From Sebastien.Carrere at toulouse.inra.fr Thu Aug 6 03:11:41 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 06 Aug 2009 09:11:41 +0200 Subject: [MOBY-dev] error when invoking asynchronous services Message-ID: <4A7A822D.9040206@toulouse.inra.fr> Bonjour, for now two days, I've got frequently errors like the following one when I try to invoke asynchronous webservices (written in Perl with WSRF::Lite): Service description 'http://docs.oasis-open.org/wsrf/rpw-2.wsdl' can't be loaded: 500 Server closed connection without sending any data back Anyone has an idea ? This error does not happen each time (with same input data) ... that's why I'm a bit confused. And it's only 2 days that the problem occurs. Merci Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From jmfernandez at cnio.es Thu Aug 6 08:57:44 2009 From: jmfernandez at cnio.es (=?ISO-8859-15?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 06 Aug 2009 14:57:44 +0200 Subject: [MOBY-dev] error when invoking asynchronous services In-Reply-To: <4A7A822D.9040206@toulouse.inra.fr> References: <4A7A822D.9040206@toulouse.inra.fr> Message-ID: <4A7AD348.9020406@cnio.es> Hi Sebastien, it seems a problem from docs.oasis-open.org side. As the WSDL generated for asynchronous services reuse (i.e. points to) some WSRF resource properties WSDL definitions, each time the generated WSDL is fully parsed the libraries must fetch http://docs.oasis-open.org/wsrf/rpw-2.wsdl (among others) in order to check the generated WSDL's validity. Best Regards, Jos? Mar?a Sebastien Carrere wrote: > Bonjour, > > for now two days, I've got frequently errors like the following one when > I try to invoke asynchronous webservices (written in Perl with WSRF::Lite): > > Service description 'http://docs.oasis-open.org/wsrf/rpw-2.wsdl' can't > be loaded: 500 Server closed connection without sending any data back > > Anyone has an idea ? > This error does not happen each time (with same input data) ... that's > why I'm a bit confused. > And it's only 2 days that the problem occurs. > > > Merci > > Sebastien > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From richard.finkers at wur.nl Sun Aug 9 08:07:03 2009 From: richard.finkers at wur.nl (Finkers, Richard) Date: Sun, 9 Aug 2009 14:07:03 +0200 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> Hi All, I am working on implementing an own moby client (based on the simpleclient example / Java Moby API) in the backbone of my database system. For this, we use a custom biomoby repository. All goes fine (service lookup / service call) however in the default situation I run into the following error while processing the XML: Problem: org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MeasurementSet) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. This is logic since the object MeasurementSet was not registered in the default (Calgary) registry but in our private project repository. I was able to hack a work-around by changing the DEFAULT_ENDPOINT and DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and NAMESPACE of my main (project) repository. I was not able to trace back the origin of the bug (yet). Can any of you help me with this? Cheers, Richard From edward.kawas at gmail.com Mon Aug 10 09:58:39 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 10 Aug 2009 06:58:39 -0700 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> Message-ID: <4a802795.25bb720a.3747.5e47@mx.google.com> Hi Richard, Are you running into this problem using MoSeS? You say composite MOBY object, so does that mean you are using MobyComposite? Did you try creating a Registry object that is primed with your registries information? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Finkers, Richard Sent: August-09-09 5:07 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private Hi All, I am working on implementing an own moby client (based on the simpleclient example / Java Moby API) in the backbone of my database system. For this, we use a custom biomoby repository. All goes fine (service lookup / service call) however in the default situation I run into the following error while processing the XML: Problem: org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MeasurementSet) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. This is logic since the object MeasurementSet was not registered in the default (Calgary) registry but in our private project repository. I was able to hack a work-around by changing the DEFAULT_ENDPOINT and DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and NAMESPACE of my main (project) repository. I was not able to trace back the origin of the bug (yet). Can any of you help me with this? Cheers, Richard _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Aug 10 10:27:42 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Aug 2009 08:27:42 -0600 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> Message-ID: <4A802E5E.7040209@ucalgary.ca> Hi Roger, If you are not using the default registry, you need to pas a Registry object into data object creation methods and others. If you can send me the code that got this error, I can help you ensure you are properly telling Moby which registry should be referenced. Thanks, Paul Finkers, Richard wrote: > Hi All, > > I am working on implementing an own moby client (based on the simpleclient example / Java Moby API) in the backbone of my database system. For this, we use a custom biomoby repository. > > All goes fine (service lookup / service call) however in the default situation I run into the following error while processing the XML: > > Problem: org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MeasurementSet) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. > > This is logic since the object MeasurementSet was not registered in the default (Calgary) registry but in our private project repository. > > I was able to hack a work-around by changing the DEFAULT_ENDPOINT and DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and NAMESPACE of my main (project) repository. > > I was not able to trace back the origin of the bug (yet). Can any of you help me with this? > > Cheers, > Richard > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From richard.finkers at wur.nl Mon Aug 10 10:55:19 2009 From: richard.finkers at wur.nl (Richard Finkers) Date: Mon, 10 Aug 2009 16:55:19 +0200 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <4a802795.25bb720a.3747.5e47@mx.google.com> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> <4a802795.25bb720a.3747.5e47@mx.google.com> Message-ID: <1249916119.17360.206.camel@localhost> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From edward.kawas at gmail.com Mon Aug 10 11:05:45 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 10 Aug 2009 08:05:45 -0700 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <1249916119.17360.206.camel@localhost> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> <4a802795.25bb720a.3747.5e47@mx.google.com> <1249916119.17360.206.camel@localhost> Message-ID: <4a803750.1cba720a.1ec6.6bb7@mx.google.com> I guess it does seem redundant, but if you consider that CentralImpl is used to interact with a registry and the other class is utilized when invoking the services, then there is a separation of concerns there. If you do create a Registry object and pass it to MobyDataType, then you will solve your problems (as Paul mentioned). Let us know if you need help with anything that we mentioned here. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Richard Finkers Sent: August-10-09 7:55 AM To: Core developer announcements Subject: Re: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private Hi Eddy, I am using the Java API and not MoSes. Correct, I am using the MobyComposite Object. I did not try to create a Registry object, instead, I am using the CentralImpl object for service discovery. Do you suggest that the registry information then will be lost for service invocation? I would naively expect that initialisation of the CentralImpl object also would prime the Registry object since it seems redundant to me to do it twice. Richard On Mon, 2009-08-10 at 06:58 -0700, Edward Kawas wrote: > Hi Richard, > > Are you running into this problem using MoSeS? You say composite MOBY > object, so does that mean you are using MobyComposite? > > Did you try creating a Registry object that is primed with your registries > information? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Finkers, Richard > Sent: August-09-09 5:07 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of > accessing private > > Hi All, > > I am working on implementing an own moby client (based on the simpleclient > example / Java Moby API) in the backbone of my database system. For this, we > use a custom biomoby repository. > > All goes fine (service lookup / service call) however in the default > situation I run into the following error while processing the XML: > > Problem: org.biomoby.shared.MobyException: Attempted to build a composite > MOBY object from XML, but the tag (MeasurementSet) does not correspond to an > existing data type in the registry (default). Please check the spelling and > capitalization of the XML tag, to match a registered data type. > > This is logic since the object MeasurementSet was not registered in the > default (Calgary) registry but in our private project repository. > > I was able to hack a work-around by changing the DEFAULT_ENDPOINT and > DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and > NAMESPACE of my main (project) repository. > > I was not able to trace back the origin of the bug (yet). Can any of you > help me with this? > > Cheers, > Richard > > > _______________________________________________ > 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 > Dr. Richard Finkers Researcher Plant Breeding Wageningen UR Plant Breeding P.O. Box 16, 6700 AA, Wageningen, The Netherlands Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands Tel. +31-317-484165 Fax +31-317-418094 http://www.plantbreeding.wur.nl/ https://www.eu-sol.wur.nl/ https://cbsgdbase.wur.nl/ http://www.disclaimer-uk.wur.nl/ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Aug 10 11:49:29 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Aug 2009 09:49:29 -0600 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <4a803750.1cba720a.1ec6.6bb7@mx.google.com> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> <4a802795.25bb720a.3747.5e47@mx.google.com> <1249916119.17360.206.camel@localhost> <4a803750.1cba720a.1ec6.6bb7@mx.google.com> Message-ID: <4A804189.501@ucalgary.ca> Eddie is indeed correct. This is especially true if you consider applications like Seahawk, which can access multiple registries at once, but whose data objects are obviously registry-specific. While it would be possible to make data objects registry-less at creation time, this also means that they could not be validated (like the error you got) until service invocation. As the libraries are used in interactive applications, I felt this was too late a point to tell the user they messed up in creating the data. -Paul Edward Kawas wrote: > I guess it does seem redundant, but if you consider that CentralImpl is used > to interact with a registry and the other class is utilized when invoking > the services, then there is a separation of concerns there. > > If you do create a Registry object and pass it to MobyDataType, then you > will solve your problems (as Paul mentioned). > > Let us know if you need help with anything that we mentioned here. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Richard Finkers > Sent: August-10-09 7:55 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] bug report: jMoby Registry refers to default instead > of accessing private > > Hi Eddy, > > I am using the Java API and not MoSes. Correct, I am using the > MobyComposite Object. > > I did not try to create a Registry object, instead, I am using the > CentralImpl object for service discovery. Do you suggest that the > registry information then will be lost for service invocation? I would > naively expect that initialisation of the CentralImpl object also would > prime the Registry object since it seems redundant to me to do it twice. > > Richard > > > > > > On Mon, 2009-08-10 at 06:58 -0700, Edward Kawas wrote: > > >> Hi Richard, >> >> Are you running into this problem using MoSeS? You say composite MOBY >> object, so does that mean you are using MobyComposite? >> >> Did you try creating a Registry object that is primed with your registries >> information? >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Finkers, Richard >> Sent: August-09-09 5:07 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead >> > of > >> accessing private >> >> Hi All, >> >> I am working on implementing an own moby client (based on the simpleclient >> example / Java Moby API) in the backbone of my database system. For this, >> > we > >> use a custom biomoby repository. >> >> All goes fine (service lookup / service call) however in the default >> situation I run into the following error while processing the XML: >> >> Problem: org.biomoby.shared.MobyException: Attempted to build a composite >> MOBY object from XML, but the tag (MeasurementSet) does not correspond to >> > an > >> existing data type in the registry (default). Please check the spelling >> > and > >> capitalization of the XML tag, to match a registered data type. >> >> This is logic since the object MeasurementSet was not registered in the >> default (Calgary) registry but in our private project repository. >> >> I was able to hack a work-around by changing the DEFAULT_ENDPOINT and >> DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and >> NAMESPACE of my main (project) repository. >> >> I was not able to trace back the origin of the bug (yet). Can any of you >> help me with this? >> >> Cheers, >> Richard >> >> >> _______________________________________________ >> 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 >> >> > > Dr. Richard Finkers > Researcher Plant Breeding > Wageningen UR Plant Breeding > P.O. Box 16, 6700 AA, Wageningen, The Netherlands > Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB > Wageningen, The Netherlands > Tel. +31-317-484165 Fax +31-317-418094 > http://www.plantbreeding.wur.nl/ > https://www.eu-sol.wur.nl/ > https://cbsgdbase.wur.nl/ > http://www.disclaimer-uk.wur.nl/ > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From edward.kawas at gmail.com Wed Aug 19 11:39:11 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Aug 2009 08:39:11 -0700 Subject: [MOBY-dev] update of the test registry URL/URI Message-ID: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> Hello All, I have set up a new test registry that will replace the one currently hosted at bioinfo.icapture.ubc.ca. The endpoint for the new registry is http://mobytest.biordf.net/MOBY-Central.pl and the URI of that registry is http://mobytest.biordf.net/MOBY/Central. Please update your registry clients to reflect the new test registry, as the older test registry is going to be taken offline in the very near future. Thanks, Eddie From gordonp at ucalgary.ca Wed Aug 19 11:57:16 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 19 Aug 2009 09:57:16 -0600 Subject: [MOBY-dev] update of the test registry URL/URI In-Reply-To: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> References: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> Message-ID: <4A8C20DC.3090903@ucalgary.ca> Hi all, Changes I committed to CVS two days ago are not showing up in the javadocs on http://biomoby.open-bio.org/. Additionally, CVS commits don't seem to be popping up in the public CVS very quickly...anyone aware of issues on the open-bio server? -Paul From edward.kawas at gmail.com Wed Aug 19 12:24:54 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Aug 2009 09:24:54 -0700 Subject: [MOBY-dev] update of the test registry URL/URI In-Reply-To: <4A8C20DC.3090903@ucalgary.ca> References: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> <4A8C20DC.3090903@ucalgary.ca> Message-ID: <4a8c2761.25578c0a.4750.173d@mx.google.com> Hi Paul, I asked Martin about this and he noticed some irregularities. I (this morning) have asked Chris about this. I will relay anything that I have learned when I get word. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: August-19-09 8:57 AM To: Core developer announcements Subject: Re: [MOBY-dev] update of the test registry URL/URI Hi all, Changes I committed to CVS two days ago are not showing up in the javadocs on http://biomoby.open-bio.org/. Additionally, CVS commits don't seem to be popping up in the public CVS very quickly...anyone aware of issues on the open-bio server? -Paul _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Sebastien.Carrere at toulouse.inra.fr Thu Aug 6 07:11:41 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Thu, 06 Aug 2009 09:11:41 +0200 Subject: [MOBY-dev] error when invoking asynchronous services Message-ID: <4A7A822D.9040206@toulouse.inra.fr> Bonjour, for now two days, I've got frequently errors like the following one when I try to invoke asynchronous webservices (written in Perl with WSRF::Lite): Service description 'http://docs.oasis-open.org/wsrf/rpw-2.wsdl' can't be loaded: 500 Server closed connection without sending any data back Anyone has an idea ? This error does not happen each time (with same input data) ... that's why I'm a bit confused. And it's only 2 days that the problem occurs. Merci Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From jmfernandez at cnio.es Thu Aug 6 12:57:44 2009 From: jmfernandez at cnio.es (=?ISO-8859-15?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Thu, 06 Aug 2009 14:57:44 +0200 Subject: [MOBY-dev] error when invoking asynchronous services In-Reply-To: <4A7A822D.9040206@toulouse.inra.fr> References: <4A7A822D.9040206@toulouse.inra.fr> Message-ID: <4A7AD348.9020406@cnio.es> Hi Sebastien, it seems a problem from docs.oasis-open.org side. As the WSDL generated for asynchronous services reuse (i.e. points to) some WSRF resource properties WSDL definitions, each time the generated WSDL is fully parsed the libraries must fetch http://docs.oasis-open.org/wsrf/rpw-2.wsdl (among others) in order to check the generated WSDL's validity. Best Regards, Jos? Mar?a Sebastien Carrere wrote: > Bonjour, > > for now two days, I've got frequently errors like the following one when > I try to invoke asynchronous webservices (written in Perl with WSRF::Lite): > > Service description 'http://docs.oasis-open.org/wsrf/rpw-2.wsdl' can't > be loaded: 500 Server closed connection without sending any data back > > Anyone has an idea ? > This error does not happen each time (with same input data) ... that's > why I'm a bit confused. > And it's only 2 days that the problem occurs. > > > Merci > > Sebastien > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- "There is no reason why anybody would want a computer in their home" - Ken Olson, founder of DEC 1977 "640K ought to be enough for anybody" - Bill Gates, 1981 "Nobody will ever outgrow a 20Mb hard drive." - ??? "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From richard.finkers at wur.nl Sun Aug 9 12:07:03 2009 From: richard.finkers at wur.nl (Finkers, Richard) Date: Sun, 9 Aug 2009 14:07:03 +0200 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private Message-ID: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> Hi All, I am working on implementing an own moby client (based on the simpleclient example / Java Moby