From duncan.hull at cs.man.ac.uk Mon Jan 15 10:44:44 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Mon, 15 Jan 2007 15:44:44 +0000 Subject: [MOBY-dev] Martin Sengers jMoby command line client for BioMOBY In-Reply-To: References: <20061212203611.GA9247@renci.org> <457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org> <458A3D3C.2000303@ac.uma.es> Message-ID: <45ABA16C.7050508@cs.man.ac.uk> Hello I'm having difficulties finding and using the latest version of Martins jMoby client "MobyCmdLineClient" as detailed at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CmdLineClients.html So far, I've had no luck finding it in the CVS or as a binary download (preferred). Can anybody help? Thanks Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From edward.kawas at gmail.com Mon Jan 15 13:52:01 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Jan 2007 10:52:01 -0800 Subject: [MOBY-dev] Martin Sengers jMoby command line client for BioMOBY In-Reply-To: <45ABA16C.7050508@cs.man.ac.uk> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> Message-ID: <000901c738d6$3f75a5a0$c766a8c0@notebook> Hi Duncan, I may be wrong, but I think that the clients will exist if you run the ant build on /moby-live/Java/. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Duncan Hull > Sent: Monday, January 15, 2007 7:45 AM > To: Core developer announcements > Subject: [MOBY-dev] Martin Sengers jMoby command line client > for BioMOBY > > Hello > > I'm having difficulties finding and using the latest version > of Martins jMoby client "MobyCmdLineClient" > > as detailed at > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Cm dLineClients.html > > So far, I've had no luck finding it in the CVS or as a binary > download (preferred). > > Can anybody help? > > Thanks > > Duncan > > > -- > Duncan Hull > http://www.cs.man.ac.uk/~hulld/ > Phone: +44 (0) 161 275 0677 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Wed Jan 17 05:56:55 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 17 Jan 2007 10:56:55 +0000 Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? In-Reply-To: <000901c738d6$3f75a5a0$c766a8c0@notebook> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> <000901c738d6$3f75a5a0$c766a8c0@notebook> Message-ID: <45AE00F7.1060502@cs.man.ac.uk> Hello Edward Kawas wrote: > I may be wrong, but I think that the clients will exist if you run the ant build > on /moby-live/Java/. > Thanks eddie, I'll give this a try. While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? SELECT ?x FROM WHERE { ?x hasInput DNASequence . } Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From gordonp at ucalgary.ca Wed Jan 17 08:28:45 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 17 Jan 2007 06:28:45 -0700 Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? In-Reply-To: <45AE00F7.1060502@cs.man.ac.uk> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> <000901c738d6$3f75a5a0$c766a8c0@notebook> <45AE00F7.1060502@cs.man.ac.uk> Message-ID: <45AE248D.1070407@ucalgary.ca> Not that I'm aware of. There are a few SPARQL engines around (for Perl and Java), but none of them seems complete yet. Like everything in the MOBY-S community, if you build it, we will come :-) > Hello > > Edward Kawas wrote: > >> I may be wrong, but I think that the clients will exist if you run the ant build >> on /moby-live/Java/. >> >> > Thanks eddie, I'll give this a try. > > While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? > > SELECT ?x > FROM > > WHERE { ?x hasInput DNASequence . } > > > Duncan > > From markw at illuminae.com Wed Jan 17 09:27:01 2007 From: markw at illuminae.com (mark wilkinson) Date: Wed, 17 Jan 2007 14:27:01 +0000 GMT Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? In-Reply-To: <45AE248D.1070407@ucalgary.ca> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> <000901c738d6$3f75a5a0$c766a8c0@notebook><45AE00F7.1060502@cs.man.ac.uk> <45AE248D.1070407@ucalgary.ca> Message-ID: <320276136-1169044020-cardhu_blackberry.rim.net-18095-@engine26-cell01> You can SPARQL the RDF representation of the registry at: http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances Let me know how it goes! In fact, you *should* be able to use Feta to query the same document :-). (That's certainly what we were planning to do very soon!) M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Wed, 17 Jan 2007 06:28:45 To:Core developer announcements Subject: Re: [MOBY-dev] SPARQL-able endpoint for BioMOBY? Not that I'm aware of. There are a few SPARQL engines around (for Perl and Java), but none of them seems complete yet. Like everything in the MOBY-S community, if you build it, we will come :-) > Hello > > Edward Kawas wrote: > >> I may be wrong, but I think that the clients will exist if you run the ant build >> on /moby-live/Java/. >> >> > Thanks eddie, I'll give this a try. > > While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? > > SELECT ?x > FROM > > WHERE { ?x hasInput DNASequence . } > > > Duncan > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Jan 17 09:28:31 2007 From: markw at illuminae.com (mark wilkinson) Date: Wed, 17 Jan 2007 14:28:31 +0000 GMT Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? Message-ID: <1457199527-1169044110-cardhu_blackberry.rim.net-26214-@engine26-cell01> By the way, I set-up an instance of Longwell on top of that document to explore it for myself - if that is any use to you I'll install it on mobycentral as well... Let me know, M ------Original Message------ To: Core developer announcements Sent: Jan 17, 2007 6:27 AM Subject: Re: [MOBY-dev] SPARQL-able endpoint for BioMOBY? You can SPARQL the RDF representation of the registry at: http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances Let me know how it goes! In fact, you *should* be able to use Feta to query the same document :-). (That's certainly what we were planning to do very soon!) M ------Original Message------ From: Paul Gordon Sender: moby-dev-bounces at lists.open-bio.org To: Core developer announcements ReplyTo: Core developer announcements Sent: Jan 17, 2007 5:28 AM Subject: Re: [MOBY-dev] SPARQL-able endpoint for BioMOBY? Not that I'm aware of. There are a few SPARQL engines around (for Perl and Java), but none of them seems complete yet. Like everything in the MOBY-S community, if you build it, we will come :-) > Hello > > Edward Kawas wrote: > >> I may be wrong, but I think that the clients will exist if you run the ant build >> on /moby-live/Java/. >> >> > Thanks eddie, I'll give this a try. > > While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? > > SELECT ?x > FROM > > WHERE { ?x hasInput DNASequence . } > > > Duncan > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark Wilkinson ...on the road! From groscurt at mpiz-koeln.mpg.de Wed Jan 17 10:13:49 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 17 Jan 2007 16:13:49 +0100 Subject: [MOBY-dev] Handling of different LSIDs if the services are equal Message-ID: <200701171613.49295.groscurt@mpiz-koeln.mpg.de> Hi everybody, I have the following situation: I have two local repositories. One is used as my central repository, the other one as a secondary repository. My central repository was updated via my syncronisation procedure from the BioMoby central and the secondary repository was initialised with the database dumps from BioMoby. I found out that the LSID of a service is changed or updated if a service is registered at a central, so now I have the situation that if I run the update mechanism for the secondary repository, that services may have different LSIDs (because of an update of the central rep.), but the services are equal. In my application I check whether the LSDIs have changed and if so, I call the RDFagent to apply the changes. The agent by itself calls a internal comparison method to check if the services are different or equal. So my question is how to handle services with different LSIDs which are actually equal, which means, where the LSID has only changed due to local registration ? One possibility could be not to compare the LSID but to use the comparasion method as it is used in the RDFagent. Another thought is, if two services differ only in the LSID, but are actually equal, shall the 