From Sebastien.Carrere at toulouse.inra.fr Wed May 13 04:27:46 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 13 May 2009 10:27:46 +0200 Subject: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR Message-ID: <4A0A8482.5010503@toulouse.inra.fr> Bonjour, I try to deploy asynchronous web-services using perl API. I've got a SOAP error message when calling "http://docs.oasis-open.org/wsrf/rp-2/GetMultipleResourceProperties" (call for poll I think): ERROR: Failed to access class (wsrf::rp-2) at /www/www-bioinfo/biomoby/analysis/test/lib//SOAP/Lite.pm line 2628. Does someone already have such a problem ? I use SOAP::Lite rel 0.710.05. Here is a part of what my dispatcher contains: use SOAP::Transport::HTTP; use SOAP::Lite; use MOBY::Async::WSRF; use MOBY::Async::SimpleServer; MAIN: { my $cgi_object = new SOAP::Transport::HTTP::CGI; $cgi_object->serializer(WSRF::Serializer->new); $cgi_object->deserializer(WSRF::Deserializer->new); $cgi_object->on_action(sub{}); my $rh_services = &GetServicesFromDispatcherScriptName(); #$WSRF::Constants::WSRP = 'http://docs.oasis-open.org/wsrf/rp-2'; #$WSRF::Constants::WSRL = 'http://docs.oasis-open.org/wsrf/rl-2'; $rh_services->{$WSRF::Constants::WSRP.'/GetResourceProperty/GetResourcePropertyRequest'} = 'MOBY::Async::SimpleServer'; $rh_services->{$WSRF::Constants::WSRP.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest'} = 'MOBY::Async::SimpleServer'; $rh_services->{$WSRF::Constants::WSRL.'/ImmediateResourceTermination/DestroyRequest'} = 'MOBY::Async::SimpleServer'; $cgi_object->dispatch_with($rh_services); $cgi_object->handle; } merci, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From jmrodriguez at cnio.es Wed May 13 05:19:32 2009 From: jmrodriguez at cnio.es (jmrodriguez) Date: Wed, 13 May 2009 11:19:32 +0200 Subject: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR In-Reply-To: <4A0A8482.5010503@toulouse.inra.fr> References: <4A0A8482.5010503@toulouse.inra.fr> Message-ID: <4A0A90A4.1080309@cnio.es> Bonjour, I guess one problem is the WSRF constants that you use. You have to use these ones: $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest' $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' $WSRF::Constants::WSRPW='http://docs.oasis-open.org/wsrf/rpw-2' $WSRF::Constants::WSRLW='http://docs.oasis-open.org/wsrf/rlw-2' I hope is useful Cheer, J Sebastien Carrere wrote: > Bonjour, > > I try to deploy asynchronous web-services using perl API. > I've got a SOAP error message when calling > "http://docs.oasis-open.org/wsrf/rp-2/GetMultipleResourceProperties" > (call for poll I think): > > ERROR: Failed to access class (wsrf::rp-2) at > /www/www-bioinfo/biomoby/analysis/test/lib//SOAP/Lite.pm line 2628. > > Does someone already have such a problem ? > I use SOAP::Lite rel 0.710.05. > > > Here is a part of what my dispatcher contains: > > use SOAP::Transport::HTTP; > use SOAP::Lite; > use MOBY::Async::WSRF; > use MOBY::Async::SimpleServer; > > MAIN: > { > my $cgi_object = new SOAP::Transport::HTTP::CGI; > $cgi_object->serializer(WSRF::Serializer->new); > $cgi_object->deserializer(WSRF::Deserializer->new); > $cgi_object->on_action(sub{}); > > my $rh_services = &GetServicesFromDispatcherScriptName(); > > #$WSRF::Constants::WSRP = 'http://docs.oasis-open.org/wsrf/rp-2'; > #$WSRF::Constants::WSRL = 'http://docs.oasis-open.org/wsrf/rl-2'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetResourceProperty/GetResourcePropertyRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRL.'/ImmediateResourceTermination/DestroyRequest'} > = 'MOBY::Async::SimpleServer'; > $cgi_object->dispatch_with($rh_services); > $cgi_object->handle; > } > > > merci, > > Sebastien > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Have you tried CARGO? http://cargo2.bioinfo.cnio.es/ ********************* Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fern?ndez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Wed May 13 13:16:02 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 13 May 2009 10:16:02 -0700 Subject: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR In-Reply-To: <4A0A90A4.1080309@cnio.es> References: <4A0A8482.5010503@toulouse.inra.fr> <4A0A90A4.1080309@cnio.es> Message-ID: <4a0b0055.14b48c0a.1d28.1024@mx.google.com> As an aside, have you looked at http://search.cpan.org/dist/MOSES-MOBY/ It can handle moby-async services. Tutorial here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/const ruct_moses_async_service.html Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of jmrodriguez Sent: May-13-09 2:20 AM To: Core developer announcements Subject: Re: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR Bonjour, I guess one problem is the WSRF constants that you use. You have to use these ones: $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' $WSRF::Constants::WSRPW='http://docs.oasis-open.org/wsrf/rpw-2' $WSRF::Constants::WSRLW='http://docs.oasis-open.org/wsrf/rlw-2' I hope is useful Cheer, J Sebastien Carrere wrote: > Bonjour, > > I try to deploy asynchronous web-services using perl API. > I've got a SOAP error message when calling > "http://docs.oasis-open.org/wsrf/rp-2/GetMultipleResourceProperties" > (call for poll I think): > > ERROR: Failed to access class (wsrf::rp-2) at > /www/www-bioinfo/biomoby/analysis/test/lib//SOAP/Lite.pm line 2628. > > Does someone already have such a problem ? > I use SOAP::Lite rel 0.710.05. > > > Here is a part of what my dispatcher contains: > > use SOAP::Transport::HTTP; > use SOAP::Lite; > use MOBY::Async::WSRF; > use MOBY::Async::SimpleServer; > > MAIN: > { > my $cgi_object = new SOAP::Transport::HTTP::CGI; > $cgi_object->serializer(WSRF::Serializer->new); > $cgi_object->deserializer(WSRF::Deserializer->new); > $cgi_object->on_action(sub{}); > > my $rh_services = &GetServicesFromDispatcherScriptName(); > > #$WSRF::Constants::WSRP = 'http://docs.oasis-open.org/wsrf/rp-2'; > #$WSRF::Constants::WSRL = 'http://docs.oasis-open.org/wsrf/rl-2'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetResourceProperty/GetResourcePrope rtyRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetMultipleResourceProperties/GetMul tipleResourcePropertiesRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRL.'/ImmediateResourceTermination/Destroy Request'} > = 'MOBY::Async::SimpleServer'; > $cgi_object->dispatch_with($rh_services); > $cgi_object->handle; > } > > > merci, > > Sebastien > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Have you tried CARGO? http://cargo2.bioinfo.cnio.es/ ********************* Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fern?ndez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From joseluisdelarosa at gmail.com Thu May 14 14:05:19 2009 From: joseluisdelarosa at gmail.com (JoseLuis de la Rosa) Date: Thu, 14 May 2009 20:05:19 +0200 Subject: [MOBY-dev] Error reading services Message-ID: Hello all, I am newbie using biomoby and I am trying to read the registry using these statements: String endpoint = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; String cache = "cachemoby"; String namespace = "http://moby.ucalgary.ca/moby/MOBY-Central"; CentralDigestCachedImpl cdci = new org.biomoby.client.CentralDigestCachedImpl(endpoint, namespace, cache); System.out.println(cdci.getFullServiceTypes().length); However I am getting this error: Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDigestCachedImpl.java:676) at org.biomoby.client.CentralDigestCachedImpl.readServiceTypes(CentralDigestCachedImpl.java:872) at org.biomoby.client.CentralDigestImpl.getFullServiceTypes(CentralDigestImpl.java:283) at com.swstranslator.app.App.main(App.java:90) Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:223) at org.biomoby.client.CentralImpl.getServiceTypesAsXML(CentralImpl.java:859) at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDigestCachedImpl.java:601) ...3 more Caused by: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1083) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(libgcj.so.90) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:173) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:219) ...5 more Can anyone give me any hint about what I am doing wrong? Thanks in advance From edward.kawas at gmail.com Thu May 14 14:06:43 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 14 May 2009 11:06:43 -0700 Subject: [MOBY-dev] Error reading services In-Reply-To: References: Message-ID: <4a0c5db9.08b38c0a.72ae.ffff81ff@mx.google.com> Hi, The namespace should read: http://moby.ucalgary.ca/MOBY/Central That should fix things 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 JoseLuis de la Rosa Sent: May-14-09 11:05 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Error reading services Hello all, I am newbie using biomoby and I am trying to read the registry using these statements: String endpoint = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; String cache = "cachemoby"; String namespace = "http://moby.ucalgary.ca/moby/MOBY-Central"; CentralDigestCachedImpl cdci = new org.biomoby.client.CentralDigestCachedImpl(endpoint, namespace, cache); System.out.println(cdci.getFullServiceTypes().length); However I am getting this error: Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige stCachedImpl.java:676) at org.biomoby.client.CentralDigestCachedImpl.readServiceTypes(CentralDigestCac hedImpl.java:872) at org.biomoby.client.CentralDigestImpl.getFullServiceTypes(CentralDigestImpl.j ava:283) at com.swstranslator.app.App.main(App.java:90) Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:223) at org.biomoby.client.CentralImpl.getServiceTypesAsXML(CentralImpl.java:859) at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige stCachedImpl.java:601) ...3 more Caused by: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2 21) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12 8) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo ntext.java:1083) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc her.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(libgcj.so.90) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext .java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChe cker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:173) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:219) ...5 more Can anyone give me any hint about what I am doing wrong? Thanks in advance _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From joseluisdelarosa at gmail.com Sat May 16 13:08:59 2009 From: joseluisdelarosa at gmail.com (JoseLuis de la Rosa) Date: Sat, 16 May 2009 19:08:59 +0200 Subject: [MOBY-dev] Error reading services In-Reply-To: <4a0c5db9.08b38c0a.72ae.ffff81ff@mx.google.com> References: <4a0c5db9.08b38c0a.72ae.ffff81ff@mx.google.com> Message-ID: That's the mistake Thanks! On Thu, May 14, 2009 at 8:06 PM, Edward Kawas wrote: > Hi, > > The namespace should read: > http://moby.ucalgary.ca/MOBY/Central > > That should fix things 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 JoseLuis de la > Rosa > Sent: May-14-09 11:05 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Error reading services > > Hello all, > > I am newbie using biomoby and I am trying to read the registry using these > statements: > > String endpoint = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; > String cache = "cachemoby"; > String namespace = "http://moby.ucalgary.ca/moby/MOBY-Central"; > > CentralDigestCachedImpl cdci = new > org.biomoby.client.CentralDigestCachedImpl(endpoint, namespace, cache); > System.out.println(cdci.getFullServiceTypes().length); > > However I am getting this error: > > Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: Failed to access class (moby::MOBY-Central) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line > 54. > > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client > Fault actor: null > When calling: > http://moby.ucalgary.ca/moby/MOBY-Central.pl > =========== > > at > > org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige > stCachedImpl.java:676) > at > > org.biomoby.client.CentralDigestCachedImpl.readServiceTypes(CentralDigestCac > hedImpl.java:872) > at > > org.biomoby.client.CentralDigestImpl.getFullServiceTypes(CentralDigestImpl.j > ava:283) > at com.swstranslator.app.App.main(App.java:90) > Caused by: org.biomoby.shared.MobyException: ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: Failed to access class (moby::MOBY-Central) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line > 54. > > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client > Fault actor: null > When calling: > http://moby.ucalgary.ca/moby/MOBY-Central.pl > =========== > > at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:223) > at > org.biomoby.client.CentralImpl.getServiceTypesAsXML(CentralImpl.java:859) > at > > org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige > stCachedImpl.java:601) > ...3 more > Caused by: Failed to access class (moby::MOBY-Central) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line > 54. > > at > > org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2 > 21) > at > > org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12 > 8) > at > > org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo > ntext.java:1083) > at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) > at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown > Source) > at > > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc > her.dispatch(Unknown > Source) > at > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown > Source) > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) > at javax.xml.parsers.SAXParser.parse(libgcj.so.90) > at > > org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext > .java:226) > at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) > at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) > at > > org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChe > cker.java:62) > at org.apache.axis.client.AxisClient.invoke(AxisClient.java:173) > at org.apache.axis.client.Call.invokeEngine(Call.java:2719) > at org.apache.axis.client.Call.invoke(Call.java:2702) > at org.apache.axis.client.Call.invoke(Call.java:2378) > at org.apache.axis.client.Call.invoke(Call.java:2301) > at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:219) > ...5 more > > > Can anyone give me any hint about what I am doing wrong? > > Thanks in advance > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From edward.kawas at gmail.com Wed May 20 13:28:13 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 20 May 2009 10:28:13 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 Message-ID: <4a143db1.1a36720a.03b1.7297@mx.google.com> Hello All, I would like to remove the ports named 'input' and 'output' from t2. They aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x will not. Any objections? Thanks, Eddie From markw at illuminae.com Wed May 20 13:28:15 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 20 May 2009 10:28:15 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4a143db1.1a36720a.03b1.7297@mx.google.com> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> Message-ID: I am 100% in favour of this! M On Wed, 20 May 2009 10:28:13 -0700, Edward Kawas wrote: > Hello All, > > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna > 2.x > will not. > > Any objections? > > Thanks, > > Eddie > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From py at pingoured.fr Wed May 20 13:31:54 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 20 May 2009 19:31:54 +0200 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4a143db1.1a36720a.03b1.7297@mx.google.com> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> Message-ID: <1242840714.8582.7.camel@red.localdomain> On Wed, 2009-05-20 at 10:28 -0700, Edward Kawas wrote: > Hello All, > > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? Remove or substitute ? If substitute, by what ? Regards, Pierre From edward.kawas at gmail.com Wed May 20 13:53:54 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 20 May 2009 10:53:54 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <1242840714.8582.7.camel@red.localdomain> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> <1242840714.8582.7.camel@red.localdomain> Message-ID: <4a1443b6.1cba720a.18de.762f@mx.google.com> No substitute. There are named ports, Datatype(Articlename), and then there is 'input'/'output'. Most services wont function correctly if you use input/output anyways. Those ports were left intact for legacy reasons. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: May-20-09 10:32 AM To: Core developer announcements Subject: Re: [MOBY-dev] removing input/output ports from taverna 2 On Wed, 2009-05-20 at 10:28 -0700, Edward Kawas wrote: > Hello All, > > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? Remove or substitute ? If substitute, by what ? Regards, Pierre _______________________________________________ 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 May 20 13:54:44 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 20 May 2009 10:54:44 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <1242840714.8582.7.camel@red.localdomain> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> <1242840714.8582.7.camel@red.localdomain> Message-ID: remove. they are already ~duplicated in the taverna interface with the updated object-bound inputs and outputs; we've only keept supporting them this long in order to support (distant!) legacy workflows... but most services wont support legacy workflows now either, so I don't see the point of preserving support for them in Taverna. M On Wed, 20 May 2009 10:31:54 -0700, Pierre-Yves Chibon wrote: > On Wed, 2009-05-20 at 10:28 -0700, Edward Kawas wrote: >> Hello All, >> >> I would like to remove the ports named 'input' and 'output' from t2. >> They >> aren't used and confuse newbies. Taverna 1.x will keep them, but >> Taverna 2.x >> will not. >> >> Any objections? > > Remove or substitute ? > If substitute, by what ? > > Regards, > > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Wed May 20 20:09:55 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Thu, 21 May 2009 00:09:55 +0000 Subject: [MOBY-dev] Thanks Martin and Eddie! Message-ID: <1333389024-1242864659-cardhu_decombobulator_blackberry.rim.net-303208248-@bxe1299.bisx.prod.on.blackberry> Hi all! I just wanted to send a thank-you out to Martin and Eddie! I *finally* used MoSeS+Dashboard to write and deploy a Moby service. I timed myself - it took 5 minutes in total to write the service, register it, and deploy it on my server. A total of 158 characters typing (including *all* Perl code and the service metadata!), 6 menu choices, one radio button selection, and two button presses. For many services now it is actually *easier* to write and deploy a Moby service than it is to access the Website, enter the data, and copy/paste the result into a spreadsheet!! WOW!! Thanks for all your hard work, brilliant brain-power and planning!! Mark On the Road! From alanrw at cs.man.ac.uk Thu May 21 04:31:50 2009 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Thu, 21 May 2009 09:31:50 +0100 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4a143db1.1a36720a.03b1.7297@mx.google.com> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> Message-ID: <4A151176.4050000@cs.man.ac.uk> Edward Kawas wrote: > Hello All, Hello Eddie, > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? With a Taverna hat on, what will this mean? Also, when some types of services are added in the development version of Taverna 2, it now automatically brings up a configuraton panel e.g. for Beanshell or Biomart. Should it bring up the "Moby Service Details" panel for BioMoby services? > Thanks, > > Eddie Alan From edward.kawas at gmail.com Thu May 21 09:15:53 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 21 May 2009 06:15:53 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4A151176.4050000@cs.man.ac.uk> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> <4A151176.4050000@cs.man.ac.uk> Message-ID: <4a15540f.1ed7720a.35c8.0fdb@mx.google.com> Hi Alan, This doesn't mean anything to Taverna except there would be 2 fewer ports shown to users. I don't think that it should pop up anything automatically... if anything, it could maybe pop up the 'configure' panel. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Alan Williams Sent: May-21-09 1:32 AM To: Core developer announcements Subject: Re: [MOBY-dev] removing input/output ports from taverna 2 Edward Kawas wrote: > Hello All, Hello Eddie, > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? With a Taverna hat on, what will this mean? Also, when some types of services are added in the development version of Taverna 2, it now automatically brings up a configuraton panel e.g. for Beanshell or Biomart. Should it bring up the "Moby Service Details" panel for BioMoby services? > Thanks, > > Eddie Alan _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From soiland-reyes at cs.manchester.ac.uk Tue May 26 06:50:27 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Tue, 26 May 2009 11:50:27 +0100 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? Message-ID: I am get connection time-out trying to connect to http://biomoby.org/m2repo/ - and even to http://biomoby.org/ Ping works: : stain at rpc268 ~;ping biomoby.org PING biomoby.org (207.154.17.70) 56(84) bytes of data. 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=1 ttl=48 time=87.7 ms 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=2 ttl=48 time=87.8 ms Connecting to HTTP however seems to time out: : stain at rpc268 ~;wget http://biomoby.org/ --2009-05-26 11:49:26-- http://biomoby.org/ Resolving biomoby.org... 207.154.17.70 Connecting to biomoby.org|207.154.17.70|:80... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From edward.kawas at gmail.com Tue May 26 10:05:38 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 26 May 2009 07:05:38 -0700 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: References: Message-ID: <4a1bf739.0ebb720a.0609.7721@mx.google.com> I can connect to the repo ... Is it still down 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 Stian Soiland-Reyes Sent: May-26-09 3:50 AM To: Core developer announcements Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? I am get connection time-out trying to connect to http://biomoby.org/m2repo/ - and even to http://biomoby.org/ Ping works: : stain at rpc268 ~;ping biomoby.org PING biomoby.org (207.154.17.70) 56(84) bytes of data. 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=1 ttl=48 time=87.7 ms 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=2 ttl=48 time=87.8 ms Connecting to HTTP however seems to time out: : stain at rpc268 ~;wget http://biomoby.org/ --2009-05-26 11:49:26-- http://biomoby.org/ Resolving biomoby.org... 207.154.17.70 Connecting to biomoby.org|207.154.17.70|:80... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester _______________________________________________ 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 May 26 10:05:47 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Tue, 26 May 2009 14:05:47 +0000 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: <4a1bf739.0ebb720a.0609.7721@mx.google.com> References: <4a1bf739.0ebb720a.0609.7721@mx.google.com> Message-ID: <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> Works for me from Alberta too... On the Road! -----Original Message----- From: "Edward Kawas" Date: Tue, 26 May 2009 07:05:38 To: 'Core developer announcements' Subject: Re: [MOBY-dev] Maven repository and http://biomoby.org down..? I can connect to the repo ... Is it still down 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 Stian Soiland-Reyes Sent: May-26-09 3:50 AM To: Core developer announcements Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? I am get connection time-out trying to connect to http://biomoby.org/m2repo/ - and even to http://biomoby.org/ Ping works: : stain at rpc268 ~;ping biomoby.org PING biomoby.org (207.154.17.70) 56(84) bytes of data. 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=1 ttl=48 time=87.7 ms 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=2 ttl=48 time=87.8 ms Connecting to HTTP however seems to time out: : stain at rpc268 ~;wget http://biomoby.org/ --2009-05-26 11:49:26-- http://biomoby.org/ Resolving biomoby.org... 207.154.17.70 Connecting to biomoby.org|207.154.17.70|:80... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester _______________________________________________ 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 soiland-reyes at cs.manchester.ac.uk Fri May 29 05:19:46 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 29 May 2009 10:19:46 +0100 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> References: <4a1bf739.0ebb720a.0609.7721@mx.google.com> <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> Message-ID: On Tue, May 26, 2009 at 15:05, wrote: > Works for me from Alberta too... yeah, up again now :-) Perhaps there were some clouds over the Atlantic.. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From markw at illuminae.com Fri May 29 13:32:49 2009 From: markw at illuminae.com (Mark) Date: Fri, 29 May 2009 10:32:49 -0700 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: References: <4a1bf739.0ebb720a.0609.7721@mx.google.com> <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> Message-ID: Must be cloudy over the atlantic again... I am unable to get through to taverna.org.uk today! M On Fri, 29 May 2009 02:19:46 -0700, Stian Soiland-Reyes wrote: > On Tue, May 26, 2009 at 15:05, wrote: >> Works for me from Alberta too... > > yeah, up again now :-) > > Perhaps there were some clouds over the Atlantic.. > > > From alanrw at cs.man.ac.uk Fri May 29 19:52:08 2009 From: alanrw at cs.man.ac.uk (Alan R Williams) Date: Sat, 30 May 2009 00:52:08 +0100 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? Message-ID: Can you see http://www.mygrid.org.uk or http://rosalind.cs.man.ac.uk ? If not, how about http://www.cs.man.ac.uk or http://www.man.ac.uk ? Alan From Sebastien.Carrere at toulouse.inra.fr Wed May 13 08:27:46 2009 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 13 May 2009 10:27:46 +0200 Subject: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR Message-ID: <4A0A8482.5010503@toulouse.inra.fr> Bonjour, I try to deploy asynchronous web-services using perl API. I've got a SOAP error message when calling "http://docs.oasis-open.org/wsrf/rp-2/GetMultipleResourceProperties" (call for poll I think): ERROR: Failed to access class (wsrf::rp-2) at /www/www-bioinfo/biomoby/analysis/test/lib//SOAP/Lite.pm line 2628. Does someone already have such a problem ? I use SOAP::Lite rel 0.710.05. Here is a part of what my dispatcher contains: use SOAP::Transport::HTTP; use SOAP::Lite; use MOBY::Async::WSRF; use MOBY::Async::SimpleServer; MAIN: { my $cgi_object = new SOAP::Transport::HTTP::CGI; $cgi_object->serializer(WSRF::Serializer->new); $cgi_object->deserializer(WSRF::Deserializer->new); $cgi_object->on_action(sub{}); my $rh_services = &GetServicesFromDispatcherScriptName(); #$WSRF::Constants::WSRP = 'http://docs.oasis-open.org/wsrf/rp-2'; #$WSRF::Constants::WSRL = 'http://docs.oasis-open.org/wsrf/rl-2'; $rh_services->{$WSRF::Constants::WSRP.'/GetResourceProperty/GetResourcePropertyRequest'} = 'MOBY::Async::SimpleServer'; $rh_services->{$WSRF::Constants::WSRP.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest'} = 'MOBY::Async::SimpleServer'; $rh_services->{$WSRF::Constants::WSRL.'/ImmediateResourceTermination/DestroyRequest'} = 'MOBY::Async::SimpleServer'; $cgi_object->dispatch_with($rh_services); $cgi_object->handle; } merci, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From jmrodriguez at cnio.es Wed May 13 09:19:32 2009 From: jmrodriguez at cnio.es (jmrodriguez) Date: Wed, 13 May 2009 11:19:32 +0200 Subject: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR In-Reply-To: <4A0A8482.5010503@toulouse.inra.fr> References: <4A0A8482.5010503@toulouse.inra.fr> Message-ID: <4A0A90A4.1080309@cnio.es> Bonjour, I guess one problem is the WSRF constants that you use. You have to use these ones: $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest' $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' $WSRF::Constants::WSRPW='http://docs.oasis-open.org/wsrf/rpw-2' $WSRF::Constants::WSRLW='http://docs.oasis-open.org/wsrf/rlw-2' I hope is useful Cheer, J Sebastien Carrere wrote: > Bonjour, > > I try to deploy asynchronous web-services using perl API. > I've got a SOAP error message when calling > "http://docs.oasis-open.org/wsrf/rp-2/GetMultipleResourceProperties" > (call for poll I think): > > ERROR: Failed to access class (wsrf::rp-2) at > /www/www-bioinfo/biomoby/analysis/test/lib//SOAP/Lite.pm line 2628. > > Does someone already have such a problem ? > I use SOAP::Lite rel 0.710.05. > > > Here is a part of what my dispatcher contains: > > use SOAP::Transport::HTTP; > use SOAP::Lite; > use MOBY::Async::WSRF; > use MOBY::Async::SimpleServer; > > MAIN: > { > my $cgi_object = new SOAP::Transport::HTTP::CGI; > $cgi_object->serializer(WSRF::Serializer->new); > $cgi_object->deserializer(WSRF::Deserializer->new); > $cgi_object->on_action(sub{}); > > my $rh_services = &GetServicesFromDispatcherScriptName(); > > #$WSRF::Constants::WSRP = 'http://docs.oasis-open.org/wsrf/rp-2'; > #$WSRF::Constants::WSRL = 'http://docs.oasis-open.org/wsrf/rl-2'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetResourceProperty/GetResourcePropertyRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRL.'/ImmediateResourceTermination/DestroyRequest'} > = 'MOBY::Async::SimpleServer'; > $cgi_object->dispatch_with($rh_services); > $cgi_object->handle; > } > > > merci, > > Sebastien > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Have you tried CARGO? http://cargo2.bioinfo.cnio.es/ ********************* Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fern?ndez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From edward.kawas at gmail.com Wed May 13 17:16:02 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 13 May 2009 10:16:02 -0700 Subject: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR In-Reply-To: <4A0A90A4.1080309@cnio.es> References: <4A0A8482.5010503@toulouse.inra.fr> <4A0A90A4.1080309@cnio.es> Message-ID: <4a0b0055.14b48c0a.1d28.1024@mx.google.com> As an aside, have you looked at http://search.cpan.org/dist/MOSES-MOBY/ It can handle moby-async services. Tutorial here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/const ruct_moses_async_service.html Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of jmrodriguez Sent: May-13-09 2:20 AM To: Core developer announcements Subject: Re: [MOBY-dev] Asynchronous web-service SOAP::Lite ERROR Bonjour, I guess one problem is the WSRF constants that you use. You have to use these ones: $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP ropertiesRequest' $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' $WSRF::Constants::WSRPW='http://docs.oasis-open.org/wsrf/rpw-2' $WSRF::Constants::WSRLW='http://docs.oasis-open.org/wsrf/rlw-2' I hope is useful Cheer, J Sebastien Carrere wrote: > Bonjour, > > I try to deploy asynchronous web-services using perl API. > I've got a SOAP error message when calling > "http://docs.oasis-open.org/wsrf/rp-2/GetMultipleResourceProperties" > (call for poll I think): > > ERROR: Failed to access class (wsrf::rp-2) at > /www/www-bioinfo/biomoby/analysis/test/lib//SOAP/Lite.pm line 2628. > > Does someone already have such a problem ? > I use SOAP::Lite rel 0.710.05. > > > Here is a part of what my dispatcher contains: > > use SOAP::Transport::HTTP; > use SOAP::Lite; > use MOBY::Async::WSRF; > use MOBY::Async::SimpleServer; > > MAIN: > { > my $cgi_object = new SOAP::Transport::HTTP::CGI; > $cgi_object->serializer(WSRF::Serializer->new); > $cgi_object->deserializer(WSRF::Deserializer->new); > $cgi_object->on_action(sub{}); > > my $rh_services = &GetServicesFromDispatcherScriptName(); > > #$WSRF::Constants::WSRP = 'http://docs.oasis-open.org/wsrf/rp-2'; > #$WSRF::Constants::WSRL = 'http://docs.oasis-open.org/wsrf/rl-2'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetResourceProperty/GetResourcePrope rtyRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRP.'/GetMultipleResourceProperties/GetMul tipleResourcePropertiesRequest'} > = 'MOBY::Async::SimpleServer'; > > $rh_services->{$WSRF::Constants::WSRL.'/ImmediateResourceTermination/Destroy Request'} > = 'MOBY::Async::SimpleServer'; > $cgi_object->dispatch_with($rh_services); > $cgi_object->handle; > } > > > merci, > > Sebastien > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Have you tried CARGO? http://cargo2.bioinfo.cnio.es/ ********************* Jos? Manuel Rodr?guez Carrasco e-mail: jmrodriguez at cnio.es Tlfn: (+34) 91 732 80 00 ext: 2256 Fax: (+34) 91 224 69 76 Bioinformatic Unit Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029 Address: C/. Melchor Fern?ndez Almagro n? 3, Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From joseluisdelarosa at gmail.com Thu May 14 18:05:19 2009 From: joseluisdelarosa at gmail.com (JoseLuis de la Rosa) Date: Thu, 14 May 2009 20:05:19 +0200 Subject: [MOBY-dev] Error reading services Message-ID: Hello all, I am newbie using biomoby and I am trying to read the registry using these statements: String endpoint = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; String cache = "cachemoby"; String namespace = "http://moby.ucalgary.ca/moby/MOBY-Central"; CentralDigestCachedImpl cdci = new org.biomoby.client.CentralDigestCachedImpl(endpoint, namespace, cache); System.out.println(cdci.getFullServiceTypes().length); However I am getting this error: Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDigestCachedImpl.java:676) at org.biomoby.client.CentralDigestCachedImpl.readServiceTypes(CentralDigestCachedImpl.java:872) at org.biomoby.client.CentralDigestImpl.getFullServiceTypes(CentralDigestImpl.java:283) at com.swstranslator.app.App.main(App.java:90) Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:223) at org.biomoby.client.CentralImpl.getServiceTypesAsXML(CentralImpl.java:859) at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDigestCachedImpl.java:601) ...3 more Caused by: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:221) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:128) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1083) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(libgcj.so.90) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:173) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:219) ...5 more Can anyone give me any hint about what I am doing wrong? Thanks in advance From edward.kawas at gmail.com Thu May 14 18:06:43 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 14 May 2009 11:06:43 -0700 Subject: [MOBY-dev] Error reading services In-Reply-To: References: Message-ID: <4a0c5db9.08b38c0a.72ae.ffff81ff@mx.google.com> Hi, The namespace should read: http://moby.ucalgary.ca/MOBY/Central That should fix things 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 JoseLuis de la Rosa Sent: May-14-09 11:05 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] Error reading services Hello all, I am newbie using biomoby and I am trying to read the registry using these statements: String endpoint = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; String cache = "cachemoby"; String namespace = "http://moby.ucalgary.ca/moby/MOBY-Central"; CentralDigestCachedImpl cdci = new org.biomoby.client.CentralDigestCachedImpl(endpoint, namespace, cache); System.out.println(cdci.getFullServiceTypes().length); However I am getting this error: Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige stCachedImpl.java:676) at org.biomoby.client.CentralDigestCachedImpl.readServiceTypes(CentralDigestCac hedImpl.java:872) at org.biomoby.client.CentralDigestImpl.getFullServiceTypes(CentralDigestImpl.j ava:283) at com.swstranslator.app.App.main(App.java:90) Caused by: org.biomoby.shared.MobyException: ===ERROR=== Fault details: [stackTrace: null] [hostname: null] Fault string: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client Fault actor: null When calling: http://moby.ucalgary.ca/moby/MOBY-Central.pl =========== at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:223) at org.biomoby.client.CentralImpl.getServiceTypesAsXML(CentralImpl.java:859) at org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige stCachedImpl.java:601) ...3 more Caused by: Failed to access class (moby::MOBY-Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line 54. at org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2 21) at org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12 8) at org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo ntext.java:1083) at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc her.dispatch(Unknown Source) at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(libgcj.so.90) at org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext .java:226) at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) at org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChe cker.java:62) at org.apache.axis.client.AxisClient.invoke(AxisClient.java:173) at org.apache.axis.client.Call.invokeEngine(Call.java:2719) at org.apache.axis.client.Call.invoke(Call.java:2702) at org.apache.axis.client.Call.invoke(Call.java:2378) at org.apache.axis.client.Call.invoke(Call.java:2301) at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:219) ...5 more Can anyone give me any hint about what I am doing wrong? Thanks in advance _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From joseluisdelarosa at gmail.com Sat May 16 17:08:59 2009 From: joseluisdelarosa at gmail.com (JoseLuis de la Rosa) Date: Sat, 16 May 2009 19:08:59 +0200 Subject: [MOBY-dev] Error reading services In-Reply-To: <4a0c5db9.08b38c0a.72ae.ffff81ff@mx.google.com> References: <4a0c5db9.08b38c0a.72ae.ffff81ff@mx.google.com> Message-ID: That's the mistake Thanks! On Thu, May 14, 2009 at 8:06 PM, Edward Kawas wrote: > Hi, > > The namespace should read: > http://moby.ucalgary.ca/MOBY/Central > > That should fix things 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 JoseLuis de la > Rosa > Sent: May-14-09 11:05 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Error reading services > > Hello all, > > I am newbie using biomoby and I am trying to read the registry using these > statements: > > String endpoint = "http://moby.ucalgary.ca/moby/MOBY-Central.pl"; > String cache = "cachemoby"; > String namespace = "http://moby.ucalgary.ca/moby/MOBY-Central"; > > CentralDigestCachedImpl cdci = new > org.biomoby.client.CentralDigestCachedImpl(endpoint, namespace, cache); > System.out.println(cdci.getFullServiceTypes().length); > > However I am getting this error: > > Exception in thread "main" org.biomoby.shared.MobyException: ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: Failed to access class (moby::MOBY-Central) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line > 54. > > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client > Fault actor: null > When calling: > http://moby.ucalgary.ca/moby/MOBY-Central.pl > =========== > > at > > org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige > stCachedImpl.java:676) > at > > org.biomoby.client.CentralDigestCachedImpl.readServiceTypes(CentralDigestCac > hedImpl.java:872) > at > > org.biomoby.client.CentralDigestImpl.getFullServiceTypes(CentralDigestImpl.j > ava:283) > at com.swstranslator.app.App.main(App.java:90) > Caused by: org.biomoby.shared.MobyException: ===ERROR=== > Fault details: > [stackTrace: null] > [hostname: null] > Fault string: Failed to access class (moby::MOBY-Central) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line > 54. > > Fault code: {http://schemas.xmlsoap.org/soap/envelope/}Client > Fault actor: null > When calling: > http://moby.ucalgary.ca/moby/MOBY-Central.pl > =========== > > at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:223) > at > org.biomoby.client.CentralImpl.getServiceTypesAsXML(CentralImpl.java:859) > at > > org.biomoby.client.CentralDigestCachedImpl.fillServiceTypesCache(CentralDige > stCachedImpl.java:601) > ...3 more > Caused by: Failed to access class (moby::MOBY-Central) at > /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm line 2473, line > 54. > > at > > org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:2 > 21) > at > > org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:12 > 8) > at > > org.apache.axis.encoding.DeserializationContext.endElement(DeserializationCo > ntext.java:1083) > at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source) > at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown > Source) > at > > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatc > her.dispatch(Unknown > Source) > at > org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown > Source) > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) > at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) > at javax.xml.parsers.SAXParser.parse(libgcj.so.90) > at > > org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext > .java:226) > at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:645) > at org.apache.axis.Message.getSOAPEnvelope(Message.java:424) > at > > org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChe > cker.java:62) > at org.apache.axis.client.AxisClient.invoke(AxisClient.java:173) > at org.apache.axis.client.Call.invokeEngine(Call.java:2719) > at org.apache.axis.client.Call.invoke(Call.java:2702) > at org.apache.axis.client.Call.invoke(Call.java:2378) > at org.apache.axis.client.Call.invoke(Call.java:2301) > at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:219) > ...5 more > > > Can anyone give me any hint about what I am doing wrong? > > Thanks in advance > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From edward.kawas at gmail.com Wed May 20 17:28:13 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 20 May 2009 10:28:13 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 Message-ID: <4a143db1.1a36720a.03b1.7297@mx.google.com> Hello All, I would like to remove the ports named 'input' and 'output' from t2. They aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x will not. Any objections? Thanks, Eddie From markw at illuminae.com Wed May 20 17:28:15 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 20 May 2009 10:28:15 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4a143db1.1a36720a.03b1.7297@mx.google.com> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> Message-ID: I am 100% in favour of this! M On Wed, 20 May 2009 10:28:13 -0700, Edward Kawas wrote: > Hello All, > > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna > 2.x > will not. > > Any objections? > > Thanks, > > Eddie > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From py at pingoured.fr Wed May 20 17:31:54 2009 From: py at pingoured.fr (Pierre-Yves Chibon) Date: Wed, 20 May 2009 19:31:54 +0200 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4a143db1.1a36720a.03b1.7297@mx.google.com> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> Message-ID: <1242840714.8582.7.camel@red.localdomain> On Wed, 2009-05-20 at 10:28 -0700, Edward Kawas wrote: > Hello All, > > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? Remove or substitute ? If substitute, by what ? Regards, Pierre From edward.kawas at gmail.com Wed May 20 17:53:54 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 20 May 2009 10:53:54 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <1242840714.8582.7.camel@red.localdomain> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> <1242840714.8582.7.camel@red.localdomain> Message-ID: <4a1443b6.1cba720a.18de.762f@mx.google.com> No substitute. There are named ports, Datatype(Articlename), and then there is 'input'/'output'. Most services wont function correctly if you use input/output anyways. Those ports were left intact for legacy reasons. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pierre-Yves Chibon Sent: May-20-09 10:32 AM To: Core developer announcements Subject: Re: [MOBY-dev] removing input/output ports from taverna 2 On Wed, 2009-05-20 at 10:28 -0700, Edward Kawas wrote: > Hello All, > > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? Remove or substitute ? If substitute, by what ? Regards, Pierre _______________________________________________ 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 May 20 17:54:44 2009 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 20 May 2009 10:54:44 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <1242840714.8582.7.camel@red.localdomain> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> <1242840714.8582.7.camel@red.localdomain> Message-ID: remove. they are already ~duplicated in the taverna interface with the updated object-bound inputs and outputs; we've only keept supporting them this long in order to support (distant!) legacy workflows... but most services wont support legacy workflows now either, so I don't see the point of preserving support for them in Taverna. M On Wed, 20 May 2009 10:31:54 -0700, Pierre-Yves Chibon wrote: > On Wed, 2009-05-20 at 10:28 -0700, Edward Kawas wrote: >> Hello All, >> >> I would like to remove the ports named 'input' and 'output' from t2. >> They >> aren't used and confuse newbies. Taverna 1.x will keep them, but >> Taverna 2.x >> will not. >> >> Any objections? > > Remove or substitute ? > If substitute, by what ? > > Regards, > > Pierre > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From markw at illuminae.com Thu May 21 00:09:55 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Thu, 21 May 2009 00:09:55 +0000 Subject: [MOBY-dev] Thanks Martin and Eddie! Message-ID: <1333389024-1242864659-cardhu_decombobulator_blackberry.rim.net-303208248-@bxe1299.bisx.prod.on.blackberry> Hi all! I just wanted to send a thank-you out to Martin and Eddie! I *finally* used MoSeS+Dashboard to write and deploy a Moby service. I timed myself - it took 5 minutes in total to write the service, register it, and deploy it on my server. A total of 158 characters typing (including *all* Perl code and the service metadata!), 6 menu choices, one radio button selection, and two button presses. For many services now it is actually *easier* to write and deploy a Moby service than it is to access the Website, enter the data, and copy/paste the result into a spreadsheet!! WOW!! Thanks for all your hard work, brilliant brain-power and planning!! Mark On the Road! From alanrw at cs.man.ac.uk Thu May 21 08:31:50 2009 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Thu, 21 May 2009 09:31:50 +0100 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4a143db1.1a36720a.03b1.7297@mx.google.com> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> Message-ID: <4A151176.4050000@cs.man.ac.uk> Edward Kawas wrote: > Hello All, Hello Eddie, > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? With a Taverna hat on, what will this mean? Also, when some types of services are added in the development version of Taverna 2, it now automatically brings up a configuraton panel e.g. for Beanshell or Biomart. Should it bring up the "Moby Service Details" panel for BioMoby services? > Thanks, > > Eddie Alan From edward.kawas at gmail.com Thu May 21 13:15:53 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 21 May 2009 06:15:53 -0700 Subject: [MOBY-dev] removing input/output ports from taverna 2 In-Reply-To: <4A151176.4050000@cs.man.ac.uk> References: <4a143db1.1a36720a.03b1.7297@mx.google.com> <4A151176.4050000@cs.man.ac.uk> Message-ID: <4a15540f.1ed7720a.35c8.0fdb@mx.google.com> Hi Alan, This doesn't mean anything to Taverna except there would be 2 fewer ports shown to users. I don't think that it should pop up anything automatically... if anything, it could maybe pop up the 'configure' panel. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Alan Williams Sent: May-21-09 1:32 AM To: Core developer announcements Subject: Re: [MOBY-dev] removing input/output ports from taverna 2 Edward Kawas wrote: > Hello All, Hello Eddie, > I would like to remove the ports named 'input' and 'output' from t2. They > aren't used and confuse newbies. Taverna 1.x will keep them, but Taverna 2.x > will not. > > Any objections? With a Taverna hat on, what will this mean? Also, when some types of services are added in the development version of Taverna 2, it now automatically brings up a configuraton panel e.g. for Beanshell or Biomart. Should it bring up the "Moby Service Details" panel for BioMoby services? > Thanks, > > Eddie Alan _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From soiland-reyes at cs.manchester.ac.uk Tue May 26 10:50:27 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Tue, 26 May 2009 11:50:27 +0100 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? Message-ID: I am get connection time-out trying to connect to http://biomoby.org/m2repo/ - and even to http://biomoby.org/ Ping works: : stain at rpc268 ~;ping biomoby.org PING biomoby.org (207.154.17.70) 56(84) bytes of data. 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=1 ttl=48 time=87.7 ms 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=2 ttl=48 time=87.8 ms Connecting to HTTP however seems to time out: : stain at rpc268 ~;wget http://biomoby.org/ --2009-05-26 11:49:26-- http://biomoby.org/ Resolving biomoby.org... 207.154.17.70 Connecting to biomoby.org|207.154.17.70|:80... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From edward.kawas at gmail.com Tue May 26 14:05:38 2009 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 26 May 2009 07:05:38 -0700 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: References: Message-ID: <4a1bf739.0ebb720a.0609.7721@mx.google.com> I can connect to the repo ... Is it still down 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 Stian Soiland-Reyes Sent: May-26-09 3:50 AM To: Core developer announcements Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? I am get connection time-out trying to connect to http://biomoby.org/m2repo/ - and even to http://biomoby.org/ Ping works: : stain at rpc268 ~;ping biomoby.org PING biomoby.org (207.154.17.70) 56(84) bytes of data. 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=1 ttl=48 time=87.7 ms 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=2 ttl=48 time=87.8 ms Connecting to HTTP however seems to time out: : stain at rpc268 ~;wget http://biomoby.org/ --2009-05-26 11:49:26-- http://biomoby.org/ Resolving biomoby.org... 207.154.17.70 Connecting to biomoby.org|207.154.17.70|:80... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester _______________________________________________ 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 May 26 14:05:47 2009 From: markw at illuminae.com (markw at illuminae.com) Date: Tue, 26 May 2009 14:05:47 +0000 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: <4a1bf739.0ebb720a.0609.7721@mx.google.com> References: <4a1bf739.0ebb720a.0609.7721@mx.google.com> Message-ID: <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> Works for me from Alberta too... On the Road! -----Original Message----- From: "Edward Kawas" Date: Tue, 26 May 2009 07:05:38 To: 'Core developer announcements' Subject: Re: [MOBY-dev] Maven repository and http://biomoby.org down..? I can connect to the repo ... Is it still down 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 Stian Soiland-Reyes Sent: May-26-09 3:50 AM To: Core developer announcements Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? I am get connection time-out trying to connect to http://biomoby.org/m2repo/ - and even to http://biomoby.org/ Ping works: : stain at rpc268 ~;ping biomoby.org PING biomoby.org (207.154.17.70) 56(84) bytes of data. 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=1 ttl=48 time=87.7 ms 64 bytes from newportal.open-bio.org (207.154.17.70): icmp_seq=2 ttl=48 time=87.8 ms Connecting to HTTP however seems to time out: : stain at rpc268 ~;wget http://biomoby.org/ --2009-05-26 11:49:26-- http://biomoby.org/ Resolving biomoby.org... 207.154.17.70 Connecting to biomoby.org|207.154.17.70|:80... -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester _______________________________________________ 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 soiland-reyes at cs.manchester.ac.uk Fri May 29 09:19:46 2009 From: soiland-reyes at cs.manchester.ac.uk (Stian Soiland-Reyes) Date: Fri, 29 May 2009 10:19:46 +0100 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> References: <4a1bf739.0ebb720a.0609.7721@mx.google.com> <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> Message-ID: On Tue, May 26, 2009 at 15:05, wrote: > Works for me from Alberta too... yeah, up again now :-) Perhaps there were some clouds over the Atlantic.. -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester From markw at illuminae.com Fri May 29 17:32:49 2009 From: markw at illuminae.com (Mark) Date: Fri, 29 May 2009 10:32:49 -0700 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? In-Reply-To: References: <4a1bf739.0ebb720a.0609.7721@mx.google.com> <397902770-1243346816-cardhu_decombobulator_blackberry.rim.net-1081505344-@bxe1299.bisx.prod.on.blackberry> Message-ID: Must be cloudy over the atlantic again... I am unable to get through to taverna.org.uk today! M On Fri, 29 May 2009 02:19:46 -0700, Stian Soiland-Reyes wrote: > On Tue, May 26, 2009 at 15:05, wrote: >> Works for me from Alberta too... > > yeah, up again now :-) > > Perhaps there were some clouds over the Atlantic.. > > > From alanrw at cs.man.ac.uk Fri May 29 23:52:08 2009 From: alanrw at cs.man.ac.uk (Alan R Williams) Date: Sat, 30 May 2009 00:52:08 +0100 Subject: [MOBY-dev] Maven repository and http://biomoby.org down..? Message-ID: Can you see http://www.mygrid.org.uk or http://rosalind.cs.man.ac.uk ? If not, how about http://www.cs.man.ac.uk or http://www.man.ac.uk ? Alan