API) in the backbone of my database system. For this, we use a custom biomoby repository. All goes fine (service lookup / service call) however in the default situation I run into the following error while processing the XML: Problem: org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MeasurementSet) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. This is logic since the object MeasurementSet was not registered in the default (Calgary) registry but in our private project repository. I was able to hack a work-around by changing the DEFAULT_ENDPOINT and DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and NAMESPACE of my main (project) repository. I was not able to trace back the origin of the bug (yet). Can any of you help me with this? Cheers, Richard From edward.kawas at gmail.com Mon Aug 10 13:58:39 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 10 Aug 2009 06:58:39 -0700 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> Message-ID: <4a802795.25bb720a.3747.5e47@mx.google.com> Hi Richard, Are you running into this problem using MoSeS? You say composite MOBY object, so does that mean you are using MobyComposite? Did you try creating a Registry object that is primed with your registries information? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Finkers, Richard Sent: August-09-09 5:07 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private Hi All, I am working on implementing an own moby client (based on the simpleclient example / Java Moby API) in the backbone of my database system. For this, we use a custom biomoby repository. All goes fine (service lookup / service call) however in the default situation I run into the following error while processing the XML: Problem: org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MeasurementSet) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. This is logic since the object MeasurementSet was not registered in the default (Calgary) registry but in our private project repository. I was able to hack a work-around by changing the DEFAULT_ENDPOINT and DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and NAMESPACE of my main (project) repository. I was not able to trace back the origin of the bug (yet). Can any of you help me with this? Cheers, Richard _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Aug 10 14:27:42 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Aug 2009 08:27:42 -0600 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> Message-ID: <4A802E5E.7040209@ucalgary.ca> Hi Roger, If you are not using the default registry, you need to pas a Registry object into data object creation methods and others. If you can send me the code that got this error, I can help you ensure you are properly telling Moby which registry should be referenced. Thanks, Paul Finkers, Richard wrote: > Hi All, > > I am working on implementing an own moby client (based on the simpleclient example / Java Moby API) in the backbone of my database system. For this, we use a custom biomoby repository. > > All goes fine (service lookup / service call) however in the default situation I run into the following error while processing the XML: > > Problem: org.biomoby.shared.MobyException: Attempted to build a composite MOBY object from XML, but the tag (MeasurementSet) does not correspond to an existing data type in the registry (default). Please check the spelling and capitalization of the XML tag, to match a registered data type. > > This is logic since the object MeasurementSet was not registered in the default (Calgary) registry but in our private project repository. > > I was able to hack a work-around by changing the DEFAULT_ENDPOINT and DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and NAMESPACE of my main (project) repository. > > I was not able to trace back the origin of the bug (yet). Can any of you help me with this? > > Cheers, > Richard > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From richard.finkers at wur.nl Mon Aug 10 14:55:19 2009 From: richard.finkers at wur.nl (Richard Finkers) Date: Mon, 10 Aug 2009 16:55:19 +0200 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <4a802795.25bb720a.3747.5e47@mx.google.com> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> <4a802795.25bb720a.3747.5e47@mx.google.com> Message-ID: <1249916119.17360.206.camel@localhost> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From edward.kawas at gmail.com Mon Aug 10 15:05:45 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 10 Aug 2009 08:05:45 -0700 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <1249916119.17360.206.camel@localhost> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> <4a802795.25bb720a.3747.5e47@mx.google.com> <1249916119.17360.206.camel@localhost> Message-ID: <4a803750.1cba720a.1ec6.6bb7@mx.google.com> I guess it does seem redundant, but if you consider that CentralImpl is used to interact with a registry and the other class is utilized when invoking the services, then there is a separation of concerns there. If you do create a Registry object and pass it to MobyDataType, then you will solve your problems (as Paul mentioned). Let us know if you need help with anything that we mentioned here. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Richard Finkers Sent: August-10-09 7:55 AM To: Core developer announcements Subject: Re: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private Hi Eddy, I am using the Java API and not MoSes. Correct, I am using the MobyComposite Object. I did not try to create a Registry object, instead, I am using the CentralImpl object for service discovery. Do you suggest that the registry information then will be lost for service invocation? I would naively expect that initialisation of the CentralImpl object also would prime the Registry object since it seems redundant to me to do it twice. Richard On Mon, 2009-08-10 at 06:58 -0700, Edward Kawas wrote: > Hi Richard, > > Are you running into this problem using MoSeS? You say composite MOBY > object, so does that mean you are using MobyComposite? > > Did you try creating a Registry object that is primed with your registries > information? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Finkers, Richard > Sent: August-09-09 5:07 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of > accessing private > > Hi All, > > I am working on implementing an own moby client (based on the simpleclient > example / Java Moby API) in the backbone of my database system. For this, we > use a custom biomoby repository. > > All goes fine (service lookup / service call) however in the default > situation I run into the following error while processing the XML: > > Problem: org.biomoby.shared.MobyException: Attempted to build a composite > MOBY object from XML, but the tag (MeasurementSet) does not correspond to an > existing data type in the registry (default). Please check the spelling and > capitalization of the XML tag, to match a registered data type. > > This is logic since the object MeasurementSet was not registered in the > default (Calgary) registry but in our private project repository. > > I was able to hack a work-around by changing the DEFAULT_ENDPOINT and > DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and > NAMESPACE of my main (project) repository. > > I was not able to trace back the origin of the bug (yet). Can any of you > help me with this? > > Cheers, > Richard > > > _______________________________________________ > 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 > Dr. Richard Finkers Researcher Plant Breeding Wageningen UR Plant Breeding P.O. Box 16, 6700 AA, Wageningen, The Netherlands Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands Tel. +31-317-484165 Fax +31-317-418094 http://www.plantbreeding.wur.nl/ https://www.eu-sol.wur.nl/ https://cbsgdbase.wur.nl/ http://www.disclaimer-uk.wur.nl/ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Mon Aug 10 15:49:29 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 10 Aug 2009 09:49:29 -0600 Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead of accessing private In-Reply-To: <4a803750.1cba720a.1ec6.6bb7@mx.google.com> References: <33AFFE3255BCA043AF09514A6F6BFBAED04AF4@scomp0039.wurnet.nl> <4a802795.25bb720a.3747.5e47@mx.google.com> <1249916119.17360.206.camel@localhost> <4a803750.1cba720a.1ec6.6bb7@mx.google.com> Message-ID: <4A804189.501@ucalgary.ca> Eddie is indeed correct. This is especially true if you consider applications like Seahawk, which can access multiple registries at once, but whose data objects are obviously registry-specific. While it would be possible to make data objects registry-less at creation time, this also means that they could not be validated (like the error you got) until service invocation. As the libraries are used in interactive applications, I felt this was too late a point to tell the user they messed up in creating the data. -Paul Edward Kawas wrote: > I guess it does seem redundant, but if you consider that CentralImpl is used > to interact with a registry and the other class is utilized when invoking > the services, then there is a separation of concerns there. > > If you do create a Registry object and pass it to MobyDataType, then you > will solve your problems (as Paul mentioned). > > Let us know if you need help with anything that we mentioned here. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Richard Finkers > Sent: August-10-09 7:55 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] bug report: jMoby Registry refers to default instead > of accessing private > > Hi Eddy, > > I am using the Java API and not MoSes. Correct, I am using the > MobyComposite Object. > > I did not try to create a Registry object, instead, I am using the > CentralImpl object for service discovery. Do you suggest that the > registry information then will be lost for service invocation? I would > naively expect that initialisation of the CentralImpl object also would > prime the Registry object since it seems redundant to me to do it twice. > > Richard > > > > > > On Mon, 2009-08-10 at 06:58 -0700, Edward Kawas wrote: > > >> Hi Richard, >> >> Are you running into this problem using MoSeS? You say composite MOBY >> object, so does that mean you are using MobyComposite? >> >> Did you try creating a Registry object that is primed with your registries >> information? >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Finkers, Richard >> Sent: August-09-09 5:07 AM >> To: moby-dev at lists.open-bio.org >> Subject: [MOBY-dev] bug report: jMoby Registry refers to default instead >> > of > >> accessing private >> >> Hi All, >> >> I am working on implementing an own moby client (based on the simpleclient >> example / Java Moby API) in the backbone of my database system. For this, >> > we > >> use a custom biomoby repository. >> >> All goes fine (service lookup / service call) however in the default >> situation I run into the following error while processing the XML: >> >> Problem: org.biomoby.shared.MobyException: Attempted to build a composite >> MOBY object from XML, but the tag (MeasurementSet) does not correspond to >> > an > >> existing data type in the registry (default). Please check the spelling >> > and > >> capitalization of the XML tag, to match a registered data type. >> >> This is logic since the object MeasurementSet was not registered in the >> default (Calgary) registry but in our private project repository. >> >> I was able to hack a work-around by changing the DEFAULT_ENDPOINT and >> DEFAULT_NAMESPACE in the CentralImple.java class to the ENDPOINT and >> NAMESPACE of my main (project) repository. >> >> I was not able to trace back the origin of the bug (yet). Can any of you >> help me with this? >> >> Cheers, >> Richard >> >> >> _______________________________________________ >> 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 >> >> > > Dr. Richard Finkers > Researcher Plant Breeding > Wageningen UR Plant Breeding > P.O. Box 16, 6700 AA, Wageningen, The Netherlands > Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB > Wageningen, The Netherlands > Tel. +31-317-484165 Fax +31-317-418094 > http://www.plantbreeding.wur.nl/ > https://www.eu-sol.wur.nl/ > https://cbsgdbase.wur.nl/ > http://www.disclaimer-uk.wur.nl/ > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From edward.kawas at gmail.com Wed Aug 19 15:39:11 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Aug 2009 08:39:11 -0700 Subject: [MOBY-dev] update of the test registry URL/URI Message-ID: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> Hello All, I have set up a new test registry that will replace the one currently hosted at bioinfo.icapture.ubc.ca. The endpoint for the new registry is http://mobytest.biordf.net/MOBY-Central.pl and the URI of that registry is http://mobytest.biordf.net/MOBY/Central. Please update your registry clients to reflect the new test registry, as the older test registry is going to be taken offline in the very near future. Thanks, Eddie From gordonp at ucalgary.ca Wed Aug 19 15:57:16 2009 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 19 Aug 2009 09:57:16 -0600 Subject: [MOBY-dev] update of the test registry URL/URI In-Reply-To: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> References: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> Message-ID: <4A8C20DC.3090903@ucalgary.ca> Hi all, Changes I committed to CVS two days ago are not showing up in the javadocs on http://biomoby.open-bio.org/. Additionally, CVS commits don't seem to be popping up in the public CVS very quickly...anyone aware of issues on the open-bio server? -Paul From edward.kawas at gmail.com Wed Aug 19 16:24:54 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 19 Aug 2009 09:24:54 -0700 Subject: [MOBY-dev] update of the test registry URL/URI In-Reply-To: <4A8C20DC.3090903@ucalgary.ca> References: <4a8c1caa.1bbc720a.37e7.478f@mx.google.com> <4A8C20DC.3090903@ucalgary.ca> Message-ID: <4a8c2761.25578c0a.4750.173d@mx.google.com> Hi Paul, I asked Martin about this and he noticed some irregularities. I (this morning) have asked Chris about this. I will relay anything that I have learned when I get word. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: August-19-09 8:57 AM To: Core developer announcements Subject: Re: [MOBY-dev] update of the test registry URL/URI Hi all, Changes I committed to CVS two days ago are not showing up in the javadocs on http://biomoby.open-bio.org/. Additionally, CVS commits don't seem to be popping up in the public CVS very quickly...anyone aware of issues on the open-bio server? -Paul _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev