its ONLY the description. >>> I respectfully disagree: the description is the *essence* of the >>> data type. Otherwise the data type is just a random assortment of >>> fields with no implied meaning in the real world, and therefore >>> useless. If you change the description, you change the version, >>> even if you think its minor, others may not. >>> >>> I agree that you should be able to change it without deregistering >>> though, that's a major flaw... >>> _______________________________________________ >>> 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: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From groscurt at mpiz-koeln.mpg.de Wed Jan 28 02:29:33 2009 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Wed, 28 Jan 2009 08:29:33 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <19477C3C-7825-46B9-918C-5120ADACEB13@gmail.com> Message-ID: I never disagreed that the description is in moby basically the only source of the meaning. I just complaint about the way it is used and how people can describe things - that free text is 'not an optimal way to do'... so imo this discussion leads the wrong way here. I totally agree with you Pieter - I just say with the current situation its not how it should be... BYGONES. Fact is - the description is not changeable currently in an easy way so my suggestion is not doable. End Cheers Andreas ----------------original message----------------- From: "Pieter Neerincx" To: "Core developer announcements" moby-dev at lists.open-bio.org Date: Tue, 27 Jan 2009 23:47:45 +0100 ------------------------------------------------- > > On 27 Jan 2009, at 16:07, Paul Gordon wrote: > >> But in Moby, the description is what tells you the meaning. The >> user will infer the appropriateness of using a term based on that >> free text. Whether that inference is reasonable or not depends on >> the user and the person who created the term. I didn't say that the >> description is necessarily *correct* or precise, but that it *is* >> the usage contract in Moby. > > Yep, I totally agree. The description is what gives you the meaning, > especially for the primitives: String, DateTime, Float, Integer and > Boolean. The fact that something is a string is not extremely > informative. So we add an articleName attribute. Let's say I use a > String primitive to store the name of a species. So now we have > ... . That still doesn't tell > me if I should use the systematical Latin name like for example Homo > sapiens or the common name like human and in the case of a common name > it doesn't have to be in English anyway, there could be case > sensitivity issues, etc.... So there are a million ways to use this > object. If this object was designed properly the description will take > any confusion away and make it 100% clear what grammar to use for the > species names. If the description doesn't specify it you'll end up > trying to find out how the service works by painstaking trial and > error. Note that the namespaces are not helping here as they cover > only the context of the id attributes, but not the CDATA content of > primitives nor the context of the element names. > > It's virtually impossible for BioMoby Central to figure out if you are > only trying to correct a typo / add a more meaningful description or > whether you are changing the meaning. The only way to make a shortcut > as compared to taking "the long way" to update an object with many > dependencies is if it's changed/hacked by someone with "raw" access to > the SQL database, which basically means we got back to whether or not > to curate Moby Central... > > >> Andreas Groscurth wrote: >>> Of course the description is important for the understanding and >>> the use of the datatype - but as its free text where everybody can >>> add any information (and therefore also less information) i wouldnt >>> count this as the *essence* of the datatype. If we would talk about >>> a description ontology or other controlled vocabulary... I would >>> agree. You could also say that random characters do not give an >>> implied meaning - thats basically what the description is. >>> >>> Just as an example what i mean (actually this shows it for the >>> description of a service) - if you have a service called >>> "runBlast"... the description about is "Runs a Blast". >>> Does this give you any implied meaning ? what version of blast, >>> against what database, what blast program etc etc... >>> >>> Sorry - this is a general issue ... a random user based text should >>> not be seen as the essence of any element in the ontology..... >>> >>> And my suggestion in the way i want to change them is basically add >>> new information, being more specific or erazing typos... I know >>> that allow this would also enable people to completly change the >>> description of a datatype... but as we allow people already being >>> that much I wouldnt dare to give this opportunity. >>> >>> Cheers >>> Andreas >>> >>> Paul Gordon wrote: >>>> >>>>> I agree here with Martin ... i dont want to change anything which >>>>> will change the LSID and therefore which might change any >>>>> dependencies - in my case its ONLY the description. >>>> I respectfully disagree: the description is the *essence* of the >>>> data type. Otherwise the data type is just a random assortment of >>>> fields with no implied meaning in the real world, and therefore >>>> useless. If you change the description, you change the version, >>>> even if you think its minor, others may not. >>>> >>>> I agree that you should be able to change it without deregistering >>>> though, that's a major flaw... >>>> _______________________________________________ >>>> 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: +31 (0)317-483 060 > mobile: +31 (0)6-143 66 783 > e-mail: pieter.neerincx at gmail.com > skype: pieter.online > ------------------------------------------------------------- > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Wed Jan 28 02:33:18 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Jan 2009 15:33:18 +0800 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4961DE42.1080203@googlemail.com> References: <4961DE42.1080203@googlemail.com> Message-ID: <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> > The major difference is that now all 'tomcat' properties are renamed to > 'server' (e.g. tomcat.host = server.host) to reflect the generalization. But I hope that the old properties work, as well - right? Thanks for all the changes you did. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Jan 28 05:00:13 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Jan 2009 11:00:13 +0100 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> Message-ID: <49802CAD.9070808@mpiz-koeln.mpg.de> I didnt encounter any problems with the "new" properties... as I said - it was mainly a renaming process. I tested it on my tomcat and jboss on my local machine and also on a tomcat and jboss and a remote machine - and it worked. Cheers andreas Martin Senger wrote: >> The major difference is that now all 'tomcat' properties are renamed to >> 'server' (e.g. tomcat.host = server.host) to reflect the generalization. >> > > > But I hope that the old properties work, as well - right? > > Thanks for all the changes you did. > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Wed Jan 28 09:44:20 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Jan 2009 22:44:20 +0800 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <49802CAD.9070808@mpiz-koeln.mpg.de> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> > I didnt encounter any problems with the "new" properties... as I said - it > was mainly a renaming process. No, that's not what I meant. I suggested that it would be nice if *both*properties work. I would like to be able to use 'tomcat.host' *or* 'server.host'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Jan 28 09:54:34 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Jan 2009 15:54:34 +0100 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> Message-ID: <498071AA.8010301@mpiz-koeln.mpg.de> In this case - no thats not possible currently... I changed it that way that all tomcat.xxx are replaced by server.xxx ... the question is why you want that ? except existing applications relying on the exact naming I couldnt think of another reason as this is a pure naming change Andreas Martin Senger wrote: >> I didnt encounter any problems with the "new" properties... as I said - it >> was mainly a renaming process. >> > > > No, that's not what I meant. I suggested that it would be nice if > *both*properties work. I would like to be able to use 'tomcat.host' > *or* 'server.host'. > > Cheers, > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Wed Jan 28 10:03:08 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Jan 2009 23:03:08 +0800 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <498071AA.8010301@mpiz-koeln.mpg.de> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> <498071AA.8010301@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901280703s3917e9a5ved75816a796bbf71@mail.gmail.com> > the question is why you want that ? except existing applications relying on > the exact naming I couldnt think of another reason as this is a pure naming > change But it is exactly the reason I have: the backwards compatibility. Something similar already was there before: you could use, from historical reasons, both properties tomcat.home or catalina.home. Now, you just added the server.YYY properties but the old ones should still be valid. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Jan 28 10:15:40 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Jan 2009 16:15:40 +0100 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4d93f07c0901280703s3917e9a5ved75816a796bbf71@mail.gmail.com> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> <498071AA.8010301@mpiz-koeln.mpg.de> <4d93f07c0901280703s3917e9a5ved75816a796bbf71@mail.gmail.com> Message-ID: <4980769C.9080608@mpiz-koeln.mpg.de> The backwards compatibility cant be guaranteed however you doing it. The problem was that in the existing build scripts it was hardcoded that it shall use tomcat and with the internal structure of tomcat (the webapps/ path) - so it wasnt possible at all to deploy on another server... Of course I can go back to *tomcat.host* instead of *server.host* so that existing applications run without problems - but still they would fail because the build files dont rely on the hard coded information anymore. And if any application does so - it will fail no matter how we name the properties. And honestly, I dont want to go back to the tomcat hard coded situation to be able to deploy only on tomcat... If you have a good solution for this - guarantee backwards compatibility and dont having the hardcoded paths in the build file - I'm more than happy to do that.... Andreas Martin Senger wrote: >> the question is why you want that ? except existing applications relying on >> the exact naming I couldnt think of another reason as this is a pure naming >> change >> > > > But it is exactly the reason I have: the backwards compatibility. Something > similar already was there before: you could use, from historical reasons, > both properties tomcat.home or catalina.home. Now, you just added the > server.YYY properties but the old ones should still be valid. > > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From meredith at cantab.net Wed Jan 14 17:59:27 2009 From: meredith at cantab.net (Tom Oinn) Date: Wed, 14 Jan 2009 22:59:27 -0000 Subject: [MOBY-dev] HTTPS Moby services without importing certificates manually Message-ID: <496E6A78.7060306@cantab.net> Hi Moby people, A recent thread on the myGrid list pointed out that for services accessed through HTTPS you have to download and manually add the server certificates to a keystore. This struck me as rather inelegant so I did a bit of digging around java.security and wrote a socket factory that allows you to selectively ignore the signature chain and therefore access such services as if you'd already installed everything. Code's in CVS, link at http://taverna.cvs.sourceforge.net/viewvc/taverna/t2infrastructure/platform-core/src/main/java/net/sf/taverna/t2/platform/util/net/ThreadLocalSSLSocketFactory.java?view=markup Feel free to just grab it (as far as I'm concerned) and use it. Basically you call install() to register it as the socket factory that'll be used by all HTTPS connections, then when you want to temporarily ignore certificate signatures you just do 'startTrustingEverything()'. This isn't a global, it actually uses ThreadLocal to cause the change to only affect the current thread, so as long as you're not randomly spawning threads and you remember to call 'stopTrustingEverything()' it won't affect anything other than that execution thread. Enjoy. Tom From meredith at cantab.net Fri Jan 23 05:24:50 2009 From: meredith at cantab.net (Tom Oinn) Date: Fri, 23 Jan 2009 10:24:50 -0000 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <4d93f07c0901221316l5928bfbfyecd5619f31a50353@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> <4d93f07c0901221316l5928bfbfyecd5619f31a50353@mail.gmail.com> Message-ID: <49799AEF.6040208@cantab.net> Martin Senger wrote: >> No and for good reasons. > > > IMHO, well no, not really a good reason. In BioMoby, descriptions are just > descriptions, they have nothing to do with ontology (like data types, > namespaces, etc.). If I change its description, a service still has the same > behaviour. > > I agree with you in one point, however. *Any* change, even a change in > typos, should be reflected in the LSID revision, and, consequently, in all > dependent LSID revisions (in the same way as it would be done by the long > procedure of de- and re-registering). But because such change does not > change behaviour of services and, therefore, does not jeopardize any > clients, the all revision changes could be done hiddenly, by the registry > code - which would guarantee the "atomicity" of such operation (which we > cannot achieve easily from the clients). As I understood the LSID specification metadata is allowed to be mutable, couldn't you use this to create an indication in the metadata that there was a more up to date description? I'd have thought this would have been in the metadata anyway rather than the data part of the LSID but I don't know Moby particularly well so am probably wrong (given this discussion). Tom From groscurt at mpiz-koeln.mpg.de Fri Jan 2 10:17:24 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 02 Jan 2009 11:17:24 +0100 Subject: [MOBY-dev] my fault Message-ID: <495DE9B4.6030409@mpiz-koeln.mpg.de> ok... o didnt see the context menu in the tree... there is a unregister option there. but still this is not intuitiv i think... anyone has any objection if i add a button as it is with the services ? thanks andreas -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Fri Jan 2 10:06:26 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 02 Jan 2009 11:06:26 +0100 Subject: [MOBY-dev] Unregister datatypes / namespaces in dashboard? Message-ID: <495DE722.9060007@mpiz-koeln.mpg.de> Hi, is there any reason why there is no button for unregistering a datatype or namespace or service type in dashboard as it is for service ? thanks Andreas oh.. and happy new year :) -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From andreas.groscurth at googlemail.com Mon Jan 5 10:17:38 2009 From: andreas.groscurth at googlemail.com (Andreas Groscurth) Date: Mon, 05 Jan 2009 11:17:38 +0100 Subject: [MOBY-dev] Minor changes in JMoby Message-ID: <4961DE42.1080203@googlemail.com> Hi all, during the winter break I made some changes in jmoby and committed them today (without any formatting... no guarantee though). 1. DEPLOYMENT Deployment via dashboard was only possible for Tomcat. I changed this that it is now also possible for JBoss (and probably other servers, but i couldnt test this). For the user the only difference is now that he/she has to enter the complete path to axis on the server. Before that it was sufficient to enter 'axis' in the field 'Axis relative path in Tomcat', now you have to enter e.g. 'webapps/axis' for tomcat or e.g. 'server/default/deploy/axis.war' for JBoss. I also replaced all 'Tomcat' entries in the labels of the fields in the MoSeS generator tab to 'Server' to reflect this generalization and I changed the corresponding build files and the documentation. The major difference is that now all 'tomcat' properties are renamed to 'server' (e.g. tomcat.host = server.host) to reflect the generalization. I'm still not happy that now there is the tomcat.xml file which is used for the deployment - but honestly i dont trust currently the renaming in the cvs via Eclipse (as i would love to rename it to server.xml or so) and so i kept it as it is. 2. SERVICE IMPLEMENTATION If a service returns a collection of datatypes, the skeleton will now also have a method which accepts a collection and not only an array. To be consistent with the existing jmoby API I kept the method which accepts the array. So now there are always two methods which the service provider can choose, based on the service implementation. If a datatype has any other primitives as relationship than String/Boolean it is now possible to pass the Java primitive and not only the moby primitive. E.g. AminoAcidSequence has the SequenceString which is a String and Length which is an Integer. Before there was the method setSequenceString(String sequence) and setSequenceString(MobyString sequence), but for Length there was only setLength(MobyInteger length). I added the templates for float and integer, so that now every datatype which has children of these primitives also have the methods for the Java corresponding primitives.. 3. DASHBOARD I added an unregistration button at the bar at the bottom (with the other buttons) to the registration panel of Namespaces, Data Types and Service Types in Dashboard, to be consistent with the unregistration button of the service regisration panel. The changes are tested and are compilable - if you find any errors or problems or have any objections let me know. Thanks and a happy new year. Andreas From andreas.groscurth at googlemail.com Tue Jan 6 09:29:05 2009 From: andreas.groscurth at googlemail.com (Andreas Groscurth) Date: Tue, 06 Jan 2009 10:29:05 +0100 Subject: [MOBY-dev] Cleaning the registry ? Message-ID: <49632461.7030201@googlemail.com> Hi all, I wrote a short script which basically fetches all namespaces and all datatypes registered at the Moby central in Canada. Both are then compared to all datatypes and namespaces of all registered services used for the input and the output definition. Assuming the retrieval methods in jmoby work correctly and my script does it also we have the following numbers: Registered Data Types: 721 Unused Data Types: 388 Registered Namespaces: 459 Unused Namespaces: 232 This means 53% of all registered datatypes are not used - and 50% of all Namespaces !!! How do you think about cleaning the registry once in a while and erase unsused datatypes and namespaces ? Of course they might be useable for a service provider someday, but for the sake of clarity I would suggest to do that. Cleaning both would reduce the number of entries by more than the half, which would result in smaller, more compact, better understandable and better browsable ontologies. What do you think ? Cheers Andreas From groscurt at mpiz-koeln.mpg.de Tue Jan 6 09:31:12 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 10:31:12 +0100 Subject: [MOBY-dev] Cleaning the registry Message-ID: <496324E0.9010509@mpiz-koeln.mpg.de> Hi all, I wrote a short script which basically fetches all namespaces and all datatypes registered at the Moby central in Canada. Both are then compared to all datatypes and namespaces of all registered services used for the input and the output definition. Assuming the retrieval methods in jmoby work correctly and my script does it also we have the following numbers: Registered Data Types: 721 Unused Data Types: 388 Registered Namespaces: 459 Unused Namespaces: 232 This means 53% of all registered datatypes are not used - and 50% of all Namespaces !!! How do you think about cleaning the registry once in a while and erase unsused datatypes and namespaces ? Of course they might be useable for a service provider someday, but for the sake of clarity I would suggest to do that. Cleaning both would reduce the number of entries by more than the half, which would result in smaller, more compact, better understandable and better browsable ontologies. What do you think ? Cheers Andreas PS: Sorry if you receive this email twice now... I (again) wrote the first mail from another, not registered, email account.... -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From py at pingoured.fr Tue Jan 6 09:37:26 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 06 Jan 2009 10:37:26 +0100 Subject: [MOBY-dev] Cleaning the registry In-Reply-To: <496324E0.9010509@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> Message-ID: <49632656.3060901@pingoured.fr> Andreas Groscurth wrote: > This means 53% of all registered datatypes are not used - and 50% of all > Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but for > the sake of clarity I would suggest to do that. Cleaning both would > reduce the number of entries by more than the half, which would result > in smaller, more compact, better understandable and better browsable > ontologies. > > What do you think ? For the theory, I think this is good idea but why not start by mailing the owner of the datatypes/namespaces to tell them that their creation is not used. I think that would be the first step before removing anything :) Could you provide the list of the datatypes and namespace you found somewhere ? Thanks and regards , Pierre From Sebastien.Carrere at toulouse.inra.fr Tue Jan 6 09:37:07 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Tue, 06 Jan 2009 10:37:07 +0100 Subject: [MOBY-dev] Cleaning the registry ? In-Reply-To: <49632461.7030201@googlemail.com> References: <49632461.7030201@googlemail.com> Message-ID: <49632643.9000700@toulouse.inra.fr> Hi all and Bonne Annee ! I totally agree with Andreas. This is what I do in Remora: I propose only used Datatypes and Namespaces in the starting page. The large amount of datatypes is a real (and old) problem for biologists (and bioinformaticians !) endusers. Sebastien Andreas Groscurth wrote: > Hi all, > > I wrote a short script which basically fetches all namespaces and all > datatypes registered at the Moby central in Canada. Both are then > compared to all datatypes and namespaces of all registered services > used for the input and the output definition. > > Assuming the retrieval methods in jmoby work correctly and my script > does it also we have the following numbers: > > Registered Data Types: 721 > Unused Data Types: 388 > > Registered Namespaces: 459 > Unused Namespaces: 232 > > This means 53% of all registered datatypes are not used - and 50% of > all Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but > for the sake of clarity I would suggest to do that. Cleaning both > would reduce the number of entries by more than the half, which would > result in smaller, more compact, better understandable and better > browsable ontologies. > > What do you think ? > > Cheers > Andreas > _______________________________________________ > 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 groscurt at mpiz-koeln.mpg.de Tue Jan 6 11:10:21 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 12:10:21 +0100 Subject: [MOBY-dev] Cleaning the registry In-Reply-To: <49632656.3060901@pingoured.fr> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49632656.3060901@pingoured.fr> Message-ID: <49633C1D.5010209@mpiz-koeln.mpg.de> Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: > >> This means 53% of all registered datatypes are not used - and 50% of >> all Namespaces !!! >> >> How do you think about cleaning the registry once in a while and >> erase unsused datatypes and namespaces ? >> >> Of course they might be useable for a service provider someday, but >> for the sake of clarity I would suggest to do that. Cleaning both >> would reduce the number of entries by more than the half, which would >> result in smaller, more compact, better understandable and better >> browsable ontologies. >> >> What do you think ? > > For the theory, I think this is good idea but why not start by mailing > the owner of the datatypes/namespaces to tell them that their creation > is not used. I think that would be the first step before removing > anything :) > > Could you provide the list of the datatypes and namespace you found > somewhere ? > > Thanks and regards > , Of course it would be nice to ask the owner to remove it, but honestly - the question is a) is the owner still reachable via this email, b) does he/she respond to it and c) does she/he unregister it ? The automatic way is more reliable ... BUT - I have found an error in my numbers... I count datatypes which are children of an used datatype as unused.... As soon as I correct this i will post the list with the unsused types and numbers on a web page. Cheers Andreas -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 6 13:32:28 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 14:32:28 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <496324E0.9010509@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> Message-ID: <49635D6C.3040608@mpiz-koeln.mpg.de> Hi, I uploaded to html files showing the unsused elements: http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html The corrected number for the datatypes is 331 / 721 (45%). I assume that people register their namespaces / datatypes in advance to their service. So of course their mightbe elements which will be used in the near future - I'm not talking about cleaning it every week or so. But thinking about a monthly basis is fair to me and via the LSID it can be checked how old the entry is. As you can see on the page - there are entries unused which are registered in 2001 etc... Cheers Andreas Andreas Groscurth wrote: > Hi all, > > I wrote a short script which basically fetches all namespaces and all > datatypes registered at the Moby central in Canada. Both are then > compared to all datatypes and namespaces of all registered services > used for the input and the output definition. > > Assuming the retrieval methods in jmoby work correctly and my script > does it also we have the following numbers: > > Registered Data Types: 721 > Unused Data Types: 388 > > Registered Namespaces: 459 > Unused Namespaces: 232 > > This means 53% of all registered datatypes are not used - and 50% of > all Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but > for the sake of clarity I would suggest to do that. Cleaning both > would reduce the number of entries by more than the half, which would > result in smaller, more compact, better understandable and better > browsable ontologies. > > What do you think ? > > Cheers > Andreas > > PS: Sorry if you receive this email twice now... I (again) wrote the > first mail from another, not registered, email account.... > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From py at pingoured.fr Tue Jan 6 13:43:15 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 06 Jan 2009 14:43:15 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49635D6C.3040608@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> Message-ID: <49635FF3.4040100@pingoured.fr> Andreas Groscurth wrote: > Hi, > > I uploaded to html files showing the unsused elements: > > http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html > http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html > > The corrected number for the datatypes is 331 / 721 (45%). I think there is still a bug, I see: OSE_object avilin05.avignon.inra.fr 2008-08-20 and I know this object (I created it), it has a bunch of children (OSE_author, OSE_experiment...) that are used by webservices :) We can not remove object that have children that are used. Thanks for the lists, Regards, Pierre From groscurt at mpiz-koeln.mpg.de Tue Jan 6 13:56:39 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 14:56:39 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49635FF3.4040100@pingoured.fr> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> Message-ID: <49636317.8070808@mpiz-koeln.mpg.de> If a datatype has children that are used by a webservice than they dont have anything to do with that datatype - so we can delete it. E.g. AminoAcidSequence has a String... String is a widely used datatype. Assuming AminoAcidSequence is not used at all it can be deregistered although it has a child String. Of course you can deregister a parent type which children are in use, but you cant deregister a child type which parent is in use.... Cheers Andreas Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> >> I uploaded to html files showing the unsused elements: >> >> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >> >> The corrected number for the datatypes is 331 / 721 (45%). > > I think there is still a bug, I see: > OSE_object avilin05.avignon.inra.fr 2008-08-20 > and I know this object (I created it), it has a bunch of children > (OSE_author, OSE_experiment...) that are used by webservices :) > > We can not remove object that have children that are used. > > Thanks for the lists, > > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 6 14:03:59 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 15:03:59 +0100 Subject: [MOBY-dev] test registry not working In-Reply-To: References: <494A3961.2060605@mpiz-koeln.mpg.de> Message-ID: <496364CF.5020601@mpiz-koeln.mpg.de> Hi Mark, any new information on the test exchange process ? Cheers Andreas Mark wrote: > We're having LOTS of problems with that machine at the moment. I'm in > the process of setting up a new server (two, actually) that will > replace the bioinfo machine. The address will, unfortunately, change > for the test registry but I'll try to convince our IT team to set-up > auto-forwarding. > > Thanks for your patience, > > M > > > > On Thu, 18 Dec 2008 03:52:01 -0800, Andreas Groscurth > wrote: > >> Hi, >> >> when i try to register anything at the test repository i receive >> >> ===ERROR=== >> Fault details: >> [stackTrace: null] >> [hostname: null] >> Fault string: DBI >> connect('moby_central:bioinfo.icapture.ubc.ca:3306','moby',...) >> failed: Can't connect to MySQL server on 'bioinfo.icapture.ubc.ca' >> (111) at >> /usr/lib/perl5/site_perl/5.8.5/MOBY/Adaptor/moby/queryapi/mysql.pm >> line 93 >> >> Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Server >> Fault actor: null >> When calling: >> http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl >> =========== >> >> Cheers >> Andreas >> > > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From edward.kawas at gmail.com Tue Jan 6 14:27:36 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Jan 2009 06:27:36 -0800 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49636317.8070808@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> <49636317.8070808@mpiz-koeln.mpg.de> Message-ID: <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> Hey Andreas, I think that he meant something like ... you can't remove the datatype Object because it has a child DNASequence that is being used. 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: January-06-09 5:57 AM To: Core developer announcements Subject: Re: [MOBY-dev] [MOBY-l] Cleaning the registry If a datatype has children that are used by a webservice than they dont have anything to do with that datatype - so we can delete it. E.g. AminoAcidSequence has a String... String is a widely used datatype. Assuming AminoAcidSequence is not used at all it can be deregistered although it has a child String. Of course you can deregister a parent type which children are in use, but you cant deregister a child type which parent is in use.... Cheers Andreas Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> >> I uploaded to html files showing the unsused elements: >> >> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >> >> The corrected number for the datatypes is 331 / 721 (45%). > > I think there is still a bug, I see: > OSE_object avilin05.avignon.inra.fr 2008-08-20 > and I know this object (I created it), it has a bunch of children > (OSE_author, OSE_experiment...) that are used by webservices :) > > We can not remove object that have children that are used. > > Thanks for the lists, > > Regards, > > Pierre > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ _______________________________________________ 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 Jan 6 14:42:14 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 06 Jan 2009 15:42:14 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> <49636317.8070808@mpiz-koeln.mpg.de> <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> Message-ID: <49636DC6.7030203@mpiz-koeln.mpg.de> Ah... in the sense of the hierarchy... not the children (attributes / relationship or however this should be called). Then of course you are right... Edward Kawas wrote: > Hey Andreas, > > I think that he meant something like ... you can't remove the datatype > Object because it has a child DNASequence that is being used. > > 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: January-06-09 5:57 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [MOBY-l] Cleaning the registry > > If a datatype has children that are used by a webservice than they dont > have anything to do with that datatype - so we can delete it. > > E.g. > > AminoAcidSequence has a String... String is a widely used datatype. > Assuming AminoAcidSequence is not used at all it can be deregistered > although it has a child String. > > Of course you can deregister a parent type which children are in use, > but you cant deregister a child type which parent is in use.... > > Cheers > Andreas > > Pierre-Yves Chibon wrote: > >> Andreas Groscurth wrote: >> >>> Hi, >>> >>> I uploaded to html files showing the unsused elements: >>> >>> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >>> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >>> >>> The corrected number for the datatypes is 331 / 721 (45%). >>> >> I think there is still a bug, I see: >> OSE_object avilin05.avignon.inra.fr 2008-08-20 >> and I know this object (I created it), it has a bunch of children >> (OSE_author, OSE_experiment...) that are used by webservices :) >> >> We can not remove object that have children that are used. >> >> Thanks for the lists, >> >> Regards, >> >> Pierre >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From py at pingoured.fr Tue Jan 6 15:29:15 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Tue, 06 Jan 2009 16:29:15 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49636DC6.7030203@mpiz-koeln.mpg.de> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> <49636317.8070808@mpiz-koeln.mpg.de> <49636a5d.02578c0a.2484.ffffcc6f@mx.google.com> <49636DC6.7030203@mpiz-koeln.mpg.de> Message-ID: <496378CB.4070208@pingoured.fr> Andreas Groscurth wrote: > Ah... in the sense of the hierarchy... not the children (attributes / > relationship or however this should be called). > > Then of course you are right... > > > Edward Kawas wrote: > >> Hey Andreas, >> >> I think that he meant something like ... you can't remove the datatype >> Object because it has a child DNASequence that is being used. >> Thanks for clarifying that's what I meant :) Regards, Pierre From pieter.neerincx at gmail.com Tue Jan 6 15:29:28 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Tue, 6 Jan 2009 16:29:28 +0100 Subject: [MOBY-dev] [MOBY-l] Cleaning the registry In-Reply-To: <49635FF3.4040100@pingoured.fr> References: <496324E0.9010509@mpiz-koeln.mpg.de> <49635D6C.3040608@mpiz-koeln.mpg.de> <49635FF3.4040100@pingoured.fr> Message-ID: <4C2DC0E2-DA21-4334-82CE-84EA92A1B8FC@gmail.com> Hi, On 06 Jan 2009, at 14:43, Pierre-Yves Chibon wrote: > Andreas Groscurth wrote: >> Hi, >> I uploaded to html files showing the unsused elements: >> http://bioinfo.mpiz-koeln.mpg.de/datatypes2Delete.html >> http://bioinfo.mpiz-koeln.mpg.de/namespaces2Delete.html >> The corrected number for the datatypes is 331 / 721 (45%). > > I think there is still a bug, I see: > OSE_object avilin05.avignon.inra.fr 2008-08-20 > and I know this object (I created it), it has a bunch of children > (OSE_author, OSE_experiment...) that are used by webservices :) > > We can not remove object that have children that are used. Check, same here. I've registered a more generic object which I don't use directly in any service, but I do use a more specialized object that inherits from this one (ISA relationship). For all the other object and namespace "orphans" registered by www.bioinformatics.nl : they are actually used, but you can't figure that out using the ontologies (yet). Long time ago I ran into scalability issues. After trying several different solutions to the problem I started to use "pass-by-reference". Hence when I expect large inputs or outputs I replace them with a URL object. This URL points to a file somewhere on a server, which contains the actual data in BioMoby format. If one day pass-by-reference will become standardised as part of the official BioMoby specs, I expect to be able to take advantage of it with only minor tweaks as all the data I send around is already BioMoby compliant :). Registering those objects and namespace made sense to me because: 1. It allows me to use BioMoby tools to explore the registry + structure of the objects when designing/maintaining my own services. 2. Others might recycle these objects preventing the registration of objects/namespace which are virtually the same, but just with a slightly different name creating yet another alias. 3. It prevents others from registering objects/namespace with the same name, but a for a different purpose or with a different meaning. That would require me to rename lots of objects/namespace once pass-by- reference makes it into the BioMoby specs. Hence it makes my current services more potentially forward compatible... On a side note: Martin, any news on an official pass-by-reference RFC? I remember some time ago we had lengthy discussion on the mailinglist... I do realise that right now a BioMoby "enduser" can not see the difference between depreciated orphan objects/namespaces catching dust and the ones I registered with the future of a standardised pass-by- reference machanism for BioMoby in mind... Cheers, Pi > Thanks for the lists, > > Regards, > > Pierre > _______________________________________________ > 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: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Tue Jan 6 23:42:02 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 6 Jan 2009 23:42:02 +0000 Subject: [MOBY-dev] Cleaning the registry ? In-Reply-To: <49632643.9000700@toulouse.inra.fr> References: <49632461.7030201@googlemail.com> <49632643.9000700@toulouse.inra.fr> Message-ID: <4d93f07c0901061542y6db34503gcd84597a3dfec2fa@mail.gmail.com> > I totally agree with Andreas. Actually, I don't. Or: I agree only partially. The data types can be part of a domain model (as they are for the GCP project) - even without existing services, the model is still useful (and, for example, with Moses generated data types can be at once used in various Java programs). I may agree with namespaces - but because I am still not sure (and never been) what exactly namespaces in BioMoby mean, I cannot be even here sure :-) Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From jason at bioteam.net Wed Jan 7 00:11:42 2009 From: jason at bioteam.net (jason) Date: Tue, 06 Jan 2009 16:11:42 -0800 Subject: [MOBY-dev] Cleaning the registry Message-ID: <4963F33E.5070105@bioteam.net> Hi, all I think some manual clean is needed, too. For example, there are two text plain data type: text_plain and text-plain. I guess there are no difference between these two types. Another example is FASTA nucleotide sequence. What type is FASTA nucleotide sequence ? It can be FASTA_NA or NucleotideSequence. Here a piece of data can be represented by two types and there is no connection between these two types. If the user thinks his data as FASTA_NA and searches for service, he will miss the service for NucleotideSequence. Service producing FASTA_NA can not be chained to service accepting NucleotideSequence as input. This brings up another question: whether uncurated data type management works in reality or not. My understanding is that data type is the heart of biomoby. If the data type is not carefully managed, the beauty of biomoby only works in theory. -jason Andreas Groscurth wrote: > Hi all, > > I wrote a short script which basically fetches all namespaces and all > datatypes registered at the Moby central in Canada. Both are then > compared to all datatypes and namespaces of all registered services > used for the input and the output definition. > > Assuming the retrieval methods in jmoby work correctly and my script > does it also we have the following numbers: > > Registered Data Types: 721 > Unused Data Types: 388 > > Registered Namespaces: 459 > Unused Namespaces: 232 > > This means 53% of all registered datatypes are not used - and 50% of > all Namespaces !!! > > How do you think about cleaning the registry once in a while and erase > unsused datatypes and namespaces ? > > Of course they might be useable for a service provider someday, but > for the sake of clarity I would suggest to do that. Cleaning both > would reduce the number of entries by more than the half, which would > result in smaller, more compact, better understandable and better > browsable ontologies. > > What do you think ? > > Cheers > Andreas > _______________________________________________ > 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 Wed Jan 7 07:03:24 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 07 Jan 2009 08:03:24 +0100 Subject: [MOBY-dev] Cleaning the registry In-Reply-To: <4963F33E.5070105@bioteam.net> References: <4963F33E.5070105@bioteam.net> Message-ID: <496453BC.9030907@mpiz-koeln.mpg.de> > My understanding is that data type is the heart of biomoby. If the data type is not carefully managed, the beauty of biomoby only works in theory. Thats of course a way more broader topic you are talking about - this is not only cleaning unused datatypes but curating existing ones. Although I agree with you this comes with some problems. The main problem would be who to decide which datatype is the correct one or what is the truth in general... And of course what to do with the numerous datatypes which might be the children of a "wrong" datatype - and with all the services which use them.... and so on. > Actually, I don't. Or: I agree only partially. The data types can be part of > a domain model (as they are for the GCP project) - even without existing > services, the model is still useful (and, for example, with Moses generated > data types can be at once used in various Java programs). mhm sorry I dont get that point. Why are datatypes registered at the official production central of BioMoby if they are not used in BioMoby ? Just because they might be relevant for various Java programs ? Is the central then a collection of all domain models which are relevant for everything ? This sounds like abuse to me... I guess I dont get that one, but still for me the central repository of BioMoby should only contain elements which are useable and relevant for the BioMoby world (This excludes those datatypes and services which are not reachable for the public) Cheers Andreas jason wrote: > Hi, all > > I think some manual clean is needed, too. > For example, there are two text plain data type: text_plain and > text-plain. I guess there are no difference between these two types. > Another example is FASTA nucleotide sequence. What type is FASTA > nucleotide sequence ? It can be FASTA_NA or NucleotideSequence. Here > a piece of data can be represented by two types and there is no > connection between these two types. If the user thinks his data as > FASTA_NA and searches for service, he will miss the service for > NucleotideSequence. Service producing FASTA_NA can not be chained to > service accepting NucleotideSequence as input. > This brings up another question: whether uncurated data type > management works in reality or not. > > > -jason > > Andreas Groscurth wrote: >> Hi all, >> >> I wrote a short script which basically fetches all namespaces and all >> datatypes registered at the Moby central in Canada. Both are then >> compared to all datatypes and namespaces of all registered services >> used for the input and the output definition. >> >> Assuming the retrieval methods in jmoby work correctly and my script >> does it also we have the following numbers: >> >> Registered Data Types: 721 >> Unused Data Types: 388 >> >> Registered Namespaces: 459 >> Unused Namespaces: 232 >> >> This means 53% of all registered datatypes are not used - and 50% of >> all Namespaces !!! >> >> How do you think about cleaning the registry once in a while and >> erase unsused datatypes and namespaces ? >> >> Of course they might be useable for a service provider someday, but >> for the sake of clarity I would suggest to do that. Cleaning both >> would reduce the number of entries by more than the half, which would >> result in smaller, more compact, better understandable and better >> browsable ontologies. >> >> What do you think ? >> >> Cheers >> 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 -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Wed Jan 21 22:10:15 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Jan 2009 23:10:15 +0100 Subject: [MOBY-dev] Unregister datatypes / namespaces in dashboard? In-Reply-To: <495DE722.9060007@mpiz-koeln.mpg.de> References: <495DE722.9060007@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901211410l1ec689b6n42e61e70d1c9bc59@mail.gmail.com> > is there any reason why there is no button for unregistering a datatype or > namespace or service type in dashboard as it is for service ? I cannot start Dashboard now (on this computer) to check all answers but I definitely remember that most entities can be unregistered from the Dashboard. However, some (from various technical and UI aspects) entities can be unregistered by right-click on their names in the tree (and not by a button). Have you tried and still some are not covered? Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Wed Jan 21 22:14:32 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Jan 2009 23:14:32 +0100 Subject: [MOBY-dev] my fault In-Reply-To: <495DE9B4.6030409@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> > but still this is not intuitiv i think... anyone has any objection if i add > a button as it is with the services ? Please wait until I can check it (see my previous email) - [which will be on Monday 26th when I am back in the office at IRRI]. When I see it I will remember why it is this way and not the other one :-) Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From andreas.groscurth at googlemail.com Thu Jan 22 08:41:13 2009 From: andreas.groscurth at googlemail.com (Andreas Groscurth) Date: Thu, 22 Jan 2009 09:41:13 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> Message-ID: <49783129.6010309@googlemail.com> Hi all, I was wondering if there is an easy and fast way to change the description of an ontology entry (such as datatype for example). Or do you have to follow the whole procedure of unregister it and then register it again ? This would be very problematic as you can unregister it as long as services are using it... So is there a way to change the description of an entity without going the long, stony way ? Thanks Andreas From martin.senger at gmail.com Thu Jan 22 11:16:03 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 22 Jan 2009 12:16:03 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <49783129.6010309@googlemail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> Message-ID: <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> > So is there a way to change the description of an entity without going the > long, stony way ? No, there is no such way in the BioMOBY API. I agree with you that it is paintful as it is now. The only thing we (you :-) ) can do is to write a Java method that does the whole long procedure for you, hidden from the end-users. But the quetsion is how safe such procedure can be (because during its run, the repository state is changed). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From pieter.neerincx at gmail.com Thu Jan 22 13:17:36 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Thu, 22 Jan 2009 14:17:36 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <49783129.6010309@googlemail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> Message-ID: <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> Hi, On 22 Jan 2009, at 09:41, Andreas Groscurth wrote: > Hi all, > > I was wondering if there is an easy and fast way to change the > description of an ontology entry (such as datatype for example). Or > do you have to follow the whole procedure of unregister it and then > register it again ? This would be very problematic as you can > unregister it as long as services are using it... > > So is there a way to change the description of an entity without > going the long, stony way ? No and for good reasons. If I designed a service for which I recycled one of the objects you designed and you change how this object is supposed to be used by changing the description, I have a problem. Hence it might brake any of the other entries in the ontologies that depend on it. Basically for BioMoby this means you have to de- and re- registering the object "the long way" to make sure all dependancies will be updated and all their LSIDs will change so everyone can easily determine these things have changed. I'd have to admit though it can be complicated procedure if all you want to is correct a typo for example, but for BioMoby it's very difficult to determine whether you just corrected a typo or changed the whole meaning of the object. Cheers, Pi > > > Thanks > Andreas > _______________________________________________ > 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: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From martin.senger at gmail.com Thu Jan 22 21:16:07 2009 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 22 Jan 2009 21:16:07 +0000 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> Message-ID: <4d93f07c0901221316l5928bfbfyecd5619f31a50353@mail.gmail.com> > No and for good reasons. IMHO, well no, not really a good reason. In BioMoby, descriptions are just descriptions, they have nothing to do with ontology (like data types, namespaces, etc.). If I change its description, a service still has the same behaviour. I agree with you in one point, however. *Any* change, even a change in typos, should be reflected in the LSID revision, and, consequently, in all dependent LSID revisions (in the same way as it would be done by the long procedure of de- and re-registering). But because such change does not change behaviour of services and, therefore, does not jeopardize any clients, the all revision changes could be done hiddenly, by the registry code - which would guarantee the "atomicity" of such operation (which we cannot achieve easily from the clients). Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Mon Jan 26 08:25:07 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 26 Jan 2009 09:25:07 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> Message-ID: <497D7363.5090605@mpiz-koeln.mpg.de> I agree here with Martin ... i dont want to change anything which will change the LSID and therefore which might change any dependencies - in my case its ONLY the description. Still I dont see how this method should be easily written... Because if I do the whole procedure in the background I still need to unregister the datatype, meaning unregister all services which uses this datatype - and how to do that ? If the services provide a rdf, I would need to delete that rdf to unregister the services successfully - and this I cant do for all services. So if there isnt any other way - I dont see a possibility to have such all-in-once method ?! Andreas Martin Senger wrote: >> So is there a way to change the description of an entity without going the >> long, stony way ? >> > > > No, there is no such way in the BioMOBY API. I agree with you that it is > paintful as it is now. The only thing we (you :-) ) can do is to write a > Java method that does the whole long procedure for you, hidden from the > end-users. But the quetsion is how safe such procedure can be (because > during its run, the repository state is changed). > > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Mon Jan 26 09:16:53 2009 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 26 Jan 2009 17:16:53 +0800 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497D7363.5090605@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901260116g1ad7513apeac886459464d7fa@mail.gmail.com> > Still I dont see how this method should be easily written... If the > services provide a rdf For services with the RDF, I also do not see a way how to automate it. This is yet another argument why such change should be done completely on the registry site (but it would need a new method - or methods - in the Moby API). Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From gordonp at ucalgary.ca Mon Jan 26 16:01:51 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 26 Jan 2009 09:01:51 -0700 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497D7363.5090605@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> Message-ID: <497DDE6F.7000906@ucalgary.ca> > I agree here with Martin ... i dont want to change anything which will > change the LSID and therefore which might change any dependencies - in > my case its ONLY the description. I respectfully disagree: the description is the *essence* of the data type. Otherwise the data type is just a random assortment of fields with no implied meaning in the real world, and therefore useless. If you change the description, you change the version, even if you think its minor, others may not. I agree that you should be able to change it without deregistering though, that's a major flaw... From martin.senger at gmail.com Tue Jan 27 00:50:26 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Jan 2009 08:50:26 +0800 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> Message-ID: <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> > Please wait until I can check it (see my previous email) - [which will be > on Monday 26th when I am back in the office at IRRI]. When I see it I will > remember why it is this way and not the other one :-) > The "normal" way to unregister an entity is by using the right-click popup menu. It is used consistently anywhere where there is a list of entities. Which is not the case for services (there is no list of all services in this panel) - and, therefore, the service panel has a separate "Unregister" button. I am not in favour to add the "Unregister" button to other subpanels. If we do that, we should remove it from the popup menu (otherwise it would be confusing to have two alternatives to do the same thing). But removing it from the popup menu will change the current functionality without a really good cause. People may be used to use this way and when it suddenly disappears, they may be confused. I do not see this, perhaps inconsistent, look&feel a big issue, therefore, I suggest to keep it as it is. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From markw at illuminae.com Tue Jan 27 03:00:42 2009 From: markw at illuminae.com (Mark) Date: Mon, 26 Jan 2009 19:00:42 -0800 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> Message-ID: I know that I am going to be crucified for this, but... Martin, I disagree with you :-) If we look at widely-used software like MS Word, the right-click context-menu contains all of the same options as you would get if you clicked on the main menu-bar and navigated to the appropriate place! Context-menu's are important (critical!). It isn't "a different way", it is THE SAME WAY, only presented in-context... M On Mon, 26 Jan 2009 16:50:26 -0800, Martin Senger wrote: >> Please wait until I can check it (see my previous email) - [which will >> be >> on Monday 26th when I am back in the office at IRRI]. When I see it I >> will >> remember why it is this way and not the other one :-) >> > > The "normal" way to unregister an entity is by using the right-click > popup > menu. It is used consistently anywhere where there is a list of entities. > Which is not the case for services (there is no list of all services in > this > panel) - and, therefore, the service panel has a separate "Unregister" > button. > > I am not in favour to add the "Unregister" button to other subpanels. If > we > do that, we should remove it from the popup menu (otherwise it would be > confusing to have two alternatives to do the same thing). But removing it > from the popup menu will change the current functionality without a > really > good cause. People may be used to use this way and when it suddenly > disappears, they may be confused. > > I do not see this, perhaps inconsistent, look&feel a big issue, > therefore, I > suggest to keep it as it is. > > Cheers, > Martin > From martin.senger at gmail.com Tue Jan 27 03:30:17 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Jan 2009 11:30:17 +0800 Subject: [MOBY-dev] my fault In-Reply-To: References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> Message-ID: <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> Then go ahead and implement the buttons.... [but make sure that the button is disabled when nothing is displayed in the subpanel, or, preferable, when what is displayed really exists in the registry (in the tree)]. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From martin.senger at gmail.com Tue Jan 27 03:51:02 2009 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Jan 2009 11:51:02 +0800 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> Message-ID: <4d93f07c0901261951u6476f990i31039fe6adb21700@mail.gmail.com> > Then go ahead and implement the buttons.... Sorry, I thought that I was talking to Andreas who expressed the wish to implement these buttons. Andreas, please go ahead and implement it, it's fine with me. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Tue Jan 27 07:32:08 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 27 Jan 2009 08:32:08 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497DDE6F.7000906@ucalgary.ca> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> Message-ID: <497EB878.8070402@mpiz-koeln.mpg.de> Of course the description is important for the understanding and the use of the datatype - but as its free text where everybody can add any information (and therefore also less information) i wouldnt count this as the *essence* of the datatype. If we would talk about a description ontology or other controlled vocabulary... I would agree. You could also say that random characters do not give an implied meaning - thats basically what the description is. Just as an example what i mean (actually this shows it for the description of a service) - if you have a service called "runBlast"... the description about is "Runs a Blast". Does this give you any implied meaning ? what version of blast, against what database, what blast program etc etc... Sorry - this is a general issue ... a random user based text should not be seen as the essence of any element in the ontology..... And my suggestion in the way i want to change them is basically add new information, being more specific or erazing typos... I know that allow this would also enable people to completly change the description of a datatype... but as we allow people already being that much I wouldnt dare to give this opportunity. Cheers Andreas Paul Gordon wrote: > >> I agree here with Martin ... i dont want to change anything which >> will change the LSID and therefore which might change any >> dependencies - in my case its ONLY the description. > I respectfully disagree: the description is the *essence* of the data > type. Otherwise the data type is just a random assortment of fields > with no implied meaning in the real world, and therefore useless. If > you change the description, you change the version, even if you think > its minor, others may not. > > I agree that you should be able to change it without deregistering > though, that's a major flaw... > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 27 07:35:21 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 27 Jan 2009 08:35:21 +0100 Subject: [MOBY-dev] my fault In-Reply-To: <4d93f07c0901261951u6476f990i31039fe6adb21700@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <4d93f07c0901261650x1c495cb9w2300337eb61765df@mail.gmail.com> <4d93f07c0901261930m29bf8f09vd03002711b7e664e@mail.gmail.com> <4d93f07c0901261951u6476f990i31039fe6adb21700@mail.gmail.com> Message-ID: <497EB939.4040800@mpiz-koeln.mpg.de> Basically I already did - they are currently just commented out ;-) I will uncomment them and take care that if nothing is selected they will be disabled etc Cheers Andreas Martin Senger wrote: >> Then go ahead and implement the buttons.... >> > > > Sorry, I thought that I was talking to Andreas who expressed the wish to > implement these buttons. Andreas, please go ahead and implement it, it's > fine with me. > > Cheers, > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From groscurt at mpiz-koeln.mpg.de Tue Jan 27 07:40:19 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 27 Jan 2009 08:40:19 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497EB878.8070402@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> <497EB878.8070402@mpiz-koeln.mpg.de> Message-ID: <497EBA63.8050200@mpiz-koeln.mpg.de> *ups* sorry for some mistakes in my email.... too early here :( > but as we allow people already being that much I wouldnt dare to give this opportunity. i meant "I would dare...." of course... i should sleep longer... Andreas Groscurth wrote: > Of course the description is important for the understanding and the > use of the datatype - but as its free text where everybody can add any > information (and therefore also less information) i wouldnt count this > as the *essence* of the datatype. If we would talk about a description > ontology or other controlled vocabulary... I would agree. You could > also say that random characters do not give an implied meaning - thats > basically what the description is. > > Just as an example what i mean (actually this shows it for the > description of a service) - if you have a service called "runBlast"... > the description about is "Runs a Blast". > Does this give you any implied meaning ? what version of blast, > against what database, what blast program etc etc... > > Sorry - this is a general issue ... a random user based text should > not be seen as the essence of any element in the ontology..... > > And my suggestion in the way i want to change them is basically add > new information, being more specific or erazing typos... I know that > allow this would also enable people to completly change the > description of a datatype... but as we allow people already being that > much I wouldnt dare to give this opportunity. > > Cheers > Andreas > > Paul Gordon wrote: >> >>> I agree here with Martin ... i dont want to change anything which >>> will change the LSID and therefore which might change any >>> dependencies - in my case its ONLY the description. >> I respectfully disagree: the description is the *essence* of the data >> type. Otherwise the data type is just a random assortment of fields >> with no implied meaning in the real world, and therefore useless. If >> you change the description, you change the version, even if you think >> its minor, others may not. >> >> I agree that you should be able to change it without deregistering >> though, that's a major flaw... >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From gordonp at ucalgary.ca Tue Jan 27 15:07:05 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 27 Jan 2009 08:07:05 -0700 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497EB878.8070402@mpiz-koeln.mpg.de> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> <497EB878.8070402@mpiz-koeln.mpg.de> Message-ID: <497F2319.9020704@ucalgary.ca> But in Moby, the description is what tells you the meaning. The user will infer the appropriateness of using a term based on that free text. Whether that inference is reasonable or not depends on the user and the person who created the term. I didn't say that the description is necessarily *correct* or precise, but that it *is* the usage contract in Moby. Andreas Groscurth wrote: > Of course the description is important for the understanding and the > use of the datatype - but as its free text where everybody can add any > information (and therefore also less information) i wouldnt count this > as the *essence* of the datatype. If we would talk about a description > ontology or other controlled vocabulary... I would agree. You could > also say that random characters do not give an implied meaning - thats > basically what the description is. > > Just as an example what i mean (actually this shows it for the > description of a service) - if you have a service called "runBlast"... > the description about is "Runs a Blast". > Does this give you any implied meaning ? what version of blast, > against what database, what blast program etc etc... > > Sorry - this is a general issue ... a random user based text should > not be seen as the essence of any element in the ontology..... > > And my suggestion in the way i want to change them is basically add > new information, being more specific or erazing typos... I know that > allow this would also enable people to completly change the > description of a datatype... but as we allow people already being that > much I wouldnt dare to give this opportunity. > > Cheers > Andreas > > Paul Gordon wrote: >> >>> I agree here with Martin ... i dont want to change anything which >>> will change the LSID and therefore which might change any >>> dependencies - in my case its ONLY the description. >> I respectfully disagree: the description is the *essence* of the data >> type. Otherwise the data type is just a random assortment of fields >> with no implied meaning in the real world, and therefore useless. If >> you change the description, you change the version, even if you think >> its minor, others may not. >> >> I agree that you should be able to change it without deregistering >> though, that's a major flaw... >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > From pieter.neerincx at gmail.com Tue Jan 27 22:47:45 2009 From: pieter.neerincx at gmail.com (Pieter Neerincx) Date: Tue, 27 Jan 2009 23:47:45 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <497F2319.9020704@ucalgary.ca> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <4d93f07c0901220316x615232fbx798b85e41212d5f2@mail.gmail.com> <497D7363.5090605@mpiz-koeln.mpg.de> <497DDE6F.7000906@ucalgary.ca> <497EB878.8070402@mpiz-koeln.mpg.de> <497F2319.9020704@ucalgary.ca> Message-ID: <19477C3C-7825-46B9-918C-5120ADACEB13@gmail.com> On 27 Jan 2009, at 16:07, Paul Gordon wrote: > But in Moby, the description is what tells you the meaning. The > user will infer the appropriateness of using a term based on that > free text. Whether that inference is reasonable or not depends on > the user and the person who created the term. I didn't say that the > description is necessarily *correct* or precise, but that it *is* > the usage contract in Moby. Yep, I totally agree. The description is what gives you the meaning, especially for the primitives: String, DateTime, Float, Integer and Boolean. The fact that something is a string is not extremely informative. So we add an articleName attribute. Let's say I use a String primitive to store the name of a species. So now we have ... . That still doesn't tell me if I should use the systematical Latin name like for example Homo sapiens or the common name like human and in the case of a common name it doesn't have to be in English anyway, there could be case sensitivity issues, etc.... So there are a million ways to use this object. If this object was designed properly the description will take any confusion away and make it 100% clear what grammar to use for the species names. If the description doesn't specify it you'll end up trying to find out how the service works by painstaking trial and error. Note that the namespaces are not helping here as they cover only the context of the id attributes, but not the CDATA content of primitives nor the context of the element names. It's virtually impossible for BioMoby Central to figure out if you are only trying to correct a typo / add a more meaningful description or whether you are changing the meaning. The only way to make a shortcut as compared to taking "the long way" to update an object with many dependencies is if it's changed/hacked by someone with "raw" access to the SQL database, which basically means we got back to whether or not to curate Moby Central... > Andreas Groscurth wrote: >> Of course the description is important for the understanding and >> the use of the datatype - but as its free text where everybody can >> add any information (and therefore also less information) i wouldnt >> count this as the *essence* of the datatype. If we would talk about >> a description ontology or other controlled vocabulary... I would >> agree. You could also say that random characters do not give an >> implied meaning - thats basically what the description is. >> >> Just as an example what i mean (actually this shows it for the >> description of a service) - if you have a service called >> "runBlast"... the description about is "Runs a Blast". >> Does this give you any implied meaning ? what version of blast, >> against what database, what blast program etc etc... >> >> Sorry - this is a general issue ... a random user based text should >> not be seen as the essence of any element in the ontology..... >> >> And my suggestion in the way i want to change them is basically add >> new information, being more specific or erazing typos... I know >> that allow this would also enable people to completly change the >> description of a datatype... but as we allow people already being >> that much I wouldnt dare to give this opportunity. >> >> Cheers >> Andreas >> >> Paul Gordon wrote: >>> >>>> I agree here with Martin ... i dont want to change anything which >>>> will change the LSID and therefore which might change any >>>> dependencies - in my case its ONLY the description. >>> I respectfully disagree: the description is the *essence* of the >>> data type. Otherwise the data type is just a random assortment of >>> fields with no implied meaning in the real world, and therefore >>> useless. If you change the description, you change the version, >>> even if you think its minor, others may not. >>> >>> I agree that you should be able to change it without deregistering >>> though, that's a major flaw... >>> _______________________________________________ >>> 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: +31 (0)317-483 060 mobile: +31 (0)6-143 66 783 e-mail: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- From groscurt at mpiz-koeln.mpg.de Wed Jan 28 07:29:33 2009 From: groscurt at mpiz-koeln.mpg.de (groscurt) Date: Wed, 28 Jan 2009 08:29:33 +0100 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <19477C3C-7825-46B9-918C-5120ADACEB13@gmail.com> Message-ID: I never disagreed that the description is in moby basically the only source of the meaning. I just complaint about the way it is used and how people can describe things - that free text is 'not an optimal way to do'... so imo this discussion leads the wrong way here. I totally agree with you Pieter - I just say with the current situation its not how it should be... BYGONES. Fact is - the description is not changeable currently in an easy way so my suggestion is not doable. End Cheers Andreas ----------------original message----------------- From: "Pieter Neerincx" To: "Core developer announcements" moby-dev at lists.open-bio.org Date: Tue, 27 Jan 2009 23:47:45 +0100 ------------------------------------------------- > > On 27 Jan 2009, at 16:07, Paul Gordon wrote: > >> But in Moby, the description is what tells you the meaning. The >> user will infer the appropriateness of using a term based on that >> free text. Whether that inference is reasonable or not depends on >> the user and the person who created the term. I didn't say that the >> description is necessarily *correct* or precise, but that it *is* >> the usage contract in Moby. > > Yep, I totally agree. The description is what gives you the meaning, > especially for the primitives: String, DateTime, Float, Integer and > Boolean. The fact that something is a string is not extremely > informative. So we add an articleName attribute. Let's say I use a > String primitive to store the name of a species. So now we have > ... . That still doesn't tell > me if I should use the systematical Latin name like for example Homo > sapiens or the common name like human and in the case of a common name > it doesn't have to be in English anyway, there could be case > sensitivity issues, etc.... So there are a million ways to use this > object. If this object was designed properly the description will take > any confusion away and make it 100% clear what grammar to use for the > species names. If the description doesn't specify it you'll end up > trying to find out how the service works by painstaking trial and > error. Note that the namespaces are not helping here as they cover > only the context of the id attributes, but not the CDATA content of > primitives nor the context of the element names. > > It's virtually impossible for BioMoby Central to figure out if you are > only trying to correct a typo / add a more meaningful description or > whether you are changing the meaning. The only way to make a shortcut > as compared to taking "the long way" to update an object with many > dependencies is if it's changed/hacked by someone with "raw" access to > the SQL database, which basically means we got back to whether or not > to curate Moby Central... > > >> Andreas Groscurth wrote: >>> Of course the description is important for the understanding and >>> the use of the datatype - but as its free text where everybody can >>> add any information (and therefore also less information) i wouldnt >>> count this as the *essence* of the datatype. If we would talk about >>> a description ontology or other controlled vocabulary... I would >>> agree. You could also say that random characters do not give an >>> implied meaning - thats basically what the description is. >>> >>> Just as an example what i mean (actually this shows it for the >>> description of a service) - if you have a service called >>> "runBlast"... the description about is "Runs a Blast". >>> Does this give you any implied meaning ? what version of blast, >>> against what database, what blast program etc etc... >>> >>> Sorry - this is a general issue ... a random user based text should >>> not be seen as the essence of any element in the ontology..... >>> >>> And my suggestion in the way i want to change them is basically add >>> new information, being more specific or erazing typos... I know >>> that allow this would also enable people to completly change the >>> description of a datatype... but as we allow people already being >>> that much I wouldnt dare to give this opportunity. >>> >>> Cheers >>> Andreas >>> >>> Paul Gordon wrote: >>>> >>>>> I agree here with Martin ... i dont want to change anything which >>>>> will change the LSID and therefore which might change any >>>>> dependencies - in my case its ONLY the description. >>>> I respectfully disagree: the description is the *essence* of the >>>> data type. Otherwise the data type is just a random assortment of >>>> fields with no implied meaning in the real world, and therefore >>>> useless. If you change the description, you change the version, >>>> even if you think its minor, others may not. >>>> >>>> I agree that you should be able to change it without deregistering >>>> though, that's a major flaw... >>>> _______________________________________________ >>>> 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: +31 (0)317-483 060 > mobile: +31 (0)6-143 66 783 > e-mail: pieter.neerincx at gmail.com > skype: pieter.online > ------------------------------------------------------------- > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From martin.senger at gmail.com Wed Jan 28 07:33:18 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Jan 2009 15:33:18 +0800 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4961DE42.1080203@googlemail.com> References: <4961DE42.1080203@googlemail.com> Message-ID: <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> > The major difference is that now all 'tomcat' properties are renamed to > 'server' (e.g. tomcat.host = server.host) to reflect the generalization. But I hope that the old properties work, as well - right? Thanks for all the changes you did. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Jan 28 10:00:13 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Jan 2009 11:00:13 +0100 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> Message-ID: <49802CAD.9070808@mpiz-koeln.mpg.de> I didnt encounter any problems with the "new" properties... as I said - it was mainly a renaming process. I tested it on my tomcat and jboss on my local machine and also on a tomcat and jboss and a remote machine - and it worked. Cheers andreas Martin Senger wrote: >> The major difference is that now all 'tomcat' properties are renamed to >> 'server' (e.g. tomcat.host = server.host) to reflect the generalization. >> > > > But I hope that the old properties work, as well - right? > > Thanks for all the changes you did. > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Wed Jan 28 14:44:20 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Jan 2009 22:44:20 +0800 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <49802CAD.9070808@mpiz-koeln.mpg.de> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> > I didnt encounter any problems with the "new" properties... as I said - it > was mainly a renaming process. No, that's not what I meant. I suggested that it would be nice if *both*properties work. I would like to be able to use 'tomcat.host' *or* 'server.host'. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Jan 28 14:54:34 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Jan 2009 15:54:34 +0100 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> Message-ID: <498071AA.8010301@mpiz-koeln.mpg.de> In this case - no thats not possible currently... I changed it that way that all tomcat.xxx are replaced by server.xxx ... the question is why you want that ? except existing applications relying on the exact naming I couldnt think of another reason as this is a pure naming change Andreas Martin Senger wrote: >> I didnt encounter any problems with the "new" properties... as I said - it >> was mainly a renaming process. >> > > > No, that's not what I meant. I suggested that it would be nice if > *both*properties work. I would like to be able to use 'tomcat.host' > *or* 'server.host'. > > Cheers, > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From martin.senger at gmail.com Wed Jan 28 15:03:08 2009 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Jan 2009 23:03:08 +0800 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <498071AA.8010301@mpiz-koeln.mpg.de> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> <498071AA.8010301@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0901280703s3917e9a5ved75816a796bbf71@mail.gmail.com> > the question is why you want that ? except existing applications relying on > the exact naming I couldnt think of another reason as this is a pure naming > change But it is exactly the reason I have: the backwards compatibility. Something similar already was there before: you could use, from historical reasons, both properties tomcat.home or catalina.home. Now, you just added the server.YYY properties but the old ones should still be valid. Martin -- Martin Senger email: martin.senger at gmail.com,m.senger at cgiar.org skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Jan 28 15:15:40 2009 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Jan 2009 16:15:40 +0100 Subject: [MOBY-dev] Minor changes in JMoby In-Reply-To: <4d93f07c0901280703s3917e9a5ved75816a796bbf71@mail.gmail.com> References: <4961DE42.1080203@googlemail.com> <4d93f07c0901272333p2e8974fbu6b4878b1de09d70d@mail.gmail.com> <49802CAD.9070808@mpiz-koeln.mpg.de> <4d93f07c0901280644na14ea91iee118ad01086db85@mail.gmail.com> <498071AA.8010301@mpiz-koeln.mpg.de> <4d93f07c0901280703s3917e9a5ved75816a796bbf71@mail.gmail.com> Message-ID: <4980769C.9080608@mpiz-koeln.mpg.de> The backwards compatibility cant be guaranteed however you doing it. The problem was that in the existing build scripts it was hardcoded that it shall use tomcat and with the internal structure of tomcat (the webapps/ path) - so it wasnt possible at all to deploy on another server... Of course I can go back to *tomcat.host* instead of *server.host* so that existing applications run without problems - but still they would fail because the build files dont rely on the hard coded information anymore. And if any application does so - it will fail no matter how we name the properties. And honestly, I dont want to go back to the tomcat hard coded situation to be able to deploy only on tomcat... If you have a good solution for this - guarantee backwards compatibility and dont having the hardcoded paths in the build file - I'm more than happy to do that.... Andreas Martin Senger wrote: >> the question is why you want that ? except existing applications relying on >> the exact naming I couldnt think of another reason as this is a pure naming >> change >> > > > But it is exactly the reason I have: the backwards compatibility. Something > similar already was there before: you could use, from historical reasons, > both properties tomcat.home or catalina.home. Now, you just added the > server.YYY properties but the old ones should still be valid. > > Martin > > -- /*************************************************** Dipl. Bioinf. Andreas Groscurth Software developer Plant Computational Biology group Max-Planck Institute for plant breeding research Carl-von-Linne Weg 10 50829 Cologne Germany +49(0) 221 5062449 ***************************************************/ From meredith at cantab.net Wed Jan 14 22:59:27 2009 From: meredith at cantab.net (Tom Oinn) Date: Wed, 14 Jan 2009 22:59:27 -0000 Subject: [MOBY-dev] HTTPS Moby services without importing certificates manually Message-ID: <496E6A78.7060306@cantab.net> Hi Moby people, A recent thread on the myGrid list pointed out that for services accessed through HTTPS you have to download and manually add the server certificates to a keystore. This struck me as rather inelegant so I did a bit of digging around java.security and wrote a socket factory that allows you to selectively ignore the signature chain and therefore access such services as if you'd already installed everything. Code's in CVS, link at http://taverna.cvs.sourceforge.net/viewvc/taverna/t2infrastructure/platform-core/src/main/java/net/sf/taverna/t2/platform/util/net/ThreadLocalSSLSocketFactory.java?view=markup Feel free to just grab it (as far as I'm concerned) and use it. Basically you call install() to register it as the socket factory that'll be used by all HTTPS connections, then when you want to temporarily ignore certificate signatures you just do 'startTrustingEverything()'. This isn't a global, it actually uses ThreadLocal to cause the change to only affect the current thread, so as long as you're not randomly spawning threads and you remember to call 'stopTrustingEverything()' it won't affect anything other than that execution thread. Enjoy. Tom From meredith at cantab.net Fri Jan 23 10:24:50 2009 From: meredith at cantab.net (Tom Oinn) Date: Fri, 23 Jan 2009 10:24:50 -0000 Subject: [MOBY-dev] Changing only the description of an ontolgy entry In-Reply-To: <4d93f07c0901221316l5928bfbfyecd5619f31a50353@mail.gmail.com> References: <495DE9B4.6030409@mpiz-koeln.mpg.de> <4d93f07c0901211414x30692bbcw2fb91b9ab7914a1c@mail.gmail.com> <49783129.6010309@googlemail.com> <7D169E51-ABEE-4E0F-84E4-977E1825259B@gmail.com> <4d93f07c0901221316l5928bfbfyecd5619f31a50353@mail.gmail.com> Message-ID: <49799AEF.6040208@cantab.net> Martin Senger wrote: >> No and for good reasons. > > > IMHO, well no, not really a good reason. In BioMoby, descriptions are just > descriptions, they have nothing to do with ontology (like data types, > namespaces, etc.). If I change its description, a service still has the same > behaviour. > > I agree with you in one point, however. *Any* change, even a change in > typos, should be reflected in the LSID revision, and, consequently, in all > dependent LSID revisions (in the same way as it would be done by the long > procedure of de- and re-registering). But because such change does not > change behaviour of services and, therefore, does not jeopardize any > clients, the all revision changes could be done hiddenly, by the registry > code - which would guarantee the "atomicity" of such operation (which we > cannot achieve easily from the clients). As I understood the LSID specification metadata is allowed to be mutable, couldn't you use this to create an indication in the metadata that there was a more up to date description? I'd have thought this would have been in the metadata anyway rather than the data part of the LSID but I don't know Moby particularly well so am probably wrong (given this discussion). Tom