'older' service just get the LSID from the younger one ? Thanks for your input Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Fri Jan 19 03:40:31 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 19 Jan 2007 09:40:31 +0100 Subject: [MOBY-dev] Registration situation Message-ID: <200701190940.31363.groscurt@mpiz-koeln.mpg.de> Hi everybody, as far as I heared BioMoby planned to switch the registration process completly to the RDFagent and that there is a transitional period that people can register their service via the BioMoby API without providing a signature URL. I was wondering how this plans are still on ? So is there still a date at which the registration will only work with a signature URL (with the RDFagent) or will the registration via the BioMoby api without a signature URL carried on ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From d.haase at gsf.de Fri Jan 19 04:42:35 2007 From: d.haase at gsf.de (Haase, Dirk) Date: Fri, 19 Jan 2007 10:42:35 +0100 Subject: [MOBY-dev] Registration situation References: <200701190940.31363.groscurt@mpiz-koeln.mpg.de> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> Hi Andreas, afaik, this is settled: full MOBY compliance requires a signature URL. However, registration without is and will be possible and legal, but services are considered to be in test stage as long as they don't have one. Clients are free to ignore services lacking an accessible RDF description (like eg. gbrowse_moby at icapture does). Best, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Andreas Groscurth Sent: Fri 1/19/2007 9:40 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Registration situation Hi everybody, as far as I heared BioMoby planned to switch the registration process completly to the RDFagent and that there is a transitional period that people can register their service via the BioMoby API without providing a signature URL. I was wondering how this plans are still on ? So is there still a date at which the registration will only work with a signature URL (with the RDFagent) or will the registration via the BioMoby api without a signature URL carried on ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: groscurt at mpiz-koeln.mpg.de Phone: +49(0)221-5062-447 _______________________________________________ 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: not available Type: application/ms-tnef Size: 3318 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20070119/abbeddaa/attachment.bin From markw at illuminae.com Fri Jan 19 07:31:16 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 19 Jan 2007 04:31:16 -0800 Subject: [MOBY-dev] Registration situation In-Reply-To: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> References: <200701190940.31363.groscurt@mpiz-koeln.mpg.de> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> Message-ID: Hi Andreas and Dirk, The current situation is that the RDF agent has replaced the ability to deregister "stable" services via the API, for security purposes; however the registration of services (both "test" and "stable"), and the deregistration of "test" services is still possible via the API. I don't think that the gbrowse moby instance at iCAPTURE ignores services without an RDF description (that certainly wasn't my intent!), but it does ignore services that have been determined (by a moby-ping) to be inaccessible. Eddie has a cron that pings every service regularly (every couple of hours?). If gbrowse is filtering "test" services please let me know because that wasn't my intention... M On Fri, 19 Jan 2007 01:42:35 -0800, Haase, Dirk wrote: > Hi Andreas, > > afaik, this is settled: full MOBY compliance requires a signature URL. > However, registration without is and will be possible and legal, but > services are considered to be in test stage as long as they don't have > one. > Clients are free to ignore services lacking an accessible RDF description > (like eg. gbrowse_moby at icapture does). > > Best, > dirk > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Andreas Groscurth > Sent: Fri 1/19/2007 9:40 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Registration situation > Hi everybody, > > as far as I heared BioMoby planned to switch the registration process > completly to the RDFagent and that there is a transitional period that > people > can register their service via the BioMoby API without providing a > signature > URL. > > I was wondering how this plans are still on ? So is there still a date at > which the registration will only work with a signature URL (with the > RDFagent) or will the registration via the BioMoby api without a > signature > URL carried on ? > > Thanks > Andreas > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From d.haase at gsf.de Fri Jan 19 08:53:54 2007 From: d.haase at gsf.de (Haase, Dirk) Date: Fri, 19 Jan 2007 14:53:54 +0100 Subject: [MOBY-dev] Registration situation References: <200701190940.31363.groscurt@mpiz-koeln.mpg.de><1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A4@sw-rz010.gsf.de> Hi Mark, thanks for clarification. And sorry for spreading lies about the behaviour of gbrowse_moby at iCAPTURE! It definetely does consider services without RDF description, I just confused things... Regards, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Mark Wilkinson Sent: Fri 1/19/2007 1:31 PM To: Core developer announcements Subject: Re: [MOBY-dev] Registration situation Hi Andreas and Dirk, The current situation is that the RDF agent has replaced the ability to deregister "stable" services via the API, for security purposes; however the registration of services (both "test" and "stable"), and the deregistration of "test" services is still possible via the API. I don't think that the gbrowse moby instance at iCAPTURE ignores services without an RDF description (that certainly wasn't my intent!), but it does ignore services that have been determined (by a moby-ping) to be inaccessible. Eddie has a cron that pings every service regularly (every couple of hours?). If gbrowse is filtering "test" services please let me know because that wasn't my intention... M On Fri, 19 Jan 2007 01:42:35 -0800, Haase, Dirk wrote: > Hi Andreas, > > afaik, this is settled: full MOBY compliance requires a signature URL. > However, registration without is and will be possible and legal, but > services are considered to be in test stage as long as they don't have > one. > Clients are free to ignore services lacking an accessible RDF description > (like eg. gbrowse_moby at icapture does). > > Best, > dirk > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Andreas Groscurth > Sent: Fri 1/19/2007 9:40 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Registration situation > Hi everybody, > > as far as I heared BioMoby planned to switch the registration process > completly to the RDFagent and that there is a transitional period that > people > can register their service via the BioMoby API without providing a > signature > URL. > > I was wondering how this plans are still on ? So is there still a date at > which the registration will only work with a signature URL (with the > RDFagent) or will the registration via the BioMoby api without a > signature > URL carried on ? > > Thanks > Andreas > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ _______________________________________________ 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: not available Type: application/ms-tnef Size: 3914 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20070119/29a99dcb/attachment.bin From rroyo at lsi.upc.edu Fri Jan 19 10:33:46 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Fri, 19 Jan 2007 16:33:46 +0100 Subject: [MOBY-dev] getSignatureForm Message-ID: <45B0E4DA.8010801@lsi.upc.edu> Hello, Is there a problem with the getSignatureForm: http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm I've been trying to use it for the past couple of weeks and I always get an error: *type* Exception report *message* *description* _The server encountered an internal error () that prevented it from fulfilling this request._ *exception* java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:129) org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.doGet(GetSignatureRDFResponse.java:91) javax.servlet.http.HttpServlet.service(HttpServlet.java:689) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) *note* _The full stack trace of the root cause is available in the Apache Tomcat/5.5.9 logs._ Thank you! Romina From d.haase at gsf.de Fri Jan 19 15:15:46 2007 From: d.haase at gsf.de (Haase, Dirk) Date: Fri, 19 Jan 2007 21:15:46 +0100 Subject: [MOBY-dev] getSignatureForm References: <45B0E4DA.8010801@lsi.upc.edu> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> I had a similar problem last month or so and learned that the form had moved to http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm But I have a - somehow related - question: did that RDFAgent_test.html page also change its URL, and if yes, where has it gone? Thanks, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Romina Royo Sent: Fri 1/19/2007 4:33 PM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] getSignatureForm Hello, Is there a problem with the getSignatureForm: http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm I've been trying to use it for the past couple of weeks and I always get an error: *type* Exception report *message* *description* _The server encountered an internal error () that prevented it from fulfilling this request._ *exception* java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:129) org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.doGet(GetSignatureRDFResponse.java:91) javax.servlet.http.HttpServlet.service(HttpServlet.java:689) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) *note* _The full stack trace of the root cause is available in the Apache Tomcat/5.5.9 logs._ Thank you! Romina _______________________________________________ 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: not available Type: application/ms-tnef Size: 3176 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/moby-dev/attachments/20070119/70c6669d/attachment-0001.bin From edward.kawas at gmail.com Sat Jan 20 18:18:38 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Sat, 20 Jan 2007 15:18:38 -0800 Subject: [MOBY-dev] getSignatureForm In-Reply-To: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> References: <45B0E4DA.8010801@lsi.upc.edu> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> Message-ID: <000b01c73ce9$521df510$6900a8c0@notebook> A while back, I updated the locations of those servlets. The new location is at http://mobycentral.icapture.ubc.ca/authority/moby.jsp >From there, you will find the form for the agent and the signatureForm. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Haase, Dirk > Sent: Friday, January 19, 2007 12:16 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] getSignatureForm > > I had a similar problem last month or so and learned that the > form had moved to > > http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm > > But I have a - somehow related - question: did that > RDFAgent_test.html page also change its URL, and if yes, > where has it gone? > > Thanks, > dirk > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Romina Royo > Sent: Fri 1/19/2007 4:33 PM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] getSignatureForm > > Hello, > > Is there a problem with the getSignatureForm: > http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm > > I've been trying to use it for the past couple of weeks and I > always get an error: > > *type* Exception report > > *message* > > *description* _The server encountered an internal error () > that prevented it from fulfilling this request._ > > *exception* > > java.lang.NullPointerException > > org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFR > esponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:129) > > org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFR > esponse.doGet(GetSignatureRDFResponse.java:91) > javax.servlet.http.HttpServlet.service(HttpServlet.java:689) > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > *note* _The full stack trace of the root cause is available > in the Apache Tomcat/5.5.9 logs._ > > Thank you! > Romina > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From markw at illuminae.com Wed Jan 24 17:57:41 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Jan 2007 14:57:41 -0800 Subject: [MOBY-dev] MOBY Central code updated Message-ID: Hi all, I've just restarted MOBY Central with the couple of new changes to the code - support for Async (I haven't tried this yet... can somoene from INB confirm that it works?), and the fix to the mysql query regarding searching for simples versus collections. All tests pass, but please let me know if you notice anything unusual. M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From d.haase at gsf.de Thu Jan 25 04:59:30 2007 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 25 Jan 2007 10:59:30 +0100 Subject: [MOBY-dev] getSignatureForm In-Reply-To: <000b01c73ce9$521df510$6900a8c0@notebook> References: <45B0E4DA.8010801@lsi.upc.edu> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> <000b01c73ce9$521df510$6900a8c0@notebook> Message-ID: <200701251059.30572.d.haase@gsf.de> On Sunday 21 January 2007 00:18, Edward Kawas wrote: > A while back, I updated the locations of those servlets. The new location > is at http://mobycentral.icapture.ubc.ca/authority/moby.jsp Wow, there's lots of useful stuff collected there! Wouldn't it make sense to list this and/or some of the contained links on the biomoby.org Wordpress, e.g. under the 'Tools and Toys' section? Best, dirk From johan at ac.uma.es Thu Jan 25 06:08:58 2007 From: johan at ac.uma.es (johan at ac.uma.es) Date: Thu, 25 Jan 2007 12:08:58 +0100 Subject: [MOBY-dev] MOBY Central code updated In-Reply-To: Message-ID: Great news, we will install and try the new version of MOBY Central. As far as I know, the latest version of the perl-library Enrique de Andres wrote for clients/services should already be commited to the CVS. We would in turn appreciate comments or bug-reports about this library. As a side-note, the internal service enactor in MOWServ is able to handle asynchronous services. A nice side-effect is a client-side library in C++ that handles the execution details of calling to asynchronous BioMOBY services (WSRF/LSAE status interpretation etc). This client-side library we would also like to offer if anyone is interested to use it (we are currently in a meeting but will send more information about this). Anyway, thanks to Mark and his team for updating MOBY Central. Kind regards, Johan Karlsson, GNV5 On 1/24/2007, "Mark Wilkinson" wrote: >Hi all, > >I've just restarted MOBY Central with the couple of new changes to the >code - support for Async (I haven't tried this yet... can somoene from INB >confirm that it works?), and the fix to the mysql query regarding >searching for simples versus collections. > >All tests pass, but please let me know if you notice anything unusual. > >M > > >-- >-- >Mark Wilkinson >Assistant Professor, Dept. Medical Genetics >University of British Columbia >PI Bioinformatics >iCAPTURE Centre, St. Paul's Hospital > >***CONFIDENTIALITY NOTICE*** >This electronic message is intended only for the use of the addressee and >may contain information that is privileged and confidential. Any >dissemination, distribution or copying of this communication by >unauthorized individuals is strictly prohibited. If you have received this >communication in error, please notify the sender immediately by reply >e-mail and delete the original and all copies from your system. > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------------------------- Webmail de SATD usando IlohaMail From markw at illuminae.com Thu Jan 25 13:31:42 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 25 Jan 2007 10:31:42 -0800 Subject: [MOBY-dev] getSignatureForm In-Reply-To: <200701251059.30572.d.haase@gsf.de> References: <45B0E4DA.8010801@lsi.upc.edu> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> <000b01c73ce9$521df510$6900a8c0@notebook> <200701251059.30572.d.haase@gsf.de> Message-ID: On Thu, 25 Jan 2007 01:59:30 -0800, Dirk Haase wrote: > e.g. under the 'Tools and Toys' section? Done! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From markw at illuminae.com Fri Jan 26 17:15:51 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 26 Jan 2007 14:15:51 -0800 Subject: [MOBY-dev] A message to ensure transparency Message-ID: Hi All, we're starting a research project in my lab that looks at better ways to discover appropriate web services and combinations of web services. One way we want to pursue is to log MOBY Central usage such that we can better prioritize the output of a findService call to MOBY Central (e.g. 9/10 people chose THIS service as their next step). To do this effectively I will be adding a "listener" to MOBY Central such that it records and catalogues the retrieveService requests from individual IP addresses in order to track usage behaviour and make better search outputs. I will hash the IP address so that I cannot easily go back and look-up who made the request - it isn't 100% private/secure, but frankly we're not interested in who requested the service, only in which service they requested immediately before and afterwards... besides, I suspect that anyone who was *that* concerned about privacy would have set-up their own mirror of MOBY Central :-) In any case, I wanted to make sure that there were no violent objections to me doing this before I do it. Please let me know, and if I hear no objections I'll add a line into the "Policy" document associated with the Vancouver MOBY Central on the homepage. Cheers all! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From martin.senger at gmail.com Fri Jan 26 18:14:55 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Jan 2007 17:14:55 -0600 Subject: [MOBY-dev] A message to ensure transparency In-Reply-To: References: Message-ID: <4d93f07c0701261514o71587961p71dd2afe9c86e986@mail.gmail.com> Hi, I do not see any problem with privacy, it is not my cup of tea, anyway. But I would like to mention that the findService() requests do not need to be done at all when somebody calls a service, and - vice-versa - many/many times a findService() request is done when Dashboard local cache is updated, without calling any service at all. What I am saying is that the findService() is a pure way how to measure service calls. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Jan 26 18:14:55 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Jan 2007 17:14:55 -0600 Subject: [MOBY-dev] A message to ensure transparency In-Reply-To: References: Message-ID: <4d93f07c0701261514o71587961p71dd2afe9c86e986@mail.gmail.com> Hi, I do not see any problem with privacy, it is not my cup of tea, anyway. But I would like to mention that the findService() requests do not need to be done at all when somebody calls a service, and - vice-versa - many/many times a findService() request is done when Dashboard local cache is updated, without calling any service at all. What I am saying is that the findService() is a pure way how to measure service calls. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Fri Jan 26 18:43:22 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 26 Jan 2007 15:43:22 -0800 Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Message-ID: Hi all, Given that we now have Asynchronous services being registered in MOBY Central, an unpleasant behaviour has become apparent that really needs to be fixed (with no change in the API). At the moment, calls to findService will automatically set the Category to "moby" if it is not specified in the request. This was fine when there were only "moby" services in the registry, but now that we have "moby-async" services it would be better to remove this default and have the "Category" parameter behave like all other findService parameters - where leaving it out is the same as a wildcard (i.e. "all"). This is unlikely to require that anyone change their software since having the parameter there, or not, will still give you "moby" services as it always has, and moreover, the "moby-async" services are supposed to be backwards-compatible with "moby" synchronous services, so even if you discover "moby-async" services your software will be able to call them (perhaps with a timeout, however). I'm going to make this change today. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From edward.kawas at gmail.com Fri Jan 26 22:48:47 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Jan 2007 19:48:47 -0800 Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central In-Reply-To: References: Message-ID: <000301c741c6$0db9d100$6900a8c0@notebook> Hey Mark, The following find service call doesn't work. I was hoping to use that to get all services in the registry. Is my thinking incorrect? Eddie ; 1 1 -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson Sent: Friday, January 26, 2007 3:43 PM To: Core developer announcements Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Hi all, Given that we now have Asynchronous services being registered in MOBY Central, an unpleasant behaviour has become apparent that really needs to be fixed (with no change in the API). At the moment, calls to findService will automatically set the Category to "moby" if it is not specified in the request. This was fine when there were only "moby" services in the registry, but now that we have "moby-async" services it would be better to remove this default and have the "Category" parameter behave like all other findService parameters - where leaving it out is the same as a wildcard (i.e. "all"). This is unlikely to require that anyone change their software since having the parameter there, or not, will still give you "moby" services as it always has, and moreover, the "moby-async" services are supposed to be backwards-compatible with "moby" synchronous services, so even if you discover "moby-async" services your software will be able to call them (perhaps with a timeout, however). I'm going to make this change today. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Sat Jan 27 00:33:24 2007 From: markw at illuminae.com (mark wilkinson) Date: Sat, 27 Jan 2007 05:33:24 +0000 GMT Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central In-Reply-To: <000301c741c6$0db9d100$6900a8c0@notebook> References: <000301c741c6$0db9d100$6900a8c0@notebook> Message-ID: <409337980-1169876054-cardhu_blackberry.rim.net-4777-@engine10-cell01> I'm working from memory now, but I think that the code does an 'if exists' on each parameter passed... So if you pass no parameters at all no query is executed... I wonder if that is a good or a bad behaviour...??? Let's think about it some more before we decide. M -- Mark Wilkinson ...on the road! -----Original Message----- From: "Edward Kawas" Date: Fri, 26 Jan 2007 19:48:47 To:"'Core developer announcements'" Subject: Re: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Hey Mark, The following find service call doesn't work. I was hoping to use that to get all services in the registry. Is my thinking incorrect? Eddie ; 1 1 -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson Sent: Friday, January 26, 2007 3:43 PM To: Core developer announcements Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Hi all, Given that we now have Asynchronous services being registered in MOBY Central, an unpleasant behaviour has become apparent that really needs to be fixed (with no change in the API). At the moment, calls to findService will automatically set the Category to "moby" if it is not specified in the request. This was fine when there were only "moby" services in the registry, but now that we have "moby-async" services it would be better to remove this default and have the "Category" parameter behave like all other findService parameters - where leaving it out is the same as a wildcard (i.e. "all"). This is unlikely to require that anyone change their software since having the parameter there, or not, will still give you "moby" services as it always has, and moreover, the "moby-async" services are supposed to be backwards-compatible with "moby" synchronous services, so even if you discover "moby-async" services your software will be able to call them (perhaps with a timeout, however). I'm going to make this change today. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Mon Jan 15 15:44:44 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Mon, 15 Jan 2007 15:44:44 +0000 Subject: [MOBY-dev] Martin Sengers jMoby command line client for BioMOBY In-Reply-To: References: <20061212203611.GA9247@renci.org> <457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org> <458A3D3C.2000303@ac.uma.es> Message-ID: <45ABA16C.7050508@cs.man.ac.uk> Hello I'm having difficulties finding and using the latest version of Martins jMoby client "MobyCmdLineClient" as detailed at http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CmdLineClients.html So far, I've had no luck finding it in the CVS or as a binary download (preferred). Can anybody help? Thanks Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From edward.kawas at gmail.com Mon Jan 15 18:52:01 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 15 Jan 2007 10:52:01 -0800 Subject: [MOBY-dev] Martin Sengers jMoby command line client for BioMOBY In-Reply-To: <45ABA16C.7050508@cs.man.ac.uk> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> Message-ID: <000901c738d6$3f75a5a0$c766a8c0@notebook> Hi Duncan, I may be wrong, but I think that the clients will exist if you run the ant build on /moby-live/Java/. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Duncan Hull > Sent: Monday, January 15, 2007 7:45 AM > To: Core developer announcements > Subject: [MOBY-dev] Martin Sengers jMoby command line client > for BioMOBY > > Hello > > I'm having difficulties finding and using the latest version > of Martins jMoby client "MobyCmdLineClient" > > as detailed at > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Cm dLineClients.html > > So far, I've had no luck finding it in the CVS or as a binary > download (preferred). > > Can anybody help? > > Thanks > > Duncan > > > -- > Duncan Hull > http://www.cs.man.ac.uk/~hulld/ > Phone: +44 (0) 161 275 0677 > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From duncan.hull at cs.man.ac.uk Wed Jan 17 10:56:55 2007 From: duncan.hull at cs.man.ac.uk (Duncan Hull) Date: Wed, 17 Jan 2007 10:56:55 +0000 Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? In-Reply-To: <000901c738d6$3f75a5a0$c766a8c0@notebook> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> <000901c738d6$3f75a5a0$c766a8c0@notebook> Message-ID: <45AE00F7.1060502@cs.man.ac.uk> Hello Edward Kawas wrote: > I may be wrong, but I think that the clients will exist if you run the ant build > on /moby-live/Java/. > Thanks eddie, I'll give this a try. While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? SELECT ?x FROM WHERE { ?x hasInput DNASequence . } Duncan -- Duncan Hull http://www.cs.man.ac.uk/~hulld/ Phone: +44 (0) 161 275 0677 From gordonp at ucalgary.ca Wed Jan 17 13:28:45 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 17 Jan 2007 06:28:45 -0700 Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? In-Reply-To: <45AE00F7.1060502@cs.man.ac.uk> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> <000901c738d6$3f75a5a0$c766a8c0@notebook> <45AE00F7.1060502@cs.man.ac.uk> Message-ID: <45AE248D.1070407@ucalgary.ca> Not that I'm aware of. There are a few SPARQL engines around (for Perl and Java), but none of them seems complete yet. Like everything in the MOBY-S community, if you build it, we will come :-) > Hello > > Edward Kawas wrote: > >> I may be wrong, but I think that the clients will exist if you run the ant build >> on /moby-live/Java/. >> >> > Thanks eddie, I'll give this a try. > > While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? > > SELECT ?x > FROM > > WHERE { ?x hasInput DNASequence . } > > > Duncan > > From markw at illuminae.com Wed Jan 17 14:27:01 2007 From: markw at illuminae.com (mark wilkinson) Date: Wed, 17 Jan 2007 14:27:01 +0000 GMT Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? In-Reply-To: <45AE248D.1070407@ucalgary.ca> References: <20061212203611.GA9247@renci.org><457F21DD.7030904@ucalgary.ca> <20061220214305.GA4523@renci.org><458A3D3C.2000303@ac.uma.es> <45ABA16C.7050508@cs.man.ac.uk> <000901c738d6$3f75a5a0$c766a8c0@notebook><45AE00F7.1060502@cs.man.ac.uk> <45AE248D.1070407@ucalgary.ca> Message-ID: <320276136-1169044020-cardhu_blackberry.rim.net-18095-@engine26-cell01> You can SPARQL the RDF representation of the registry at: http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances Let me know how it goes! In fact, you *should* be able to use Feta to query the same document :-). (That's certainly what we were planning to do very soon!) M -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Wed, 17 Jan 2007 06:28:45 To:Core developer announcements Subject: Re: [MOBY-dev] SPARQL-able endpoint for BioMOBY? Not that I'm aware of. There are a few SPARQL engines around (for Perl and Java), but none of them seems complete yet. Like everything in the MOBY-S community, if you build it, we will come :-) > Hello > > Edward Kawas wrote: > >> I may be wrong, but I think that the clients will exist if you run the ant build >> on /moby-live/Java/. >> >> > Thanks eddie, I'll give this a try. > > While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? > > SELECT ?x > FROM > > WHERE { ?x hasInput DNASequence . } > > > Duncan > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Wed Jan 17 14:28:31 2007 From: markw at illuminae.com (mark wilkinson) Date: Wed, 17 Jan 2007 14:28:31 +0000 GMT Subject: [MOBY-dev] SPARQL-able endpoint for BioMOBY? Message-ID: <1457199527-1169044110-cardhu_blackberry.rim.net-26214-@engine26-cell01> By the way, I set-up an instance of Longwell on top of that document to explore it for myself - if that is any use to you I'll install it on mobycentral as well... Let me know, M ------Original Message------ To: Core developer announcements Sent: Jan 17, 2007 6:27 AM Subject: Re: [MOBY-dev] SPARQL-able endpoint for BioMOBY? You can SPARQL the RDF representation of the registry at: http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances Let me know how it goes! In fact, you *should* be able to use Feta to query the same document :-). (That's certainly what we were planning to do very soon!) M ------Original Message------ From: Paul Gordon Sender: moby-dev-bounces at lists.open-bio.org To: Core developer announcements ReplyTo: Core developer announcements Sent: Jan 17, 2007 5:28 AM Subject: Re: [MOBY-dev] SPARQL-able endpoint for BioMOBY? Not that I'm aware of. There are a few SPARQL engines around (for Perl and Java), but none of them seems complete yet. Like everything in the MOBY-S community, if you build it, we will come :-) > Hello > > Edward Kawas wrote: > >> I may be wrong, but I think that the clients will exist if you run the ant build >> on /moby-live/Java/. >> >> > Thanks eddie, I'll give this a try. > > While I'm at it, is there a SPARQL-able endpoint for BioMOBY RDF? > > SELECT ?x > FROM > > WHERE { ?x hasInput DNASequence . } > > > Duncan > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark Wilkinson ...on the road! From groscurt at mpiz-koeln.mpg.de Wed Jan 17 15:13:49 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 17 Jan 2007 16:13:49 +0100 Subject: [MOBY-dev] Handling of different LSIDs if the services are equal Message-ID: <200701171613.49295.groscurt@mpiz-koeln.mpg.de> Hi everybody, I have the following situation: I have two local repositories. One is used as my central repository, the other one as a secondary repository. My central repository was updated via my syncronisation procedure from the BioMoby central and the secondary repository was initialised with the database dumps from BioMoby. I found out that the LSID of a service is changed or updated if a service is registered at a central, so now I have the situation that if I run the update mechanism for the secondary repository, that services may have different LSIDs (because of an update of the central rep.), but the services are equal. In my application I check whether the LSDIs have changed and if so, I call the RDFagent to apply the changes. The agent by itself calls a internal comparison method to check if the services are different or equal. So my question is how to handle services with different LSIDs which are actually equal, which means, where the LSID has only changed due to local registration ? One possibility could be not to compare the LSID but to use the comparasion method as it is used in the RDFagent. Another thought is, if two services differ only in the LSID, but are actually equal, shall the 'older' service just get the LSID from the younger one ? Thanks for your input Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From groscurt at mpiz-koeln.mpg.de Fri Jan 19 08:40:31 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 19 Jan 2007 09:40:31 +0100 Subject: [MOBY-dev] Registration situation Message-ID: <200701190940.31363.groscurt@mpiz-koeln.mpg.de> Hi everybody, as far as I heared BioMoby planned to switch the registration process completly to the RDFagent and that there is a transitional period that people can register their service via the BioMoby API without providing a signature URL. I was wondering how this plans are still on ? So is there still a date at which the registration will only work with a signature URL (with the RDFagent) or will the registration via the BioMoby api without a signature URL carried on ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From d.haase at gsf.de Fri Jan 19 09:42:35 2007 From: d.haase at gsf.de (Haase, Dirk) Date: Fri, 19 Jan 2007 10:42:35 +0100 Subject: [MOBY-dev] Registration situation References: <200701190940.31363.groscurt@mpiz-koeln.mpg.de> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> Hi Andreas, afaik, this is settled: full MOBY compliance requires a signature URL. However, registration without is and will be possible and legal, but services are considered to be in test stage as long as they don't have one. Clients are free to ignore services lacking an accessible RDF description (like eg. gbrowse_moby at icapture does). Best, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Andreas Groscurth Sent: Fri 1/19/2007 9:40 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Registration situation Hi everybody, as far as I heared BioMoby planned to switch the registration process completly to the RDFagent and that there is a transitional period that people can register their service via the BioMoby API without providing a signature URL. I was wondering how this plans are still on ? So is there still a date at which the registration will only work with a signature URL (with the RDFagent) or will the registration via the BioMoby api without a signature URL carried on ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: groscurt at mpiz-koeln.mpg.de Phone: +49(0)221-5062-447 _______________________________________________ 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: winmail.dat Type: application/ms-tnef Size: 3318 bytes Desc: not available URL: From markw at illuminae.com Fri Jan 19 12:31:16 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 19 Jan 2007 04:31:16 -0800 Subject: [MOBY-dev] Registration situation In-Reply-To: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> References: <200701190940.31363.groscurt@mpiz-koeln.mpg.de> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> Message-ID: Hi Andreas and Dirk, The current situation is that the RDF agent has replaced the ability to deregister "stable" services via the API, for security purposes; however the registration of services (both "test" and "stable"), and the deregistration of "test" services is still possible via the API. I don't think that the gbrowse moby instance at iCAPTURE ignores services without an RDF description (that certainly wasn't my intent!), but it does ignore services that have been determined (by a moby-ping) to be inaccessible. Eddie has a cron that pings every service regularly (every couple of hours?). If gbrowse is filtering "test" services please let me know because that wasn't my intention... M On Fri, 19 Jan 2007 01:42:35 -0800, Haase, Dirk wrote: > Hi Andreas, > > afaik, this is settled: full MOBY compliance requires a signature URL. > However, registration without is and will be possible and legal, but > services are considered to be in test stage as long as they don't have > one. > Clients are free to ignore services lacking an accessible RDF description > (like eg. gbrowse_moby at icapture does). > > Best, > dirk > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Andreas Groscurth > Sent: Fri 1/19/2007 9:40 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Registration situation > Hi everybody, > > as far as I heared BioMoby planned to switch the registration process > completly to the RDFagent and that there is a transitional period that > people > can register their service via the BioMoby API without providing a > signature > URL. > > I was wondering how this plans are still on ? So is there still a date at > which the registration will only work with a signature URL (with the > RDFagent) or will the registration via the BioMoby api without a > signature > URL carried on ? > > Thanks > Andreas > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From d.haase at gsf.de Fri Jan 19 13:53:54 2007 From: d.haase at gsf.de (Haase, Dirk) Date: Fri, 19 Jan 2007 14:53:54 +0100 Subject: [MOBY-dev] Registration situation References: <200701190940.31363.groscurt@mpiz-koeln.mpg.de><1D78CE9FD586024AB0E0102F6F9A7CF86A08A3@sw-rz010.gsf.de> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A4@sw-rz010.gsf.de> Hi Mark, thanks for clarification. And sorry for spreading lies about the behaviour of gbrowse_moby at iCAPTURE! It definetely does consider services without RDF description, I just confused things... Regards, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Mark Wilkinson Sent: Fri 1/19/2007 1:31 PM To: Core developer announcements Subject: Re: [MOBY-dev] Registration situation Hi Andreas and Dirk, The current situation is that the RDF agent has replaced the ability to deregister "stable" services via the API, for security purposes; however the registration of services (both "test" and "stable"), and the deregistration of "test" services is still possible via the API. I don't think that the gbrowse moby instance at iCAPTURE ignores services without an RDF description (that certainly wasn't my intent!), but it does ignore services that have been determined (by a moby-ping) to be inaccessible. Eddie has a cron that pings every service regularly (every couple of hours?). If gbrowse is filtering "test" services please let me know because that wasn't my intention... M On Fri, 19 Jan 2007 01:42:35 -0800, Haase, Dirk wrote: > Hi Andreas, > > afaik, this is settled: full MOBY compliance requires a signature URL. > However, registration without is and will be possible and legal, but > services are considered to be in test stage as long as they don't have > one. > Clients are free to ignore services lacking an accessible RDF description > (like eg. gbrowse_moby at icapture does). > > Best, > dirk > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Andreas Groscurth > Sent: Fri 1/19/2007 9:40 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Registration situation > Hi everybody, > > as far as I heared BioMoby planned to switch the registration process > completly to the RDFagent and that there is a transitional period that > people > can register their service via the BioMoby API without providing a > signature > URL. > > I was wondering how this plans are still on ? So is there still a date at > which the registration will only work with a signature URL (with the > RDFagent) or will the registration via the BioMoby api without a > signature > URL carried on ? > > Thanks > Andreas > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ _______________________________________________ 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: winmail.dat Type: application/ms-tnef Size: 3914 bytes Desc: not available URL: From rroyo at lsi.upc.edu Fri Jan 19 15:33:46 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Fri, 19 Jan 2007 16:33:46 +0100 Subject: [MOBY-dev] getSignatureForm Message-ID: <45B0E4DA.8010801@lsi.upc.edu> Hello, Is there a problem with the getSignatureForm: http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm I've been trying to use it for the past couple of weeks and I always get an error: *type* Exception report *message* *description* _The server encountered an internal error () that prevented it from fulfilling this request._ *exception* java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:129) org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.doGet(GetSignatureRDFResponse.java:91) javax.servlet.http.HttpServlet.service(HttpServlet.java:689) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) *note* _The full stack trace of the root cause is available in the Apache Tomcat/5.5.9 logs._ Thank you! Romina From d.haase at gsf.de Fri Jan 19 20:15:46 2007 From: d.haase at gsf.de (Haase, Dirk) Date: Fri, 19 Jan 2007 21:15:46 +0100 Subject: [MOBY-dev] getSignatureForm References: <45B0E4DA.8010801@lsi.upc.edu> Message-ID: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> I had a similar problem last month or so and learned that the form had moved to http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm But I have a - somehow related - question: did that RDFAgent_test.html page also change its URL, and if yes, where has it gone? Thanks, dirk -----Original Message----- From: moby-dev-bounces at lists.open-bio.org on behalf of Romina Royo Sent: Fri 1/19/2007 4:33 PM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] getSignatureForm Hello, Is there a problem with the getSignatureForm: http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm I've been trying to use it for the past couple of weeks and I always get an error: *type* Exception report *message* *description* _The server encountered an internal error () that prevented it from fulfilling this request._ *exception* java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:129) org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.doGet(GetSignatureRDFResponse.java:91) javax.servlet.http.HttpServlet.service(HttpServlet.java:689) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) *note* _The full stack trace of the root cause is available in the Apache Tomcat/5.5.9 logs._ Thank you! Romina _______________________________________________ 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: winmail.dat Type: application/ms-tnef Size: 3176 bytes Desc: not available URL: From edward.kawas at gmail.com Sat Jan 20 23:18:38 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Sat, 20 Jan 2007 15:18:38 -0800 Subject: [MOBY-dev] getSignatureForm In-Reply-To: <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> References: <45B0E4DA.8010801@lsi.upc.edu> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> Message-ID: <000b01c73ce9$521df510$6900a8c0@notebook> A while back, I updated the locations of those servlets. The new location is at http://mobycentral.icapture.ubc.ca/authority/moby.jsp >From there, you will find the form for the agent and the signatureForm. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Haase, Dirk > Sent: Friday, January 19, 2007 12:16 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] getSignatureForm > > I had a similar problem last month or so and learned that the > form had moved to > > http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm > > But I have a - somehow related - question: did that > RDFAgent_test.html page also change its URL, and if yes, > where has it gone? > > Thanks, > dirk > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org on behalf of Romina Royo > Sent: Fri 1/19/2007 4:33 PM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] getSignatureForm > > Hello, > > Is there a problem with the getSignatureForm: > http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm > > I've been trying to use it for the past couple of weeks and I > always get an error: > > *type* Exception report > > *message* > > *description* _The server encountered an internal error () > that prevented it from fulfilling this request._ > > *exception* > > java.lang.NullPointerException > > org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFR > esponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:129) > > org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFR > esponse.doGet(GetSignatureRDFResponse.java:91) > javax.servlet.http.HttpServlet.service(HttpServlet.java:689) > javax.servlet.http.HttpServlet.service(HttpServlet.java:802) > > *note* _The full stack trace of the root cause is available > in the Apache Tomcat/5.5.9 logs._ > > Thank you! > Romina > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > From markw at illuminae.com Wed Jan 24 22:57:41 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 24 Jan 2007 14:57:41 -0800 Subject: [MOBY-dev] MOBY Central code updated Message-ID: Hi all, I've just restarted MOBY Central with the couple of new changes to the code - support for Async (I haven't tried this yet... can somoene from INB confirm that it works?), and the fix to the mysql query regarding searching for simples versus collections. All tests pass, but please let me know if you notice anything unusual. M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From d.haase at gsf.de Thu Jan 25 09:59:30 2007 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 25 Jan 2007 10:59:30 +0100 Subject: [MOBY-dev] getSignatureForm In-Reply-To: <000b01c73ce9$521df510$6900a8c0@notebook> References: <45B0E4DA.8010801@lsi.upc.edu> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> <000b01c73ce9$521df510$6900a8c0@notebook> Message-ID: <200701251059.30572.d.haase@gsf.de> On Sunday 21 January 2007 00:18, Edward Kawas wrote: > A while back, I updated the locations of those servlets. The new location > is at http://mobycentral.icapture.ubc.ca/authority/moby.jsp Wow, there's lots of useful stuff collected there! Wouldn't it make sense to list this and/or some of the contained links on the biomoby.org Wordpress, e.g. under the 'Tools and Toys' section? Best, dirk From johan at ac.uma.es Thu Jan 25 11:08:58 2007 From: johan at ac.uma.es (johan at ac.uma.es) Date: Thu, 25 Jan 2007 12:08:58 +0100 Subject: [MOBY-dev] MOBY Central code updated In-Reply-To: Message-ID: Great news, we will install and try the new version of MOBY Central. As far as I know, the latest version of the perl-library Enrique de Andres wrote for clients/services should already be commited to the CVS. We would in turn appreciate comments or bug-reports about this library. As a side-note, the internal service enactor in MOWServ is able to handle asynchronous services. A nice side-effect is a client-side library in C++ that handles the execution details of calling to asynchronous BioMOBY services (WSRF/LSAE status interpretation etc). This client-side library we would also like to offer if anyone is interested to use it (we are currently in a meeting but will send more information about this). Anyway, thanks to Mark and his team for updating MOBY Central. Kind regards, Johan Karlsson, GNV5 On 1/24/2007, "Mark Wilkinson" wrote: >Hi all, > >I've just restarted MOBY Central with the couple of new changes to the >code - support for Async (I haven't tried this yet... can somoene from INB >confirm that it works?), and the fix to the mysql query regarding >searching for simples versus collections. > >All tests pass, but please let me know if you notice anything unusual. > >M > > >-- >-- >Mark Wilkinson >Assistant Professor, Dept. Medical Genetics >University of British Columbia >PI Bioinformatics >iCAPTURE Centre, St. Paul's Hospital > >***CONFIDENTIALITY NOTICE*** >This electronic message is intended only for the use of the addressee and >may contain information that is privileged and confidential. Any >dissemination, distribution or copying of this communication by >unauthorized individuals is strictly prohibited. If you have received this >communication in error, please notify the sender immediately by reply >e-mail and delete the original and all copies from your system. > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------------------------- Webmail de SATD usando IlohaMail From markw at illuminae.com Thu Jan 25 18:31:42 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 25 Jan 2007 10:31:42 -0800 Subject: [MOBY-dev] getSignatureForm In-Reply-To: <200701251059.30572.d.haase@gsf.de> References: <45B0E4DA.8010801@lsi.upc.edu> <1D78CE9FD586024AB0E0102F6F9A7CF86A08A5@sw-rz010.gsf.de> <000b01c73ce9$521df510$6900a8c0@notebook> <200701251059.30572.d.haase@gsf.de> Message-ID: On Thu, 25 Jan 2007 01:59:30 -0800, Dirk Haase wrote: > e.g. under the 'Tools and Toys' section? Done! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From markw at illuminae.com Fri Jan 26 22:15:51 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 26 Jan 2007 14:15:51 -0800 Subject: [MOBY-dev] A message to ensure transparency Message-ID: Hi All, we're starting a research project in my lab that looks at better ways to discover appropriate web services and combinations of web services. One way we want to pursue is to log MOBY Central usage such that we can better prioritize the output of a findService call to MOBY Central (e.g. 9/10 people chose THIS service as their next step). To do this effectively I will be adding a "listener" to MOBY Central such that it records and catalogues the retrieveService requests from individual IP addresses in order to track usage behaviour and make better search outputs. I will hash the IP address so that I cannot easily go back and look-up who made the request - it isn't 100% private/secure, but frankly we're not interested in who requested the service, only in which service they requested immediately before and afterwards... besides, I suspect that anyone who was *that* concerned about privacy would have set-up their own mirror of MOBY Central :-) In any case, I wanted to make sure that there were no violent objections to me doing this before I do it. Please let me know, and if I hear no objections I'll add a line into the "Policy" document associated with the Vancouver MOBY Central on the homepage. Cheers all! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From martin.senger at gmail.com Fri Jan 26 23:14:55 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Jan 2007 17:14:55 -0600 Subject: [MOBY-dev] A message to ensure transparency In-Reply-To: References: Message-ID: <4d93f07c0701261514o71587961p71dd2afe9c86e986@mail.gmail.com> Hi, I do not see any problem with privacy, it is not my cup of tea, anyway. But I would like to mention that the findService() requests do not need to be done at all when somebody calls a service, and - vice-versa - many/many times a findService() request is done when Dashboard local cache is updated, without calling any service at all. What I am saying is that the findService() is a pure way how to measure service calls. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Fri Jan 26 23:14:55 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 26 Jan 2007 17:14:55 -0600 Subject: [MOBY-dev] A message to ensure transparency In-Reply-To: References: Message-ID: <4d93f07c0701261514o71587961p71dd2afe9c86e986@mail.gmail.com> Hi, I do not see any problem with privacy, it is not my cup of tea, anyway. But I would like to mention that the findService() requests do not need to be done at all when somebody calls a service, and - vice-versa - many/many times a findService() request is done when Dashboard local cache is updated, without calling any service at all. What I am saying is that the findService() is a pure way how to measure service calls. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Fri Jan 26 23:43:22 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 26 Jan 2007 15:43:22 -0800 Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Message-ID: Hi all, Given that we now have Asynchronous services being registered in MOBY Central, an unpleasant behaviour has become apparent that really needs to be fixed (with no change in the API). At the moment, calls to findService will automatically set the Category to "moby" if it is not specified in the request. This was fine when there were only "moby" services in the registry, but now that we have "moby-async" services it would be better to remove this default and have the "Category" parameter behave like all other findService parameters - where leaving it out is the same as a wildcard (i.e. "all"). This is unlikely to require that anyone change their software since having the parameter there, or not, will still give you "moby" services as it always has, and moreover, the "moby-async" services are supposed to be backwards-compatible with "moby" synchronous services, so even if you discover "moby-async" services your software will be able to call them (perhaps with a timeout, however). I'm going to make this change today. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From edward.kawas at gmail.com Sat Jan 27 03:48:47 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 26 Jan 2007 19:48:47 -0800 Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central In-Reply-To: References: Message-ID: <000301c741c6$0db9d100$6900a8c0@notebook> Hey Mark, The following find service call doesn't work. I was hoping to use that to get all services in the registry. Is my thinking incorrect? Eddie ; 1 1 -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson Sent: Friday, January 26, 2007 3:43 PM To: Core developer announcements Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Hi all, Given that we now have Asynchronous services being registered in MOBY Central, an unpleasant behaviour has become apparent that really needs to be fixed (with no change in the API). At the moment, calls to findService will automatically set the Category to "moby" if it is not specified in the request. This was fine when there were only "moby" services in the registry, but now that we have "moby-async" services it would be better to remove this default and have the "Category" parameter behave like all other findService parameters - where leaving it out is the same as a wildcard (i.e. "all"). This is unlikely to require that anyone change their software since having the parameter there, or not, will still give you "moby" services as it always has, and moreover, the "moby-async" services are supposed to be backwards-compatible with "moby" synchronous services, so even if you discover "moby-async" services your software will be able to call them (perhaps with a timeout, however). I'm going to make this change today. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Sat Jan 27 05:33:24 2007 From: markw at illuminae.com (mark wilkinson) Date: Sat, 27 Jan 2007 05:33:24 +0000 GMT Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central In-Reply-To: <000301c741c6$0db9d100$6900a8c0@notebook> References: <000301c741c6$0db9d100$6900a8c0@notebook> Message-ID: <409337980-1169876054-cardhu_blackberry.rim.net-4777-@engine10-cell01> I'm working from memory now, but I think that the code does an 'if exists' on each parameter passed... So if you pass no parameters at all no query is executed... I wonder if that is a good or a bad behaviour...??? Let's think about it some more before we decide. M -- Mark Wilkinson ...on the road! -----Original Message----- From: "Edward Kawas" Date: Fri, 26 Jan 2007 19:48:47 To:"'Core developer announcements'" Subject: Re: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Hey Mark, The following find service call doesn't work. I was hoping to use that to get all services in the registry. Is my thinking incorrect? Eddie ; 1 1 -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson Sent: Friday, January 26, 2007 3:43 PM To: Core developer announcements Subject: [MOBY-dev] Tiny modification in the behaviour of MOBY Central Hi all, Given that we now have Asynchronous services being registered in MOBY Central, an unpleasant behaviour has become apparent that really needs to be fixed (with no change in the API). At the moment, calls to findService will automatically set the Category to "moby" if it is not specified in the request. This was fine when there were only "moby" services in the registry, but now that we have "moby-async" services it would be better to remove this default and have the "Category" parameter behave like all other findService parameters - where leaving it out is the same as a wildcard (i.e. "all"). This is unlikely to require that anyone change their software since having the parameter there, or not, will still give you "moby" services as it always has, and moreover, the "moby-async" services are supposed to be backwards-compatible with "moby" synchronous services, so even if you discover "moby-async" services your software will be able to call them (perhaps with a timeout, however). I'm going to make this change today. Cheers! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev