From markw at illuminae.com Sat Feb 3 13:36:44 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 03 Feb 2007 10:36:44 -0800 Subject: [MOBY-dev] The "erroneous" RDF agent report that many of you received Message-ID: Hi all, Apologies for the erroneous RDF agent report that many of you will have received overnight. Something happened yesterday that we cannot yet explain, but it resulted in many of the Namespaces being modified in the database and appended with a "_" character. According to the API this should be impossible for namespaces that are in use, but somehow it happened anyway. The test suite has a case for this, and it seems to pass the test, so I don't know how it happened....?? I've looked at the access logs to MOBY Central and can't see anything obvious there either. Anyway, it's a mystery for the moment. The same thing happened about a year ago, and we weren't able to determine it's cause then either... it seems to be a recurring, but rare problem. The affected namespaces are listed below. Anyone with a service that uses any of these namespaces will have received an RDF Agent report of failed lookup. PLEASE IGNORE THIS REPORT - you do not have to do anything. I have solved the problem at the SQL level. If the list below looks familiar to any of you, please let me know as I would like to track-down the source of this problem. Thanks! Mark CGEN BRENDA ChEBI CL EchoBASE EcoCyc ECOGENE FB INTERPRO IPI MaizeGDB MetaCyc PANTHER PIR PINC SMART Swiss-Prot TreEMBL Reactome REBASE FLYBASE EMBL PMID From markw at illuminae.com Mon Feb 5 23:02:03 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 05 Feb 2007 20:02:03 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Message-ID: Hi all, First off, apologies to anyone who was trying to get through to MOBY Central this afternoon - Eddie and I were making the changes necessary to get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on the test server didn't work on the real MOBY Central... so it took a couple of hours of troubleshooting before we had it back up again. The good news is that it seems to work correctly with both Perl and Java clients. What we don't know is if it is backwards compatible with earlier versions of the MOBY::Client::* libraries, in particular, MOBY::Client::Service. I *think* it is, but we didn't have the opportunity to test it. In any case, the API did not change, so if you just cvs update your client libraries everything should come back to life if it isn't working. Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves subtly differently than the old one in several ways that we were not expecting. Thankfully, Pieter and Eddie had done most of the trouble-shoting already, but it still threw us for a loop in some places with incompatible SOAP version errors and a new auto-encoding of strings by SOAP::Lite that we used to do in-code by ourselves (resulting in double-coded messages). Anyway, it's done now. Please scream loudly if it doesn't work for you!! I have backups of everything so if necessary we can roll-back quickly. All of this was done primarily to get us to be compatible with the new Asynchronous services API that use the Manchester WSRF::Lite modules which depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the code to see if it works for them v.v. Async services? The database can now hold Category=moby-async (which reminds me, I need to update the database templates in the CVS...), and Eddie assures me that the code will now provide correct WSDL for an Asych interface. The myGrid folks have added moby-async as a valid service category into their ontology as well, so in principle... it should all work... (touch wood!) ********************* IMPORTANTLY this means that the new MOBY Central code will likely NOT work on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are running your own registry... ********************* Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to make the changes to gbrowse_moby such that it can also invoke asynchronous services. I think the Async modules also need to be added to the MANIFEST before they are installed by default, so I'll try to remember to do that as well. Otherwise there were just some small changes to the test suite to better clean-up the registry if something goes wrong during testing, and I cleaned-up the test database so that it also doesn't cause the test suite to fail. I will restart the test registry using the new codebase first thing in the morning so that the two are identical. We still haven't figured out why those namespace changes happened a couple of days ago. It coincided with the Gene Ontology curators making some additions to the Namespace list, so I suspect that there is a bug in the interface I have given to them (which talks directly to the database without using the MOBY API), but exactly WHY this happened is still a mystery. I've alerted Midori to the problem and she's going to hold-off on making any more changes until we can figure out what is going wrong. That's all the news from MOBY Central! Let us know ASAP if you notice anything wrong. It's been a rough ride today... Mark From markw at illuminae.com Mon Feb 5 23:04:06 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 05 Feb 2007 20:04:06 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: References: Message-ID: ALSO NOTE! The MOBY Central daemon code has changed in two lines - see moby-live/Perl/scripts/MOBY-Central.pl for the new code. M On Mon, 05 Feb 2007 20:02:03 -0800, Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary > to get it ready for SOAP::Lite 0.69 and the changes that worked > perfectly on the test server didn't work on the real MOBY Central... so > it took a couple of hours of troubleshooting before we had it back up > again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with > earlier versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to > life if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite > behaves subtly differently than the old one in several ways that we were > not expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for > you!! I have backups of everything so if necessary we can roll-back > quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules > which depend on SOAP::Lite 0.69. Can I ask the good folks at INB to > test the code to see if it works for them v.v. Async services? The > database can now hold Category=moby-async (which reminds me, I need to > update the database templates in the CVS...), and Eddie assures me that > the code will now provide correct WSDL for an Asych interface. The > myGrid folks have added moby-async as a valid service category into > their ontology as well, so in principle... it should all work... (touch > wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT > work on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if > you are running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try > to make the changes to gbrowse_moby such that it can also invoke > asynchronous services. I think the Async modules also need to be added > to the MANIFEST before they are installed by default, so I'll try to > remember to do that as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test > suite to fail. I will restart the test registry using the new codebase > first thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a > couple of days ago. It coincided with the Gene Ontology curators making > some additions to the Namespace list, so I suspect that there is a bug > in the interface I have given to them (which talks directly to the > database without using the MOBY API), but exactly WHY this happened is > still a mystery. I've alerted Midori to the problem and she's going to > hold-off on making any more changes until we can figure out what is > going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From rroyo at lsi.upc.edu Tue Feb 6 09:25:15 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 15:25:15 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: References: Message-ID: <45C88FCB.2030704@lsi.upc.edu> Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From rroyo at lsi.upc.edu Tue Feb 6 09:25:15 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 15:25:15 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: References: Message-ID: <45C88FCB.2030704@lsi.upc.edu> Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > 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 Tue Feb 6 10:13:15 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 07:13:15 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <005901c74a01$54aa2d10$6900a8c0@notebook> Hi Romina, Do you think that you could send me your code? I am having problems replicating the errors that you got (which were the ones we 'fixed' yesterday!). Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 6:25 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatch Wrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > 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 Tue Feb 6 10:13:15 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 07:13:15 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <005901c74a01$54aa2d10$6900a8c0@notebook> Hi Romina, Do you think that you could send me your code? I am having problems replicating the errors that you got (which were the ones we 'fixed' yesterday!). Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 6:25 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatch Wrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Feb 6 10:03:31 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 6 Feb 2007 15:03:31 +0000 GMT Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> Hmmmm... Well that's a bit of a disaster! Could you check what happens when you call one of my services (eg MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to each other properly (which would be a nightmare, but given our experiences yesterday, not surprising!) M -- Mark Wilkinson ...on the road! -----Original Message----- From: Romina Royo Date: Tue, 06 Feb 2007 15:25:15 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Feb 6 10:03:31 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 6 Feb 2007 15:03:31 +0000 GMT Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> Hmmmm... Well that's a bit of a disaster! Could you check what happens when you call one of my services (eg MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to each other properly (which would be a nightmare, but given our experiences yesterday, not surprising!) M -- Mark Wilkinson ...on the road! -----Original Message----- From: Romina Royo Date: Tue, 06 Feb 2007 15:25:15 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > 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 rroyo at lsi.upc.edu Tue Feb 6 10:38:59 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 16:38:59 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> Message-ID: <45C8A113.40803@lsi.upc.edu> Hello again, Mark, I just called your service and it did work. Eddy, if those are some of the errors you fixed yesterday I might be doing something wrong. Let me re-check everything and if the errors are still there I'll send you more details about the code I'm using. Thank you very much! Romina mark wilkinson wrote: > Hmmmm... Well that's a bit of a disaster! > > Could you check what happens when you call one of my services (eg MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to each other properly (which would be a nightmare, but given our experiences yesterday, not surprising!) > > M > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 15:25:15 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for > registry hosts > > Hello, > > I updated the moby-live/Perl libraries from cvs and I installed > SOAP::Lite 0.69. > > Here are some of the results I got: > > - When executing a synchronous Perl service (function execute in > Client/Service.pm) I got this error: > > SOAP-ENV:VersionMismatchWrong > SOAP version specified. Supported versions: > 1.1 (http://schemas.xmlsoap.org/soap/envelope/) > 1.2 (http://www.w3.org/2001/06/soap-envelope) > > > mm.. I guess it is OK because the service provider might be using some > other SOAP version? > > - When doing the same test on one of our services (SOAP::Lite 0.69 > installed on the service side). I got this error: > > soap:ClientApplication > failed during request deserialization: > xml declaration not at start of external entity at line 1, column 941, > byte 941 at > /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm > line 187 > > > - When executing a Java service: > > soapenv:Client > org.jboss.axis.AxisFault: Version Mismatch > > > > and again, it might be ok? > > - When trying to retrieve the wsdl of a 'moby-async' service (function > retrieveService) I got this error: > > Connection to MOBY Central at > 'http://mobycentral.icapture.ubc.ca/MOBY/Central' > died because: > Can't use string (" > /usr/lib/perl5 > /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. > > ERROR ERROR ERROR > > The function retrieveService does work when the service is not > 'moby-async' though. > > - When executing an asynchronous service (function > Async/Service/execute) everything seems ok. > > Has anyone had similar problems? Any ideas? > > Thank you! > Romina > > Mark Wilkinson wrote: > >> Hi all, >> >> First off, apologies to anyone who was trying to get through to MOBY >> Central this afternoon - Eddie and I were making the changes necessary to >> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on >> the test server didn't work on the real MOBY Central... so it took a >> couple of hours of troubleshooting before we had it back up again. >> >> The good news is that it seems to work correctly with both Perl and Java >> clients. What we don't know is if it is backwards compatible with earlier >> versions of the MOBY::Client::* libraries, in particular, >> MOBY::Client::Service. I *think* it is, but we didn't have the >> opportunity to test it. In any case, the API did not change, so if you >> just cvs update your client libraries everything should come back to life >> if it isn't working. >> >> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves >> subtly differently than the old one in several ways that we were not >> expecting. Thankfully, Pieter and Eddie had done most of the >> trouble-shoting already, but it still threw us for a loop in some places >> with incompatible SOAP version errors and a new auto-encoding of strings >> by SOAP::Lite that we used to do in-code by ourselves (resulting in >> double-coded messages). >> >> Anyway, it's done now. Please scream loudly if it doesn't work for you!! >> I have backups of everything so if necessary we can roll-back quickly. >> >> All of this was done primarily to get us to be compatible with the new >> Asynchronous services API that use the Manchester WSRF::Lite modules which >> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >> code to see if it works for them v.v. Async services? The database can >> now hold Category=moby-async (which reminds me, I need to update the >> database templates in the CVS...), and Eddie assures me that the code will >> now provide correct WSDL for an Asych interface. The myGrid folks have >> added moby-async as a valid service category into their ontology as well, >> so in principle... it should all work... (touch wood!) >> >> ********************* >> IMPORTANTLY this means that the new MOBY Central code will likely NOT work >> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are >> running your own registry... >> ********************* >> >> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to >> make the changes to gbrowse_moby such that it can also invoke asynchronous >> services. I think the Async modules also need to be added to the MANIFEST >> before they are installed by default, so I'll try to remember to do that >> as well. >> >> Otherwise there were just some small changes to the test suite to better >> clean-up the registry if something goes wrong during testing, and I >> cleaned-up the test database so that it also doesn't cause the test suite >> to fail. I will restart the test registry using the new codebase first >> thing in the morning so that the two are identical. >> >> We still haven't figured out why those namespace changes happened a couple >> of days ago. It coincided with the Gene Ontology curators making some >> additions to the Namespace list, so I suspect that there is a bug in the >> interface I have given to them (which talks directly to the database >> without using the MOBY API), but exactly WHY this happened is still a >> mystery. I've alerted Midori to the problem and she's going to hold-off >> on making any more changes until we can figure out what is going wrong. >> >> That's all the news from MOBY Central! >> >> Let us know ASAP if you notice anything wrong. It's been a rough ride >> today... >> >> Mark >> >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 Tue Feb 6 10:48:40 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Feb 2007 07:48:40 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C8A113.40803@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: Hi Romina, I can confirm that calling services running S::L 0.69 from a client running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I have not yet successfully tested is calling a service from a .69 client to an earlier version on the server-side. The way to do that would be to use gbrowse_moby on the mobycentral machine, but I don't know what versions of Perl anyone else is running so I can't reliably do that experiment... can anyone try one of their Perl services from gbrowse-moby on a server with perl 0.60 or less? MOBY Central itself seems fine... and Java invocations of services seem fine also (largely because the Java libraries don't use the WSDL from MOBY Central to create their connections... there may be a lesson in there somewhere! Ugh... WSDL!!) M On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > Hello again, > > Mark, I just called your service and it did work. > > Eddy, if those are some of the errors you fixed yesterday I might be > doing something wrong. Let me re-check everything and if the errors are > still there I'll send you more details about the code I'm using. > > Thank you very much! > Romina > > > > mark wilkinson wrote: >> Hmmmm... Well that's a bit of a disaster! >> >> Could you check what happens when you call one of my services (eg >> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >> each other properly (which would be a nightmare, but given our >> experiences yesterday, not surprising!) >> >> M >> >> >> -- >> Mark Wilkinson >> ...on the road! >> >> >> -----Original Message----- >> From: Romina Royo >> Date: Tue, 06 Feb 2007 15:25:15 >> To:Core developer announcements >> Cc:mobydev >> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >> registry hosts >> >> Hello, >> >> I updated the moby-live/Perl libraries from cvs and I installed >> SOAP::Lite 0.69. >> >> Here are some of the results I got: >> >> - When executing a synchronous Perl service (function execute in >> Client/Service.pm) I got this error: >> >> SOAP-ENV:VersionMismatchWrong >> SOAP version specified. Supported versions: >> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >> 1.2 (http://www.w3.org/2001/06/soap-envelope) >> >> >> mm.. I guess it is OK because the service provider might be using some >> other SOAP version? >> >> - When doing the same test on one of our services (SOAP::Lite 0.69 >> installed on the service side). I got this error: >> >> soap:ClientApplication >> failed during request deserialization: >> xml declaration not at start of external entity at line 1, column 941, >> byte 941 at >> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >> line 187 >> >> >> - When executing a Java service: >> >> soapenv:Client >> org.jboss.axis.AxisFault: Version Mismatch >> >> >> >> and again, it might be ok? >> >> - When trying to retrieve the wsdl of a 'moby-async' service (function >> retrieveService) I got this error: >> >> Connection to MOBY Central at >> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >> died because: >> Can't use string (" >> > /usr/lib/perl5 >> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >> >> ERROR ERROR ERROR >> >> The function retrieveService does work when the service is not >> 'moby-async' though. >> >> - When executing an asynchronous service (function >> Async/Service/execute) everything seems ok. >> >> Has anyone had similar problems? Any ideas? >> >> Thank you! >> Romina >> >> Mark Wilkinson wrote: >> >>> Hi all, >>> >>> First off, apologies to anyone who was trying to get through to MOBY >>> Central this afternoon - Eddie and I were making the changes necessary >>> to >>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>> on >>> the test server didn't work on the real MOBY Central... so it took a >>> couple of hours of troubleshooting before we had it back up again. >>> >>> The good news is that it seems to work correctly with both Perl and >>> Java >>> clients. What we don't know is if it is backwards compatible with >>> earlier >>> versions of the MOBY::Client::* libraries, in particular, >>> MOBY::Client::Service. I *think* it is, but we didn't have the >>> opportunity to test it. In any case, the API did not change, so if you >>> just cvs update your client libraries everything should come back to >>> life >>> if it isn't working. >>> >>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>> behaves >>> subtly differently than the old one in several ways that we were not >>> expecting. Thankfully, Pieter and Eddie had done most of the >>> trouble-shoting already, but it still threw us for a loop in some >>> places >>> with incompatible SOAP version errors and a new auto-encoding of >>> strings >>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>> double-coded messages). >>> >>> Anyway, it's done now. Please scream loudly if it doesn't work for >>> you!! >>> I have backups of everything so if necessary we can roll-back quickly. >>> >>> All of this was done primarily to get us to be compatible with the new >>> Asynchronous services API that use the Manchester WSRF::Lite modules >>> which >>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>> code to see if it works for them v.v. Async services? The database can >>> now hold Category=moby-async (which reminds me, I need to update the >>> database templates in the CVS...), and Eddie assures me that the code >>> will >>> now provide correct WSDL for an Asych interface. The myGrid folks have >>> added moby-async as a valid service category into their ontology as >>> well, >>> so in principle... it should all work... (touch wood!) >>> >>> ********************* >>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>> work >>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>> are >>> running your own registry... >>> ********************* >>> >>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>> try to >>> make the changes to gbrowse_moby such that it can also invoke >>> asynchronous >>> services. I think the Async modules also need to be added to the >>> MANIFEST >>> before they are installed by default, so I'll try to remember to do >>> that >>> as well. >>> >>> Otherwise there were just some small changes to the test suite to >>> better >>> clean-up the registry if something goes wrong during testing, and I >>> cleaned-up the test database so that it also doesn't cause the test >>> suite >>> to fail. I will restart the test registry using the new codebase first >>> thing in the morning so that the two are identical. >>> >>> We still haven't figured out why those namespace changes happened a >>> couple >>> of days ago. It coincided with the Gene Ontology curators making some >>> additions to the Namespace list, so I suspect that there is a bug in >>> the >>> interface I have given to them (which talks directly to the database >>> without using the MOBY API), but exactly WHY this happened is still a >>> mystery. I've alerted Midori to the problem and she's going to >>> hold-off >>> on making any more changes until we can figure out what is going wrong. >>> >>> That's all the news from MOBY Central! >>> >>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>> today... >>> >>> Mark >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From markw at illuminae.com Tue Feb 6 10:48:40 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Feb 2007 07:48:40 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C8A113.40803@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: Hi Romina, I can confirm that calling services running S::L 0.69 from a client running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I have not yet successfully tested is calling a service from a .69 client to an earlier version on the server-side. The way to do that would be to use gbrowse_moby on the mobycentral machine, but I don't know what versions of Perl anyone else is running so I can't reliably do that experiment... can anyone try one of their Perl services from gbrowse-moby on a server with perl 0.60 or less? MOBY Central itself seems fine... and Java invocations of services seem fine also (largely because the Java libraries don't use the WSDL from MOBY Central to create their connections... there may be a lesson in there somewhere! Ugh... WSDL!!) M On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > Hello again, > > Mark, I just called your service and it did work. > > Eddy, if those are some of the errors you fixed yesterday I might be > doing something wrong. Let me re-check everything and if the errors are > still there I'll send you more details about the code I'm using. > > Thank you very much! > Romina > > > > mark wilkinson wrote: >> Hmmmm... Well that's a bit of a disaster! >> >> Could you check what happens when you call one of my services (eg >> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >> each other properly (which would be a nightmare, but given our >> experiences yesterday, not surprising!) >> >> M >> >> >> -- >> Mark Wilkinson >> ...on the road! >> >> >> -----Original Message----- >> From: Romina Royo >> Date: Tue, 06 Feb 2007 15:25:15 >> To:Core developer announcements >> Cc:mobydev >> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >> registry hosts >> >> Hello, >> >> I updated the moby-live/Perl libraries from cvs and I installed >> SOAP::Lite 0.69. >> >> Here are some of the results I got: >> >> - When executing a synchronous Perl service (function execute in >> Client/Service.pm) I got this error: >> >> SOAP-ENV:VersionMismatchWrong >> SOAP version specified. Supported versions: >> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >> 1.2 (http://www.w3.org/2001/06/soap-envelope) >> >> >> mm.. I guess it is OK because the service provider might be using some >> other SOAP version? >> >> - When doing the same test on one of our services (SOAP::Lite 0.69 >> installed on the service side). I got this error: >> >> soap:ClientApplication >> failed during request deserialization: >> xml declaration not at start of external entity at line 1, column 941, >> byte 941 at >> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >> line 187 >> >> >> - When executing a Java service: >> >> soapenv:Client >> org.jboss.axis.AxisFault: Version Mismatch >> >> >> >> and again, it might be ok? >> >> - When trying to retrieve the wsdl of a 'moby-async' service (function >> retrieveService) I got this error: >> >> Connection to MOBY Central at >> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >> died because: >> Can't use string (" >> > /usr/lib/perl5 >> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >> >> ERROR ERROR ERROR >> >> The function retrieveService does work when the service is not >> 'moby-async' though. >> >> - When executing an asynchronous service (function >> Async/Service/execute) everything seems ok. >> >> Has anyone had similar problems? Any ideas? >> >> Thank you! >> Romina >> >> Mark Wilkinson wrote: >> >>> Hi all, >>> >>> First off, apologies to anyone who was trying to get through to MOBY >>> Central this afternoon - Eddie and I were making the changes necessary >>> to >>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>> on >>> the test server didn't work on the real MOBY Central... so it took a >>> couple of hours of troubleshooting before we had it back up again. >>> >>> The good news is that it seems to work correctly with both Perl and >>> Java >>> clients. What we don't know is if it is backwards compatible with >>> earlier >>> versions of the MOBY::Client::* libraries, in particular, >>> MOBY::Client::Service. I *think* it is, but we didn't have the >>> opportunity to test it. In any case, the API did not change, so if you >>> just cvs update your client libraries everything should come back to >>> life >>> if it isn't working. >>> >>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>> behaves >>> subtly differently than the old one in several ways that we were not >>> expecting. Thankfully, Pieter and Eddie had done most of the >>> trouble-shoting already, but it still threw us for a loop in some >>> places >>> with incompatible SOAP version errors and a new auto-encoding of >>> strings >>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>> double-coded messages). >>> >>> Anyway, it's done now. Please scream loudly if it doesn't work for >>> you!! >>> I have backups of everything so if necessary we can roll-back quickly. >>> >>> All of this was done primarily to get us to be compatible with the new >>> Asynchronous services API that use the Manchester WSRF::Lite modules >>> which >>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>> code to see if it works for them v.v. Async services? The database can >>> now hold Category=moby-async (which reminds me, I need to update the >>> database templates in the CVS...), and Eddie assures me that the code >>> will >>> now provide correct WSDL for an Asych interface. The myGrid folks have >>> added moby-async as a valid service category into their ontology as >>> well, >>> so in principle... it should all work... (touch wood!) >>> >>> ********************* >>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>> work >>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>> are >>> running your own registry... >>> ********************* >>> >>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>> try to >>> make the changes to gbrowse_moby such that it can also invoke >>> asynchronous >>> services. I think the Async modules also need to be added to the >>> MANIFEST >>> before they are installed by default, so I'll try to remember to do >>> that >>> as well. >>> >>> Otherwise there were just some small changes to the test suite to >>> better >>> clean-up the registry if something goes wrong during testing, and I >>> cleaned-up the test database so that it also doesn't cause the test >>> suite >>> to fail. I will restart the test registry using the new codebase first >>> thing in the morning so that the two are identical. >>> >>> We still haven't figured out why those namespace changes happened a >>> couple >>> of days ago. It coincided with the Gene Ontology curators making some >>> additions to the Namespace list, so I suspect that there is a bug in >>> the >>> interface I have given to them (which talks directly to the database >>> without using the MOBY API), but exactly WHY this happened is still a >>> mystery. I've alerted Midori to the problem and she's going to >>> hold-off >>> on making any more changes until we can figure out what is going wrong. >>> >>> That's all the news from MOBY Central! >>> >>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>> today... >>> >>> Mark >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From rroyo at lsi.upc.edu Tue Feb 6 11:18:33 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 17:18:33 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: <45C8AA59.3020508@lsi.upc.edu> Hello Mark, I used gbrowse to call one of our services: - first test we had .69 on the server side and as you said it worked ok - second test we had 0.60 on the server side and it also worked ok. I hope this is the test you were asking for :-) Thanks! Romina Mark Wilkinson wrote: > Hi Romina, > > I can confirm that calling services running S::L 0.69 from a client > running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I > have not yet successfully tested is calling a service from a .69 client to > an earlier version on the server-side. The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? > > MOBY Central itself seems fine... and Java invocations of services seem > fine also (largely because the Java libraries don't use the WSDL from MOBY > Central to create their connections... there may be a lesson in there > somewhere! Ugh... WSDL!!) > > M > > > > > On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > > >> Hello again, >> >> Mark, I just called your service and it did work. >> >> Eddy, if those are some of the errors you fixed yesterday I might be >> doing something wrong. Let me re-check everything and if the errors are >> still there I'll send you more details about the code I'm using. >> >> Thank you very much! >> Romina >> >> >> >> mark wilkinson wrote: >> >>> Hmmmm... Well that's a bit of a disaster! >>> >>> Could you check what happens when you call one of my services (eg >>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>> each other properly (which would be a nightmare, but given our >>> experiences yesterday, not surprising!) >>> >>> M >>> >>> >>> -- >>> Mark Wilkinson >>> ...on the road! >>> >>> >>> -----Original Message----- >>> From: Romina Royo >>> Date: Tue, 06 Feb 2007 15:25:15 >>> To:Core developer announcements >>> Cc:mobydev >>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>> registry hosts >>> >>> Hello, >>> >>> I updated the moby-live/Perl libraries from cvs and I installed >>> SOAP::Lite 0.69. >>> >>> Here are some of the results I got: >>> >>> - When executing a synchronous Perl service (function execute in >>> Client/Service.pm) I got this error: >>> >>> SOAP-ENV:VersionMismatchWrong >>> SOAP version specified. Supported versions: >>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>> >>> >>> mm.. I guess it is OK because the service provider might be using some >>> other SOAP version? >>> >>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>> installed on the service side). I got this error: >>> >>> soap:ClientApplication >>> failed during request deserialization: >>> xml declaration not at start of external entity at line 1, column 941, >>> byte 941 at >>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>> line 187 >>> >>> >>> - When executing a Java service: >>> >>> soapenv:Client >>> org.jboss.axis.AxisFault: Version Mismatch >>> >>> >>> >>> and again, it might be ok? >>> >>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>> retrieveService) I got this error: >>> >>> Connection to MOBY Central at >>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>> died because: >>> Can't use string (" >>> >> /usr/lib/perl5 >>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>> >>> ERROR ERROR ERROR >>> >>> The function retrieveService does work when the service is not >>> 'moby-async' though. >>> >>> - When executing an asynchronous service (function >>> Async/Service/execute) everything seems ok. >>> >>> Has anyone had similar problems? Any ideas? >>> >>> Thank you! >>> Romina >>> >>> Mark Wilkinson wrote: >>> >>> >>>> Hi all, >>>> >>>> First off, apologies to anyone who was trying to get through to MOBY >>>> Central this afternoon - Eddie and I were making the changes necessary >>>> to >>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>> on >>>> the test server didn't work on the real MOBY Central... so it took a >>>> couple of hours of troubleshooting before we had it back up again. >>>> >>>> The good news is that it seems to work correctly with both Perl and >>>> Java >>>> clients. What we don't know is if it is backwards compatible with >>>> earlier >>>> versions of the MOBY::Client::* libraries, in particular, >>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>> opportunity to test it. In any case, the API did not change, so if you >>>> just cvs update your client libraries everything should come back to >>>> life >>>> if it isn't working. >>>> >>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>> behaves >>>> subtly differently than the old one in several ways that we were not >>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>> trouble-shoting already, but it still threw us for a loop in some >>>> places >>>> with incompatible SOAP version errors and a new auto-encoding of >>>> strings >>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>> double-coded messages). >>>> >>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>> you!! >>>> I have backups of everything so if necessary we can roll-back quickly. >>>> >>>> All of this was done primarily to get us to be compatible with the new >>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>> which >>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>> code to see if it works for them v.v. Async services? The database can >>>> now hold Category=moby-async (which reminds me, I need to update the >>>> database templates in the CVS...), and Eddie assures me that the code >>>> will >>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>> added moby-async as a valid service category into their ontology as >>>> well, >>>> so in principle... it should all work... (touch wood!) >>>> >>>> ********************* >>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>> work >>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>> are >>>> running your own registry... >>>> ********************* >>>> >>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>> try to >>>> make the changes to gbrowse_moby such that it can also invoke >>>> asynchronous >>>> services. I think the Async modules also need to be added to the >>>> MANIFEST >>>> before they are installed by default, so I'll try to remember to do >>>> that >>>> as well. >>>> >>>> Otherwise there were just some small changes to the test suite to >>>> better >>>> clean-up the registry if something goes wrong during testing, and I >>>> cleaned-up the test database so that it also doesn't cause the test >>>> suite >>>> to fail. I will restart the test registry using the new codebase first >>>> thing in the morning so that the two are identical. >>>> >>>> We still haven't figured out why those namespace changes happened a >>>> couple >>>> of days ago. It coincided with the Gene Ontology curators making some >>>> additions to the Namespace list, so I suspect that there is a bug in >>>> the >>>> interface I have given to them (which talks directly to the database >>>> without using the MOBY API), but exactly WHY this happened is still a >>>> mystery. I've alerted Midori to the problem and she's going to >>>> hold-off >>>> on making any more changes until we can figure out what is going wrong. >>>> >>>> That's all the news from MOBY Central! >>>> >>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>> today... >>>> >>>> Mark >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 rroyo at lsi.upc.edu Tue Feb 6 11:18:33 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 17:18:33 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: <45C8AA59.3020508@lsi.upc.edu> Hello Mark, I used gbrowse to call one of our services: - first test we had .69 on the server side and as you said it worked ok - second test we had 0.60 on the server side and it also worked ok. I hope this is the test you were asking for :-) Thanks! Romina Mark Wilkinson wrote: > Hi Romina, > > I can confirm that calling services running S::L 0.69 from a client > running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I > have not yet successfully tested is calling a service from a .69 client to > an earlier version on the server-side. The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? > > MOBY Central itself seems fine... and Java invocations of services seem > fine also (largely because the Java libraries don't use the WSDL from MOBY > Central to create their connections... there may be a lesson in there > somewhere! Ugh... WSDL!!) > > M > > > > > On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > > >> Hello again, >> >> Mark, I just called your service and it did work. >> >> Eddy, if those are some of the errors you fixed yesterday I might be >> doing something wrong. Let me re-check everything and if the errors are >> still there I'll send you more details about the code I'm using. >> >> Thank you very much! >> Romina >> >> >> >> mark wilkinson wrote: >> >>> Hmmmm... Well that's a bit of a disaster! >>> >>> Could you check what happens when you call one of my services (eg >>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>> each other properly (which would be a nightmare, but given our >>> experiences yesterday, not surprising!) >>> >>> M >>> >>> >>> -- >>> Mark Wilkinson >>> ...on the road! >>> >>> >>> -----Original Message----- >>> From: Romina Royo >>> Date: Tue, 06 Feb 2007 15:25:15 >>> To:Core developer announcements >>> Cc:mobydev >>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>> registry hosts >>> >>> Hello, >>> >>> I updated the moby-live/Perl libraries from cvs and I installed >>> SOAP::Lite 0.69. >>> >>> Here are some of the results I got: >>> >>> - When executing a synchronous Perl service (function execute in >>> Client/Service.pm) I got this error: >>> >>> SOAP-ENV:VersionMismatchWrong >>> SOAP version specified. Supported versions: >>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>> >>> >>> mm.. I guess it is OK because the service provider might be using some >>> other SOAP version? >>> >>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>> installed on the service side). I got this error: >>> >>> soap:ClientApplication >>> failed during request deserialization: >>> xml declaration not at start of external entity at line 1, column 941, >>> byte 941 at >>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>> line 187 >>> >>> >>> - When executing a Java service: >>> >>> soapenv:Client >>> org.jboss.axis.AxisFault: Version Mismatch >>> >>> >>> >>> and again, it might be ok? >>> >>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>> retrieveService) I got this error: >>> >>> Connection to MOBY Central at >>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>> died because: >>> Can't use string (" >>> >> /usr/lib/perl5 >>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>> >>> ERROR ERROR ERROR >>> >>> The function retrieveService does work when the service is not >>> 'moby-async' though. >>> >>> - When executing an asynchronous service (function >>> Async/Service/execute) everything seems ok. >>> >>> Has anyone had similar problems? Any ideas? >>> >>> Thank you! >>> Romina >>> >>> Mark Wilkinson wrote: >>> >>> >>>> Hi all, >>>> >>>> First off, apologies to anyone who was trying to get through to MOBY >>>> Central this afternoon - Eddie and I were making the changes necessary >>>> to >>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>> on >>>> the test server didn't work on the real MOBY Central... so it took a >>>> couple of hours of troubleshooting before we had it back up again. >>>> >>>> The good news is that it seems to work correctly with both Perl and >>>> Java >>>> clients. What we don't know is if it is backwards compatible with >>>> earlier >>>> versions of the MOBY::Client::* libraries, in particular, >>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>> opportunity to test it. In any case, the API did not change, so if you >>>> just cvs update your client libraries everything should come back to >>>> life >>>> if it isn't working. >>>> >>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>> behaves >>>> subtly differently than the old one in several ways that we were not >>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>> trouble-shoting already, but it still threw us for a loop in some >>>> places >>>> with incompatible SOAP version errors and a new auto-encoding of >>>> strings >>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>> double-coded messages). >>>> >>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>> you!! >>>> I have backups of everything so if necessary we can roll-back quickly. >>>> >>>> All of this was done primarily to get us to be compatible with the new >>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>> which >>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>> code to see if it works for them v.v. Async services? The database can >>>> now hold Category=moby-async (which reminds me, I need to update the >>>> database templates in the CVS...), and Eddie assures me that the code >>>> will >>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>> added moby-async as a valid service category into their ontology as >>>> well, >>>> so in principle... it should all work... (touch wood!) >>>> >>>> ********************* >>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>> work >>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>> are >>>> running your own registry... >>>> ********************* >>>> >>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>> try to >>>> make the changes to gbrowse_moby such that it can also invoke >>>> asynchronous >>>> services. I think the Async modules also need to be added to the >>>> MANIFEST >>>> before they are installed by default, so I'll try to remember to do >>>> that >>>> as well. >>>> >>>> Otherwise there were just some small changes to the test suite to >>>> better >>>> clean-up the registry if something goes wrong during testing, and I >>>> cleaned-up the test database so that it also doesn't cause the test >>>> suite >>>> to fail. I will restart the test registry using the new codebase first >>>> thing in the morning so that the two are identical. >>>> >>>> We still haven't figured out why those namespace changes happened a >>>> couple >>>> of days ago. It coincided with the Gene Ontology curators making some >>>> additions to the Namespace list, so I suspect that there is a bug in >>>> the >>>> interface I have given to them (which talks directly to the database >>>> without using the MOBY API), but exactly WHY this happened is still a >>>> mystery. I've alerted Midori to the problem and she's going to >>>> hold-off >>>> on making any more changes until we can figure out what is going wrong. >>>> >>>> That's all the news from MOBY Central! >>>> >>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>> today... >>>> >>>> Mark >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > > From markw at illuminae.com Tue Feb 6 11:30:28 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 6 Feb 2007 16:30:28 +0000 GMT Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <45C8AA59.3020508@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> Message-ID: <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> Super! That's great news! So, does that mean that everything is OK? M -- Mark Wilkinson ...on the road! -----Original Message----- From: Romina Royo Date: Tue, 06 Feb 2007 17:18:33 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts Hello Mark, I used gbrowse to call one of our services: - first test we had .69 on the server side and as you said it worked ok - second test we had 0.60 on the server side and it also worked ok. I hope this is the test you were asking for :-) Thanks! Romina Mark Wilkinson wrote: > Hi Romina, > > I can confirm that calling services running S::L 0.69 from a client > running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I > have not yet successfully tested is calling a service from a .69 client to > an earlier version on the server-side. The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? > > MOBY Central itself seems fine... and Java invocations of services seem > fine also (largely because the Java libraries don't use the WSDL from MOBY > Central to create their connections... there may be a lesson in there > somewhere! Ugh... WSDL!!) > > M > > > > > On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > > >> Hello again, >> >> Mark, I just called your service and it did work. >> >> Eddy, if those are some of the errors you fixed yesterday I might be >> doing something wrong. Let me re-check everything and if the errors are >> still there I'll send you more details about the code I'm using. >> >> Thank you very much! >> Romina >> >> >> >> mark wilkinson wrote: >> >>> Hmmmm... Well that's a bit of a disaster! >>> >>> Could you check what happens when you call one of my services (eg >>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>> each other properly (which would be a nightmare, but given our >>> experiences yesterday, not surprising!) >>> >>> M >>> >>> >>> -- >>> Mark Wilkinson >>> ...on the road! >>> >>> >>> -----Original Message----- >>> From: Romina Royo >>> Date: Tue, 06 Feb 2007 15:25:15 >>> To:Core developer announcements >>> Cc:mobydev >>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>> registry hosts >>> >>> Hello, >>> >>> I updated the moby-live/Perl libraries from cvs and I installed >>> SOAP::Lite 0.69. >>> >>> Here are some of the results I got: >>> >>> - When executing a synchronous Perl service (function execute in >>> Client/Service.pm) I got this error: >>> >>> SOAP-ENV:VersionMismatchWrong >>> SOAP version specified. Supported versions: >>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>> >>> >>> mm.. I guess it is OK because the service provider might be using some >>> other SOAP version? >>> >>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>> installed on the service side). I got this error: >>> >>> soap:ClientApplication >>> failed during request deserialization: >>> xml declaration not at start of external entity at line 1, column 941, >>> byte 941 at >>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>> line 187 >>> >>> >>> - When executing a Java service: >>> >>> soapenv:Client >>> org.jboss.axis.AxisFault: Version Mismatch >>> >>> >>> >>> and again, it might be ok? >>> >>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>> retrieveService) I got this error: >>> >>> Connection to MOBY Central at >>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>> died because: >>> Can't use string (" >>> >> /usr/lib/perl5 >>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>> >>> ERROR ERROR ERROR >>> >>> The function retrieveService does work when the service is not >>> 'moby-async' though. >>> >>> - When executing an asynchronous service (function >>> Async/Service/execute) everything seems ok. >>> >>> Has anyone had similar problems? Any ideas? >>> >>> Thank you! >>> Romina >>> >>> Mark Wilkinson wrote: >>> >>> >>>> Hi all, >>>> >>>> First off, apologies to anyone who was trying to get through to MOBY >>>> Central this afternoon - Eddie and I were making the changes necessary >>>> to >>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>> on >>>> the test server didn't work on the real MOBY Central... so it took a >>>> couple of hours of troubleshooting before we had it back up again. >>>> >>>> The good news is that it seems to work correctly with both Perl and >>>> Java >>>> clients. What we don't know is if it is backwards compatible with >>>> earlier >>>> versions of the MOBY::Client::* libraries, in particular, >>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>> opportunity to test it. In any case, the API did not change, so if you >>>> just cvs update your client libraries everything should come back to >>>> life >>>> if it isn't working. >>>> >>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>> behaves >>>> subtly differently than the old one in several ways that we were not >>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>> trouble-shoting already, but it still threw us for a loop in some >>>> places >>>> with incompatible SOAP version errors and a new auto-encoding of >>>> strings >>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>> double-coded messages). >>>> >>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>> you!! >>>> I have backups of everything so if necessary we can roll-back quickly. >>>> >>>> All of this was done primarily to get us to be compatible with the new >>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>> which >>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>> code to see if it works for them v.v. Async services? The database can >>>> now hold Category=moby-async (which reminds me, I need to update the >>>> database templates in the CVS...), and Eddie assures me that the code >>>> will >>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>> added moby-async as a valid service category into their ontology as >>>> well, >>>> so in principle... it should all work... (touch wood!) >>>> >>>> ********************* >>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>> work >>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>> are >>>> running your own registry... >>>> ********************* >>>> >>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>> try to >>>> make the changes to gbrowse_moby such that it can also invoke >>>> asynchronous >>>> services. I think the Async modules also need to be added to the >>>> MANIFEST >>>> before they are installed by default, so I'll try to remember to do >>>> that >>>> as well. >>>> >>>> Otherwise there were just some small changes to the test suite to >>>> better >>>> clean-up the registry if something goes wrong during testing, and I >>>> cleaned-up the test database so that it also doesn't cause the test >>>> suite >>>> to fail. I will restart the test registry using the new codebase first >>>> thing in the morning so that the two are identical. >>>> >>>> We still haven't figured out why those namespace changes happened a >>>> couple >>>> of days ago. It coincided with the Gene Ontology curators making some >>>> additions to the Namespace list, so I suspect that there is a bug in >>>> the >>>> interface I have given to them (which talks directly to the database >>>> without using the MOBY API), but exactly WHY this happened is still a >>>> mystery. I've alerted Midori to the problem and she's going to >>>> hold-off >>>> on making any more changes until we can figure out what is going wrong. >>>> >>>> That's all the news from MOBY Central! >>>> >>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>> today... >>>> >>>> Mark >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 >> > > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Tue Feb 6 11:12:31 2007 From: d.haase at gsf.de (Dirk Haase) Date: Tue, 6 Feb 2007 17:12:31 +0100 Subject: [MOBY-dev] =?iso-8859-1?q?Updates_to_MOBY_Central_and_IMPORTANT_N?= =?iso-8859-1?q?OTES=09forregistry_hosts?= In-Reply-To: References: <45C8A113.40803@lsi.upc.edu> Message-ID: <200702061712.31415.d.haase@gsf.de> On Tuesday 06 February 2007 16:48, Mark Wilkinson wrote: > The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? The mips services (using S::L 0.60) are fine when invoked from your gbrowse_moby. Also interaction between client (also 0.60) and Canadian registry is OK. Best, dirk From rroyo at lsi.upc.edu Tue Feb 6 12:09:45 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 18:09:45 +0100 Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> Message-ID: <45C8B659.7090209@lsi.upc.edu> Hello, The retrieveService function of the Perl API still doesn't seem to work for me (while using soap 0.69)... I get this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 1378. ERROR ERROR ERROR It works for 'moby' services but it does not work for 'moby-async' services. Here's an exmple of the scripts I'm using: ------------------ #!/usr/bin/perl -w use FindBin qw($Bin); use lib "$Bin"; use MOBY::Client::Central; use MOBY::Client::Service; use MOBY::CommonSubs; #use SOAP::Lite + trace; use strict; my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; my $Central = MOBY::Client::Central->new( Registries => {mobycentral => {URL => $URL,URI => $URI}}); my ($ServiceInstances, $RegObject) = $Central->findService( serviceName=> 'runClustalwFast', authURI => 'inb.bsc.es' ); print "ServiceInstances? " . $ServiceInstances->[0]->name . "\n"; my $WSDL = $Central->retrieveService($ServiceInstances->[0]); print "WSDL:::::::\n" . $WSDL . "\n"; ----------------- Thanks! Romina mark wilkinson wrote: > Super! That's great news! > > So, does that mean that everything is OK? > > M > > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 17:18:33 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and > IMPORTANT NOTES forregistry hosts > > Hello Mark, > > I used gbrowse to call one of our services: > > - first test we had .69 on the server side and as you said it worked ok > > - second test we had 0.60 on the server side and it also worked ok. > > I hope this is the test you were asking for :-) > > Thanks! > Romina > > > Mark Wilkinson wrote: > >> Hi Romina, >> >> I can confirm that calling services running S::L 0.69 from a client >> running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I >> have not yet successfully tested is calling a service from a .69 client to >> an earlier version on the server-side. The way to do that would be to use >> gbrowse_moby on the mobycentral machine, but I don't know what versions of >> Perl anyone else is running so I can't reliably do that experiment... can >> anyone try one of their Perl services from gbrowse-moby on a server with >> perl 0.60 or less? >> >> MOBY Central itself seems fine... and Java invocations of services seem >> fine also (largely because the Java libraries don't use the WSDL from MOBY >> Central to create their connections... there may be a lesson in there >> somewhere! Ugh... WSDL!!) >> >> M >> >> >> >> >> On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: >> >> >> >>> Hello again, >>> >>> Mark, I just called your service and it did work. >>> >>> Eddy, if those are some of the errors you fixed yesterday I might be >>> doing something wrong. Let me re-check everything and if the errors are >>> still there I'll send you more details about the code I'm using. >>> >>> Thank you very much! >>> Romina >>> >>> >>> >>> mark wilkinson wrote: >>> >>> >>>> Hmmmm... Well that's a bit of a disaster! >>>> >>>> Could you check what happens when you call one of my services (eg >>>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>>> each other properly (which would be a nightmare, but given our >>>> experiences yesterday, not surprising!) >>>> >>>> M >>>> >>>> >>>> -- >>>> Mark Wilkinson >>>> ...on the road! >>>> >>>> >>>> -----Original Message----- >>>> From: Romina Royo >>>> Date: Tue, 06 Feb 2007 15:25:15 >>>> To:Core developer announcements >>>> Cc:mobydev >>>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>>> registry hosts >>>> >>>> Hello, >>>> >>>> I updated the moby-live/Perl libraries from cvs and I installed >>>> SOAP::Lite 0.69. >>>> >>>> Here are some of the results I got: >>>> >>>> - When executing a synchronous Perl service (function execute in >>>> Client/Service.pm) I got this error: >>>> >>>> SOAP-ENV:VersionMismatchWrong >>>> SOAP version specified. Supported versions: >>>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>>> >>>> >>>> mm.. I guess it is OK because the service provider might be using some >>>> other SOAP version? >>>> >>>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>>> installed on the service side). I got this error: >>>> >>>> soap:ClientApplication >>>> failed during request deserialization: >>>> xml declaration not at start of external entity at line 1, column 941, >>>> byte 941 at >>>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>>> line 187 >>>> >>>> >>>> - When executing a Java service: >>>> >>>> soapenv:Client >>>> org.jboss.axis.AxisFault: Version Mismatch >>>> >>>> >>>> >>>> and again, it might be ok? >>>> >>>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>>> retrieveService) I got this error: >>>> >>>> Connection to MOBY Central at >>>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>>> died because: >>>> Can't use string (" >>>> >>> /usr/lib/perl5 >>>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>>> >>>> ERROR ERROR ERROR >>>> >>>> The function retrieveService does work when the service is not >>>> 'moby-async' though. >>>> >>>> - When executing an asynchronous service (function >>>> Async/Service/execute) everything seems ok. >>>> >>>> Has anyone had similar problems? Any ideas? >>>> >>>> Thank you! >>>> Romina >>>> >>>> Mark Wilkinson wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> First off, apologies to anyone who was trying to get through to MOBY >>>>> Central this afternoon - Eddie and I were making the changes necessary >>>>> to >>>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>>> on >>>>> the test server didn't work on the real MOBY Central... so it took a >>>>> couple of hours of troubleshooting before we had it back up again. >>>>> >>>>> The good news is that it seems to work correctly with both Perl and >>>>> Java >>>>> clients. What we don't know is if it is backwards compatible with >>>>> earlier >>>>> versions of the MOBY::Client::* libraries, in particular, >>>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>>> opportunity to test it. In any case, the API did not change, so if you >>>>> just cvs update your client libraries everything should come back to >>>>> life >>>>> if it isn't working. >>>>> >>>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>>> behaves >>>>> subtly differently than the old one in several ways that we were not >>>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>>> trouble-shoting already, but it still threw us for a loop in some >>>>> places >>>>> with incompatible SOAP version errors and a new auto-encoding of >>>>> strings >>>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>>> double-coded messages). >>>>> >>>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>>> you!! >>>>> I have backups of everything so if necessary we can roll-back quickly. >>>>> >>>>> All of this was done primarily to get us to be compatible with the new >>>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>>> which >>>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>>> code to see if it works for them v.v. Async services? The database can >>>>> now hold Category=moby-async (which reminds me, I need to update the >>>>> database templates in the CVS...), and Eddie assures me that the code >>>>> will >>>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>>> added moby-async as a valid service category into their ontology as >>>>> well, >>>>> so in principle... it should all work... (touch wood!) >>>>> >>>>> ********************* >>>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>>> work >>>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>>> are >>>>> running your own registry... >>>>> ********************* >>>>> >>>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>>> try to >>>>> make the changes to gbrowse_moby such that it can also invoke >>>>> asynchronous >>>>> services. I think the Async modules also need to be added to the >>>>> MANIFEST >>>>> before they are installed by default, so I'll try to remember to do >>>>> that >>>>> as well. >>>>> >>>>> Otherwise there were just some small changes to the test suite to >>>>> better >>>>> clean-up the registry if something goes wrong during testing, and I >>>>> cleaned-up the test database so that it also doesn't cause the test >>>>> suite >>>>> to fail. I will restart the test registry using the new codebase first >>>>> thing in the morning so that the two are identical. >>>>> >>>>> We still haven't figured out why those namespace changes happened a >>>>> couple >>>>> of days ago. It coincided with the Gene Ontology curators making some >>>>> additions to the Namespace list, so I suspect that there is a bug in >>>>> the >>>>> interface I have given to them (which talks directly to the database >>>>> without using the MOBY API), but exactly WHY this happened is still a >>>>> mystery. I've alerted Midori to the problem and she's going to >>>>> hold-off >>>>> on making any more changes until we can figure out what is going wrong. >>>>> >>>>> That's all the news from MOBY Central! >>>>> >>>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>>> today... >>>>> >>>>> Mark >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> > > _______________________________________________ > 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 Tue Feb 6 12:49:13 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 09:49:13 -0800 Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <45C8B659.7090209@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> Message-ID: <006801c74a17$1ea4f9a0$6900a8c0@notebook> So something is wrong with the routine that is sending the async wsdl, because there is nothing wrong with your script using category == moby. I will track down the culprit and get back to you! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 9:10 AM To: markw at illuminae.com; Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts Hello, The retrieveService function of the Perl API still doesn't seem to work for me (while using soap 0.69)... I get this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 1378. ERROR ERROR ERROR It works for 'moby' services but it does not work for 'moby-async' services. Here's an exmple of the scripts I'm using: ------------------ #!/usr/bin/perl -w use FindBin qw($Bin); use lib "$Bin"; use MOBY::Client::Central; use MOBY::Client::Service; use MOBY::CommonSubs; #use SOAP::Lite + trace; use strict; my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; my $Central = MOBY::Client::Central->new( Registries => {mobycentral => {URL => $URL,URI => $URI}}); my ($ServiceInstances, $RegObject) = $Central->findService( serviceName=> 'runClustalwFast', authURI => 'inb.bsc.es' ); print "ServiceInstances? " . $ServiceInstances->[0]->name . "\n"; my $WSDL = $Central->retrieveService($ServiceInstances->[0]); print "WSDL:::::::\n" . $WSDL . "\n"; ----------------- Thanks! Romina mark wilkinson wrote: > Super! That's great news! > > So, does that mean that everything is OK? > > M > > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 17:18:33 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and > IMPORTANT NOTES forregistry hosts > > Hello Mark, > > I used gbrowse to call one of our services: > > - first test we had .69 on the server side and as you said it worked ok > > - second test we had 0.60 on the server side and it also worked ok. > > I hope this is the test you were asking for :-) > > Thanks! > Romina > > > Mark Wilkinson wrote: > >> Hi Romina, >> >> I can confirm that calling services running S::L 0.69 from a client >> running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I >> have not yet successfully tested is calling a service from a .69 client to >> an earlier version on the server-side. The way to do that would be to use >> gbrowse_moby on the mobycentral machine, but I don't know what versions of >> Perl anyone else is running so I can't reliably do that experiment... can >> anyone try one of their Perl services from gbrowse-moby on a server with >> perl 0.60 or less? >> >> MOBY Central itself seems fine... and Java invocations of services seem >> fine also (largely because the Java libraries don't use the WSDL from MOBY >> Central to create their connections... there may be a lesson in there >> somewhere! Ugh... WSDL!!) >> >> M >> >> >> >> >> On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: >> >> >> >>> Hello again, >>> >>> Mark, I just called your service and it did work. >>> >>> Eddy, if those are some of the errors you fixed yesterday I might be >>> doing something wrong. Let me re-check everything and if the errors are >>> still there I'll send you more details about the code I'm using. >>> >>> Thank you very much! >>> Romina >>> >>> >>> >>> mark wilkinson wrote: >>> >>> >>>> Hmmmm... Well that's a bit of a disaster! >>>> >>>> Could you check what happens when you call one of my services (eg >>>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>>> each other properly (which would be a nightmare, but given our >>>> experiences yesterday, not surprising!) >>>> >>>> M >>>> >>>> >>>> -- >>>> Mark Wilkinson >>>> ...on the road! >>>> >>>> >>>> -----Original Message----- >>>> From: Romina Royo >>>> Date: Tue, 06 Feb 2007 15:25:15 >>>> To:Core developer announcements >>>> Cc:mobydev >>>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>>> registry hosts >>>> >>>> Hello, >>>> >>>> I updated the moby-live/Perl libraries from cvs and I installed >>>> SOAP::Lite 0.69. >>>> >>>> Here are some of the results I got: >>>> >>>> - When executing a synchronous Perl service (function execute in >>>> Client/Service.pm) I got this error: >>>> >>>> SOAP-ENV:VersionMismatch Wrong >>>> SOAP version specified. Supported versions: >>>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>>> >>>> >>>> mm.. I guess it is OK because the service provider might be using some >>>> other SOAP version? >>>> >>>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>>> installed on the service side). I got this error: >>>> >>>> soap:ClientApplication >>>> failed during request deserialization: >>>> xml declaration not at start of external entity at line 1, column 941, >>>> byte 941 at >>>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>>> line 187 >>>> >>>> >>>> - When executing a Java service: >>>> >>>> soapenv:Client >>>> org.jboss.axis.AxisFault: Version Mismatch >>>> >>>> >>>> >>>> and again, it might be ok? >>>> >>>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>>> retrieveService) I got this error: >>>> >>>> Connection to MOBY Central at >>>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>>> died because: >>>> Can't use string (" >>>> >>> /usr/lib/perl5 >>>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>>> >>>> ERROR ERROR ERROR >>>> >>>> The function retrieveService does work when the service is not >>>> 'moby-async' though. >>>> >>>> - When executing an asynchronous service (function >>>> Async/Service/execute) everything seems ok. >>>> >>>> Has anyone had similar problems? Any ideas? >>>> >>>> Thank you! >>>> Romina >>>> >>>> Mark Wilkinson wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> First off, apologies to anyone who was trying to get through to MOBY >>>>> Central this afternoon - Eddie and I were making the changes necessary >>>>> to >>>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>>> on >>>>> the test server didn't work on the real MOBY Central... so it took a >>>>> couple of hours of troubleshooting before we had it back up again. >>>>> >>>>> The good news is that it seems to work correctly with both Perl and >>>>> Java >>>>> clients. What we don't know is if it is backwards compatible with >>>>> earlier >>>>> versions of the MOBY::Client::* libraries, in particular, >>>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>>> opportunity to test it. In any case, the API did not change, so if you >>>>> just cvs update your client libraries everything should come back to >>>>> life >>>>> if it isn't working. >>>>> >>>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>>> behaves >>>>> subtly differently than the old one in several ways that we were not >>>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>>> trouble-shoting already, but it still threw us for a loop in some >>>>> places >>>>> with incompatible SOAP version errors and a new auto-encoding of >>>>> strings >>>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>>> double-coded messages). >>>>> >>>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>>> you!! >>>>> I have backups of everything so if necessary we can roll-back quickly. >>>>> >>>>> All of this was done primarily to get us to be compatible with the new >>>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>>> which >>>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>>> code to see if it works for them v.v. Async services? The database can >>>>> now hold Category=moby-async (which reminds me, I need to update the >>>>> database templates in the CVS...), and Eddie assures me that the code >>>>> will >>>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>>> added moby-async as a valid service category into their ontology as >>>>> well, >>>>> so in principle... it should all work... (touch wood!) >>>>> >>>>> ********************* >>>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>>> work >>>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>>> are >>>>> running your own registry... >>>>> ********************* >>>>> >>>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>>> try to >>>>> make the changes to gbrowse_moby such that it can also invoke >>>>> asynchronous >>>>> services. I think the Async modules also need to be added to the >>>>> MANIFEST >>>>> before they are installed by default, so I'll try to remember to do >>>>> that >>>>> as well. >>>>> >>>>> Otherwise there were just some small changes to the test suite to >>>>> better >>>>> clean-up the registry if something goes wrong during testing, and I >>>>> cleaned-up the test database so that it also doesn't cause the test >>>>> suite >>>>> to fail. I will restart the test registry using the new codebase first >>>>> thing in the morning so that the two are identical. >>>>> >>>>> We still haven't figured out why those namespace changes happened a >>>>> couple >>>>> of days ago. It coincided with the Gene Ontology curators making some >>>>> additions to the Namespace list, so I suspect that there is a bug in >>>>> the >>>>> interface I have given to them (which talks directly to the database >>>>> without using the MOBY API), but exactly WHY this happened is still a >>>>> mystery. I've alerted Midori to the problem and she's going to >>>>> hold-off >>>>> on making any more changes until we can figure out what is going wrong. >>>>> >>>>> That's all the news from MOBY Central! >>>>> >>>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>>> today... >>>>> >>>>> Mark >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> > > _______________________________________________ > 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 > _______________________________________________ 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 Tue Feb 6 13:06:43 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 10:06:43 -0800 Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <45C8B659.7090209@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> Message-ID: <006901c74a19$907716b0$6900a8c0@notebook> Hi Romina, I just committed into the cvs a fix to this problem. There should be no more errors (fingers crossed ;-) Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 9:10 AM To: markw at illuminae.com; Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts Hello, The retrieveService function of the Perl API still doesn't seem to work for me (while using soap 0.69)... I get this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 1378. ERROR ERROR ERROR It works for 'moby' services but it does not work for 'moby-async' services. Here's an exmple of the scripts I'm using: ------------------ #!/usr/bin/perl -w use FindBin qw($Bin); use lib "$Bin"; use MOBY::Client::Central; use MOBY::Client::Service; use MOBY::CommonSubs; #use SOAP::Lite + trace; use strict; my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; my $Central = MOBY::Client::Central->new( Registries => {mobycentral => {URL => $URL,URI => $URI}}); my ($ServiceInstances, $RegObject) = $Central->findService( serviceName=> 'runClustalwFast', authURI => 'inb.bsc.es' ); print "ServiceInstances? " . $ServiceInstances->[0]->name . "\n"; my $WSDL = $Central->retrieveService($ServiceInstances->[0]); print "WSDL:::::::\n" . $WSDL . "\n"; ----------------- Thanks! Romina mark wilkinson wrote: > Super! That's great news! > > So, does that mean that everything is OK? > > M > > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 17:18:33 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and > IMPORTANT NOTES forregistry hosts > > Hello Mark, > > I used gbrowse to call one of our services: > > - first test we had .69 on the server side and as you said it worked ok > > - second test we had 0.60 on the server side and it also worked ok. > > I hope this is the test you were asking for :-) > > Thanks! > Romina > > > Mark Wilkinson wrote: > >> Hi Romina, >> >> I can confirm that calling services running S::L 0.69 from a client >> running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I >> have not yet successfully tested is calling a service from a .69 client to >> an earlier version on the server-side. The way to do that would be to use >> gbrowse_moby on the mobycentral machine, but I don't know what versions of >> Perl anyone else is running so I can't reliably do that experiment... can >> anyone try one of their Perl services from gbrowse-moby on a server with >> perl 0.60 or less? >> >> MOBY Central itself seems fine... and Java invocations of services seem >> fine also (largely because the Java libraries don't use the WSDL from MOBY >> Central to create their connections... there may be a lesson in there >> somewhere! Ugh... WSDL!!) >> >> M >> >> >> >> >> On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: >> >> >> >>> Hello again, >>> >>> Mark, I just called your service and it did work. >>> >>> Eddy, if those are some of the errors you fixed yesterday I might be >>> doing something wrong. Let me re-check everything and if the errors are >>> still there I'll send you more details about the code I'm using. >>> >>> Thank you very much! >>> Romina >>> >>> >>> >>> mark wilkinson wrote: >>> >>> >>>> Hmmmm... Well that's a bit of a disaster! >>>> >>>> Could you check what happens when you call one of my services (eg >>>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>>> each other properly (which would be a nightmare, but given our >>>> experiences yesterday, not surprising!) >>>> >>>> M >>>> >>>> >>>> -- >>>> Mark Wilkinson >>>> ...on the road! >>>> >>>> >>>> -----Original Message----- >>>> From: Romina Royo >>>> Date: Tue, 06 Feb 2007 15:25:15 >>>> To:Core developer announcements >>>> Cc:mobydev >>>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>>> registry hosts >>>> >>>> Hello, >>>> >>>> I updated the moby-live/Perl libraries from cvs and I installed >>>> SOAP::Lite 0.69. >>>> >>>> Here are some of the results I got: >>>> >>>> - When executing a synchronous Perl service (function execute in >>>> Client/Service.pm) I got this error: >>>> >>>> SOAP-ENV:VersionMismatch Wrong >>>> SOAP version specified. Supported versions: >>>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>>> >>>> >>>> mm.. I guess it is OK because the service provider might be using some >>>> other SOAP version? >>>> >>>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>>> installed on the service side). I got this error: >>>> >>>> soap:ClientApplication >>>> failed during request deserialization: >>>> xml declaration not at start of external entity at line 1, column 941, >>>> byte 941 at >>>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>>> line 187 >>>> >>>> >>>> - When executing a Java service: >>>> >>>> soapenv:Client >>>> org.jboss.axis.AxisFault: Version Mismatch >>>> >>>> >>>> >>>> and again, it might be ok? >>>> >>>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>>> retrieveService) I got this error: >>>> >>>> Connection to MOBY Central at >>>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>>> died because: >>>> Can't use string (" >>>> >>> /usr/lib/perl5 >>>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>>> >>>> ERROR ERROR ERROR >>>> >>>> The function retrieveService does work when the service is not >>>> 'moby-async' though. >>>> >>>> - When executing an asynchronous service (function >>>> Async/Service/execute) everything seems ok. >>>> >>>> Has anyone had similar problems? Any ideas? >>>> >>>> Thank you! >>>> Romina >>>> >>>> Mark Wilkinson wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> First off, apologies to anyone who was trying to get through to MOBY >>>>> Central this afternoon - Eddie and I were making the changes necessary >>>>> to >>>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>>> on >>>>> the test server didn't work on the real MOBY Central... so it took a >>>>> couple of hours of troubleshooting before we had it back up again. >>>>> >>>>> The good news is that it seems to work correctly with both Perl and >>>>> Java >>>>> clients. What we don't know is if it is backwards compatible with >>>>> earlier >>>>> versions of the MOBY::Client::* libraries, in particular, >>>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>>> opportunity to test it. In any case, the API did not change, so if you >>>>> just cvs update your client libraries everything should come back to >>>>> life >>>>> if it isn't working. >>>>> >>>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>>> behaves >>>>> subtly differently than the old one in several ways that we were not >>>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>>> trouble-shoting already, but it still threw us for a loop in some >>>>> places >>>>> with incompatible SOAP version errors and a new auto-encoding of >>>>> strings >>>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>>> double-coded messages). >>>>> >>>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>>> you!! >>>>> I have backups of everything so if necessary we can roll-back quickly. >>>>> >>>>> All of this was done primarily to get us to be compatible with the new >>>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>>> which >>>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>>> code to see if it works for them v.v. Async services? The database can >>>>> now hold Category=moby-async (which reminds me, I need to update the >>>>> database templates in the CVS...), and Eddie assures me that the code >>>>> will >>>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>>> added moby-async as a valid service category into their ontology as >>>>> well, >>>>> so in principle... it should all work... (touch wood!) >>>>> >>>>> ********************* >>>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>>> work >>>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>>> are >>>>> running your own registry... >>>>> ********************* >>>>> >>>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>>> try to >>>>> make the changes to gbrowse_moby such that it can also invoke >>>>> asynchronous >>>>> services. I think the Async modules also need to be added to the >>>>> MANIFEST >>>>> before they are installed by default, so I'll try to remember to do >>>>> that >>>>> as well. >>>>> >>>>> Otherwise there were just some small changes to the test suite to >>>>> better >>>>> clean-up the registry if something goes wrong during testing, and I >>>>> cleaned-up the test database so that it also doesn't cause the test >>>>> suite >>>>> to fail. I will restart the test registry using the new codebase first >>>>> thing in the morning so that the two are identical. >>>>> >>>>> We still haven't figured out why those namespace changes happened a >>>>> couple >>>>> of days ago. It coincided with the Gene Ontology curators making some >>>>> additions to the Namespace list, so I suspect that there is a bug in >>>>> the >>>>> interface I have given to them (which talks directly to the database >>>>> without using the MOBY API), but exactly WHY this happened is still a >>>>> mystery. I've alerted Midori to the problem and she's going to >>>>> hold-off >>>>> on making any more changes until we can figure out what is going wrong. >>>>> >>>>> That's all the news from MOBY Central! >>>>> >>>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>>> today... >>>>> >>>>> Mark >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> > > _______________________________________________ > 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 > _______________________________________________ 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 Tue Feb 6 16:56:04 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Feb 2007 13:56:04 -0800 Subject: [MOBY-dev] Q about Async services Message-ID: Hi INB team! I have a quick question about some parts of the last version of the MOBY Async proposal (or at least, the last version that I printed for myself that I am reading now). One of the aspects in the proposal was the addition of a boolean parameter to the service registration and also some additional RDF in the LSID metadata indicating that the service was asynchronous. What seems to have happened is that these two aspects were abandoned and in their place the new Category "moby-async" was added to the list of acceptable service categories. Is this your understanding also (i.e. that these two pieces of the proposal are now deprecated) or are you still expecting these changes to happen? I believe that the status quo fulfils all of the requirements, but please correct me if I am wrong. Mark -- -- 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 johan at ac.uma.es Wed Feb 7 04:25:20 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Wed, 07 Feb 2007 10:25:20 +0100 Subject: [MOBY-dev] Q about Async services In-Reply-To: References: Message-ID: <45C99B00.2030602@ac.uma.es> Hi Mark, You are completely right, the "moby-async" category covers what is needed but we missed to update some things in the document. So "moby-async" should be allowed in: * registerService: the input field "category" * findService: the input field "protocol" and the output field "category". * RDF for service instances: "dc:format" predicate Anywhere else? Kind regards, Johan Karlsson -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 Mark Wilkinson wrote: > Hi INB team! > > I have a quick question about some parts of the last version of the MOBY > Async proposal (or at least, the last version that I printed for myself > that I am reading now). > > One of the aspects in the proposal was the addition of a boolean parameter > to the service registration and also some additional RDF in the LSID > metadata indicating that the service was asynchronous. What seems to have > happened is that these two aspects were abandoned and in their place the > new Category "moby-async" was added to the list of acceptable service > categories. Is this your understanding also (i.e. that these two pieces > of the proposal are now deprecated) or are you still expecting these > changes to happen? I believe that the status quo fulfils all of the > requirements, but please correct me if I am wrong. > > Mark > > > > From markw at illuminae.com Wed Feb 7 22:38:57 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 07 Feb 2007 19:38:57 -0800 Subject: [MOBY-dev] Q about Async services In-Reply-To: <45C99B00.2030602@ac.uma.es> References: <45C99B00.2030602@ac.uma.es> Message-ID: I think those are the only three places. Okay great, I just wanted to be sure that you have all the changes you require. We're still working out some bugs with Romina, but hopefully we'll have those sorted out in a day or two. Cheers! Mark On Wed, 07 Feb 2007 01:25:20 -0800, Johan Karlsson wrote: > Hi Mark, > > You are completely right, the "moby-async" category covers what is > needed but we missed to update some things in the document. > > So "moby-async" should be allowed in: > > * registerService: the input field "category" > * findService: the input field "protocol" and the output field > "category". > * RDF for service instances: "dc:format" predicate > > Anywhere else? > > Kind regards, > Johan Karlsson > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From Pieter.Neerincx at wur.nl Thu Feb 8 15:01:15 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 8 Feb 2007 21:01:15 +0100 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <006901c74a19$907716b0$6900a8c0@notebook> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> <006901c74a19$907716b0$6900a8c0@notebook> Message-ID: Hi Eddie, I think I ran into a small problem. When I use MOBY::Client::Central::DUMP I get the following error: ------------------- Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ MOBY/Central' died because: String value expected instead of ARRAY reference ERROR ERROR ERROR ------------------- This happens both with: * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY Central with S::L 0.69 * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY Central with S::L 0.69 I'm suspecting the following line to be the cruel-pit: MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; I'm guessing your new S::L (de-)serializer expects an XML string instead of the array ref... Is that possible? Cheers, Pi in update mode :) From edward.kawas at gmail.com Thu Feb 8 15:58:02 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 8 Feb 2007 12:58:02 -0800 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01><45C8B659.7090209@lsi.upc.edu><006901c74a19$907716b0$6900a8c0@notebook> Message-ID: <007201c74bc3$d35cf8e0$6900a8c0@notebook> Hi Pieter, You are right. The serializer (MOBY::SOAP::Serializer) expects a string. I have fixed it, but I think that my patch is very sub optimal. What I did was wrap the code contained in do { ... } if $_[1] =~ /^(?:method|response)$/; With: do { do { ... } unless ref($_[3]) =~ /ARRAY/; } if $_[1] =~ /^(?:method|response)$/; This seems to work, i.e. I see something in the soap trace. However, when I attempt to use the array ref, things don't work for me ... I am wondering if I should encode the strings in the array!?! Thoughts anyone? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: Thursday, February 08, 2007 12:01 PM To: Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central Hi Eddie, I think I ran into a small problem. When I use MOBY::Client::Central::DUMP I get the following error: ------------------- Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ MOBY/Central' died because: String value expected instead of ARRAY reference ERROR ERROR ERROR ------------------- This happens both with: * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY Central with S::L 0.69 * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY Central with S::L 0.69 I'm suspecting the following line to be the cruel-pit: MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; I'm guessing your new S::L (de-)serializer expects an XML string instead of the array ref... Is that possible? Cheers, Pi in update mode :) _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Feb 8 16:47:35 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Feb 2007 13:47:35 -0800 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <007201c74bc3$d35cf8e0$6900a8c0@notebook> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> <006901c74a19$907716b0$6900a8c0@notebook> <007201c74bc3$d35cf8e0$6900a8c0@notebook> Message-ID: Hmmmm... that DUMP subroutine has always been a bit "odd" compared to the rest of the API (actually... is it even IN the API?). I guess if it is causing problems now then it should be fixed properly. M On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas wrote: > Hi Pieter, > > You are right. The serializer (MOBY::SOAP::Serializer) expects a string. > I > have fixed it, but I think that my patch is very sub optimal. What I did > was > wrap the code contained in > > do { > ... > } if $_[1] =~ /^(?:method|response)$/; > > With: > do { > do { > ... > } unless ref($_[3]) =~ /ARRAY/; > } if $_[1] =~ /^(?:method|response)$/; > > This seems to work, i.e. I see something in the soap trace. However, > when I > attempt to use the array ref, things don't work for me ... I am > wondering if > I should encode the strings in the array!?! > > Thoughts anyone? > > Eddie > > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx > Sent: Thursday, February 08, 2007 12:01 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Updates to MOBY Central > > Hi Eddie, > > I think I ran into a small problem. When I use > MOBY::Client::Central::DUMP I get the following error: > ------------------- > Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ > MOBY/Central' died because: > String value expected instead of ARRAY reference > > ERROR ERROR ERROR > ------------------- > > This happens both with: > * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY > Central with S::L 0.69 > * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY > Central with S::L 0.69 > > I'm suspecting the following line to be the cruel-pit: > > MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; > > I'm guessing your new S::L (de-)serializer expects an XML string > instead of the array ref... Is that possible? > > Cheers, > > Pi in update mode :) > _______________________________________________ > 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From Pieter.Neerincx at wur.nl Thu Feb 8 17:15:32 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 8 Feb 2007 23:15:32 +0100 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> <006901c74a19$907716b0$6900a8c0@notebook> <007201c74bc3$d35cf8e0$6900a8c0@notebook> Message-ID: <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> On 08 Feb 2007, at 22:47, Mark Wilkinson wrote: > Hmmmm... that DUMP subroutine has always been a bit "odd" compared > to the > rest of the API (actually... is it even IN the API?). Yeah it's bit of a weird one, but it's also extremely useful for duplicating a Central :). > I guess if it is > causing problems now then it should be fixed properly. > > M > > > > > > On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas > > wrote: > >> Hi Pieter, >> >> You are right. The serializer (MOBY::SOAP::Serializer) expects a >> string. >> I >> have fixed it, but I think that my patch is very sub optimal. What >> I did >> was >> wrap the code contained in >> >> do { >> ... >> } if $_[1] =~ /^(?:method|response)$/; >> >> With: >> do { >> do { >> ... >> } unless ref($_[3]) =~ /ARRAY/; >> } if $_[1] =~ /^(?:method|response)$/; >> >> This seems to work, i.e. I see something in the soap trace. However, >> when I >> attempt to use the array ref, things don't work for me ... I am >> wondering if >> I should encode the strings in the array!?! I guess. If the BioMOBY Perl libs are not encoding the strings in the array and the new serializer is not doing that either it must cause trouble with not escaped characters... I'll try to dig further tomorrow. Cheers, Pi >> >> Thoughts anyone? >> >> Eddie >> >> >> >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter >> Neerincx >> Sent: Thursday, February 08, 2007 12:01 PM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Updates to MOBY Central >> >> Hi Eddie, >> >> I think I ran into a small problem. When I use >> MOBY::Client::Central::DUMP I get the following error: >> ------------------- >> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ >> MOBY/Central' died because: >> String value expected instead of ARRAY reference >> >> ERROR ERROR ERROR >> ------------------- >> >> This happens both with: >> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY >> Central with S::L 0.69 >> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY >> Central with S::L 0.69 >> >> I'm suspecting the following line to be the cruel-pit: >> >> MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; >> >> I'm guessing your new S::L (de-)serializer expects an XML string >> instead of the array ref... Is that possible? >> >> Cheers, >> >> Pi in update mode :) >> _______________________________________________ >> 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 > > > > -- > 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 Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From edward.kawas at gmail.com Thu Feb 8 18:12:54 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 8 Feb 2007 15:12:54 -0800 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> References: <45C88FCB.2030704@lsi.upc.edu><1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01><45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01><45C8B659.7090209@lsi.upc.edu><006901c74a19$907716b0$6900a8c0@notebook><007201c74bc3$d35cf8e0$6900a8c0@notebook> <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> Message-ID: <007c01c74bd6$aa6c0940$6900a8c0@notebook> Pieter, Okay, I have committed a fix. It should be backwards compatible. Let me know if this works for you! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: Thursday, February 08, 2007 2:16 PM To: Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central On 08 Feb 2007, at 22:47, Mark Wilkinson wrote: > Hmmmm... that DUMP subroutine has always been a bit "odd" compared > to the > rest of the API (actually... is it even IN the API?). Yeah it's bit of a weird one, but it's also extremely useful for duplicating a Central :). > I guess if it is > causing problems now then it should be fixed properly. > > M > > > > > > On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas > > wrote: > >> Hi Pieter, >> >> You are right. The serializer (MOBY::SOAP::Serializer) expects a >> string. >> I >> have fixed it, but I think that my patch is very sub optimal. What >> I did >> was >> wrap the code contained in >> >> do { >> ... >> } if $_[1] =~ /^(?:method|response)$/; >> >> With: >> do { >> do { >> ... >> } unless ref($_[3]) =~ /ARRAY/; >> } if $_[1] =~ /^(?:method|response)$/; >> >> This seems to work, i.e. I see something in the soap trace. However, >> when I >> attempt to use the array ref, things don't work for me ... I am >> wondering if >> I should encode the strings in the array!?! I guess. If the BioMOBY Perl libs are not encoding the strings in the array and the new serializer is not doing that either it must cause trouble with not escaped characters... I'll try to dig further tomorrow. Cheers, Pi >> >> Thoughts anyone? >> >> Eddie >> >> >> >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter >> Neerincx >> Sent: Thursday, February 08, 2007 12:01 PM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Updates to MOBY Central >> >> Hi Eddie, >> >> I think I ran into a small problem. When I use >> MOBY::Client::Central::DUMP I get the following error: >> ------------------- >> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ >> MOBY/Central' died because: >> String value expected instead of ARRAY reference >> >> ERROR ERROR ERROR >> ------------------- >> >> This happens both with: >> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY >> Central with S::L 0.69 >> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY >> Central with S::L 0.69 >> >> I'm suspecting the following line to be the cruel-pit: >> >> MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; >> >> I'm guessing your new S::L (de-)serializer expects an XML string >> instead of the array ref... Is that possible? >> >> Cheers, >> >> Pi in update mode :) >> _______________________________________________ >> 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 > > > > -- > 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 Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Fri Feb 9 06:01:24 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 9 Feb 2007 12:01:24 +0100 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <007c01c74bd6$aa6c0940$6900a8c0@notebook> References: <45C88FCB.2030704@lsi.upc.edu><1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01><45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01><45C8B659.7090209@lsi.upc.edu><006901c74a19$907716b0$6900a8c0@notebook><007201c74bc3$d35cf8e0$6900a8c0@notebook> <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> <007c01c74bd6$aa6c0940$6900a8c0@notebook> Message-ID: <4B1A3610-AB88-4926-8B28-ABFB146020F3@wur.nl> On 9-Feb-2007, at 12:12 AM, Edward Kawas wrote: > Pieter, > > Okay, I have committed a fix. > > It should be backwards compatible. > > Let me know if this works for you! It does :). Thanks! Pi > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: Thursday, February 08, 2007 2:16 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Updates to MOBY Central > > > On 08 Feb 2007, at 22:47, Mark Wilkinson wrote: > >> Hmmmm... that DUMP subroutine has always been a bit "odd" compared >> to the >> rest of the API (actually... is it even IN the API?). > > Yeah it's bit of a weird one, but it's also extremely useful for > duplicating a Central :). > >> I guess if it is >> causing problems now then it should be fixed properly. >> >> M >> >> >> >> >> >> On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas >> >> wrote: >> >>> Hi Pieter, >>> >>> You are right. The serializer (MOBY::SOAP::Serializer) expects a >>> string. >>> I >>> have fixed it, but I think that my patch is very sub optimal. What >>> I did >>> was >>> wrap the code contained in >>> >>> do { >>> ... >>> } if $_[1] =~ /^(?:method|response)$/; >>> >>> With: >>> do { >>> do { >>> ... >>> } unless ref($_[3]) =~ /ARRAY/; >>> } if $_[1] =~ /^(?:method|response)$/; >>> >>> This seems to work, i.e. I see something in the soap trace. However, >>> when I >>> attempt to use the array ref, things don't work for me ... I am >>> wondering if >>> I should encode the strings in the array!?! > > I guess. If the BioMOBY Perl libs are not encoding the strings in the > array and the new serializer is not doing that either it must cause > trouble with not escaped characters... > > I'll try to dig further tomorrow. > > Cheers, > > Pi > >>> >>> Thoughts anyone? >>> >>> Eddie >>> >>> >>> >>> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter >>> Neerincx >>> Sent: Thursday, February 08, 2007 12:01 PM >>> To: Core developer announcements >>> Subject: Re: [MOBY-dev] Updates to MOBY Central >>> >>> Hi Eddie, >>> >>> I think I ran into a small problem. When I use >>> MOBY::Client::Central::DUMP I get the following error: >>> ------------------- >>> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ >>> MOBY/Central' died because: >>> String value expected instead of ARRAY reference >>> >>> ERROR ERROR ERROR >>> ------------------- >>> >>> This happens both with: >>> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY >>> Central with S::L 0.69 >>> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY >>> Central with S::L 0.69 >>> >>> I'm suspecting the following line to be the cruel-pit: >>> >>> MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; >>> >>> I'm guessing your new S::L (de-)serializer expects an XML string >>> instead of the array ref... Is that possible? >>> >>> Cheers, >>> >>> Pi in update mode :) >>> _______________________________________________ >>> 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 >> >> >> >> -- >> 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 > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1038 > Dreijenlaan 3 > 6703 HA Wageningen > phone: 0317-484 706 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at 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 Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Fri Feb 9 21:59:04 2007 From: markw at illuminae.com (mark wilkinson) Date: Sat, 10 Feb 2007 02:59:04 +0000 GMT Subject: [MOBY-dev] New Perl Client::Service Function Message-ID: <1196561465-1171076434-cardhu_blackberry.rim.net-19978-@engine02-cell01> Just a heads-up that I just committed a new function to the MOBY::Client::Service module "enumerated_execute", that allows the client to set the queryID's (as opposed to them being autogenerated by the module). This is more reflective of how we (I?) envisioned that service execution should happen, since there is a need for the client to be able to keep track of which inputs led to which outputs in a multi-invocation service call. I know that this should have been an available function years ago... Sorry!! The Java code (eg Taverna) already does this, but I have been negligent in adding this functionality on the Perl side. INB folks, you may want to "mirror" this functionality in your Async Perl module... I haven't tested it (because I wrote it in the pub just now ;-) ) but it was only a small modification from what we had already so I'm fairly sure it will work. I'm going to test it tomorrow, but if any brave mobyers are bored on a Friday night (why would that be??) And want to try it themselves please let me know if it works for you! Cheers all! M -- Mark Wilkinson ...on the road! From d.haase at gsf.de Thu Feb 15 04:40:58 2007 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 15 Feb 2007 10:40:58 +0100 Subject: [MOBY-dev] getSignatureForm doesn't work Message-ID: <200702151040.58811.d.haase@gsf.de> Hello Canadians, the servlet at http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm for registration of signature URLs does not work. When I enter my data and press 'submit' it takes ages and then an error message (see below) is displayed. Moreover, the signature URL is not stored in the database. Regards, dirk And this is the error message: java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:179) 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) From edward.kawas at gmail.com Thu Feb 15 09:34:25 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 15 Feb 2007 06:34:25 -0800 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <200702151040.58811.d.haase@gsf.de> References: <200702151040.58811.d.haase@gsf.de> Message-ID: <001801c7510e$64ff8d90$6900a8c0@notebook> Hi Dirk, You do know that the form isn't supposed to be used to register services from a signatureURL, right? With that said, you are correct, the form seems to be broken... Did it work in the recent past? I am asking, because it is failing at an odd point in the code ... I will have it up soon. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase Sent: Thursday, February 15, 2007 1:41 AM To: Moby-dev at biomoby.org Subject: [MOBY-dev] getSignatureForm doesn't work Hello Canadians, the servlet at http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm for registration of signature URLs does not work. When I enter my data and press 'submit' it takes ages and then an error message (see below) is displayed. Moreover, the signature URL is not stored in the database. Regards, dirk And this is the error message: java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.update MobyCentralDatabase(GetSignatureRDFResponse.java:179) org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.doGet( GetSignatureRDFResponse.java:91) javax.servlet.http.HttpServlet.service(HttpServlet.java:689) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Feb 15 09:44:46 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 15 Feb 2007 06:44:46 -0800 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <200702151040.58811.d.haase@gsf.de> References: <200702151040.58811.d.haase@gsf.de> Message-ID: <001901c7510f$d730b000$6900a8c0@notebook> Dirk, The form is up and running again. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase Sent: Thursday, February 15, 2007 1:41 AM To: Moby-dev at biomoby.org Subject: [MOBY-dev] getSignatureForm doesn't work Hello Canadians, the servlet at http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm for registration of signature URLs does not work. When I enter my data and press 'submit' it takes ages and then an error message (see below) is displayed. Moreover, the signature URL is not stored in the database. Regards, dirk And this is the error message: java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.update MobyCentralDatabase(GetSignatureRDFResponse.java:179) 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) _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Thu Feb 15 09:46:38 2007 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 15 Feb 2007 15:46:38 +0100 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <001801c7510e$64ff8d90$6900a8c0@notebook> References: <200702151040.58811.d.haase@gsf.de> <001801c7510e$64ff8d90$6900a8c0@notebook> Message-ID: <200702151546.38647.d.haase@gsf.de> On Thursday 15 February 2007 15:34, Edward Kawas wrote: > Hi Dirk, > > You do know that the form isn't supposed to be used to register services > from a signatureURL, right? I thought I could use it to add a signature URL for a service which existed before in the registry but had no RDF description yet. Is that correct? > With that said, you are correct, the form seems to be broken... Did it work > in the recent past? I am asking, because it is failing at an odd point in > the code ... I got a message from a project partner last Friday. Before that I can't say anything. > I will have it up soon. Great! Regards, dirk From edward.kawas at gmail.com Thu Feb 15 09:55:51 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 15 Feb 2007 06:55:51 -0800 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <200702151546.38647.d.haase@gsf.de> References: <200702151040.58811.d.haase@gsf.de><001801c7510e$64ff8d90$6900a8c0@notebook> <200702151546.38647.d.haase@gsf.de> Message-ID: <002b01c75111$6391ec70$6900a8c0@notebook> >I thought I could use it to add a signature URL for a service which existed >before in the registry but had no RDF description yet. Is that correct? That is correct. I thought something else (although, I didn't understand how!), because someone else sent me a message about using it to register services from an RDF. Thanks Dirk, Eddie From Yogaraj.Khanal at usd.edu Thu Feb 15 12:45:52 2007 From: Yogaraj.Khanal at usd.edu (Yogaraj.Khanal at usd.edu) Date: Thu, 15 Feb 2007 11:45:52 -0600 Subject: [MOBY-dev] Regarding XML conversion Message-ID: <1ad0b71aacdf.1aacdf1ad0b7@usd.edu> Dear Mark, I was reading your comment form http://lists.open-bio.org/pipermail/moby-dev/2006-September/003798.html I was doing a similar projects like "Take any two arbitrary Web Services out there and try to automatically feed the output of one into the input of another" I was wondering if you could provide me with an example or the tutorial that explains how it works. I thank you in advance for your help and support. Regards, Y From gordonp at ucalgary.ca Fri Feb 16 10:15:56 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 16 Feb 2007 08:15:56 -0700 Subject: [MOBY-dev] Regarding XML conversion In-Reply-To: <1ad0b71aacdf.1aacdf1ad0b7@usd.edu> References: <1ad0b71aacdf.1aacdf1ad0b7@usd.edu> Message-ID: <45D5CAAC.60609@ucalgary.ca> Hi Yogaraj, This is, unfortunately, a near-impossible task because although you can take data from one service and pass it to another, you have no idea whether the xsd:String output in the WSDL of one service is semantically the same as the xsd:String input to another service. Web services deal with syntax (structure) only, whereas you need semantic (meaning) compatibility for real interoperability. That's why MOBY has a central ontology, and we are calling them Semantic Web Services (though not really as the W3C uses the term). One approach is to retrofit services to a semantic standard such as MOBY. It's a LOT of work to even semi-automate this (I am doing this now). If you want to do this generically for any WSDL, the best I can suggest is to restrict yourself to some easily recognizable data formats that you can detect as data comes out of services, such as strings encoding URLs or e-mail addresses. That way you can seamlessly and fairly confidently make services that output and consume URLs compatible. Trying to make all services compatible, I believe, is a sisyphean task. Regards, Paul ** > Dear Mark, > I was reading your comment form > http://lists.open-bio.org/pipermail/moby-dev/2006-September/003798.html > > I was doing a similar projects like > "Take any two arbitrary Web Services out > there and try to automatically feed the output of one into the input of > another" > > > I was wondering if you could provide me with an example or the tutorial that explains how it works. > > I thank you in advance for your help and support. > Regards, > Y > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,45d4b7937098222965079! > > > > From ivanp at mmb.pcb.ub.es Tue Feb 20 18:08:09 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 21 Feb 2007 00:08:09 +0100 Subject: [MOBY-dev] non-English characters & windows & jMoby Message-ID: <45DB7F59.6060607@mmb.pcb.ub.es> Dear list, I've experienced a strange effect trying to compile jmoby with the build.bat and build-dev.bat scripts under Windows. I was using Eclipse as CVS client. Eclipse needs to create a project under the selected workspace to store the local version of the code. The default workspace is created in the user folder under "Documents & Settings". In my case, my username is Iv?n (and notice this accented non-English "?"). In short, the path becomes like this: C:\Documents and Settings\Iv?n\workspace\moby-live\Java Well, when I tried to compile it, I got this message: C:\Documents and Settings\Iv?n\workspace\moby-live\Java>build-dev.bat Buildfile: build.xml BUILD FAILED Error reading project file C:\Documents and Settings\Iv?n\workspace\moby-live\Java\build.xml: no protocol: xmls/libraries.xml As you can see the "?" becomes a "?"... This can be solved in two different ways: - the easy one: move the location of moby-live to another path without non-English characters - the tricky one (works but generates ugly warnings): modify the build.xml file by replacing all the occurrences of for in lines from 3 to 12 Regards, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From markw at illuminae.com Tue Feb 20 18:44:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 15:44:43 -0800 Subject: [MOBY-dev] gbrowse moby Asynchronous service support Message-ID: It should support Async now, but there aren't any async services registered in our moby central. If someone from INB has a minute, could they register an async service in our registry and try it? (it will have to be one that consumes a simple or else gbrowse wont find it anyway, since it only operates on simples) Thanks! M From markw at illuminae.com Tue Feb 20 18:44:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 15:44:43 -0800 Subject: [MOBY-dev] gbrowse moby Asynchronous service support Message-ID: It should support Async now, but there aren't any async services registered in our moby central. If someone from INB has a minute, could they register an async service in our registry and try it? (it will have to be one that consumes a simple or else gbrowse wont find it anyway, since it only operates on simples) Thanks! M From markw at illuminae.com Tue Feb 20 18:39:20 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 15:39:20 -0800 Subject: [MOBY-dev] non-English characters & windows & jMoby In-Reply-To: <45DB7F59.6060607@mmb.pcb.ub.es> References: <45DB7F59.6060607@mmb.pcb.ub.es> Message-ID: > This can be solved in two different ways: > - the easy one: move the location of moby-live to another path without > non-English characters > - the tricky one (works but generates ugly warnings): modify the > build.xml file by replacing all the occurrences of Or even easier - you could change your name ;-) ;-) (sorry, I'll shut up now - not very helpful!) M From ivanp at mmb.pcb.ub.es Tue Feb 20 19:02:46 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 21 Feb 2007 01:02:46 +0100 Subject: [MOBY-dev] non-English characters & windows & jMoby In-Reply-To: References: <45DB7F59.6060607@mmb.pcb.ub.es> Message-ID: <45DB8C26.1040905@mmb.pcb.ub.es> Not sure if my parents would be happy about that? :-P No problemo! ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Mark Wilkinson escribi?: >> This can be solved in two different ways: >> - the easy one: move the location of moby-live to another path without >> non-English characters >> - the tricky one (works but generates ugly warnings): modify the >> build.xml file by replacing all the occurrences of >> > > Or even easier - you could change your name > > ;-) ;-) > > (sorry, I'll shut up now - not very helpful!) > > M > > > > _______________________________________________ > 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 Tue Feb 20 21:40:52 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 18:40:52 -0800 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? Message-ID: Hi all, I'm curious as to whether anyone currently uses the OWL version of the Object ontology at http://biomoby.org/RESOUR CES/MOBY-S/Objects I have a much better version of the Objects ontology now, but it is structurally very different from that one. If anyone is actually USING that one for anything, then I'll deploy the new one at a different address, if not, then I'll over-write that one with the new one. Please let me know ASAP. Thanks! Mark From rroyo at lsi.upc.edu Wed Feb 21 00:48:58 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Wed, 21 Feb 2007 06:48:58 +0100 Subject: [MOBY-dev] gbrowse moby Asynchronous service support In-Reply-To: References: Message-ID: <45DBDD4A.8070309@lsi.upc.edu> Hello Mark, I just registered another 'moby-async' service: runNCBIBlastp (inb.bsc.es). When I try to execute it (with an AminoAcidSequence previously retrieved by getFeatureAASequence (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not recieving any requests on my side (I checked temporal directories and apache logs). By the way, we're going through some changes in our node. We're replacing the remote machine where most of our services were executed. So this service is not quite working. Instead of the blast report it should reply with: error 600, A generic error during internal processing (Basically, it tries to access the remote machine but since it is not accessible it returns this error; it takes about 5 minutes, so I use it to test asynchrony). And a minor thing: the 'Configure Parameters' button. I tried it with Firefox and IExplorer. The window is too small in both browsers and it is not resizable so it's hard to use it. That's probably because I have obsolete versions of these browsers though :-) Thanks! Romina Mark Wilkinson wrote: >It should support Async now, but there aren't any async services >registered in our moby central. > >If someone from INB has a minute, could they register an async service in >our registry and try it? (it will have to be one that consumes a simple >or else gbrowse wont find it anyway, since it only operates on simples) > >Thanks! > >M > > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev > > From rroyo at lsi.upc.edu Wed Feb 21 00:48:58 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Wed, 21 Feb 2007 06:48:58 +0100 Subject: [MOBY-dev] gbrowse moby Asynchronous service support In-Reply-To: References: Message-ID: <45DBDD4A.8070309@lsi.upc.edu> Hello Mark, I just registered another 'moby-async' service: runNCBIBlastp (inb.bsc.es). When I try to execute it (with an AminoAcidSequence previously retrieved by getFeatureAASequence (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not recieving any requests on my side (I checked temporal directories and apache logs). By the way, we're going through some changes in our node. We're replacing the remote machine where most of our services were executed. So this service is not quite working. Instead of the blast report it should reply with: error 600, A generic error during internal processing (Basically, it tries to access the remote machine but since it is not accessible it returns this error; it takes about 5 minutes, so I use it to test asynchrony). And a minor thing: the 'Configure Parameters' button. I tried it with Firefox and IExplorer. The window is too small in both browsers and it is not resizable so it's hard to use it. That's probably because I have obsolete versions of these browsers though :-) Thanks! Romina Mark Wilkinson wrote: >It should support Async now, but there aren't any async services >registered in our moby central. > >If someone from INB has a minute, could they register an async service in >our registry and try it? (it will have to be one that consumes a simple >or else gbrowse wont find it anyway, since it only operates on simples) > >Thanks! > >M > > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev > > From martin.senger at gmail.com Wed Feb 21 06:01:37 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Feb 2007 11:01:37 +0000 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: References: Message-ID: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Feb 21 06:01:37 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Feb 2007 11:01:37 +0000 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: References: Message-ID: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Wed Feb 21 09:17:56 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 21 Feb 2007 06:17:56 -0800 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> Message-ID: <001201c755c3$1648ec50$6600a8c0@notebook> Mark, I use them. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: Wednesday, February 21, 2007 3:02 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ 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 Feb 21 09:17:56 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 21 Feb 2007 06:17:56 -0800 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> Message-ID: <001201c755c3$1648ec50$6600a8c0@notebook> Mark, I use them. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: Wednesday, February 21, 2007 3:02 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Feb 21 09:56:46 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 21 Feb 2007 07:56:46 -0700 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <001201c755c3$1648ec50$6600a8c0@notebook> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> <001201c755c3$1648ec50$6600a8c0@notebook> Message-ID: <45DC5DAE.6020508@ucalgary.ca> Me too (via Eddie's org.biomoby.shared.extended.DataTypeParser) > Mark, > > I use them. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Wednesday, February 21, 2007 3:02 AM > To: Core developer announcements > Cc: mobydev > Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? > > I'm curious as to whether anyone currently uses the OWL version of the > >> Object ontology at >> >> http://biomoby.org/RESOUR CES/MOBY-S/Objects >> > > > I do not know if anybody is using it - but the part of the BioMoby API is to > get these URLs and call them. Definitely jMoby has these methods. If you > intent to change the URL, make please sure that also the Central returns > the new URLs in those methods. > > Thanks, > Martin > > From gordonp at ucalgary.ca Wed Feb 21 09:56:46 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 21 Feb 2007 07:56:46 -0700 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <001201c755c3$1648ec50$6600a8c0@notebook> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> <001201c755c3$1648ec50$6600a8c0@notebook> Message-ID: <45DC5DAE.6020508@ucalgary.ca> Me too (via Eddie's org.biomoby.shared.extended.DataTypeParser) > Mark, > > I use them. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Wednesday, February 21, 2007 3:02 AM > To: Core developer announcements > Cc: mobydev > Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? > > I'm curious as to whether anyone currently uses the OWL version of the > >> Object ontology at >> >> http://biomoby.org/RESOUR CES/MOBY-S/Objects >> > > > I do not know if anybody is using it - but the part of the BioMoby API is to > get these URLs and call them. Definitely jMoby has these methods. If you > intent to change the URL, make please sure that also the Central returns > the new URLs in those methods. > > Thanks, > Martin > > From markw at illuminae.com Wed Feb 21 10:29:41 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 21 Feb 2007 07:29:41 -0800 Subject: [MOBY-dev] gbrowse moby Asynchronous service support In-Reply-To: <45DBDD4A.8070309@lsi.upc.edu> References: <45DBDD4A.8070309@lsi.upc.edu> Message-ID: Thanks Romina. As soon as I get to work today I'll fix the problem - it should only take a half hour or so. v.v. the configure windows - I'll leave that to Eddie :-) M On Tue, 20 Feb 2007 21:48:58 -0800, Romina Royo wrote: > Hello Mark, > > I just registered another 'moby-async' service: runNCBIBlastp > (inb.bsc.es). > > When I try to execute it (with an AminoAcidSequence previously retrieved > by getFeatureAASequence > (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not > recieving any requests on my side (I checked > temporal directories and apache logs). From markw at illuminae.com Wed Feb 21 16:24:34 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 21 Feb 2007 13:24:34 -0800 Subject: [MOBY-dev] Welcome Wendy Alexander Message-ID: <1172093074.16907.8.camel@bioinfo.icapture.ubc.ca> Hi Mobyers! We've finally hired another pair of hands here in Vancouver. Wendy Alexander is starting with us this week as our second BioMoby core developer, to work side by side with Eddie. I've worked with Wendy for the past two years doing primarily database development activities, so we know each other well and I know she's a solid Java coder. She's new to Moby, so it will take a few weeks for her to get caught up on all the libraries, but she'll figure it all out soon enough. Anyway, this means that we can finally spend more time at this end getting various TODO's done! YAY! Best wishes all, Mark From markw at illuminae.com Wed Feb 21 16:25:29 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 21 Feb 2007 13:25:29 -0800 Subject: [MOBY-dev] [moby] Re: gbrowse moby Asynchronous service support In-Reply-To: <45DBDD4A.8070309@lsi.upc.edu> References: <45DBDD4A.8070309@lsi.upc.edu> Message-ID: <1172093129.16907.10.camel@bioinfo.icapture.ubc.ca> Would you believe that I simply forgot to "use" the MOBY::Async::Service module :-) It works now. M On Wed, 2007-02-21 at 06:48 +0100, Romina Royo wrote: > Hello Mark, > > I just registered another 'moby-async' service: runNCBIBlastp (inb.bsc.es). > > When I try to execute it (with an AminoAcidSequence previously retrieved > by getFeatureAASequence > (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not > recieving any requests on my side (I checked > temporal directories and apache logs). From edward.kawas at gmail.com Thu Feb 22 10:41:03 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Feb 2007 07:41:03 -0800 Subject: [MOBY-dev] async services Message-ID: <003c01c75697$dd4b2b90$6600a8c0@notebook> Hi, I wanted to verify something. If a synchronous client calls an async service, the async service is meant to act in synchronous mode, right? Of the handful of services that I have seen that are asynchronous, I don't believe that is the case. I believe that I have seen them return a message that contained a job id, and not the 'normal' moby message. This question is aimed mainly at the good folks at the inb, as I believe they are the only ones to have implemented any real asynchronous services. Thanks, Eddie ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From rroyo at lsi.upc.edu Thu Feb 22 11:14:33 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Thu, 22 Feb 2007 17:14:33 +0100 Subject: [MOBY-dev] async services In-Reply-To: <003c01c75697$dd4b2b90$6600a8c0@notebook> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> Message-ID: <45DDC169.20004@lsi.upc.edu> Hello! This is how I understood that async services should work (and how I'm implementing them so far). Please anyone correct me if I'm doing it wrong! For example: The service runClustalwFast (authURI inb.bsc.es) is an asynchronous service. It can be executed in a synchronous mode (like all sync services): my $Service = MOBY::Client::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); and this would return the normal moby message. Or it can be called in an asynchronous mode: my $Service = MOBY::Async::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); which would _submit, _poll and finally return the results. Is this the behauviour everyone is expecting? Thanks! Romina Edward Kawas wrote: > Hi, > > > > I wanted to verify something. If a synchronous client calls an async > service, the async service is meant to act in synchronous mode, right? Of > the handful of services that I have seen that are asynchronous, I don't > believe that is the case. I believe that I have seen them return a message > that contained a job id, and not the 'normal' moby message. > > > > This question is aimed mainly at the good folks at the inb, as I believe > they are the only ones to have implemented any real asynchronous services. > > > > Thanks, > > > > Eddie > > > > ***CONFIDENTIALITY NOTICE*** > > This electronic message is intended only for the use of the addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by unauthorized > individuals is strictly prohibited. If you have received this communication > in error, please notify the sender immediately by reply e-mail and delete > the original and all copies from your system. > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From edward.kawas at gmail.com Thu Feb 22 11:17:37 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Feb 2007 08:17:37 -0800 Subject: [MOBY-dev] async services In-Reply-To: <45DDC169.20004@lsi.upc.edu> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> <45DDC169.20004@lsi.upc.edu> Message-ID: <004701c7569c$f8e395e0$6600a8c0@notebook> Hi Romina, So you are describing what I actually thought is supposed to happen. I am just slightly confused, because while we were debugging some of the wsdl issues, I remember that one of the async services when called in sync mode returned a job id. Maybe that was just a one time thing ... Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Thursday, February 22, 2007 8:15 AM To: Core developer announcements Subject: Re: [MOBY-dev] async services Hello! This is how I understood that async services should work (and how I'm implementing them so far). Please anyone correct me if I'm doing it wrong! For example: The service runClustalwFast (authURI inb.bsc.es) is an asynchronous service. It can be executed in a synchronous mode (like all sync services): my $Service = MOBY::Client::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); and this would return the normal moby message. Or it can be called in an asynchronous mode: my $Service = MOBY::Async::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); which would _submit, _poll and finally return the results. Is this the behauviour everyone is expecting? Thanks! Romina Edward Kawas wrote: > Hi, > > > > I wanted to verify something. If a synchronous client calls an async > service, the async service is meant to act in synchronous mode, right? Of > the handful of services that I have seen that are asynchronous, I don't > believe that is the case. I believe that I have seen them return a message > that contained a job id, and not the 'normal' moby message. > > > > This question is aimed mainly at the good folks at the inb, as I believe > they are the only ones to have implemented any real asynchronous services. > > > > Thanks, > > > > Eddie > > > > ***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 markw at illuminae.com Thu Feb 22 11:30:20 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 22 Feb 2007 08:30:20 -0800 Subject: [MOBY-dev] MOBY::Async::Service in Java? Message-ID: Hi INB'ers, Is there an equivalent to the MOBY::Async::Service module in Java? M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From ivanp at mmb.pcb.ub.es Thu Feb 22 11:43:21 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Thu, 22 Feb 2007 17:43:21 +0100 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: References: Message-ID: <45DDC829.7080804@mmb.pcb.ub.es> Hi Mark, I'm afraid not; as long as I know, myself and another lab-mate are the only ones producing Java services at INB and we've not developed any prototype for async services. Sorry, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Mark Wilkinson escribi?: > Hi INB'ers, > > Is there an equivalent to the MOBY::Async::Service module in Java? > > M > > From markw at illuminae.com Thu Feb 22 11:47:30 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 22 Feb 2007 08:47:30 -0800 Subject: [MOBY-dev] [moby] Re: MOBY::Async::Service in Java? In-Reply-To: <45DDC829.7080804@mmb.pcb.ub.es> References: <45DDC829.7080804@mmb.pcb.ub.es> Message-ID: <1172162850.20528.16.camel@bioinfo.icapture.ubc.ca> Perl wins again! ;-) ;-) Okay... Eddie and I will look into whether or not there is WSRF support in Java, and if there is, then we should probably create these modules soon, since it will be important to support Async in e.g. Taverna. Mark On Thu, 2007-02-22 at 17:43 +0100, Iv?n P?rraga Garc?a wrote: > Hi Mark, > > I'm afraid not; as long as I know, myself and another lab-mate are the > only ones producing Java services at INB and we've not developed any > prototype for async services. > > Sorry, > > ------------------------------------------------ > Iv?n P?rraga Garc?a > Computer Scientist > Molecular Modelling & Bioinformatics Unit > INB - Instituto Nacional de Bioinform?tica > Josep Samitier 1-5 > 08028 Barcelona > Spain > tel.: +34 93 403 71 55 > fax.: +34 93 403 71 57 > e-mail: ivanp at mmb.pcb.ub.es > group page: http://mmb.pcb.ub.es > pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc > ------------------------------------------------ > > > > Mark Wilkinson escribi?: > > Hi INB'ers, > > > > Is there an equivalent to the MOBY::Async::Service module in Java? > > > > M > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From johan at ac.uma.es Thu Feb 22 11:44:27 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Thu, 22 Feb 2007 17:44:27 +0100 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: References: Message-ID: <45DDC86B.60309@ac.uma.es> This is most likely being implemented as part of JMoby? Martin Senger could probably answer your question better. As far as I know INB does not have a server-side library for developing services in Java. We do have an async client-side library written in C++ (done as part of the scheduler/worker of MOWserv). More details when we finish the documentation... :-) Kind regards, Johan Mark Wilkinson wrote: > Hi INB'ers, > > Is there an equivalent to the MOBY::Async::Service module in Java? > > M > > -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 From johan at ac.uma.es Thu Feb 22 11:52:52 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Thu, 22 Feb 2007 17:52:52 +0100 Subject: [MOBY-dev] async services In-Reply-To: <004701c7569c$f8e395e0$6600a8c0@notebook> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> <45DDC169.20004@lsi.upc.edu> <004701c7569c$f8e395e0$6600a8c0@notebook> Message-ID: <45DDCA64.5080307@ac.uma.es> I think Romina is describing it correctly. Maybe the problem you experienced was a temporary bug in the async server-side library of Perl? Kind regards, Johan Edward Kawas wrote: > Hi Romina, > > So you are describing what I actually thought is supposed to happen. I am > just slightly confused, because while we were debugging some of the wsdl > issues, I remember that one of the async services when called in sync mode > returned a job id. > > Maybe that was just a one time thing ... > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo > Sent: Thursday, February 22, 2007 8:15 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] async services > > Hello! > > This is how I understood that async services should work (and how I'm > implementing them so far). > Please anyone correct me if I'm doing it wrong! > > For example: > > The service runClustalwFast (authURI inb.bsc.es) is an asynchronous > service. > > It can be executed in a synchronous mode (like all sync services): > > my $Service = MOBY::Client::Service->new(service => $WSDL); > my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] > ]]); > > and this would return the normal moby message. > > Or it can be called in an asynchronous mode: > > my $Service = MOBY::Async::Service->new(service => $WSDL); > my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] > ]]); > > which would _submit, _poll and finally return the results. > > Is this the behauviour everyone is expecting? > > Thanks! > Romina > > Edward Kawas wrote: > >> Hi, >> >> >> >> I wanted to verify something. If a synchronous client calls an async >> service, the async service is meant to act in synchronous mode, right? Of >> the handful of services that I have seen that are asynchronous, I don't >> believe that is the case. I believe that I have seen them return a message >> that contained a job id, and not the 'normal' moby message. >> >> >> >> This question is aimed mainly at the good folks at the inb, as I believe >> they are the only ones to have implemented any real asynchronous services. >> >> >> >> Thanks, >> >> >> >> Eddie >> >> >> >> ***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 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 From johan at ac.uma.es Thu Feb 22 12:01:25 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Thu, 22 Feb 2007 18:01:25 +0100 Subject: [MOBY-dev] [moby] Re: MOBY::Async::Service in Java? In-Reply-To: <1172162850.20528.16.camel@bioinfo.icapture.ubc.ca> References: <45DDC829.7080804@mmb.pcb.ub.es> <1172162850.20528.16.camel@bioinfo.icapture.ubc.ca> Message-ID: <45DDCC65.9050504@ac.uma.es> Yes, there is at least this library from Apache: http://ws.apache.org/wsrf/ Kind regards, Johan Mark Wilkinson wrote: > Perl wins again! ;-) ;-) > > Okay... Eddie and I will look into whether or not there is WSRF support > in Java, and if there is, then we should probably create these modules > soon, since it will be important to support Async in e.g. Taverna. > > Mark > > > > On Thu, 2007-02-22 at 17:43 +0100, Iv?n P?rraga Garc?a wrote: > >> Hi Mark, >> >> I'm afraid not; as long as I know, myself and another lab-mate are the >> only ones producing Java services at INB and we've not developed any >> prototype for async services. >> >> Sorry, >> >> ------------------------------------------------ >> Iv?n P?rraga Garc?a >> Computer Scientist >> Molecular Modelling & Bioinformatics Unit >> INB - Instituto Nacional de Bioinform?tica >> Josep Samitier 1-5 >> 08028 Barcelona >> Spain >> tel.: +34 93 403 71 55 >> fax.: +34 93 403 71 57 >> e-mail: ivanp at mmb.pcb.ub.es >> group page: http://mmb.pcb.ub.es >> pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc >> ------------------------------------------------ >> >> >> >> Mark Wilkinson escribi?: >> >>> Hi INB'ers, >>> >>> Is there an equivalent to the MOBY::Async::Service module in Java? >>> >>> M >>> >>> >>> >> _______________________________________________ >> 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 > > -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 From enrique.deandres at pcm.uam.es Thu Feb 22 13:31:58 2007 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 22 Feb 2007 19:31:58 +0100 Subject: [MOBY-dev] async services In-Reply-To: <45DDCA64.5080307@ac.uma.es> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> <45DDC169.20004@lsi.up c.edu><004701c7569c$f8e395e0$6600a8c0@notebook> <45DDCA64.5080307@ac.uma.es> Message-ID: <45DDE19E.6030509@pcm.uam.es> Hi, As Romina says, it is the behavior from the client side. >From the server side, it is required to have: - one method called service which answers the synchronous invocations with typical moby messages. From the perldoc MOBY::Async: sub sayHello { my $self = shift @_; # Here you can choose between sync or error return $self->sync($sayHello, 180, @_); # tries to execute #return $self->error(@_); # returns directly an exception } - one method called service_submit which answers the request (submission) of asynchrnous invocations with the job identifier. sub sayHello_submit { my $self = shift @_; return $self->async($sayHello, @_); } Note that here we use $self->async and in the previous $self->sync (or $self->error)... if not, it could be possible that sayHello return an ID. I have been checking the code and I don't see anything wrong, then I don't think it is a bug.... but could you send me more details? Which is that service which has that behavior. I hope it helps. Regards, Enrique. Johan Karlsson wrote: > I think Romina is describing it correctly. Maybe the problem you > experienced was a temporary bug in the async server-side library of Perl? > > Kind regards, > Johan > > Edward Kawas wrote: >> Hi Romina, >> >> So you are describing what I actually thought is supposed to happen. I am >> just slightly confused, because while we were debugging some of the wsdl >> issues, I remember that one of the async services when called in sync mode >> returned a job id. >> >> Maybe that was just a one time thing ... >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo >> Sent: Thursday, February 22, 2007 8:15 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] async services >> >> Hello! >> >> This is how I understood that async services should work (and how I'm >> implementing them so far). >> Please anyone correct me if I'm doing it wrong! >> >> For example: >> >> The service runClustalwFast (authURI inb.bsc.es) is an asynchronous >> service. >> >> It can be executed in a synchronous mode (like all sync services): >> >> my $Service = MOBY::Client::Service->new(service => $WSDL); >> my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] >> ]]); >> >> and this would return the normal moby message. >> >> Or it can be called in an asynchronous mode: >> >> my $Service = MOBY::Async::Service->new(service => $WSDL); >> my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] >> ]]); >> >> which would _submit, _poll and finally return the results. >> >> Is this the behauviour everyone is expecting? >> >> Thanks! >> Romina >> >> Edward Kawas wrote: >> >>> Hi, >>> >>> >>> >>> I wanted to verify something. If a synchronous client calls an async >>> service, the async service is meant to act in synchronous mode, right? Of >>> the handful of services that I have seen that are asynchronous, I don't >>> believe that is the case. I believe that I have seen them return a message >>> that contained a job id, and not the 'normal' moby message. >>> >>> >>> >>> This question is aimed mainly at the good folks at the inb, as I believe >>> they are the only ones to have implemented any real asynchronous services. >>> >>> >>> >>> Thanks, >>> >>> >>> >>> Eddie >>> >>> >>> >>> ***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 >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > -- Enrique de Andres Saiz Unidad de Bioinform?tica (INB GNHC-1) Parque Cientifico de Madrid Ctra. de Colmenar, Km. 15. Campus UAM, Cantoblanco - Pabellon C 28049 Madrid Tel. (+34) 91 497 3448 Fax. (+34) 91 497 3471 http://www.fpcm.es http://www.inab.org From Yogaraj.Khanal at usd.edu Thu Feb 22 17:25:02 2007 From: Yogaraj.Khanal at usd.edu (Yogaraj.Khanal at usd.edu) Date: Thu, 22 Feb 2007 16:25:02 -0600 Subject: [MOBY-dev] Regarding XML Message-ID: <256d5e2509b0.2509b0256d5e@usd.edu> Hi Everyone, I was trying to run the workflow through this URL http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/workflows.html but I am getting this message This XML file does not appear to have any style information associated with it. The document tree is shown below. Can anyone guide me how do I see the workflow as in Taverna or the any tutorail that guides me to build one from the code listed in the above URL. Regards, Raj From edward.kawas at gmail.com Thu Feb 22 17:27:22 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Feb 2007 14:27:22 -0800 Subject: [MOBY-dev] Regarding XML In-Reply-To: <256d5e2509b0.2509b0256d5e@usd.edu> References: <256d5e2509b0.2509b0256d5e@usd.edu> Message-ID: <008801c756d0$a01893a0$6600a8c0@notebook> Hi, You will have to either: 1. save the workflow and load it locally, or 2. copy the workflow location (the link) and load the workflow into taverna 'from URL'. Hope that helps, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Yogaraj.Khanal at usd.edu Sent: Thursday, February 22, 2007 2:25 PM To: Core developer announcements Subject: [MOBY-dev] Regarding XML Hi Everyone, I was trying to run the workflow through this URL http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/wo rkflows.html but I am getting this message This XML file does not appear to have any style information associated with it. The document tree is shown below. Can anyone guide me how do I see the workflow as in Taverna or the any tutorail that guides me to build one from the code listed in the above URL. Regards, Raj _______________________________________________ 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 Feb 3 18:36:44 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 03 Feb 2007 10:36:44 -0800 Subject: [MOBY-dev] The "erroneous" RDF agent report that many of you received Message-ID: Hi all, Apologies for the erroneous RDF agent report that many of you will have received overnight. Something happened yesterday that we cannot yet explain, but it resulted in many of the Namespaces being modified in the database and appended with a "_" character. According to the API this should be impossible for namespaces that are in use, but somehow it happened anyway. The test suite has a case for this, and it seems to pass the test, so I don't know how it happened....?? I've looked at the access logs to MOBY Central and can't see anything obvious there either. Anyway, it's a mystery for the moment. The same thing happened about a year ago, and we weren't able to determine it's cause then either... it seems to be a recurring, but rare problem. The affected namespaces are listed below. Anyone with a service that uses any of these namespaces will have received an RDF Agent report of failed lookup. PLEASE IGNORE THIS REPORT - you do not have to do anything. I have solved the problem at the SQL level. If the list below looks familiar to any of you, please let me know as I would like to track-down the source of this problem. Thanks! Mark CGEN BRENDA ChEBI CL EchoBASE EcoCyc ECOGENE FB INTERPRO IPI MaizeGDB MetaCyc PANTHER PIR PINC SMART Swiss-Prot TreEMBL Reactome REBASE FLYBASE EMBL PMID From markw at illuminae.com Tue Feb 6 04:02:03 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 05 Feb 2007 20:02:03 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Message-ID: Hi all, First off, apologies to anyone who was trying to get through to MOBY Central this afternoon - Eddie and I were making the changes necessary to get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on the test server didn't work on the real MOBY Central... so it took a couple of hours of troubleshooting before we had it back up again. The good news is that it seems to work correctly with both Perl and Java clients. What we don't know is if it is backwards compatible with earlier versions of the MOBY::Client::* libraries, in particular, MOBY::Client::Service. I *think* it is, but we didn't have the opportunity to test it. In any case, the API did not change, so if you just cvs update your client libraries everything should come back to life if it isn't working. Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves subtly differently than the old one in several ways that we were not expecting. Thankfully, Pieter and Eddie had done most of the trouble-shoting already, but it still threw us for a loop in some places with incompatible SOAP version errors and a new auto-encoding of strings by SOAP::Lite that we used to do in-code by ourselves (resulting in double-coded messages). Anyway, it's done now. Please scream loudly if it doesn't work for you!! I have backups of everything so if necessary we can roll-back quickly. All of this was done primarily to get us to be compatible with the new Asynchronous services API that use the Manchester WSRF::Lite modules which depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the code to see if it works for them v.v. Async services? The database can now hold Category=moby-async (which reminds me, I need to update the database templates in the CVS...), and Eddie assures me that the code will now provide correct WSDL for an Asych interface. The myGrid folks have added moby-async as a valid service category into their ontology as well, so in principle... it should all work... (touch wood!) ********************* IMPORTANTLY this means that the new MOBY Central code will likely NOT work on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are running your own registry... ********************* Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to make the changes to gbrowse_moby such that it can also invoke asynchronous services. I think the Async modules also need to be added to the MANIFEST before they are installed by default, so I'll try to remember to do that as well. Otherwise there were just some small changes to the test suite to better clean-up the registry if something goes wrong during testing, and I cleaned-up the test database so that it also doesn't cause the test suite to fail. I will restart the test registry using the new codebase first thing in the morning so that the two are identical. We still haven't figured out why those namespace changes happened a couple of days ago. It coincided with the Gene Ontology curators making some additions to the Namespace list, so I suspect that there is a bug in the interface I have given to them (which talks directly to the database without using the MOBY API), but exactly WHY this happened is still a mystery. I've alerted Midori to the problem and she's going to hold-off on making any more changes until we can figure out what is going wrong. That's all the news from MOBY Central! Let us know ASAP if you notice anything wrong. It's been a rough ride today... Mark From markw at illuminae.com Tue Feb 6 04:04:06 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 05 Feb 2007 20:04:06 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: References: Message-ID: ALSO NOTE! The MOBY Central daemon code has changed in two lines - see moby-live/Perl/scripts/MOBY-Central.pl for the new code. M On Mon, 05 Feb 2007 20:02:03 -0800, Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary > to get it ready for SOAP::Lite 0.69 and the changes that worked > perfectly on the test server didn't work on the real MOBY Central... so > it took a couple of hours of troubleshooting before we had it back up > again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with > earlier versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to > life if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite > behaves subtly differently than the old one in several ways that we were > not expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for > you!! I have backups of everything so if necessary we can roll-back > quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules > which depend on SOAP::Lite 0.69. Can I ask the good folks at INB to > test the code to see if it works for them v.v. Async services? The > database can now hold Category=moby-async (which reminds me, I need to > update the database templates in the CVS...), and Eddie assures me that > the code will now provide correct WSDL for an Asych interface. The > myGrid folks have added moby-async as a valid service category into > their ontology as well, so in principle... it should all work... (touch > wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT > work on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if > you are running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try > to make the changes to gbrowse_moby such that it can also invoke > asynchronous services. I think the Async modules also need to be added > to the MANIFEST before they are installed by default, so I'll try to > remember to do that as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test > suite to fail. I will restart the test registry using the new codebase > first thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a > couple of days ago. It coincided with the Gene Ontology curators making > some additions to the Namespace list, so I suspect that there is a bug > in the interface I have given to them (which talks directly to the > database without using the MOBY API), but exactly WHY this happened is > still a mystery. I've alerted Midori to the problem and she's going to > hold-off on making any more changes until we can figure out what is > going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From rroyo at lsi.upc.edu Tue Feb 6 14:25:15 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 15:25:15 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: References: Message-ID: <45C88FCB.2030704@lsi.upc.edu> Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From rroyo at lsi.upc.edu Tue Feb 6 14:25:15 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 15:25:15 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: References: Message-ID: <45C88FCB.2030704@lsi.upc.edu> Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > 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 Tue Feb 6 15:13:15 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 07:13:15 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <005901c74a01$54aa2d10$6900a8c0@notebook> Hi Romina, Do you think that you could send me your code? I am having problems replicating the errors that you got (which were the ones we 'fixed' yesterday!). Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 6:25 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatch Wrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > 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 Tue Feb 6 15:13:15 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 07:13:15 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <005901c74a01$54aa2d10$6900a8c0@notebook> Hi Romina, Do you think that you could send me your code? I am having problems replicating the errors that you got (which were the ones we 'fixed' yesterday!). Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 6:25 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatch Wrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Feb 6 15:03:31 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 6 Feb 2007 15:03:31 +0000 GMT Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> Hmmmm... Well that's a bit of a disaster! Could you check what happens when you call one of my services (eg MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to each other properly (which would be a nightmare, but given our experiences yesterday, not surprising!) M -- Mark Wilkinson ...on the road! -----Original Message----- From: Romina Royo Date: Tue, 06 Feb 2007 15:25:15 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Feb 6 15:03:31 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 6 Feb 2007 15:03:31 +0000 GMT Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C88FCB.2030704@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> Message-ID: <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> Hmmmm... Well that's a bit of a disaster! Could you check what happens when you call one of my services (eg MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to each other properly (which would be a nightmare, but given our experiences yesterday, not surprising!) M -- Mark Wilkinson ...on the road! -----Original Message----- From: Romina Royo Date: Tue, 06 Feb 2007 15:25:15 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts Hello, I updated the moby-live/Perl libraries from cvs and I installed SOAP::Lite 0.69. Here are some of the results I got: - When executing a synchronous Perl service (function execute in Client/Service.pm) I got this error: SOAP-ENV:VersionMismatchWrong SOAP version specified. Supported versions: 1.1 (http://schemas.xmlsoap.org/soap/envelope/) 1.2 (http://www.w3.org/2001/06/soap-envelope) mm.. I guess it is OK because the service provider might be using some other SOAP version? - When doing the same test on one of our services (SOAP::Lite 0.69 installed on the service side). I got this error: soap:ClientApplication failed during request deserialization: xml declaration not at start of external entity at line 1, column 941, byte 941 at /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm line 187 - When executing a Java service: soapenv:Client org.jboss.axis.AxisFault: Version Mismatch and again, it might be ok? - When trying to retrieve the wsdl of a 'moby-async' service (function retrieveService) I got this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 371. ERROR ERROR ERROR The function retrieveService does work when the service is not 'moby-async' though. - When executing an asynchronous service (function Async/Service/execute) everything seems ok. Has anyone had similar problems? Any ideas? Thank you! Romina Mark Wilkinson wrote: > Hi all, > > First off, apologies to anyone who was trying to get through to MOBY > Central this afternoon - Eddie and I were making the changes necessary to > get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on > the test server didn't work on the real MOBY Central... so it took a > couple of hours of troubleshooting before we had it back up again. > > The good news is that it seems to work correctly with both Perl and Java > clients. What we don't know is if it is backwards compatible with earlier > versions of the MOBY::Client::* libraries, in particular, > MOBY::Client::Service. I *think* it is, but we didn't have the > opportunity to test it. In any case, the API did not change, so if you > just cvs update your client libraries everything should come back to life > if it isn't working. > > Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves > subtly differently than the old one in several ways that we were not > expecting. Thankfully, Pieter and Eddie had done most of the > trouble-shoting already, but it still threw us for a loop in some places > with incompatible SOAP version errors and a new auto-encoding of strings > by SOAP::Lite that we used to do in-code by ourselves (resulting in > double-coded messages). > > Anyway, it's done now. Please scream loudly if it doesn't work for you!! > I have backups of everything so if necessary we can roll-back quickly. > > All of this was done primarily to get us to be compatible with the new > Asynchronous services API that use the Manchester WSRF::Lite modules which > depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the > code to see if it works for them v.v. Async services? The database can > now hold Category=moby-async (which reminds me, I need to update the > database templates in the CVS...), and Eddie assures me that the code will > now provide correct WSDL for an Asych interface. The myGrid folks have > added moby-async as a valid service category into their ontology as well, > so in principle... it should all work... (touch wood!) > > ********************* > IMPORTANTLY this means that the new MOBY Central code will likely NOT work > on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are > running your own registry... > ********************* > > Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to > make the changes to gbrowse_moby such that it can also invoke asynchronous > services. I think the Async modules also need to be added to the MANIFEST > before they are installed by default, so I'll try to remember to do that > as well. > > Otherwise there were just some small changes to the test suite to better > clean-up the registry if something goes wrong during testing, and I > cleaned-up the test database so that it also doesn't cause the test suite > to fail. I will restart the test registry using the new codebase first > thing in the morning so that the two are identical. > > We still haven't figured out why those namespace changes happened a couple > of days ago. It coincided with the Gene Ontology curators making some > additions to the Namespace list, so I suspect that there is a bug in the > interface I have given to them (which talks directly to the database > without using the MOBY API), but exactly WHY this happened is still a > mystery. I've alerted Midori to the problem and she's going to hold-off > on making any more changes until we can figure out what is going wrong. > > That's all the news from MOBY Central! > > Let us know ASAP if you notice anything wrong. It's been a rough ride > today... > > Mark > > > > _______________________________________________ > 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 rroyo at lsi.upc.edu Tue Feb 6 15:38:59 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 16:38:59 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> Message-ID: <45C8A113.40803@lsi.upc.edu> Hello again, Mark, I just called your service and it did work. Eddy, if those are some of the errors you fixed yesterday I might be doing something wrong. Let me re-check everything and if the errors are still there I'll send you more details about the code I'm using. Thank you very much! Romina mark wilkinson wrote: > Hmmmm... Well that's a bit of a disaster! > > Could you check what happens when you call one of my services (eg MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to each other properly (which would be a nightmare, but given our experiences yesterday, not surprising!) > > M > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 15:25:15 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for > registry hosts > > Hello, > > I updated the moby-live/Perl libraries from cvs and I installed > SOAP::Lite 0.69. > > Here are some of the results I got: > > - When executing a synchronous Perl service (function execute in > Client/Service.pm) I got this error: > > SOAP-ENV:VersionMismatchWrong > SOAP version specified. Supported versions: > 1.1 (http://schemas.xmlsoap.org/soap/envelope/) > 1.2 (http://www.w3.org/2001/06/soap-envelope) > > > mm.. I guess it is OK because the service provider might be using some > other SOAP version? > > - When doing the same test on one of our services (SOAP::Lite 0.69 > installed on the service side). I got this error: > > soap:ClientApplication > failed during request deserialization: > xml declaration not at start of external entity at line 1, column 941, > byte 941 at > /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm > line 187 > > > - When executing a Java service: > > soapenv:Client > org.jboss.axis.AxisFault: Version Mismatch > > > > and again, it might be ok? > > - When trying to retrieve the wsdl of a 'moby-async' service (function > retrieveService) I got this error: > > Connection to MOBY Central at > 'http://mobycentral.icapture.ubc.ca/MOBY/Central' > died because: > Can't use string (" > /usr/lib/perl5 > /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. > > ERROR ERROR ERROR > > The function retrieveService does work when the service is not > 'moby-async' though. > > - When executing an asynchronous service (function > Async/Service/execute) everything seems ok. > > Has anyone had similar problems? Any ideas? > > Thank you! > Romina > > Mark Wilkinson wrote: > >> Hi all, >> >> First off, apologies to anyone who was trying to get through to MOBY >> Central this afternoon - Eddie and I were making the changes necessary to >> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly on >> the test server didn't work on the real MOBY Central... so it took a >> couple of hours of troubleshooting before we had it back up again. >> >> The good news is that it seems to work correctly with both Perl and Java >> clients. What we don't know is if it is backwards compatible with earlier >> versions of the MOBY::Client::* libraries, in particular, >> MOBY::Client::Service. I *think* it is, but we didn't have the >> opportunity to test it. In any case, the API did not change, so if you >> just cvs update your client libraries everything should come back to life >> if it isn't working. >> >> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite behaves >> subtly differently than the old one in several ways that we were not >> expecting. Thankfully, Pieter and Eddie had done most of the >> trouble-shoting already, but it still threw us for a loop in some places >> with incompatible SOAP version errors and a new auto-encoding of strings >> by SOAP::Lite that we used to do in-code by ourselves (resulting in >> double-coded messages). >> >> Anyway, it's done now. Please scream loudly if it doesn't work for you!! >> I have backups of everything so if necessary we can roll-back quickly. >> >> All of this was done primarily to get us to be compatible with the new >> Asynchronous services API that use the Manchester WSRF::Lite modules which >> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >> code to see if it works for them v.v. Async services? The database can >> now hold Category=moby-async (which reminds me, I need to update the >> database templates in the CVS...), and Eddie assures me that the code will >> now provide correct WSDL for an Asych interface. The myGrid folks have >> added moby-async as a valid service category into their ontology as well, >> so in principle... it should all work... (touch wood!) >> >> ********************* >> IMPORTANTLY this means that the new MOBY Central code will likely NOT work >> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you are >> running your own registry... >> ********************* >> >> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try to >> make the changes to gbrowse_moby such that it can also invoke asynchronous >> services. I think the Async modules also need to be added to the MANIFEST >> before they are installed by default, so I'll try to remember to do that >> as well. >> >> Otherwise there were just some small changes to the test suite to better >> clean-up the registry if something goes wrong during testing, and I >> cleaned-up the test database so that it also doesn't cause the test suite >> to fail. I will restart the test registry using the new codebase first >> thing in the morning so that the two are identical. >> >> We still haven't figured out why those namespace changes happened a couple >> of days ago. It coincided with the Gene Ontology curators making some >> additions to the Namespace list, so I suspect that there is a bug in the >> interface I have given to them (which talks directly to the database >> without using the MOBY API), but exactly WHY this happened is still a >> mystery. I've alerted Midori to the problem and she's going to hold-off >> on making any more changes until we can figure out what is going wrong. >> >> That's all the news from MOBY Central! >> >> Let us know ASAP if you notice anything wrong. It's been a rough ride >> today... >> >> Mark >> >> >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 Tue Feb 6 15:48:40 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Feb 2007 07:48:40 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C8A113.40803@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: Hi Romina, I can confirm that calling services running S::L 0.69 from a client running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I have not yet successfully tested is calling a service from a .69 client to an earlier version on the server-side. The way to do that would be to use gbrowse_moby on the mobycentral machine, but I don't know what versions of Perl anyone else is running so I can't reliably do that experiment... can anyone try one of their Perl services from gbrowse-moby on a server with perl 0.60 or less? MOBY Central itself seems fine... and Java invocations of services seem fine also (largely because the Java libraries don't use the WSDL from MOBY Central to create their connections... there may be a lesson in there somewhere! Ugh... WSDL!!) M On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > Hello again, > > Mark, I just called your service and it did work. > > Eddy, if those are some of the errors you fixed yesterday I might be > doing something wrong. Let me re-check everything and if the errors are > still there I'll send you more details about the code I'm using. > > Thank you very much! > Romina > > > > mark wilkinson wrote: >> Hmmmm... Well that's a bit of a disaster! >> >> Could you check what happens when you call one of my services (eg >> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >> each other properly (which would be a nightmare, but given our >> experiences yesterday, not surprising!) >> >> M >> >> >> -- >> Mark Wilkinson >> ...on the road! >> >> >> -----Original Message----- >> From: Romina Royo >> Date: Tue, 06 Feb 2007 15:25:15 >> To:Core developer announcements >> Cc:mobydev >> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >> registry hosts >> >> Hello, >> >> I updated the moby-live/Perl libraries from cvs and I installed >> SOAP::Lite 0.69. >> >> Here are some of the results I got: >> >> - When executing a synchronous Perl service (function execute in >> Client/Service.pm) I got this error: >> >> SOAP-ENV:VersionMismatchWrong >> SOAP version specified. Supported versions: >> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >> 1.2 (http://www.w3.org/2001/06/soap-envelope) >> >> >> mm.. I guess it is OK because the service provider might be using some >> other SOAP version? >> >> - When doing the same test on one of our services (SOAP::Lite 0.69 >> installed on the service side). I got this error: >> >> soap:ClientApplication >> failed during request deserialization: >> xml declaration not at start of external entity at line 1, column 941, >> byte 941 at >> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >> line 187 >> >> >> - When executing a Java service: >> >> soapenv:Client >> org.jboss.axis.AxisFault: Version Mismatch >> >> >> >> and again, it might be ok? >> >> - When trying to retrieve the wsdl of a 'moby-async' service (function >> retrieveService) I got this error: >> >> Connection to MOBY Central at >> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >> died because: >> Can't use string (" >> > /usr/lib/perl5 >> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >> >> ERROR ERROR ERROR >> >> The function retrieveService does work when the service is not >> 'moby-async' though. >> >> - When executing an asynchronous service (function >> Async/Service/execute) everything seems ok. >> >> Has anyone had similar problems? Any ideas? >> >> Thank you! >> Romina >> >> Mark Wilkinson wrote: >> >>> Hi all, >>> >>> First off, apologies to anyone who was trying to get through to MOBY >>> Central this afternoon - Eddie and I were making the changes necessary >>> to >>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>> on >>> the test server didn't work on the real MOBY Central... so it took a >>> couple of hours of troubleshooting before we had it back up again. >>> >>> The good news is that it seems to work correctly with both Perl and >>> Java >>> clients. What we don't know is if it is backwards compatible with >>> earlier >>> versions of the MOBY::Client::* libraries, in particular, >>> MOBY::Client::Service. I *think* it is, but we didn't have the >>> opportunity to test it. In any case, the API did not change, so if you >>> just cvs update your client libraries everything should come back to >>> life >>> if it isn't working. >>> >>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>> behaves >>> subtly differently than the old one in several ways that we were not >>> expecting. Thankfully, Pieter and Eddie had done most of the >>> trouble-shoting already, but it still threw us for a loop in some >>> places >>> with incompatible SOAP version errors and a new auto-encoding of >>> strings >>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>> double-coded messages). >>> >>> Anyway, it's done now. Please scream loudly if it doesn't work for >>> you!! >>> I have backups of everything so if necessary we can roll-back quickly. >>> >>> All of this was done primarily to get us to be compatible with the new >>> Asynchronous services API that use the Manchester WSRF::Lite modules >>> which >>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>> code to see if it works for them v.v. Async services? The database can >>> now hold Category=moby-async (which reminds me, I need to update the >>> database templates in the CVS...), and Eddie assures me that the code >>> will >>> now provide correct WSDL for an Asych interface. The myGrid folks have >>> added moby-async as a valid service category into their ontology as >>> well, >>> so in principle... it should all work... (touch wood!) >>> >>> ********************* >>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>> work >>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>> are >>> running your own registry... >>> ********************* >>> >>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>> try to >>> make the changes to gbrowse_moby such that it can also invoke >>> asynchronous >>> services. I think the Async modules also need to be added to the >>> MANIFEST >>> before they are installed by default, so I'll try to remember to do >>> that >>> as well. >>> >>> Otherwise there were just some small changes to the test suite to >>> better >>> clean-up the registry if something goes wrong during testing, and I >>> cleaned-up the test database so that it also doesn't cause the test >>> suite >>> to fail. I will restart the test registry using the new codebase first >>> thing in the morning so that the two are identical. >>> >>> We still haven't figured out why those namespace changes happened a >>> couple >>> of days ago. It coincided with the Gene Ontology curators making some >>> additions to the Namespace list, so I suspect that there is a bug in >>> the >>> interface I have given to them (which talks directly to the database >>> without using the MOBY API), but exactly WHY this happened is still a >>> mystery. I've alerted Midori to the problem and she's going to >>> hold-off >>> on making any more changes until we can figure out what is going wrong. >>> >>> That's all the news from MOBY Central! >>> >>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>> today... >>> >>> Mark >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From markw at illuminae.com Tue Feb 6 15:48:40 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Feb 2007 07:48:40 -0800 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: <45C8A113.40803@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: Hi Romina, I can confirm that calling services running S::L 0.69 from a client running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I have not yet successfully tested is calling a service from a .69 client to an earlier version on the server-side. The way to do that would be to use gbrowse_moby on the mobycentral machine, but I don't know what versions of Perl anyone else is running so I can't reliably do that experiment... can anyone try one of their Perl services from gbrowse-moby on a server with perl 0.60 or less? MOBY Central itself seems fine... and Java invocations of services seem fine also (largely because the Java libraries don't use the WSDL from MOBY Central to create their connections... there may be a lesson in there somewhere! Ugh... WSDL!!) M On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > Hello again, > > Mark, I just called your service and it did work. > > Eddy, if those are some of the errors you fixed yesterday I might be > doing something wrong. Let me re-check everything and if the errors are > still there I'll send you more details about the code I'm using. > > Thank you very much! > Romina > > > > mark wilkinson wrote: >> Hmmmm... Well that's a bit of a disaster! >> >> Could you check what happens when you call one of my services (eg >> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >> each other properly (which would be a nightmare, but given our >> experiences yesterday, not surprising!) >> >> M >> >> >> -- >> Mark Wilkinson >> ...on the road! >> >> >> -----Original Message----- >> From: Romina Royo >> Date: Tue, 06 Feb 2007 15:25:15 >> To:Core developer announcements >> Cc:mobydev >> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >> registry hosts >> >> Hello, >> >> I updated the moby-live/Perl libraries from cvs and I installed >> SOAP::Lite 0.69. >> >> Here are some of the results I got: >> >> - When executing a synchronous Perl service (function execute in >> Client/Service.pm) I got this error: >> >> SOAP-ENV:VersionMismatchWrong >> SOAP version specified. Supported versions: >> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >> 1.2 (http://www.w3.org/2001/06/soap-envelope) >> >> >> mm.. I guess it is OK because the service provider might be using some >> other SOAP version? >> >> - When doing the same test on one of our services (SOAP::Lite 0.69 >> installed on the service side). I got this error: >> >> soap:ClientApplication >> failed during request deserialization: >> xml declaration not at start of external entity at line 1, column 941, >> byte 941 at >> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >> line 187 >> >> >> - When executing a Java service: >> >> soapenv:Client >> org.jboss.axis.AxisFault: Version Mismatch >> >> >> >> and again, it might be ok? >> >> - When trying to retrieve the wsdl of a 'moby-async' service (function >> retrieveService) I got this error: >> >> Connection to MOBY Central at >> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >> died because: >> Can't use string (" >> > /usr/lib/perl5 >> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >> >> ERROR ERROR ERROR >> >> The function retrieveService does work when the service is not >> 'moby-async' though. >> >> - When executing an asynchronous service (function >> Async/Service/execute) everything seems ok. >> >> Has anyone had similar problems? Any ideas? >> >> Thank you! >> Romina >> >> Mark Wilkinson wrote: >> >>> Hi all, >>> >>> First off, apologies to anyone who was trying to get through to MOBY >>> Central this afternoon - Eddie and I were making the changes necessary >>> to >>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>> on >>> the test server didn't work on the real MOBY Central... so it took a >>> couple of hours of troubleshooting before we had it back up again. >>> >>> The good news is that it seems to work correctly with both Perl and >>> Java >>> clients. What we don't know is if it is backwards compatible with >>> earlier >>> versions of the MOBY::Client::* libraries, in particular, >>> MOBY::Client::Service. I *think* it is, but we didn't have the >>> opportunity to test it. In any case, the API did not change, so if you >>> just cvs update your client libraries everything should come back to >>> life >>> if it isn't working. >>> >>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>> behaves >>> subtly differently than the old one in several ways that we were not >>> expecting. Thankfully, Pieter and Eddie had done most of the >>> trouble-shoting already, but it still threw us for a loop in some >>> places >>> with incompatible SOAP version errors and a new auto-encoding of >>> strings >>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>> double-coded messages). >>> >>> Anyway, it's done now. Please scream loudly if it doesn't work for >>> you!! >>> I have backups of everything so if necessary we can roll-back quickly. >>> >>> All of this was done primarily to get us to be compatible with the new >>> Asynchronous services API that use the Manchester WSRF::Lite modules >>> which >>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>> code to see if it works for them v.v. Async services? The database can >>> now hold Category=moby-async (which reminds me, I need to update the >>> database templates in the CVS...), and Eddie assures me that the code >>> will >>> now provide correct WSDL for an Asych interface. The myGrid folks have >>> added moby-async as a valid service category into their ontology as >>> well, >>> so in principle... it should all work... (touch wood!) >>> >>> ********************* >>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>> work >>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>> are >>> running your own registry... >>> ********************* >>> >>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>> try to >>> make the changes to gbrowse_moby such that it can also invoke >>> asynchronous >>> services. I think the Async modules also need to be added to the >>> MANIFEST >>> before they are installed by default, so I'll try to remember to do >>> that >>> as well. >>> >>> Otherwise there were just some small changes to the test suite to >>> better >>> clean-up the registry if something goes wrong during testing, and I >>> cleaned-up the test database so that it also doesn't cause the test >>> suite >>> to fail. I will restart the test registry using the new codebase first >>> thing in the morning so that the two are identical. >>> >>> We still haven't figured out why those namespace changes happened a >>> couple >>> of days ago. It coincided with the Gene Ontology curators making some >>> additions to the Namespace list, so I suspect that there is a bug in >>> the >>> interface I have given to them (which talks directly to the database >>> without using the MOBY API), but exactly WHY this happened is still a >>> mystery. I've alerted Midori to the problem and she's going to >>> hold-off >>> on making any more changes until we can figure out what is going wrong. >>> >>> That's all the news from MOBY Central! >>> >>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>> today... >>> >>> Mark >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From rroyo at lsi.upc.edu Tue Feb 6 16:18:33 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 17:18:33 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: <45C8AA59.3020508@lsi.upc.edu> Hello Mark, I used gbrowse to call one of our services: - first test we had .69 on the server side and as you said it worked ok - second test we had 0.60 on the server side and it also worked ok. I hope this is the test you were asking for :-) Thanks! Romina Mark Wilkinson wrote: > Hi Romina, > > I can confirm that calling services running S::L 0.69 from a client > running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I > have not yet successfully tested is calling a service from a .69 client to > an earlier version on the server-side. The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? > > MOBY Central itself seems fine... and Java invocations of services seem > fine also (largely because the Java libraries don't use the WSDL from MOBY > Central to create their connections... there may be a lesson in there > somewhere! Ugh... WSDL!!) > > M > > > > > On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > > >> Hello again, >> >> Mark, I just called your service and it did work. >> >> Eddy, if those are some of the errors you fixed yesterday I might be >> doing something wrong. Let me re-check everything and if the errors are >> still there I'll send you more details about the code I'm using. >> >> Thank you very much! >> Romina >> >> >> >> mark wilkinson wrote: >> >>> Hmmmm... Well that's a bit of a disaster! >>> >>> Could you check what happens when you call one of my services (eg >>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>> each other properly (which would be a nightmare, but given our >>> experiences yesterday, not surprising!) >>> >>> M >>> >>> >>> -- >>> Mark Wilkinson >>> ...on the road! >>> >>> >>> -----Original Message----- >>> From: Romina Royo >>> Date: Tue, 06 Feb 2007 15:25:15 >>> To:Core developer announcements >>> Cc:mobydev >>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>> registry hosts >>> >>> Hello, >>> >>> I updated the moby-live/Perl libraries from cvs and I installed >>> SOAP::Lite 0.69. >>> >>> Here are some of the results I got: >>> >>> - When executing a synchronous Perl service (function execute in >>> Client/Service.pm) I got this error: >>> >>> SOAP-ENV:VersionMismatchWrong >>> SOAP version specified. Supported versions: >>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>> >>> >>> mm.. I guess it is OK because the service provider might be using some >>> other SOAP version? >>> >>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>> installed on the service side). I got this error: >>> >>> soap:ClientApplication >>> failed during request deserialization: >>> xml declaration not at start of external entity at line 1, column 941, >>> byte 941 at >>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>> line 187 >>> >>> >>> - When executing a Java service: >>> >>> soapenv:Client >>> org.jboss.axis.AxisFault: Version Mismatch >>> >>> >>> >>> and again, it might be ok? >>> >>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>> retrieveService) I got this error: >>> >>> Connection to MOBY Central at >>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>> died because: >>> Can't use string (" >>> >> /usr/lib/perl5 >>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>> >>> ERROR ERROR ERROR >>> >>> The function retrieveService does work when the service is not >>> 'moby-async' though. >>> >>> - When executing an asynchronous service (function >>> Async/Service/execute) everything seems ok. >>> >>> Has anyone had similar problems? Any ideas? >>> >>> Thank you! >>> Romina >>> >>> Mark Wilkinson wrote: >>> >>> >>>> Hi all, >>>> >>>> First off, apologies to anyone who was trying to get through to MOBY >>>> Central this afternoon - Eddie and I were making the changes necessary >>>> to >>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>> on >>>> the test server didn't work on the real MOBY Central... so it took a >>>> couple of hours of troubleshooting before we had it back up again. >>>> >>>> The good news is that it seems to work correctly with both Perl and >>>> Java >>>> clients. What we don't know is if it is backwards compatible with >>>> earlier >>>> versions of the MOBY::Client::* libraries, in particular, >>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>> opportunity to test it. In any case, the API did not change, so if you >>>> just cvs update your client libraries everything should come back to >>>> life >>>> if it isn't working. >>>> >>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>> behaves >>>> subtly differently than the old one in several ways that we were not >>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>> trouble-shoting already, but it still threw us for a loop in some >>>> places >>>> with incompatible SOAP version errors and a new auto-encoding of >>>> strings >>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>> double-coded messages). >>>> >>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>> you!! >>>> I have backups of everything so if necessary we can roll-back quickly. >>>> >>>> All of this was done primarily to get us to be compatible with the new >>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>> which >>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>> code to see if it works for them v.v. Async services? The database can >>>> now hold Category=moby-async (which reminds me, I need to update the >>>> database templates in the CVS...), and Eddie assures me that the code >>>> will >>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>> added moby-async as a valid service category into their ontology as >>>> well, >>>> so in principle... it should all work... (touch wood!) >>>> >>>> ********************* >>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>> work >>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>> are >>>> running your own registry... >>>> ********************* >>>> >>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>> try to >>>> make the changes to gbrowse_moby such that it can also invoke >>>> asynchronous >>>> services. I think the Async modules also need to be added to the >>>> MANIFEST >>>> before they are installed by default, so I'll try to remember to do >>>> that >>>> as well. >>>> >>>> Otherwise there were just some small changes to the test suite to >>>> better >>>> clean-up the registry if something goes wrong during testing, and I >>>> cleaned-up the test database so that it also doesn't cause the test >>>> suite >>>> to fail. I will restart the test registry using the new codebase first >>>> thing in the morning so that the two are identical. >>>> >>>> We still haven't figured out why those namespace changes happened a >>>> couple >>>> of days ago. It coincided with the Gene Ontology curators making some >>>> additions to the Namespace list, so I suspect that there is a bug in >>>> the >>>> interface I have given to them (which talks directly to the database >>>> without using the MOBY API), but exactly WHY this happened is still a >>>> mystery. I've alerted Midori to the problem and she's going to >>>> hold-off >>>> on making any more changes until we can figure out what is going wrong. >>>> >>>> That's all the news from MOBY Central! >>>> >>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>> today... >>>> >>>> Mark >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 rroyo at lsi.upc.edu Tue Feb 6 16:18:33 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 17:18:33 +0100 Subject: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> Message-ID: <45C8AA59.3020508@lsi.upc.edu> Hello Mark, I used gbrowse to call one of our services: - first test we had .69 on the server side and as you said it worked ok - second test we had 0.60 on the server side and it also worked ok. I hope this is the test you were asking for :-) Thanks! Romina Mark Wilkinson wrote: > Hi Romina, > > I can confirm that calling services running S::L 0.69 from a client > running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I > have not yet successfully tested is calling a service from a .69 client to > an earlier version on the server-side. The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? > > MOBY Central itself seems fine... and Java invocations of services seem > fine also (largely because the Java libraries don't use the WSDL from MOBY > Central to create their connections... there may be a lesson in there > somewhere! Ugh... WSDL!!) > > M > > > > > On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > > >> Hello again, >> >> Mark, I just called your service and it did work. >> >> Eddy, if those are some of the errors you fixed yesterday I might be >> doing something wrong. Let me re-check everything and if the errors are >> still there I'll send you more details about the code I'm using. >> >> Thank you very much! >> Romina >> >> >> >> mark wilkinson wrote: >> >>> Hmmmm... Well that's a bit of a disaster! >>> >>> Could you check what happens when you call one of my services (eg >>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>> each other properly (which would be a nightmare, but given our >>> experiences yesterday, not surprising!) >>> >>> M >>> >>> >>> -- >>> Mark Wilkinson >>> ...on the road! >>> >>> >>> -----Original Message----- >>> From: Romina Royo >>> Date: Tue, 06 Feb 2007 15:25:15 >>> To:Core developer announcements >>> Cc:mobydev >>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>> registry hosts >>> >>> Hello, >>> >>> I updated the moby-live/Perl libraries from cvs and I installed >>> SOAP::Lite 0.69. >>> >>> Here are some of the results I got: >>> >>> - When executing a synchronous Perl service (function execute in >>> Client/Service.pm) I got this error: >>> >>> SOAP-ENV:VersionMismatchWrong >>> SOAP version specified. Supported versions: >>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>> >>> >>> mm.. I guess it is OK because the service provider might be using some >>> other SOAP version? >>> >>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>> installed on the service side). I got this error: >>> >>> soap:ClientApplication >>> failed during request deserialization: >>> xml declaration not at start of external entity at line 1, column 941, >>> byte 941 at >>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>> line 187 >>> >>> >>> - When executing a Java service: >>> >>> soapenv:Client >>> org.jboss.axis.AxisFault: Version Mismatch >>> >>> >>> >>> and again, it might be ok? >>> >>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>> retrieveService) I got this error: >>> >>> Connection to MOBY Central at >>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>> died because: >>> Can't use string (" >>> >> /usr/lib/perl5 >>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>> >>> ERROR ERROR ERROR >>> >>> The function retrieveService does work when the service is not >>> 'moby-async' though. >>> >>> - When executing an asynchronous service (function >>> Async/Service/execute) everything seems ok. >>> >>> Has anyone had similar problems? Any ideas? >>> >>> Thank you! >>> Romina >>> >>> Mark Wilkinson wrote: >>> >>> >>>> Hi all, >>>> >>>> First off, apologies to anyone who was trying to get through to MOBY >>>> Central this afternoon - Eddie and I were making the changes necessary >>>> to >>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>> on >>>> the test server didn't work on the real MOBY Central... so it took a >>>> couple of hours of troubleshooting before we had it back up again. >>>> >>>> The good news is that it seems to work correctly with both Perl and >>>> Java >>>> clients. What we don't know is if it is backwards compatible with >>>> earlier >>>> versions of the MOBY::Client::* libraries, in particular, >>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>> opportunity to test it. In any case, the API did not change, so if you >>>> just cvs update your client libraries everything should come back to >>>> life >>>> if it isn't working. >>>> >>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>> behaves >>>> subtly differently than the old one in several ways that we were not >>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>> trouble-shoting already, but it still threw us for a loop in some >>>> places >>>> with incompatible SOAP version errors and a new auto-encoding of >>>> strings >>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>> double-coded messages). >>>> >>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>> you!! >>>> I have backups of everything so if necessary we can roll-back quickly. >>>> >>>> All of this was done primarily to get us to be compatible with the new >>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>> which >>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>> code to see if it works for them v.v. Async services? The database can >>>> now hold Category=moby-async (which reminds me, I need to update the >>>> database templates in the CVS...), and Eddie assures me that the code >>>> will >>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>> added moby-async as a valid service category into their ontology as >>>> well, >>>> so in principle... it should all work... (touch wood!) >>>> >>>> ********************* >>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>> work >>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>> are >>>> running your own registry... >>>> ********************* >>>> >>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>> try to >>>> make the changes to gbrowse_moby such that it can also invoke >>>> asynchronous >>>> services. I think the Async modules also need to be added to the >>>> MANIFEST >>>> before they are installed by default, so I'll try to remember to do >>>> that >>>> as well. >>>> >>>> Otherwise there were just some small changes to the test suite to >>>> better >>>> clean-up the registry if something goes wrong during testing, and I >>>> cleaned-up the test database so that it also doesn't cause the test >>>> suite >>>> to fail. I will restart the test registry using the new codebase first >>>> thing in the morning so that the two are identical. >>>> >>>> We still haven't figured out why those namespace changes happened a >>>> couple >>>> of days ago. It coincided with the Gene Ontology curators making some >>>> additions to the Namespace list, so I suspect that there is a bug in >>>> the >>>> interface I have given to them (which talks directly to the database >>>> without using the MOBY API), but exactly WHY this happened is still a >>>> mystery. I've alerted Midori to the problem and she's going to >>>> hold-off >>>> on making any more changes until we can figure out what is going wrong. >>>> >>>> That's all the news from MOBY Central! >>>> >>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>> today... >>>> >>>> Mark >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > > > From markw at illuminae.com Tue Feb 6 16:30:28 2007 From: markw at illuminae.com (mark wilkinson) Date: Tue, 6 Feb 2007 16:30:28 +0000 GMT Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <45C8AA59.3020508@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> Message-ID: <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> Super! That's great news! So, does that mean that everything is OK? M -- Mark Wilkinson ...on the road! -----Original Message----- From: Romina Royo Date: Tue, 06 Feb 2007 17:18:33 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts Hello Mark, I used gbrowse to call one of our services: - first test we had .69 on the server side and as you said it worked ok - second test we had 0.60 on the server side and it also worked ok. I hope this is the test you were asking for :-) Thanks! Romina Mark Wilkinson wrote: > Hi Romina, > > I can confirm that calling services running S::L 0.69 from a client > running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I > have not yet successfully tested is calling a service from a .69 client to > an earlier version on the server-side. The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? > > MOBY Central itself seems fine... and Java invocations of services seem > fine also (largely because the Java libraries don't use the WSDL from MOBY > Central to create their connections... there may be a lesson in there > somewhere! Ugh... WSDL!!) > > M > > > > > On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: > > >> Hello again, >> >> Mark, I just called your service and it did work. >> >> Eddy, if those are some of the errors you fixed yesterday I might be >> doing something wrong. Let me re-check everything and if the errors are >> still there I'll send you more details about the code I'm using. >> >> Thank you very much! >> Romina >> >> >> >> mark wilkinson wrote: >> >>> Hmmmm... Well that's a bit of a disaster! >>> >>> Could you check what happens when you call one of my services (eg >>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>> each other properly (which would be a nightmare, but given our >>> experiences yesterday, not surprising!) >>> >>> M >>> >>> >>> -- >>> Mark Wilkinson >>> ...on the road! >>> >>> >>> -----Original Message----- >>> From: Romina Royo >>> Date: Tue, 06 Feb 2007 15:25:15 >>> To:Core developer announcements >>> Cc:mobydev >>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>> registry hosts >>> >>> Hello, >>> >>> I updated the moby-live/Perl libraries from cvs and I installed >>> SOAP::Lite 0.69. >>> >>> Here are some of the results I got: >>> >>> - When executing a synchronous Perl service (function execute in >>> Client/Service.pm) I got this error: >>> >>> SOAP-ENV:VersionMismatchWrong >>> SOAP version specified. Supported versions: >>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>> >>> >>> mm.. I guess it is OK because the service provider might be using some >>> other SOAP version? >>> >>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>> installed on the service side). I got this error: >>> >>> soap:ClientApplication >>> failed during request deserialization: >>> xml declaration not at start of external entity at line 1, column 941, >>> byte 941 at >>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>> line 187 >>> >>> >>> - When executing a Java service: >>> >>> soapenv:Client >>> org.jboss.axis.AxisFault: Version Mismatch >>> >>> >>> >>> and again, it might be ok? >>> >>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>> retrieveService) I got this error: >>> >>> Connection to MOBY Central at >>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>> died because: >>> Can't use string (" >>> >> /usr/lib/perl5 >>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>> >>> ERROR ERROR ERROR >>> >>> The function retrieveService does work when the service is not >>> 'moby-async' though. >>> >>> - When executing an asynchronous service (function >>> Async/Service/execute) everything seems ok. >>> >>> Has anyone had similar problems? Any ideas? >>> >>> Thank you! >>> Romina >>> >>> Mark Wilkinson wrote: >>> >>> >>>> Hi all, >>>> >>>> First off, apologies to anyone who was trying to get through to MOBY >>>> Central this afternoon - Eddie and I were making the changes necessary >>>> to >>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>> on >>>> the test server didn't work on the real MOBY Central... so it took a >>>> couple of hours of troubleshooting before we had it back up again. >>>> >>>> The good news is that it seems to work correctly with both Perl and >>>> Java >>>> clients. What we don't know is if it is backwards compatible with >>>> earlier >>>> versions of the MOBY::Client::* libraries, in particular, >>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>> opportunity to test it. In any case, the API did not change, so if you >>>> just cvs update your client libraries everything should come back to >>>> life >>>> if it isn't working. >>>> >>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>> behaves >>>> subtly differently than the old one in several ways that we were not >>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>> trouble-shoting already, but it still threw us for a loop in some >>>> places >>>> with incompatible SOAP version errors and a new auto-encoding of >>>> strings >>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>> double-coded messages). >>>> >>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>> you!! >>>> I have backups of everything so if necessary we can roll-back quickly. >>>> >>>> All of this was done primarily to get us to be compatible with the new >>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>> which >>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>> code to see if it works for them v.v. Async services? The database can >>>> now hold Category=moby-async (which reminds me, I need to update the >>>> database templates in the CVS...), and Eddie assures me that the code >>>> will >>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>> added moby-async as a valid service category into their ontology as >>>> well, >>>> so in principle... it should all work... (touch wood!) >>>> >>>> ********************* >>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>> work >>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>> are >>>> running your own registry... >>>> ********************* >>>> >>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>> try to >>>> make the changes to gbrowse_moby such that it can also invoke >>>> asynchronous >>>> services. I think the Async modules also need to be added to the >>>> MANIFEST >>>> before they are installed by default, so I'll try to remember to do >>>> that >>>> as well. >>>> >>>> Otherwise there were just some small changes to the test suite to >>>> better >>>> clean-up the registry if something goes wrong during testing, and I >>>> cleaned-up the test database so that it also doesn't cause the test >>>> suite >>>> to fail. I will restart the test registry using the new codebase first >>>> thing in the morning so that the two are identical. >>>> >>>> We still haven't figured out why those namespace changes happened a >>>> couple >>>> of days ago. It coincided with the Gene Ontology curators making some >>>> additions to the Namespace list, so I suspect that there is a bug in >>>> the >>>> interface I have given to them (which talks directly to the database >>>> without using the MOBY API), but exactly WHY this happened is still a >>>> mystery. I've alerted Midori to the problem and she's going to >>>> hold-off >>>> on making any more changes until we can figure out what is going wrong. >>>> >>>> That's all the news from MOBY Central! >>>> >>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>> today... >>>> >>>> Mark >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> 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 >> > > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Tue Feb 6 16:12:31 2007 From: d.haase at gsf.de (Dirk Haase) Date: Tue, 6 Feb 2007 17:12:31 +0100 Subject: [MOBY-dev] =?iso-8859-1?q?Updates_to_MOBY_Central_and_IMPORTANT_N?= =?iso-8859-1?q?OTES=09forregistry_hosts?= In-Reply-To: References: <45C8A113.40803@lsi.upc.edu> Message-ID: <200702061712.31415.d.haase@gsf.de> On Tuesday 06 February 2007 16:48, Mark Wilkinson wrote: > The way to do that would be to use > gbrowse_moby on the mobycentral machine, but I don't know what versions of > Perl anyone else is running so I can't reliably do that experiment... can > anyone try one of their Perl services from gbrowse-moby on a server with > perl 0.60 or less? The mips services (using S::L 0.60) are fine when invoked from your gbrowse_moby. Also interaction between client (also 0.60) and Canadian registry is OK. Best, dirk From rroyo at lsi.upc.edu Tue Feb 6 17:09:45 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Tue, 06 Feb 2007 18:09:45 +0100 Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> Message-ID: <45C8B659.7090209@lsi.upc.edu> Hello, The retrieveService function of the Perl API still doesn't seem to work for me (while using soap 0.69)... I get this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 1378. ERROR ERROR ERROR It works for 'moby' services but it does not work for 'moby-async' services. Here's an exmple of the scripts I'm using: ------------------ #!/usr/bin/perl -w use FindBin qw($Bin); use lib "$Bin"; use MOBY::Client::Central; use MOBY::Client::Service; use MOBY::CommonSubs; #use SOAP::Lite + trace; use strict; my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; my $Central = MOBY::Client::Central->new( Registries => {mobycentral => {URL => $URL,URI => $URI}}); my ($ServiceInstances, $RegObject) = $Central->findService( serviceName=> 'runClustalwFast', authURI => 'inb.bsc.es' ); print "ServiceInstances? " . $ServiceInstances->[0]->name . "\n"; my $WSDL = $Central->retrieveService($ServiceInstances->[0]); print "WSDL:::::::\n" . $WSDL . "\n"; ----------------- Thanks! Romina mark wilkinson wrote: > Super! That's great news! > > So, does that mean that everything is OK? > > M > > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 17:18:33 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and > IMPORTANT NOTES forregistry hosts > > Hello Mark, > > I used gbrowse to call one of our services: > > - first test we had .69 on the server side and as you said it worked ok > > - second test we had 0.60 on the server side and it also worked ok. > > I hope this is the test you were asking for :-) > > Thanks! > Romina > > > Mark Wilkinson wrote: > >> Hi Romina, >> >> I can confirm that calling services running S::L 0.69 from a client >> running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I >> have not yet successfully tested is calling a service from a .69 client to >> an earlier version on the server-side. The way to do that would be to use >> gbrowse_moby on the mobycentral machine, but I don't know what versions of >> Perl anyone else is running so I can't reliably do that experiment... can >> anyone try one of their Perl services from gbrowse-moby on a server with >> perl 0.60 or less? >> >> MOBY Central itself seems fine... and Java invocations of services seem >> fine also (largely because the Java libraries don't use the WSDL from MOBY >> Central to create their connections... there may be a lesson in there >> somewhere! Ugh... WSDL!!) >> >> M >> >> >> >> >> On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: >> >> >> >>> Hello again, >>> >>> Mark, I just called your service and it did work. >>> >>> Eddy, if those are some of the errors you fixed yesterday I might be >>> doing something wrong. Let me re-check everything and if the errors are >>> still there I'll send you more details about the code I'm using. >>> >>> Thank you very much! >>> Romina >>> >>> >>> >>> mark wilkinson wrote: >>> >>> >>>> Hmmmm... Well that's a bit of a disaster! >>>> >>>> Could you check what happens when you call one of my services (eg >>>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>>> each other properly (which would be a nightmare, but given our >>>> experiences yesterday, not surprising!) >>>> >>>> M >>>> >>>> >>>> -- >>>> Mark Wilkinson >>>> ...on the road! >>>> >>>> >>>> -----Original Message----- >>>> From: Romina Royo >>>> Date: Tue, 06 Feb 2007 15:25:15 >>>> To:Core developer announcements >>>> Cc:mobydev >>>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>>> registry hosts >>>> >>>> Hello, >>>> >>>> I updated the moby-live/Perl libraries from cvs and I installed >>>> SOAP::Lite 0.69. >>>> >>>> Here are some of the results I got: >>>> >>>> - When executing a synchronous Perl service (function execute in >>>> Client/Service.pm) I got this error: >>>> >>>> SOAP-ENV:VersionMismatchWrong >>>> SOAP version specified. Supported versions: >>>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>>> >>>> >>>> mm.. I guess it is OK because the service provider might be using some >>>> other SOAP version? >>>> >>>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>>> installed on the service side). I got this error: >>>> >>>> soap:ClientApplication >>>> failed during request deserialization: >>>> xml declaration not at start of external entity at line 1, column 941, >>>> byte 941 at >>>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>>> line 187 >>>> >>>> >>>> - When executing a Java service: >>>> >>>> soapenv:Client >>>> org.jboss.axis.AxisFault: Version Mismatch >>>> >>>> >>>> >>>> and again, it might be ok? >>>> >>>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>>> retrieveService) I got this error: >>>> >>>> Connection to MOBY Central at >>>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>>> died because: >>>> Can't use string (" >>>> >>> /usr/lib/perl5 >>>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>>> >>>> ERROR ERROR ERROR >>>> >>>> The function retrieveService does work when the service is not >>>> 'moby-async' though. >>>> >>>> - When executing an asynchronous service (function >>>> Async/Service/execute) everything seems ok. >>>> >>>> Has anyone had similar problems? Any ideas? >>>> >>>> Thank you! >>>> Romina >>>> >>>> Mark Wilkinson wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> First off, apologies to anyone who was trying to get through to MOBY >>>>> Central this afternoon - Eddie and I were making the changes necessary >>>>> to >>>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>>> on >>>>> the test server didn't work on the real MOBY Central... so it took a >>>>> couple of hours of troubleshooting before we had it back up again. >>>>> >>>>> The good news is that it seems to work correctly with both Perl and >>>>> Java >>>>> clients. What we don't know is if it is backwards compatible with >>>>> earlier >>>>> versions of the MOBY::Client::* libraries, in particular, >>>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>>> opportunity to test it. In any case, the API did not change, so if you >>>>> just cvs update your client libraries everything should come back to >>>>> life >>>>> if it isn't working. >>>>> >>>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>>> behaves >>>>> subtly differently than the old one in several ways that we were not >>>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>>> trouble-shoting already, but it still threw us for a loop in some >>>>> places >>>>> with incompatible SOAP version errors and a new auto-encoding of >>>>> strings >>>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>>> double-coded messages). >>>>> >>>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>>> you!! >>>>> I have backups of everything so if necessary we can roll-back quickly. >>>>> >>>>> All of this was done primarily to get us to be compatible with the new >>>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>>> which >>>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>>> code to see if it works for them v.v. Async services? The database can >>>>> now hold Category=moby-async (which reminds me, I need to update the >>>>> database templates in the CVS...), and Eddie assures me that the code >>>>> will >>>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>>> added moby-async as a valid service category into their ontology as >>>>> well, >>>>> so in principle... it should all work... (touch wood!) >>>>> >>>>> ********************* >>>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>>> work >>>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>>> are >>>>> running your own registry... >>>>> ********************* >>>>> >>>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>>> try to >>>>> make the changes to gbrowse_moby such that it can also invoke >>>>> asynchronous >>>>> services. I think the Async modules also need to be added to the >>>>> MANIFEST >>>>> before they are installed by default, so I'll try to remember to do >>>>> that >>>>> as well. >>>>> >>>>> Otherwise there were just some small changes to the test suite to >>>>> better >>>>> clean-up the registry if something goes wrong during testing, and I >>>>> cleaned-up the test database so that it also doesn't cause the test >>>>> suite >>>>> to fail. I will restart the test registry using the new codebase first >>>>> thing in the morning so that the two are identical. >>>>> >>>>> We still haven't figured out why those namespace changes happened a >>>>> couple >>>>> of days ago. It coincided with the Gene Ontology curators making some >>>>> additions to the Namespace list, so I suspect that there is a bug in >>>>> the >>>>> interface I have given to them (which talks directly to the database >>>>> without using the MOBY API), but exactly WHY this happened is still a >>>>> mystery. I've alerted Midori to the problem and she's going to >>>>> hold-off >>>>> on making any more changes until we can figure out what is going wrong. >>>>> >>>>> That's all the news from MOBY Central! >>>>> >>>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>>> today... >>>>> >>>>> Mark >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> > > _______________________________________________ > 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 Tue Feb 6 17:49:13 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 09:49:13 -0800 Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <45C8B659.7090209@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> Message-ID: <006801c74a17$1ea4f9a0$6900a8c0@notebook> So something is wrong with the routine that is sending the async wsdl, because there is nothing wrong with your script using category == moby. I will track down the culprit and get back to you! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 9:10 AM To: markw at illuminae.com; Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts Hello, The retrieveService function of the Perl API still doesn't seem to work for me (while using soap 0.69)... I get this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 1378. ERROR ERROR ERROR It works for 'moby' services but it does not work for 'moby-async' services. Here's an exmple of the scripts I'm using: ------------------ #!/usr/bin/perl -w use FindBin qw($Bin); use lib "$Bin"; use MOBY::Client::Central; use MOBY::Client::Service; use MOBY::CommonSubs; #use SOAP::Lite + trace; use strict; my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; my $Central = MOBY::Client::Central->new( Registries => {mobycentral => {URL => $URL,URI => $URI}}); my ($ServiceInstances, $RegObject) = $Central->findService( serviceName=> 'runClustalwFast', authURI => 'inb.bsc.es' ); print "ServiceInstances? " . $ServiceInstances->[0]->name . "\n"; my $WSDL = $Central->retrieveService($ServiceInstances->[0]); print "WSDL:::::::\n" . $WSDL . "\n"; ----------------- Thanks! Romina mark wilkinson wrote: > Super! That's great news! > > So, does that mean that everything is OK? > > M > > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 17:18:33 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and > IMPORTANT NOTES forregistry hosts > > Hello Mark, > > I used gbrowse to call one of our services: > > - first test we had .69 on the server side and as you said it worked ok > > - second test we had 0.60 on the server side and it also worked ok. > > I hope this is the test you were asking for :-) > > Thanks! > Romina > > > Mark Wilkinson wrote: > >> Hi Romina, >> >> I can confirm that calling services running S::L 0.69 from a client >> running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I >> have not yet successfully tested is calling a service from a .69 client to >> an earlier version on the server-side. The way to do that would be to use >> gbrowse_moby on the mobycentral machine, but I don't know what versions of >> Perl anyone else is running so I can't reliably do that experiment... can >> anyone try one of their Perl services from gbrowse-moby on a server with >> perl 0.60 or less? >> >> MOBY Central itself seems fine... and Java invocations of services seem >> fine also (largely because the Java libraries don't use the WSDL from MOBY >> Central to create their connections... there may be a lesson in there >> somewhere! Ugh... WSDL!!) >> >> M >> >> >> >> >> On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: >> >> >> >>> Hello again, >>> >>> Mark, I just called your service and it did work. >>> >>> Eddy, if those are some of the errors you fixed yesterday I might be >>> doing something wrong. Let me re-check everything and if the errors are >>> still there I'll send you more details about the code I'm using. >>> >>> Thank you very much! >>> Romina >>> >>> >>> >>> mark wilkinson wrote: >>> >>> >>>> Hmmmm... Well that's a bit of a disaster! >>>> >>>> Could you check what happens when you call one of my services (eg >>>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>>> each other properly (which would be a nightmare, but given our >>>> experiences yesterday, not surprising!) >>>> >>>> M >>>> >>>> >>>> -- >>>> Mark Wilkinson >>>> ...on the road! >>>> >>>> >>>> -----Original Message----- >>>> From: Romina Royo >>>> Date: Tue, 06 Feb 2007 15:25:15 >>>> To:Core developer announcements >>>> Cc:mobydev >>>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>>> registry hosts >>>> >>>> Hello, >>>> >>>> I updated the moby-live/Perl libraries from cvs and I installed >>>> SOAP::Lite 0.69. >>>> >>>> Here are some of the results I got: >>>> >>>> - When executing a synchronous Perl service (function execute in >>>> Client/Service.pm) I got this error: >>>> >>>> SOAP-ENV:VersionMismatch Wrong >>>> SOAP version specified. Supported versions: >>>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>>> >>>> >>>> mm.. I guess it is OK because the service provider might be using some >>>> other SOAP version? >>>> >>>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>>> installed on the service side). I got this error: >>>> >>>> soap:ClientApplication >>>> failed during request deserialization: >>>> xml declaration not at start of external entity at line 1, column 941, >>>> byte 941 at >>>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>>> line 187 >>>> >>>> >>>> - When executing a Java service: >>>> >>>> soapenv:Client >>>> org.jboss.axis.AxisFault: Version Mismatch >>>> >>>> >>>> >>>> and again, it might be ok? >>>> >>>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>>> retrieveService) I got this error: >>>> >>>> Connection to MOBY Central at >>>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>>> died because: >>>> Can't use string (" >>>> >>> /usr/lib/perl5 >>>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>>> >>>> ERROR ERROR ERROR >>>> >>>> The function retrieveService does work when the service is not >>>> 'moby-async' though. >>>> >>>> - When executing an asynchronous service (function >>>> Async/Service/execute) everything seems ok. >>>> >>>> Has anyone had similar problems? Any ideas? >>>> >>>> Thank you! >>>> Romina >>>> >>>> Mark Wilkinson wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> First off, apologies to anyone who was trying to get through to MOBY >>>>> Central this afternoon - Eddie and I were making the changes necessary >>>>> to >>>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>>> on >>>>> the test server didn't work on the real MOBY Central... so it took a >>>>> couple of hours of troubleshooting before we had it back up again. >>>>> >>>>> The good news is that it seems to work correctly with both Perl and >>>>> Java >>>>> clients. What we don't know is if it is backwards compatible with >>>>> earlier >>>>> versions of the MOBY::Client::* libraries, in particular, >>>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>>> opportunity to test it. In any case, the API did not change, so if you >>>>> just cvs update your client libraries everything should come back to >>>>> life >>>>> if it isn't working. >>>>> >>>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>>> behaves >>>>> subtly differently than the old one in several ways that we were not >>>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>>> trouble-shoting already, but it still threw us for a loop in some >>>>> places >>>>> with incompatible SOAP version errors and a new auto-encoding of >>>>> strings >>>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>>> double-coded messages). >>>>> >>>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>>> you!! >>>>> I have backups of everything so if necessary we can roll-back quickly. >>>>> >>>>> All of this was done primarily to get us to be compatible with the new >>>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>>> which >>>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>>> code to see if it works for them v.v. Async services? The database can >>>>> now hold Category=moby-async (which reminds me, I need to update the >>>>> database templates in the CVS...), and Eddie assures me that the code >>>>> will >>>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>>> added moby-async as a valid service category into their ontology as >>>>> well, >>>>> so in principle... it should all work... (touch wood!) >>>>> >>>>> ********************* >>>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>>> work >>>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>>> are >>>>> running your own registry... >>>>> ********************* >>>>> >>>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>>> try to >>>>> make the changes to gbrowse_moby such that it can also invoke >>>>> asynchronous >>>>> services. I think the Async modules also need to be added to the >>>>> MANIFEST >>>>> before they are installed by default, so I'll try to remember to do >>>>> that >>>>> as well. >>>>> >>>>> Otherwise there were just some small changes to the test suite to >>>>> better >>>>> clean-up the registry if something goes wrong during testing, and I >>>>> cleaned-up the test database so that it also doesn't cause the test >>>>> suite >>>>> to fail. I will restart the test registry using the new codebase first >>>>> thing in the morning so that the two are identical. >>>>> >>>>> We still haven't figured out why those namespace changes happened a >>>>> couple >>>>> of days ago. It coincided with the Gene Ontology curators making some >>>>> additions to the Namespace list, so I suspect that there is a bug in >>>>> the >>>>> interface I have given to them (which talks directly to the database >>>>> without using the MOBY API), but exactly WHY this happened is still a >>>>> mystery. I've alerted Midori to the problem and she's going to >>>>> hold-off >>>>> on making any more changes until we can figure out what is going wrong. >>>>> >>>>> That's all the news from MOBY Central! >>>>> >>>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>>> today... >>>>> >>>>> Mark >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> > > _______________________________________________ > 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 > _______________________________________________ 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 Tue Feb 6 18:06:43 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 6 Feb 2007 10:06:43 -0800 Subject: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts In-Reply-To: <45C8B659.7090209@lsi.upc.edu> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> Message-ID: <006901c74a19$907716b0$6900a8c0@notebook> Hi Romina, I just committed into the cvs a fix to this problem. There should be no more errors (fingers crossed ;-) Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Tuesday, February 06, 2007 9:10 AM To: markw at illuminae.com; Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central andIMPORTANT NOTES forregistry hosts Hello, The retrieveService function of the Perl API still doesn't seem to work for me (while using soap 0.69)... I get this error: Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/MOBY/Central' died because: Can't use string (" line 1378. ERROR ERROR ERROR It works for 'moby' services but it does not work for 'moby-async' services. Here's an exmple of the scripts I'm using: ------------------ #!/usr/bin/perl -w use FindBin qw($Bin); use lib "$Bin"; use MOBY::Client::Central; use MOBY::Client::Service; use MOBY::CommonSubs; #use SOAP::Lite + trace; use strict; my $URL = 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'; my $URI = 'http://mobycentral.icapture.ubc.ca/MOBY/Central'; my $Central = MOBY::Client::Central->new( Registries => {mobycentral => {URL => $URL,URI => $URI}}); my ($ServiceInstances, $RegObject) = $Central->findService( serviceName=> 'runClustalwFast', authURI => 'inb.bsc.es' ); print "ServiceInstances? " . $ServiceInstances->[0]->name . "\n"; my $WSDL = $Central->retrieveService($ServiceInstances->[0]); print "WSDL:::::::\n" . $WSDL . "\n"; ----------------- Thanks! Romina mark wilkinson wrote: > Super! That's great news! > > So, does that mean that everything is OK? > > M > > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: Romina Royo > Date: Tue, 06 Feb 2007 17:18:33 > To:Core developer announcements > Cc:mobydev > Subject: Re: [MOBY-dev] Updates to MOBY Central and > IMPORTANT NOTES forregistry hosts > > Hello Mark, > > I used gbrowse to call one of our services: > > - first test we had .69 on the server side and as you said it worked ok > > - second test we had 0.60 on the server side and it also worked ok. > > I hope this is the test you were asking for :-) > > Thanks! > Romina > > > Mark Wilkinson wrote: > >> Hi Romina, >> >> I can confirm that calling services running S::L 0.69 from a client >> running S::L 0.55 is succesful. .69 to .69 is obviously OK also. What I >> have not yet successfully tested is calling a service from a .69 client to >> an earlier version on the server-side. The way to do that would be to use >> gbrowse_moby on the mobycentral machine, but I don't know what versions of >> Perl anyone else is running so I can't reliably do that experiment... can >> anyone try one of their Perl services from gbrowse-moby on a server with >> perl 0.60 or less? >> >> MOBY Central itself seems fine... and Java invocations of services seem >> fine also (largely because the Java libraries don't use the WSDL from MOBY >> Central to create their connections... there may be a lesson in there >> somewhere! Ugh... WSDL!!) >> >> M >> >> >> >> >> On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo wrote: >> >> >> >>> Hello again, >>> >>> Mark, I just called your service and it did work. >>> >>> Eddy, if those are some of the errors you fixed yesterday I might be >>> doing something wrong. Let me re-check everything and if the errors are >>> still there I'll send you more details about the code I'm using. >>> >>> Thank you very much! >>> Romina >>> >>> >>> >>> mark wilkinson wrote: >>> >>> >>>> Hmmmm... Well that's a bit of a disaster! >>>> >>>> Could you check what happens when you call one of my services (eg >>>> MOBYSHoundGetGenbankff)? I wonder if SOAP::Lite versions don't talk to >>>> each other properly (which would be a nightmare, but given our >>>> experiences yesterday, not surprising!) >>>> >>>> M >>>> >>>> >>>> -- >>>> Mark Wilkinson >>>> ...on the road! >>>> >>>> >>>> -----Original Message----- >>>> From: Romina Royo >>>> Date: Tue, 06 Feb 2007 15:25:15 >>>> To:Core developer announcements >>>> Cc:mobydev >>>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for >>>> registry hosts >>>> >>>> Hello, >>>> >>>> I updated the moby-live/Perl libraries from cvs and I installed >>>> SOAP::Lite 0.69. >>>> >>>> Here are some of the results I got: >>>> >>>> - When executing a synchronous Perl service (function execute in >>>> Client/Service.pm) I got this error: >>>> >>>> SOAP-ENV:VersionMismatch Wrong >>>> SOAP version specified. Supported versions: >>>> 1.1 (http://schemas.xmlsoap.org/soap/envelope/) >>>> 1.2 (http://www.w3.org/2001/06/soap-envelope) >>>> >>>> >>>> mm.. I guess it is OK because the service provider might be using some >>>> other SOAP version? >>>> >>>> - When doing the same test on one of our services (SOAP::Lite 0.69 >>>> installed on the service side). I got this error: >>>> >>>> soap:ClientApplication >>>> failed during request deserialization: >>>> xml declaration not at start of external entity at line 1, column 941, >>>> byte 941 at >>>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm >>>> line 187 >>>> >>>> >>>> - When executing a Java service: >>>> >>>> soapenv:Client >>>> org.jboss.axis.AxisFault: Version Mismatch >>>> >>>> >>>> >>>> and again, it might be ok? >>>> >>>> - When trying to retrieve the wsdl of a 'moby-async' service (function >>>> retrieveService) I got this error: >>>> >>>> Connection to MOBY Central at >>>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central' >>>> died because: >>>> Can't use string (" >>>> >>> /usr/lib/perl5 >>>> /site_perl/5.8.5/MOBY/Central.pm line 3290, line 371. >>>> >>>> ERROR ERROR ERROR >>>> >>>> The function retrieveService does work when the service is not >>>> 'moby-async' though. >>>> >>>> - When executing an asynchronous service (function >>>> Async/Service/execute) everything seems ok. >>>> >>>> Has anyone had similar problems? Any ideas? >>>> >>>> Thank you! >>>> Romina >>>> >>>> Mark Wilkinson wrote: >>>> >>>> >>>> >>>>> Hi all, >>>>> >>>>> First off, apologies to anyone who was trying to get through to MOBY >>>>> Central this afternoon - Eddie and I were making the changes necessary >>>>> to >>>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly >>>>> on >>>>> the test server didn't work on the real MOBY Central... so it took a >>>>> couple of hours of troubleshooting before we had it back up again. >>>>> >>>>> The good news is that it seems to work correctly with both Perl and >>>>> Java >>>>> clients. What we don't know is if it is backwards compatible with >>>>> earlier >>>>> versions of the MOBY::Client::* libraries, in particular, >>>>> MOBY::Client::Service. I *think* it is, but we didn't have the >>>>> opportunity to test it. In any case, the API did not change, so if you >>>>> just cvs update your client libraries everything should come back to >>>>> life >>>>> if it isn't working. >>>>> >>>>> Upgrading to SOAP::Lite 0.69 was a nightmare! The new SOAP::Lite >>>>> behaves >>>>> subtly differently than the old one in several ways that we were not >>>>> expecting. Thankfully, Pieter and Eddie had done most of the >>>>> trouble-shoting already, but it still threw us for a loop in some >>>>> places >>>>> with incompatible SOAP version errors and a new auto-encoding of >>>>> strings >>>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in >>>>> double-coded messages). >>>>> >>>>> Anyway, it's done now. Please scream loudly if it doesn't work for >>>>> you!! >>>>> I have backups of everything so if necessary we can roll-back quickly. >>>>> >>>>> All of this was done primarily to get us to be compatible with the new >>>>> Asynchronous services API that use the Manchester WSRF::Lite modules >>>>> which >>>>> depend on SOAP::Lite 0.69. Can I ask the good folks at INB to test the >>>>> code to see if it works for them v.v. Async services? The database can >>>>> now hold Category=moby-async (which reminds me, I need to update the >>>>> database templates in the CVS...), and Eddie assures me that the code >>>>> will >>>>> now provide correct WSDL for an Asych interface. The myGrid folks have >>>>> added moby-async as a valid service category into their ontology as >>>>> well, >>>>> so in principle... it should all work... (touch wood!) >>>>> >>>>> ********************* >>>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT >>>>> work >>>>> on versions of SOAP::Lite prior to 0.69!!! Keep this in mind if you >>>>> are >>>>> running your own registry... >>>>> ********************* >>>>> >>>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll >>>>> try to >>>>> make the changes to gbrowse_moby such that it can also invoke >>>>> asynchronous >>>>> services. I think the Async modules also need to be added to the >>>>> MANIFEST >>>>> before they are installed by default, so I'll try to remember to do >>>>> that >>>>> as well. >>>>> >>>>> Otherwise there were just some small changes to the test suite to >>>>> better >>>>> clean-up the registry if something goes wrong during testing, and I >>>>> cleaned-up the test database so that it also doesn't cause the test >>>>> suite >>>>> to fail. I will restart the test registry using the new codebase first >>>>> thing in the morning so that the two are identical. >>>>> >>>>> We still haven't figured out why those namespace changes happened a >>>>> couple >>>>> of days ago. It coincided with the Gene Ontology curators making some >>>>> additions to the Namespace list, so I suspect that there is a bug in >>>>> the >>>>> interface I have given to them (which talks directly to the database >>>>> without using the MOBY API), but exactly WHY this happened is still a >>>>> mystery. I've alerted Midori to the problem and she's going to >>>>> hold-off >>>>> on making any more changes until we can figure out what is going wrong. >>>>> >>>>> That's all the news from MOBY Central! >>>>> >>>>> Let us know ASAP if you notice anything wrong. It's been a rough ride >>>>> today... >>>>> >>>>> Mark >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> >> > > _______________________________________________ > 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 > _______________________________________________ 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 Tue Feb 6 21:56:04 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 06 Feb 2007 13:56:04 -0800 Subject: [MOBY-dev] Q about Async services Message-ID: Hi INB team! I have a quick question about some parts of the last version of the MOBY Async proposal (or at least, the last version that I printed for myself that I am reading now). One of the aspects in the proposal was the addition of a boolean parameter to the service registration and also some additional RDF in the LSID metadata indicating that the service was asynchronous. What seems to have happened is that these two aspects were abandoned and in their place the new Category "moby-async" was added to the list of acceptable service categories. Is this your understanding also (i.e. that these two pieces of the proposal are now deprecated) or are you still expecting these changes to happen? I believe that the status quo fulfils all of the requirements, but please correct me if I am wrong. Mark -- -- 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 johan at ac.uma.es Wed Feb 7 09:25:20 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Wed, 07 Feb 2007 10:25:20 +0100 Subject: [MOBY-dev] Q about Async services In-Reply-To: References: Message-ID: <45C99B00.2030602@ac.uma.es> Hi Mark, You are completely right, the "moby-async" category covers what is needed but we missed to update some things in the document. So "moby-async" should be allowed in: * registerService: the input field "category" * findService: the input field "protocol" and the output field "category". * RDF for service instances: "dc:format" predicate Anywhere else? Kind regards, Johan Karlsson -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 Mark Wilkinson wrote: > Hi INB team! > > I have a quick question about some parts of the last version of the MOBY > Async proposal (or at least, the last version that I printed for myself > that I am reading now). > > One of the aspects in the proposal was the addition of a boolean parameter > to the service registration and also some additional RDF in the LSID > metadata indicating that the service was asynchronous. What seems to have > happened is that these two aspects were abandoned and in their place the > new Category "moby-async" was added to the list of acceptable service > categories. Is this your understanding also (i.e. that these two pieces > of the proposal are now deprecated) or are you still expecting these > changes to happen? I believe that the status quo fulfils all of the > requirements, but please correct me if I am wrong. > > Mark > > > > From markw at illuminae.com Thu Feb 8 03:38:57 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 07 Feb 2007 19:38:57 -0800 Subject: [MOBY-dev] Q about Async services In-Reply-To: <45C99B00.2030602@ac.uma.es> References: <45C99B00.2030602@ac.uma.es> Message-ID: I think those are the only three places. Okay great, I just wanted to be sure that you have all the changes you require. We're still working out some bugs with Romina, but hopefully we'll have those sorted out in a day or two. Cheers! Mark On Wed, 07 Feb 2007 01:25:20 -0800, Johan Karlsson wrote: > Hi Mark, > > You are completely right, the "moby-async" category covers what is > needed but we missed to update some things in the document. > > So "moby-async" should be allowed in: > > * registerService: the input field "category" > * findService: the input field "protocol" and the output field > "category". > * RDF for service instances: "dc:format" predicate > > Anywhere else? > > Kind regards, > Johan Karlsson > -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From Pieter.Neerincx at wur.nl Thu Feb 8 20:01:15 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 8 Feb 2007 21:01:15 +0100 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <006901c74a19$907716b0$6900a8c0@notebook> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> <006901c74a19$907716b0$6900a8c0@notebook> Message-ID: Hi Eddie, I think I ran into a small problem. When I use MOBY::Client::Central::DUMP I get the following error: ------------------- Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ MOBY/Central' died because: String value expected instead of ARRAY reference ERROR ERROR ERROR ------------------- This happens both with: * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY Central with S::L 0.69 * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY Central with S::L 0.69 I'm suspecting the following line to be the cruel-pit: MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; I'm guessing your new S::L (de-)serializer expects an XML string instead of the array ref... Is that possible? Cheers, Pi in update mode :) From edward.kawas at gmail.com Thu Feb 8 20:58:02 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 8 Feb 2007 12:58:02 -0800 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01><45C8B659.7090209@lsi.upc.edu><006901c74a19$907716b0$6900a8c0@notebook> Message-ID: <007201c74bc3$d35cf8e0$6900a8c0@notebook> Hi Pieter, You are right. The serializer (MOBY::SOAP::Serializer) expects a string. I have fixed it, but I think that my patch is very sub optimal. What I did was wrap the code contained in do { ... } if $_[1] =~ /^(?:method|response)$/; With: do { do { ... } unless ref($_[3]) =~ /ARRAY/; } if $_[1] =~ /^(?:method|response)$/; This seems to work, i.e. I see something in the soap trace. However, when I attempt to use the array ref, things don't work for me ... I am wondering if I should encode the strings in the array!?! Thoughts anyone? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: Thursday, February 08, 2007 12:01 PM To: Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central Hi Eddie, I think I ran into a small problem. When I use MOBY::Client::Central::DUMP I get the following error: ------------------- Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ MOBY/Central' died because: String value expected instead of ARRAY reference ERROR ERROR ERROR ------------------- This happens both with: * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY Central with S::L 0.69 * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY Central with S::L 0.69 I'm suspecting the following line to be the cruel-pit: MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; I'm guessing your new S::L (de-)serializer expects an XML string instead of the array ref... Is that possible? Cheers, Pi in update mode :) _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Feb 8 21:47:35 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Feb 2007 13:47:35 -0800 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <007201c74bc3$d35cf8e0$6900a8c0@notebook> References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> <006901c74a19$907716b0$6900a8c0@notebook> <007201c74bc3$d35cf8e0$6900a8c0@notebook> Message-ID: Hmmmm... that DUMP subroutine has always been a bit "odd" compared to the rest of the API (actually... is it even IN the API?). I guess if it is causing problems now then it should be fixed properly. M On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas wrote: > Hi Pieter, > > You are right. The serializer (MOBY::SOAP::Serializer) expects a string. > I > have fixed it, but I think that my patch is very sub optimal. What I did > was > wrap the code contained in > > do { > ... > } if $_[1] =~ /^(?:method|response)$/; > > With: > do { > do { > ... > } unless ref($_[3]) =~ /ARRAY/; > } if $_[1] =~ /^(?:method|response)$/; > > This seems to work, i.e. I see something in the soap trace. However, > when I > attempt to use the array ref, things don't work for me ... I am > wondering if > I should encode the strings in the array!?! > > Thoughts anyone? > > Eddie > > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx > Sent: Thursday, February 08, 2007 12:01 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Updates to MOBY Central > > Hi Eddie, > > I think I ran into a small problem. When I use > MOBY::Client::Central::DUMP I get the following error: > ------------------- > Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ > MOBY/Central' died because: > String value expected instead of ARRAY reference > > ERROR ERROR ERROR > ------------------- > > This happens both with: > * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY > Central with S::L 0.69 > * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY > Central with S::L 0.69 > > I'm suspecting the following line to be the cruel-pit: > > MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; > > I'm guessing your new S::L (de-)serializer expects an XML string > instead of the array ref... Is that possible? > > Cheers, > > Pi in update mode :) > _______________________________________________ > 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 -- Using Opera's revolutionary e-mail client: http://www.opera.com/mail/ From Pieter.Neerincx at wur.nl Thu Feb 8 22:15:32 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 8 Feb 2007 23:15:32 +0100 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: References: <45C88FCB.2030704@lsi.upc.edu> <1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01> <45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu> <617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01> <45C8B659.7090209@lsi.upc.edu> <006901c74a19$907716b0$6900a8c0@notebook> <007201c74bc3$d35cf8e0$6900a8c0@notebook> Message-ID: <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> On 08 Feb 2007, at 22:47, Mark Wilkinson wrote: > Hmmmm... that DUMP subroutine has always been a bit "odd" compared > to the > rest of the API (actually... is it even IN the API?). Yeah it's bit of a weird one, but it's also extremely useful for duplicating a Central :). > I guess if it is > causing problems now then it should be fixed properly. > > M > > > > > > On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas > > wrote: > >> Hi Pieter, >> >> You are right. The serializer (MOBY::SOAP::Serializer) expects a >> string. >> I >> have fixed it, but I think that my patch is very sub optimal. What >> I did >> was >> wrap the code contained in >> >> do { >> ... >> } if $_[1] =~ /^(?:method|response)$/; >> >> With: >> do { >> do { >> ... >> } unless ref($_[3]) =~ /ARRAY/; >> } if $_[1] =~ /^(?:method|response)$/; >> >> This seems to work, i.e. I see something in the soap trace. However, >> when I >> attempt to use the array ref, things don't work for me ... I am >> wondering if >> I should encode the strings in the array!?! I guess. If the BioMOBY Perl libs are not encoding the strings in the array and the new serializer is not doing that either it must cause trouble with not escaped characters... I'll try to dig further tomorrow. Cheers, Pi >> >> Thoughts anyone? >> >> Eddie >> >> >> >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter >> Neerincx >> Sent: Thursday, February 08, 2007 12:01 PM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Updates to MOBY Central >> >> Hi Eddie, >> >> I think I ran into a small problem. When I use >> MOBY::Client::Central::DUMP I get the following error: >> ------------------- >> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ >> MOBY/Central' died because: >> String value expected instead of ARRAY reference >> >> ERROR ERROR ERROR >> ------------------- >> >> This happens both with: >> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY >> Central with S::L 0.69 >> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY >> Central with S::L 0.69 >> >> I'm suspecting the following line to be the cruel-pit: >> >> MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; >> >> I'm guessing your new S::L (de-)serializer expects an XML string >> instead of the array ref... Is that possible? >> >> Cheers, >> >> Pi in update mode :) >> _______________________________________________ >> 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 > > > > -- > 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 Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From edward.kawas at gmail.com Thu Feb 8 23:12:54 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 8 Feb 2007 15:12:54 -0800 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> References: <45C88FCB.2030704@lsi.upc.edu><1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01><45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01><45C8B659.7090209@lsi.upc.edu><006901c74a19$907716b0$6900a8c0@notebook><007201c74bc3$d35cf8e0$6900a8c0@notebook> <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> Message-ID: <007c01c74bd6$aa6c0940$6900a8c0@notebook> Pieter, Okay, I have committed a fix. It should be backwards compatible. Let me know if this works for you! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: Thursday, February 08, 2007 2:16 PM To: Core developer announcements Subject: Re: [MOBY-dev] Updates to MOBY Central On 08 Feb 2007, at 22:47, Mark Wilkinson wrote: > Hmmmm... that DUMP subroutine has always been a bit "odd" compared > to the > rest of the API (actually... is it even IN the API?). Yeah it's bit of a weird one, but it's also extremely useful for duplicating a Central :). > I guess if it is > causing problems now then it should be fixed properly. > > M > > > > > > On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas > > wrote: > >> Hi Pieter, >> >> You are right. The serializer (MOBY::SOAP::Serializer) expects a >> string. >> I >> have fixed it, but I think that my patch is very sub optimal. What >> I did >> was >> wrap the code contained in >> >> do { >> ... >> } if $_[1] =~ /^(?:method|response)$/; >> >> With: >> do { >> do { >> ... >> } unless ref($_[3]) =~ /ARRAY/; >> } if $_[1] =~ /^(?:method|response)$/; >> >> This seems to work, i.e. I see something in the soap trace. However, >> when I >> attempt to use the array ref, things don't work for me ... I am >> wondering if >> I should encode the strings in the array!?! I guess. If the BioMOBY Perl libs are not encoding the strings in the array and the new serializer is not doing that either it must cause trouble with not escaped characters... I'll try to dig further tomorrow. Cheers, Pi >> >> Thoughts anyone? >> >> Eddie >> >> >> >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter >> Neerincx >> Sent: Thursday, February 08, 2007 12:01 PM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Updates to MOBY Central >> >> Hi Eddie, >> >> I think I ran into a small problem. When I use >> MOBY::Client::Central::DUMP I get the following error: >> ------------------- >> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ >> MOBY/Central' died because: >> String value expected instead of ARRAY reference >> >> ERROR ERROR ERROR >> ------------------- >> >> This happens both with: >> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY >> Central with S::L 0.69 >> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY >> Central with S::L 0.69 >> >> I'm suspecting the following line to be the cruel-pit: >> >> MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; >> >> I'm guessing your new S::L (de-)serializer expects an XML string >> instead of the array ref... Is that possible? >> >> Cheers, >> >> Pi in update mode :) >> _______________________________________________ >> 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 > > > > -- > 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 Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1038 Dreijenlaan 3 6703 HA Wageningen phone: 0317-484 706 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Fri Feb 9 11:01:24 2007 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 9 Feb 2007 12:01:24 +0100 Subject: [MOBY-dev] Updates to MOBY Central In-Reply-To: <007c01c74bd6$aa6c0940$6900a8c0@notebook> References: <45C88FCB.2030704@lsi.upc.edu><1119747513-1170774292-cardhu_blackberry.rim.net-20101-@engine25-cell01><45C8A113.40803@lsi.upc.edu> <45C8AA59.3020508@lsi.upc.edu><617661685-1170779510-cardhu_blackberry.rim.net-31375-@engine08-cell01><45C8B659.7090209@lsi.upc.edu><006901c74a19$907716b0$6900a8c0@notebook><007201c74bc3$d35cf8e0$6900a8c0@notebook> <10664F1C-0E82-4526-A7DE-76926B46C6C8@wur.nl> <007c01c74bd6$aa6c0940$6900a8c0@notebook> Message-ID: <4B1A3610-AB88-4926-8B28-ABFB146020F3@wur.nl> On 9-Feb-2007, at 12:12 AM, Edward Kawas wrote: > Pieter, > > Okay, I have committed a fix. > > It should be backwards compatible. > > Let me know if this works for you! It does :). Thanks! Pi > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter > Neerincx > Sent: Thursday, February 08, 2007 2:16 PM > To: Core developer announcements > Subject: Re: [MOBY-dev] Updates to MOBY Central > > > On 08 Feb 2007, at 22:47, Mark Wilkinson wrote: > >> Hmmmm... that DUMP subroutine has always been a bit "odd" compared >> to the >> rest of the API (actually... is it even IN the API?). > > Yeah it's bit of a weird one, but it's also extremely useful for > duplicating a Central :). > >> I guess if it is >> causing problems now then it should be fixed properly. >> >> M >> >> >> >> >> >> On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas >> >> wrote: >> >>> Hi Pieter, >>> >>> You are right. The serializer (MOBY::SOAP::Serializer) expects a >>> string. >>> I >>> have fixed it, but I think that my patch is very sub optimal. What >>> I did >>> was >>> wrap the code contained in >>> >>> do { >>> ... >>> } if $_[1] =~ /^(?:method|response)$/; >>> >>> With: >>> do { >>> do { >>> ... >>> } unless ref($_[3]) =~ /ARRAY/; >>> } if $_[1] =~ /^(?:method|response)$/; >>> >>> This seems to work, i.e. I see something in the soap trace. However, >>> when I >>> attempt to use the array ref, things don't work for me ... I am >>> wondering if >>> I should encode the strings in the array!?! > > I guess. If the BioMOBY Perl libs are not encoding the strings in the > array and the new serializer is not doing that either it must cause > trouble with not escaped characters... > > I'll try to dig further tomorrow. > > Cheers, > > Pi > >>> >>> Thoughts anyone? >>> >>> Eddie >>> >>> >>> >>> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter >>> Neerincx >>> Sent: Thursday, February 08, 2007 12:01 PM >>> To: Core developer announcements >>> Subject: Re: [MOBY-dev] Updates to MOBY Central >>> >>> Hi Eddie, >>> >>> I think I ran into a small problem. When I use >>> MOBY::Client::Central::DUMP I get the following error: >>> ------------------- >>> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/ >>> MOBY/Central' died because: >>> String value expected instead of ARRAY reference >>> >>> ERROR ERROR ERROR >>> ------------------- >>> >>> This happens both with: >>> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY >>> Central with S::L 0.69 >>> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY >>> Central with S::L 0.69 >>> >>> I'm suspecting the following line to be the cruel-pit: >>> >>> MOBY::Central.pm line 3139 sub DUMP_MySQL: return [@response]; >>> >>> I'm guessing your new S::L (de-)serializer expects an XML string >>> instead of the array ref... Is that possible? >>> >>> Cheers, >>> >>> Pi in update mode :) >>> _______________________________________________ >>> 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 >> >> >> >> -- >> 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 > > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1038 > Dreijenlaan 3 > 6703 HA Wageningen > phone: 0317-484 706 > fax: 0317-483 584 > mobile: 06-143 66 783 > pieter.neerincx at 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 Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 060 fax: 0317-483 584 mobile: 06-143 66 783 pieter.neerincx at wur.nl From markw at illuminae.com Sat Feb 10 02:59:04 2007 From: markw at illuminae.com (mark wilkinson) Date: Sat, 10 Feb 2007 02:59:04 +0000 GMT Subject: [MOBY-dev] New Perl Client::Service Function Message-ID: <1196561465-1171076434-cardhu_blackberry.rim.net-19978-@engine02-cell01> Just a heads-up that I just committed a new function to the MOBY::Client::Service module "enumerated_execute", that allows the client to set the queryID's (as opposed to them being autogenerated by the module). This is more reflective of how we (I?) envisioned that service execution should happen, since there is a need for the client to be able to keep track of which inputs led to which outputs in a multi-invocation service call. I know that this should have been an available function years ago... Sorry!! The Java code (eg Taverna) already does this, but I have been negligent in adding this functionality on the Perl side. INB folks, you may want to "mirror" this functionality in your Async Perl module... I haven't tested it (because I wrote it in the pub just now ;-) ) but it was only a small modification from what we had already so I'm fairly sure it will work. I'm going to test it tomorrow, but if any brave mobyers are bored on a Friday night (why would that be??) And want to try it themselves please let me know if it works for you! Cheers all! M -- Mark Wilkinson ...on the road! From d.haase at gsf.de Thu Feb 15 09:40:58 2007 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 15 Feb 2007 10:40:58 +0100 Subject: [MOBY-dev] getSignatureForm doesn't work Message-ID: <200702151040.58811.d.haase@gsf.de> Hello Canadians, the servlet at http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm for registration of signature URLs does not work. When I enter my data and press 'submit' it takes ages and then an error message (see below) is displayed. Moreover, the signature URL is not stored in the database. Regards, dirk And this is the error message: java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.updateMobyCentralDatabase(GetSignatureRDFResponse.java:179) 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) From edward.kawas at gmail.com Thu Feb 15 14:34:25 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 15 Feb 2007 06:34:25 -0800 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <200702151040.58811.d.haase@gsf.de> References: <200702151040.58811.d.haase@gsf.de> Message-ID: <001801c7510e$64ff8d90$6900a8c0@notebook> Hi Dirk, You do know that the form isn't supposed to be used to register services from a signatureURL, right? With that said, you are correct, the form seems to be broken... Did it work in the recent past? I am asking, because it is failing at an odd point in the code ... I will have it up soon. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase Sent: Thursday, February 15, 2007 1:41 AM To: Moby-dev at biomoby.org Subject: [MOBY-dev] getSignatureForm doesn't work Hello Canadians, the servlet at http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm for registration of signature URLs does not work. When I enter my data and press 'submit' it takes ages and then an error message (see below) is displayed. Moreover, the signature URL is not stored in the database. Regards, dirk And this is the error message: java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.update MobyCentralDatabase(GetSignatureRDFResponse.java:179) org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.doGet( GetSignatureRDFResponse.java:91) javax.servlet.http.HttpServlet.service(HttpServlet.java:689) javax.servlet.http.HttpServlet.service(HttpServlet.java:802) _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Feb 15 14:44:46 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 15 Feb 2007 06:44:46 -0800 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <200702151040.58811.d.haase@gsf.de> References: <200702151040.58811.d.haase@gsf.de> Message-ID: <001901c7510f$d730b000$6900a8c0@notebook> Dirk, The form is up and running again. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dirk Haase Sent: Thursday, February 15, 2007 1:41 AM To: Moby-dev at biomoby.org Subject: [MOBY-dev] getSignatureForm doesn't work Hello Canadians, the servlet at http://mobycentral.icapture.ubc.ca/authority/forms/getSignatureForm for registration of signature URLs does not work. When I enter my data and press 'submit' it takes ages and then an error message (see below) is displayed. Moreover, the signature URL is not stored in the database. Regards, dirk And this is the error message: java.lang.NullPointerException org.biomoby.client.ui.graphical.servlet.forms.GetSignatureRDFResponse.update MobyCentralDatabase(GetSignatureRDFResponse.java:179) 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) _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From d.haase at gsf.de Thu Feb 15 14:46:38 2007 From: d.haase at gsf.de (Dirk Haase) Date: Thu, 15 Feb 2007 15:46:38 +0100 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <001801c7510e$64ff8d90$6900a8c0@notebook> References: <200702151040.58811.d.haase@gsf.de> <001801c7510e$64ff8d90$6900a8c0@notebook> Message-ID: <200702151546.38647.d.haase@gsf.de> On Thursday 15 February 2007 15:34, Edward Kawas wrote: > Hi Dirk, > > You do know that the form isn't supposed to be used to register services > from a signatureURL, right? I thought I could use it to add a signature URL for a service which existed before in the registry but had no RDF description yet. Is that correct? > With that said, you are correct, the form seems to be broken... Did it work > in the recent past? I am asking, because it is failing at an odd point in > the code ... I got a message from a project partner last Friday. Before that I can't say anything. > I will have it up soon. Great! Regards, dirk From edward.kawas at gmail.com Thu Feb 15 14:55:51 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 15 Feb 2007 06:55:51 -0800 Subject: [MOBY-dev] getSignatureForm doesn't work In-Reply-To: <200702151546.38647.d.haase@gsf.de> References: <200702151040.58811.d.haase@gsf.de><001801c7510e$64ff8d90$6900a8c0@notebook> <200702151546.38647.d.haase@gsf.de> Message-ID: <002b01c75111$6391ec70$6900a8c0@notebook> >I thought I could use it to add a signature URL for a service which existed >before in the registry but had no RDF description yet. Is that correct? That is correct. I thought something else (although, I didn't understand how!), because someone else sent me a message about using it to register services from an RDF. Thanks Dirk, Eddie From Yogaraj.Khanal at usd.edu Thu Feb 15 17:45:52 2007 From: Yogaraj.Khanal at usd.edu (Yogaraj.Khanal at usd.edu) Date: Thu, 15 Feb 2007 11:45:52 -0600 Subject: [MOBY-dev] Regarding XML conversion Message-ID: <1ad0b71aacdf.1aacdf1ad0b7@usd.edu> Dear Mark, I was reading your comment form http://lists.open-bio.org/pipermail/moby-dev/2006-September/003798.html I was doing a similar projects like "Take any two arbitrary Web Services out there and try to automatically feed the output of one into the input of another" I was wondering if you could provide me with an example or the tutorial that explains how it works. I thank you in advance for your help and support. Regards, Y From gordonp at ucalgary.ca Fri Feb 16 15:15:56 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 16 Feb 2007 08:15:56 -0700 Subject: [MOBY-dev] Regarding XML conversion In-Reply-To: <1ad0b71aacdf.1aacdf1ad0b7@usd.edu> References: <1ad0b71aacdf.1aacdf1ad0b7@usd.edu> Message-ID: <45D5CAAC.60609@ucalgary.ca> Hi Yogaraj, This is, unfortunately, a near-impossible task because although you can take data from one service and pass it to another, you have no idea whether the xsd:String output in the WSDL of one service is semantically the same as the xsd:String input to another service. Web services deal with syntax (structure) only, whereas you need semantic (meaning) compatibility for real interoperability. That's why MOBY has a central ontology, and we are calling them Semantic Web Services (though not really as the W3C uses the term). One approach is to retrofit services to a semantic standard such as MOBY. It's a LOT of work to even semi-automate this (I am doing this now). If you want to do this generically for any WSDL, the best I can suggest is to restrict yourself to some easily recognizable data formats that you can detect as data comes out of services, such as strings encoding URLs or e-mail addresses. That way you can seamlessly and fairly confidently make services that output and consume URLs compatible. Trying to make all services compatible, I believe, is a sisyphean task. Regards, Paul ** > Dear Mark, > I was reading your comment form > http://lists.open-bio.org/pipermail/moby-dev/2006-September/003798.html > > I was doing a similar projects like > "Take any two arbitrary Web Services out > there and try to automatically feed the output of one into the input of > another" > > > I was wondering if you could provide me with an example or the tutorial that explains how it works. > > I thank you in advance for your help and support. > Regards, > Y > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,45d4b7937098222965079! > > > > From ivanp at mmb.pcb.ub.es Tue Feb 20 23:08:09 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 21 Feb 2007 00:08:09 +0100 Subject: [MOBY-dev] non-English characters & windows & jMoby Message-ID: <45DB7F59.6060607@mmb.pcb.ub.es> Dear list, I've experienced a strange effect trying to compile jmoby with the build.bat and build-dev.bat scripts under Windows. I was using Eclipse as CVS client. Eclipse needs to create a project under the selected workspace to store the local version of the code. The default workspace is created in the user folder under "Documents & Settings". In my case, my username is Iv?n (and notice this accented non-English "?"). In short, the path becomes like this: C:\Documents and Settings\Iv?n\workspace\moby-live\Java Well, when I tried to compile it, I got this message: C:\Documents and Settings\Iv?n\workspace\moby-live\Java>build-dev.bat Buildfile: build.xml BUILD FAILED Error reading project file C:\Documents and Settings\Iv?n\workspace\moby-live\Java\build.xml: no protocol: xmls/libraries.xml As you can see the "?" becomes a "?"... This can be solved in two different ways: - the easy one: move the location of moby-live to another path without non-English characters - the tricky one (works but generates ugly warnings): modify the build.xml file by replacing all the occurrences of for in lines from 3 to 12 Regards, -- ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ From markw at illuminae.com Tue Feb 20 23:44:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 15:44:43 -0800 Subject: [MOBY-dev] gbrowse moby Asynchronous service support Message-ID: It should support Async now, but there aren't any async services registered in our moby central. If someone from INB has a minute, could they register an async service in our registry and try it? (it will have to be one that consumes a simple or else gbrowse wont find it anyway, since it only operates on simples) Thanks! M From markw at illuminae.com Tue Feb 20 23:44:43 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 15:44:43 -0800 Subject: [MOBY-dev] gbrowse moby Asynchronous service support Message-ID: It should support Async now, but there aren't any async services registered in our moby central. If someone from INB has a minute, could they register an async service in our registry and try it? (it will have to be one that consumes a simple or else gbrowse wont find it anyway, since it only operates on simples) Thanks! M From markw at illuminae.com Tue Feb 20 23:39:20 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 15:39:20 -0800 Subject: [MOBY-dev] non-English characters & windows & jMoby In-Reply-To: <45DB7F59.6060607@mmb.pcb.ub.es> References: <45DB7F59.6060607@mmb.pcb.ub.es> Message-ID: > This can be solved in two different ways: > - the easy one: move the location of moby-live to another path without > non-English characters > - the tricky one (works but generates ugly warnings): modify the > build.xml file by replacing all the occurrences of Or even easier - you could change your name ;-) ;-) (sorry, I'll shut up now - not very helpful!) M From ivanp at mmb.pcb.ub.es Wed Feb 21 00:02:46 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Wed, 21 Feb 2007 01:02:46 +0100 Subject: [MOBY-dev] non-English characters & windows & jMoby In-Reply-To: References: <45DB7F59.6060607@mmb.pcb.ub.es> Message-ID: <45DB8C26.1040905@mmb.pcb.ub.es> Not sure if my parents would be happy about that? :-P No problemo! ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Mark Wilkinson escribi?: >> This can be solved in two different ways: >> - the easy one: move the location of moby-live to another path without >> non-English characters >> - the tricky one (works but generates ugly warnings): modify the >> build.xml file by replacing all the occurrences of >> > > Or even easier - you could change your name > > ;-) ;-) > > (sorry, I'll shut up now - not very helpful!) > > M > > > > _______________________________________________ > 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 Feb 21 02:40:52 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Feb 2007 18:40:52 -0800 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? Message-ID: Hi all, I'm curious as to whether anyone currently uses the OWL version of the Object ontology at http://biomoby.org/RESOUR CES/MOBY-S/Objects I have a much better version of the Objects ontology now, but it is structurally very different from that one. If anyone is actually USING that one for anything, then I'll deploy the new one at a different address, if not, then I'll over-write that one with the new one. Please let me know ASAP. Thanks! Mark From rroyo at lsi.upc.edu Wed Feb 21 05:48:58 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Wed, 21 Feb 2007 06:48:58 +0100 Subject: [MOBY-dev] gbrowse moby Asynchronous service support In-Reply-To: References: Message-ID: <45DBDD4A.8070309@lsi.upc.edu> Hello Mark, I just registered another 'moby-async' service: runNCBIBlastp (inb.bsc.es). When I try to execute it (with an AminoAcidSequence previously retrieved by getFeatureAASequence (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not recieving any requests on my side (I checked temporal directories and apache logs). By the way, we're going through some changes in our node. We're replacing the remote machine where most of our services were executed. So this service is not quite working. Instead of the blast report it should reply with: error 600, A generic error during internal processing (Basically, it tries to access the remote machine but since it is not accessible it returns this error; it takes about 5 minutes, so I use it to test asynchrony). And a minor thing: the 'Configure Parameters' button. I tried it with Firefox and IExplorer. The window is too small in both browsers and it is not resizable so it's hard to use it. That's probably because I have obsolete versions of these browsers though :-) Thanks! Romina Mark Wilkinson wrote: >It should support Async now, but there aren't any async services >registered in our moby central. > >If someone from INB has a minute, could they register an async service in >our registry and try it? (it will have to be one that consumes a simple >or else gbrowse wont find it anyway, since it only operates on simples) > >Thanks! > >M > > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev > > From rroyo at lsi.upc.edu Wed Feb 21 05:48:58 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Wed, 21 Feb 2007 06:48:58 +0100 Subject: [MOBY-dev] gbrowse moby Asynchronous service support In-Reply-To: References: Message-ID: <45DBDD4A.8070309@lsi.upc.edu> Hello Mark, I just registered another 'moby-async' service: runNCBIBlastp (inb.bsc.es). When I try to execute it (with an AminoAcidSequence previously retrieved by getFeatureAASequence (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not recieving any requests on my side (I checked temporal directories and apache logs). By the way, we're going through some changes in our node. We're replacing the remote machine where most of our services were executed. So this service is not quite working. Instead of the blast report it should reply with: error 600, A generic error during internal processing (Basically, it tries to access the remote machine but since it is not accessible it returns this error; it takes about 5 minutes, so I use it to test asynchrony). And a minor thing: the 'Configure Parameters' button. I tried it with Firefox and IExplorer. The window is too small in both browsers and it is not resizable so it's hard to use it. That's probably because I have obsolete versions of these browsers though :-) Thanks! Romina Mark Wilkinson wrote: >It should support Async now, but there aren't any async services >registered in our moby central. > >If someone from INB has a minute, could they register an async service in >our registry and try it? (it will have to be one that consumes a simple >or else gbrowse wont find it anyway, since it only operates on simples) > >Thanks! > >M > > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at lists.open-bio.org >http://lists.open-bio.org/mailman/listinfo/moby-dev > > From martin.senger at gmail.com Wed Feb 21 11:01:37 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Feb 2007 11:01:37 +0000 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: References: Message-ID: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Feb 21 11:01:37 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 21 Feb 2007 11:01:37 +0000 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: References: Message-ID: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Wed Feb 21 14:17:56 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 21 Feb 2007 06:17:56 -0800 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> Message-ID: <001201c755c3$1648ec50$6600a8c0@notebook> Mark, I use them. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: Wednesday, February 21, 2007 3:02 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ 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 Feb 21 14:17:56 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 21 Feb 2007 06:17:56 -0800 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> Message-ID: <001201c755c3$1648ec50$6600a8c0@notebook> Mark, I use them. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger Sent: Wednesday, February 21, 2007 3:02 AM To: Core developer announcements Cc: mobydev Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? I'm curious as to whether anyone currently uses the OWL version of the > Object ontology at > > http://biomoby.org/RESOUR CES/MOBY-S/Objects I do not know if anybody is using it - but the part of the BioMoby API is to get these URLs and call them. Definitely jMoby has these methods. If you intent to change the URL, make please sure that also the Central returns the new URLs in those methods. Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Feb 21 14:56:46 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 21 Feb 2007 07:56:46 -0700 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <001201c755c3$1648ec50$6600a8c0@notebook> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> <001201c755c3$1648ec50$6600a8c0@notebook> Message-ID: <45DC5DAE.6020508@ucalgary.ca> Me too (via Eddie's org.biomoby.shared.extended.DataTypeParser) > Mark, > > I use them. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Wednesday, February 21, 2007 3:02 AM > To: Core developer announcements > Cc: mobydev > Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? > > I'm curious as to whether anyone currently uses the OWL version of the > >> Object ontology at >> >> http://biomoby.org/RESOUR CES/MOBY-S/Objects >> > > > I do not know if anybody is using it - but the part of the BioMoby API is to > get these URLs and call them. Definitely jMoby has these methods. If you > intent to change the URL, make please sure that also the Central returns > the new URLs in those methods. > > Thanks, > Martin > > From gordonp at ucalgary.ca Wed Feb 21 14:56:46 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 21 Feb 2007 07:56:46 -0700 Subject: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? In-Reply-To: <001201c755c3$1648ec50$6600a8c0@notebook> References: <4d93f07c0702210301w21be290bt1129bec68a8da57e@mail.gmail.com> <001201c755c3$1648ec50$6600a8c0@notebook> Message-ID: <45DC5DAE.6020508@ucalgary.ca> Me too (via Eddie's org.biomoby.shared.extended.DataTypeParser) > Mark, > > I use them. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger > Sent: Wednesday, February 21, 2007 3:02 AM > To: Core developer announcements > Cc: mobydev > Subject: Re: [MOBY-dev] Does anyone use the MOBY Objects ontology in OWL? > > I'm curious as to whether anyone currently uses the OWL version of the > >> Object ontology at >> >> http://biomoby.org/RESOUR CES/MOBY-S/Objects >> > > > I do not know if anybody is using it - but the part of the BioMoby API is to > get these URLs and call them. Definitely jMoby has these methods. If you > intent to change the URL, make please sure that also the Central returns > the new URLs in those methods. > > Thanks, > Martin > > From markw at illuminae.com Wed Feb 21 15:29:41 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 21 Feb 2007 07:29:41 -0800 Subject: [MOBY-dev] gbrowse moby Asynchronous service support In-Reply-To: <45DBDD4A.8070309@lsi.upc.edu> References: <45DBDD4A.8070309@lsi.upc.edu> Message-ID: Thanks Romina. As soon as I get to work today I'll fix the problem - it should only take a half hour or so. v.v. the configure windows - I'll leave that to Eddie :-) M On Tue, 20 Feb 2007 21:48:58 -0800, Romina Royo wrote: > Hello Mark, > > I just registered another 'moby-async' service: runNCBIBlastp > (inb.bsc.es). > > When I try to execute it (with an AminoAcidSequence previously retrieved > by getFeatureAASequence > (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not > recieving any requests on my side (I checked > temporal directories and apache logs). From markw at illuminae.com Wed Feb 21 21:24:34 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 21 Feb 2007 13:24:34 -0800 Subject: [MOBY-dev] Welcome Wendy Alexander Message-ID: <1172093074.16907.8.camel@bioinfo.icapture.ubc.ca> Hi Mobyers! We've finally hired another pair of hands here in Vancouver. Wendy Alexander is starting with us this week as our second BioMoby core developer, to work side by side with Eddie. I've worked with Wendy for the past two years doing primarily database development activities, so we know each other well and I know she's a solid Java coder. She's new to Moby, so it will take a few weeks for her to get caught up on all the libraries, but she'll figure it all out soon enough. Anyway, this means that we can finally spend more time at this end getting various TODO's done! YAY! Best wishes all, Mark From markw at illuminae.com Wed Feb 21 21:25:29 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 21 Feb 2007 13:25:29 -0800 Subject: [MOBY-dev] [moby] Re: gbrowse moby Asynchronous service support In-Reply-To: <45DBDD4A.8070309@lsi.upc.edu> References: <45DBDD4A.8070309@lsi.upc.edu> Message-ID: <1172093129.16907.10.camel@bioinfo.icapture.ubc.ca> Would you believe that I simply forgot to "use" the MOBY::Async::Service module :-) It works now. M On Wed, 2007-02-21 at 06:48 +0100, Romina Royo wrote: > Hello Mark, > > I just registered another 'moby-async' service: runNCBIBlastp (inb.bsc.es). > > When I try to execute it (with an AminoAcidSequence previously retrieved > by getFeatureAASequence > (inb.bsc.es)), it doesn't seem to do anything... I'm afraid I'm not > recieving any requests on my side (I checked > temporal directories and apache logs). From edward.kawas at gmail.com Thu Feb 22 15:41:03 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Feb 2007 07:41:03 -0800 Subject: [MOBY-dev] async services Message-ID: <003c01c75697$dd4b2b90$6600a8c0@notebook> Hi, I wanted to verify something. If a synchronous client calls an async service, the async service is meant to act in synchronous mode, right? Of the handful of services that I have seen that are asynchronous, I don't believe that is the case. I believe that I have seen them return a message that contained a job id, and not the 'normal' moby message. This question is aimed mainly at the good folks at the inb, as I believe they are the only ones to have implemented any real asynchronous services. Thanks, Eddie ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From rroyo at lsi.upc.edu Thu Feb 22 16:14:33 2007 From: rroyo at lsi.upc.edu (Romina Royo) Date: Thu, 22 Feb 2007 17:14:33 +0100 Subject: [MOBY-dev] async services In-Reply-To: <003c01c75697$dd4b2b90$6600a8c0@notebook> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> Message-ID: <45DDC169.20004@lsi.upc.edu> Hello! This is how I understood that async services should work (and how I'm implementing them so far). Please anyone correct me if I'm doing it wrong! For example: The service runClustalwFast (authURI inb.bsc.es) is an asynchronous service. It can be executed in a synchronous mode (like all sync services): my $Service = MOBY::Client::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); and this would return the normal moby message. Or it can be called in an asynchronous mode: my $Service = MOBY::Async::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); which would _submit, _poll and finally return the results. Is this the behauviour everyone is expecting? Thanks! Romina Edward Kawas wrote: > Hi, > > > > I wanted to verify something. If a synchronous client calls an async > service, the async service is meant to act in synchronous mode, right? Of > the handful of services that I have seen that are asynchronous, I don't > believe that is the case. I believe that I have seen them return a message > that contained a job id, and not the 'normal' moby message. > > > > This question is aimed mainly at the good folks at the inb, as I believe > they are the only ones to have implemented any real asynchronous services. > > > > Thanks, > > > > Eddie > > > > ***CONFIDENTIALITY NOTICE*** > > This electronic message is intended only for the use of the addressee and > may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by unauthorized > individuals is strictly prohibited. If you have received this communication > in error, please notify the sender immediately by reply e-mail and delete > the original and all copies from your system. > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From edward.kawas at gmail.com Thu Feb 22 16:17:37 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Feb 2007 08:17:37 -0800 Subject: [MOBY-dev] async services In-Reply-To: <45DDC169.20004@lsi.upc.edu> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> <45DDC169.20004@lsi.upc.edu> Message-ID: <004701c7569c$f8e395e0$6600a8c0@notebook> Hi Romina, So you are describing what I actually thought is supposed to happen. I am just slightly confused, because while we were debugging some of the wsdl issues, I remember that one of the async services when called in sync mode returned a job id. Maybe that was just a one time thing ... Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo Sent: Thursday, February 22, 2007 8:15 AM To: Core developer announcements Subject: Re: [MOBY-dev] async services Hello! This is how I understood that async services should work (and how I'm implementing them so far). Please anyone correct me if I'm doing it wrong! For example: The service runClustalwFast (authURI inb.bsc.es) is an asynchronous service. It can be executed in a synchronous mode (like all sync services): my $Service = MOBY::Client::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); and this would return the normal moby message. Or it can be called in an asynchronous mode: my $Service = MOBY::Async::Service->new(service => $WSDL); my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] ]]); which would _submit, _poll and finally return the results. Is this the behauviour everyone is expecting? Thanks! Romina Edward Kawas wrote: > Hi, > > > > I wanted to verify something. If a synchronous client calls an async > service, the async service is meant to act in synchronous mode, right? Of > the handful of services that I have seen that are asynchronous, I don't > believe that is the case. I believe that I have seen them return a message > that contained a job id, and not the 'normal' moby message. > > > > This question is aimed mainly at the good folks at the inb, as I believe > they are the only ones to have implemented any real asynchronous services. > > > > Thanks, > > > > Eddie > > > > ***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 markw at illuminae.com Thu Feb 22 16:30:20 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 22 Feb 2007 08:30:20 -0800 Subject: [MOBY-dev] MOBY::Async::Service in Java? Message-ID: Hi INB'ers, Is there an equivalent to the MOBY::Async::Service module in Java? M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital From ivanp at mmb.pcb.ub.es Thu Feb 22 16:43:21 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Thu, 22 Feb 2007 17:43:21 +0100 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: References: Message-ID: <45DDC829.7080804@mmb.pcb.ub.es> Hi Mark, I'm afraid not; as long as I know, myself and another lab-mate are the only ones producing Java services at INB and we've not developed any prototype for async services. Sorry, ------------------------------------------------ Iv?n P?rraga Garc?a Computer Scientist Molecular Modelling & Bioinformatics Unit INB - Instituto Nacional de Bioinform?tica Josep Samitier 1-5 08028 Barcelona Spain tel.: +34 93 403 71 55 fax.: +34 93 403 71 57 e-mail: ivanp at mmb.pcb.ub.es group page: http://mmb.pcb.ub.es pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc ------------------------------------------------ Mark Wilkinson escribi?: > Hi INB'ers, > > Is there an equivalent to the MOBY::Async::Service module in Java? > > M > > From markw at illuminae.com Thu Feb 22 16:47:30 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 22 Feb 2007 08:47:30 -0800 Subject: [MOBY-dev] [moby] Re: MOBY::Async::Service in Java? In-Reply-To: <45DDC829.7080804@mmb.pcb.ub.es> References: <45DDC829.7080804@mmb.pcb.ub.es> Message-ID: <1172162850.20528.16.camel@bioinfo.icapture.ubc.ca> Perl wins again! ;-) ;-) Okay... Eddie and I will look into whether or not there is WSRF support in Java, and if there is, then we should probably create these modules soon, since it will be important to support Async in e.g. Taverna. Mark On Thu, 2007-02-22 at 17:43 +0100, Iv?n P?rraga Garc?a wrote: > Hi Mark, > > I'm afraid not; as long as I know, myself and another lab-mate are the > only ones producing Java services at INB and we've not developed any > prototype for async services. > > Sorry, > > ------------------------------------------------ > Iv?n P?rraga Garc?a > Computer Scientist > Molecular Modelling & Bioinformatics Unit > INB - Instituto Nacional de Bioinform?tica > Josep Samitier 1-5 > 08028 Barcelona > Spain > tel.: +34 93 403 71 55 > fax.: +34 93 403 71 57 > e-mail: ivanp at mmb.pcb.ub.es > group page: http://mmb.pcb.ub.es > pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc > ------------------------------------------------ > > > > Mark Wilkinson escribi?: > > Hi INB'ers, > > > > Is there an equivalent to the MOBY::Async::Service module in Java? > > > > M > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From johan at ac.uma.es Thu Feb 22 16:44:27 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Thu, 22 Feb 2007 17:44:27 +0100 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: References: Message-ID: <45DDC86B.60309@ac.uma.es> This is most likely being implemented as part of JMoby? Martin Senger could probably answer your question better. As far as I know INB does not have a server-side library for developing services in Java. We do have an async client-side library written in C++ (done as part of the scheduler/worker of MOWserv). More details when we finish the documentation... :-) Kind regards, Johan Mark Wilkinson wrote: > Hi INB'ers, > > Is there an equivalent to the MOBY::Async::Service module in Java? > > M > > -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 From johan at ac.uma.es Thu Feb 22 16:52:52 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Thu, 22 Feb 2007 17:52:52 +0100 Subject: [MOBY-dev] async services In-Reply-To: <004701c7569c$f8e395e0$6600a8c0@notebook> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> <45DDC169.20004@lsi.upc.edu> <004701c7569c$f8e395e0$6600a8c0@notebook> Message-ID: <45DDCA64.5080307@ac.uma.es> I think Romina is describing it correctly. Maybe the problem you experienced was a temporary bug in the async server-side library of Perl? Kind regards, Johan Edward Kawas wrote: > Hi Romina, > > So you are describing what I actually thought is supposed to happen. I am > just slightly confused, because while we were debugging some of the wsdl > issues, I remember that one of the async services when called in sync mode > returned a job id. > > Maybe that was just a one time thing ... > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo > Sent: Thursday, February 22, 2007 8:15 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] async services > > Hello! > > This is how I understood that async services should work (and how I'm > implementing them so far). > Please anyone correct me if I'm doing it wrong! > > For example: > > The service runClustalwFast (authURI inb.bsc.es) is an asynchronous > service. > > It can be executed in a synchronous mode (like all sync services): > > my $Service = MOBY::Client::Service->new(service => $WSDL); > my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] > ]]); > > and this would return the normal moby message. > > Or it can be called in an asynchronous mode: > > my $Service = MOBY::Async::Service->new(service => $WSDL); > my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] > ]]); > > which would _submit, _poll and finally return the results. > > Is this the behauviour everyone is expecting? > > Thanks! > Romina > > Edward Kawas wrote: > >> Hi, >> >> >> >> I wanted to verify something. If a synchronous client calls an async >> service, the async service is meant to act in synchronous mode, right? Of >> the handful of services that I have seen that are asynchronous, I don't >> believe that is the case. I believe that I have seen them return a message >> that contained a job id, and not the 'normal' moby message. >> >> >> >> This question is aimed mainly at the good folks at the inb, as I believe >> they are the only ones to have implemented any real asynchronous services. >> >> >> >> Thanks, >> >> >> >> Eddie >> >> >> >> ***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 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 From johan at ac.uma.es Thu Feb 22 17:01:25 2007 From: johan at ac.uma.es (Johan Karlsson) Date: Thu, 22 Feb 2007 18:01:25 +0100 Subject: [MOBY-dev] [moby] Re: MOBY::Async::Service in Java? In-Reply-To: <1172162850.20528.16.camel@bioinfo.icapture.ubc.ca> References: <45DDC829.7080804@mmb.pcb.ub.es> <1172162850.20528.16.camel@bioinfo.icapture.ubc.ca> Message-ID: <45DDCC65.9050504@ac.uma.es> Yes, there is at least this library from Apache: http://ws.apache.org/wsrf/ Kind regards, Johan Mark Wilkinson wrote: > Perl wins again! ;-) ;-) > > Okay... Eddie and I will look into whether or not there is WSRF support > in Java, and if there is, then we should probably create these modules > soon, since it will be important to support Async in e.g. Taverna. > > Mark > > > > On Thu, 2007-02-22 at 17:43 +0100, Iv?n P?rraga Garc?a wrote: > >> Hi Mark, >> >> I'm afraid not; as long as I know, myself and another lab-mate are the >> only ones producing Java services at INB and we've not developed any >> prototype for async services. >> >> Sorry, >> >> ------------------------------------------------ >> Iv?n P?rraga Garc?a >> Computer Scientist >> Molecular Modelling & Bioinformatics Unit >> INB - Instituto Nacional de Bioinform?tica >> Josep Samitier 1-5 >> 08028 Barcelona >> Spain >> tel.: +34 93 403 71 55 >> fax.: +34 93 403 71 57 >> e-mail: ivanp at mmb.pcb.ub.es >> group page: http://mmb.pcb.ub.es >> pgp key: http://mmb.pcb.ub.es/~ivanp/pubkey.asc >> ------------------------------------------------ >> >> >> >> Mark Wilkinson escribi?: >> >>> Hi INB'ers, >>> >>> Is there an equivalent to the MOBY::Async::Service module in Java? >>> >>> M >>> >>> >>> >> _______________________________________________ >> 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 > > -- Johan Karlsson Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 From enrique.deandres at pcm.uam.es Thu Feb 22 18:31:58 2007 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 22 Feb 2007 19:31:58 +0100 Subject: [MOBY-dev] async services In-Reply-To: <45DDCA64.5080307@ac.uma.es> References: <003c01c75697$dd4b2b90$6600a8c0@notebook> <45DDC169.20004@lsi.up c.edu><004701c7569c$f8e395e0$6600a8c0@notebook> <45DDCA64.5080307@ac.uma.es> Message-ID: <45DDE19E.6030509@pcm.uam.es> Hi, As Romina says, it is the behavior from the client side. >From the server side, it is required to have: - one method called service which answers the synchronous invocations with typical moby messages. From the perldoc MOBY::Async: sub sayHello { my $self = shift @_; # Here you can choose between sync or error return $self->sync($sayHello, 180, @_); # tries to execute #return $self->error(@_); # returns directly an exception } - one method called service_submit which answers the request (submission) of asynchrnous invocations with the job identifier. sub sayHello_submit { my $self = shift @_; return $self->async($sayHello, @_); } Note that here we use $self->async and in the previous $self->sync (or $self->error)... if not, it could be possible that sayHello return an ID. I have been checking the code and I don't see anything wrong, then I don't think it is a bug.... but could you send me more details? Which is that service which has that behavior. I hope it helps. Regards, Enrique. Johan Karlsson wrote: > I think Romina is describing it correctly. Maybe the problem you > experienced was a temporary bug in the async server-side library of Perl? > > Kind regards, > Johan > > Edward Kawas wrote: >> Hi Romina, >> >> So you are describing what I actually thought is supposed to happen. I am >> just slightly confused, because while we were debugging some of the wsdl >> issues, I remember that one of the async services when called in sync mode >> returned a job id. >> >> Maybe that was just a one time thing ... >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Romina Royo >> Sent: Thursday, February 22, 2007 8:15 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] async services >> >> Hello! >> >> This is how I understood that async services should work (and how I'm >> implementing them so far). >> Please anyone correct me if I'm doing it wrong! >> >> For example: >> >> The service runClustalwFast (authURI inb.bsc.es) is an asynchronous >> service. >> >> It can be executed in a synchronous mode (like all sync services): >> >> my $Service = MOBY::Client::Service->new(service => $WSDL); >> my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] >> ]]); >> >> and this would return the normal moby message. >> >> Or it can be called in an asynchronous mode: >> >> my $Service = MOBY::Async::Service->new(service => $WSDL); >> my $result = $Service->execute(XMLinputlist => [['sequences', [$data,$data2] >> ]]); >> >> which would _submit, _poll and finally return the results. >> >> Is this the behauviour everyone is expecting? >> >> Thanks! >> Romina >> >> Edward Kawas wrote: >> >>> Hi, >>> >>> >>> >>> I wanted to verify something. If a synchronous client calls an async >>> service, the async service is meant to act in synchronous mode, right? Of >>> the handful of services that I have seen that are asynchronous, I don't >>> believe that is the case. I believe that I have seen them return a message >>> that contained a job id, and not the 'normal' moby message. >>> >>> >>> >>> This question is aimed mainly at the good folks at the inb, as I believe >>> they are the only ones to have implemented any real asynchronous services. >>> >>> >>> >>> Thanks, >>> >>> >>> >>> Eddie >>> >>> >>> >>> ***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 >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > -- Enrique de Andres Saiz Unidad de Bioinform?tica (INB GNHC-1) Parque Cientifico de Madrid Ctra. de Colmenar, Km. 15. Campus UAM, Cantoblanco - Pabellon C 28049 Madrid Tel. (+34) 91 497 3448 Fax. (+34) 91 497 3471 http://www.fpcm.es http://www.inab.org From Yogaraj.Khanal at usd.edu Thu Feb 22 22:25:02 2007 From: Yogaraj.Khanal at usd.edu (Yogaraj.Khanal at usd.edu) Date: Thu, 22 Feb 2007 16:25:02 -0600 Subject: [MOBY-dev] Regarding XML Message-ID: <256d5e2509b0.2509b0256d5e@usd.edu> Hi Everyone, I was trying to run the workflow through this URL http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/workflows.html but I am getting this message This XML file does not appear to have any style information associated with it. The document tree is shown below. Can anyone guide me how do I see the workflow as in Taverna or the any tutorail that guides me to build one from the code listed in the above URL. Regards, Raj From edward.kawas at gmail.com Thu Feb 22 22:27:22 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Feb 2007 14:27:22 -0800 Subject: [MOBY-dev] Regarding XML In-Reply-To: <256d5e2509b0.2509b0256d5e@usd.edu> References: <256d5e2509b0.2509b0256d5e@usd.edu> Message-ID: <008801c756d0$a01893a0$6600a8c0@notebook> Hi, You will have to either: 1. save the workflow and load it locally, or 2. copy the workflow location (the link) and load the workflow into taverna 'from URL'. Hope that helps, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Yogaraj.Khanal at usd.edu Sent: Thursday, February 22, 2007 2:25 PM To: Core developer announcements Subject: [MOBY-dev] Regarding XML Hi Everyone, I was trying to run the workflow through this URL http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/wo rkflows.html but I am getting this message This XML file does not appear to have any style information associated with it. The document tree is shown below. Can anyone guide me how do I see the workflow as in Taverna or the any tutorail that guides me to build one from the code listed in the above URL. Regards, Raj _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev