From martin.senger at gmail.com Thu Mar 1 19:11:12 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Mar 2007 00:11:12 +0000 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: References: Message-ID: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> > Is there an equivalent to the MOBY::Async::Service module in Java? I will be looking into in during March and April (with a definitive target date to be fully completed before I meet with Mark and few others in Vancouver in June). I will be looking how to make async services in Moses, both Java and Perl Moses. (BTW - and out of the topic - why do we still have two Perl versions?) Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Thu Mar 1 19:16:35 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 1 Mar 2007 16:16:35 -0800 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> References: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> Message-ID: <00a001c75c60$0a7e1780$6900a8c0@notebook> Hey Martin, I have been working on a java client, recently. I must say that I have given up on using any third party libraries that advertise support for wsrf. It may be that I am a really bad programmer, but I couldn't figure out how to those libraries to work. The prototype that I got working today uses the java SOAP api and http posts. 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: Thursday, March 01, 2007 4:11 PM To: Core developer announcements Subject: Re: [MOBY-dev] MOBY::Async::Service in Java? > Is there an equivalent to the MOBY::Async::Service module in Java? I will be looking into in during March and April (with a definitive target date to be fully completed before I meet with Mark and few others in Vancouver in June). I will be looking how to make async services in Moses, both Java and Perl Moses. (BTW - and out of the topic - why do we still have two Perl versions?) 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 martin.senger at gmail.com Thu Mar 1 19:20:54 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Mar 2007 00:20:54 +0000 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: <00a001c75c60$0a7e1780$6900a8c0@notebook> References: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> <00a001c75c60$0a7e1780$6900a8c0@notebook> Message-ID: <4d93f07c0703011620i10f2f5c4jd934908e4bbc027d@mail.gmail.com> > The prototype that I got working today uses the java SOAP api and http > posts. Thanks, Eddie. I will use your expertise when I dive into it myself. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Thu Mar 1 19:25:30 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 02 Mar 2007 01:25:30 +0100 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> References: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> Message-ID: <45E76EFA.2070802@mmb.pcb.ub.es> Hi, If you need somebody providing Java async services, just let me know it. I'll be happy to check any version/prototype. Iv?n Martin Senger escribi?: >> Is there an equivalent to the MOBY::Async::Service module in Java? >> > > > I will be looking into in during March and April (with a definitive target > date to be fully completed before I meet with Mark and few others in > Vancouver in June). I will be looking how to make async services in Moses, > both Java and Perl Moses. (BTW - and out of the topic - why do we still have > two Perl versions?) > > Martin > > -- ------------------------------------------------ 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 Thu Mar 8 11:51:57 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Mar 2007 08:51:57 -0800 Subject: [MOBY-dev] Who is "jmrc"? Message-ID: Hiya, Just going through the commits log to get the authorship list for the MOBY 1.0 manuscript, but I can't figure out who "jmrc" is? Anyone know? Mark From markw at illuminae.com Thu Mar 8 12:08:31 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Mar 2007 09:08:31 -0800 Subject: [MOBY-dev] Who is "jmrc"? In-Reply-To: References: Message-ID: Nix that - I got it from the /etc/passwd file. It's Jose :-) M On Thu, 08 Mar 2007 08:51:57 -0800, Mark Wilkinson wrote: > Hiya, > > Just going through the commits log to get the authorship list for the > MOBY > 1.0 manuscript, but I can't figure out who "jmrc" is? > > Anyone know? > > Mark > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From markw at illuminae.com Thu Mar 8 12:08:31 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Mar 2007 09:08:31 -0800 Subject: [MOBY-dev] Who is "jmrc"? In-Reply-To: References: Message-ID: Nix that - I got it from the /etc/passwd file. It's Jose :-) M On Thu, 08 Mar 2007 08:51:57 -0800, Mark Wilkinson wrote: > Hiya, > > Just going through the commits log to get the authorship list for the > MOBY > 1.0 manuscript, but I can't figure out who "jmrc" is? > > Anyone know? > > Mark > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From markw at illuminae.com Thu Mar 8 20:44:07 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 9 Mar 2007 01:44:07 +0000 GMT Subject: [MOBY-dev] The Moby 1.0 paper authorship Message-ID: <1627174959-1173404654-cardhu_blackberry.rim.net-26838-@engine09-cell01> Hi all moby dev'ers! I'm just doing the final edit of the moby 1.0 manuscript - I'll commit it to the CVS (as a PDF) in a day or two for comment from you all. The target journal is PLoS Computational Biology (unless anyone can suggest a better open-access forum for this work?) My question to you is regarding authorship. Almost everyone on this list is a co-author. Would you prefer to be individually named (as was done with the 1.0 release of BioPerl) or would you prefer to be called "The BioMoby Consortium" (as was done for the Gene Ontology's Nature paper)? I'm ambivalent, so if the wider community has any preference please let me know. Cheers all! Mark -- Mark Wilkinson ...on the road! From darin.london at duke.edu Tue Mar 6 11:03:59 2007 From: darin.london at duke.edu (Darin London) Date: Tue, 06 Mar 2007 11:03:59 -0500 Subject: [MOBY-dev] Announcing BOSC 2007 Message-ID: <45ED90EF.7030000@duke.edu> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From gordonp at ucalgary.ca Fri Mar 9 09:57:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 09 Mar 2007 07:57:37 -0700 Subject: [MOBY-dev] The Moby 1.0 paper authorship In-Reply-To: <1627174959-1173404654-cardhu_blackberry.rim.net-26838-@engine09-cell01> References: <1627174959-1173404654-cardhu_blackberry.rim.net-26838-@engine09-cell01> Message-ID: <45F175E1.6060406@ucalgary.ca> The question is, how long is the list? 30-40 authors is not uncommon for genome papers, for example. More than 50 is probably unreasonable, in which case you'd want to go the Consortium root... > Hi all moby dev'ers! > > I'm just doing the final edit of the moby 1.0 manuscript - I'll commit it to the CVS (as a PDF) in a day or two for comment from you all. The target journal is PLoS Computational Biology (unless anyone can suggest a better open-access forum for this work?) > > My question to you is regarding authorship. Almost everyone on this list is a co-author. Would you prefer to be individually named (as was done with the 1.0 release of BioPerl) or would you prefer to be called "The BioMoby Consortium" (as was done for the Gene Ontology's Nature paper)? > > I'm ambivalent, so if the wider community has any preference please let me know. > > Cheers all! > > Mark > > > > > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From enrique.deandres at pcm.uam.es Thu Mar 15 07:45:07 2007 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 15 Mar 2007 12:45:07 +0100 Subject: [MOBY-dev] Bug in MOBY::Client::SimpleArticle and MOBY::Client::CollectionArticle? Message-ID: <45F931C3.4030608@pcm.uam.es> Hello, I think I have detected a bug in MOBY/Client/SimpleArticle.pm. At the subroutine createFromDOM (line 277), when getting the articleName, it doesn't take into account the moby namespace (while MOBY::Client::Service adds the moby namespace to the articleName attribute): my $attr = $dom->getAttributeNode( 'articleName' ); It happens the same in MOBY/Client/CollectionArticle.pm (line 265). Thanks, Enrique. -- 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 enrique.deandres at pcm.uam.es Thu Mar 15 10:40:48 2007 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 15 Mar 2007 15:40:48 +0100 Subject: [MOBY-dev] Bug in MOBY::Client::SimpleArticle andMOBY::Client::CollectionArticle? In-Reply-To: <45F931C3.4030608@pcm.uam.es> References: <45F931C3.4030608@pcm.uam.es> Message-ID: <45F95AF0.4090207@pcm.uam.es> I think it is not a bug... it works well. I'm sorry for the alert, but there was something working wrong in my code and I thought that it was the reason. Sorry again. Enrique. Enrique de Andres Saiz wrote: > Hello, > > I think I have detected a bug in MOBY/Client/SimpleArticle.pm. At the > subroutine createFromDOM (line 277), when getting the articleName, it > doesn't take into account the moby namespace (while > MOBY::Client::Service adds the moby namespace to the articleName attribute): > > my $attr = $dom->getAttributeNode( 'articleName' ); > > It happens the same in MOBY/Client/CollectionArticle.pm (line 265). > > Thanks, > Enrique. > > -- Enrique de Andres Saiz Unidad de Bioinform?tica (INB GNHC-1) Parque Cientifico de Madrid Ctra. de Colmenar, Km. 15. Campus UAM, Cantoblanco - Pabellon C 28049 Madrid Tel. (+34) 91 497 3448 Fax. (+34) 91 497 3471 http://www.fpcm.es http://www.inab.org From jmrodriguez at cnio.es Thu Mar 22 05:32:29 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Thu, 22 Mar 2007 10:32:29 +0100 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs Message-ID: <46024D2D.5070502@cnio.es> Hi everyone, I am executing a MOBY services in Perl which needs multiple Simple inputs. To extract the MOBY messages, when the service are called, I am using the "serviceInputParser" but I have seen that the returned hashref which contains the Simple inputs is wrong. I mean, the hashref ,whose structure is "$inputs->{$queryID}->{articleName}", has always empty articleName value. That means the articleName of Simple Object is not obtained correctly. (if we have multiple simple inputs in one mobyData, the hashref returned by "serviceInputParser" will contain the last MOBY Object). I have been checking the code and I have seen in the method "createFromDOM" from "MOBY::Client::SimpleArticle" file that the 'articleNames' attribute is not extracted when this belongs to the namespace of "moby". my $attr = $dom->getAttributeNode( 'articleName' ); my $articleName = $attr ? $attr->getValue : ""; Here you are one solution in this particular problem: my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', 'articleName' ); $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; my $articleName = $attr ? $attr->getValue : ""; (but I think this is one of more problems regarding MOBY namespaces) Best Regards, Jos?. -- 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 Adress: C/. Melchor Fernandez 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 markw at illuminae.com Thu Mar 22 11:53:10 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 22 Mar 2007 07:53:10 -0800 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <46024D2D.5070502@cnio.es> References: <46024D2D.5070502@cnio.es> Message-ID: <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> Hi Jose, please go ahead and fix this in the CVS. It's interesting that there is no attribute-equivalent to getElementsByLocalName, where "local" means whatever namespace you are currently in... M On Thu, 2007-03-22 at 10:32 +0100, Jose Manuel Rodriguez wrote: > Hi everyone, > > I am executing a MOBY services in Perl which needs multiple Simple inputs. > To extract the MOBY messages, when the service are called, I am using > the "serviceInputParser" but I have seen that the returned hashref which > contains the Simple inputs is wrong. I mean, the hashref > > ,whose structure is "$inputs->{$queryID}->{articleName}", > > has always empty articleName value. That means the articleName of Simple > Object is not obtained correctly. (if we have multiple simple inputs in > one mobyData, the hashref returned by "serviceInputParser" will contain > the last MOBY Object). > > > > I have been checking the code and I have seen in the method > "createFromDOM" from "MOBY::Client::SimpleArticle" file that the > 'articleNames' attribute is not extracted when this belongs to the > namespace of "moby". > > > my $attr = $dom->getAttributeNode( 'articleName' ); > my $articleName = $attr ? $attr->getValue : ""; > > > Here you are one solution in this particular problem: > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > 'articleName' ); > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > my $articleName = $attr ? $attr->getValue : ""; > > > > (but I think this is one of more problems regarding MOBY namespaces) > > Best Regards, > Jos?. > From edward.kawas at gmail.com Thu Mar 22 12:35:33 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Mar 2007 09:35:33 -0700 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method whenthe mobyservice receives multiple Simple inputs In-Reply-To: <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> References: <46024D2D.5070502@cnio.es> <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> Message-ID: <003f01c76ca0$1ced0110$6800a8c0@notebook> To get an attribute regardless of the prefix, use: getAttributeNS("", "articleName") This seems to work on my machine. Does it work for you Jose? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Thursday, March 22, 2007 8:53 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] Problems using serviceInputParser method > whenthe mobyservice receives multiple Simple inputs > > Hi Jose, > > please go ahead and fix this in the CVS. > > It's interesting that there is no attribute-equivalent to > getElementsByLocalName, where "local" means whatever namespace you are > currently in... > > M > > > > > > On Thu, 2007-03-22 at 10:32 +0100, Jose Manuel Rodriguez wrote: > > Hi everyone, > > > > I am executing a MOBY services in Perl which needs multiple Simple > inputs. > > To extract the MOBY messages, when the service are called, I am using > > the "serviceInputParser" but I have seen that the returned hashref which > > contains the Simple inputs is wrong. I mean, the hashref > > > > ,whose structure is "$inputs->{$queryID}->{articleName}", > > > > has always empty articleName value. That means the articleName of Simple > > Object is not obtained correctly. (if we have multiple simple inputs in > > one mobyData, the hashref returned by "serviceInputParser" will contain > > the last MOBY Object). > > > > > > > > I have been checking the code and I have seen in the method > > "createFromDOM" from "MOBY::Client::SimpleArticle" file that the > > 'articleNames' attribute is not extracted when this belongs to the > > namespace of "moby". > > > > > > my $attr = $dom->getAttributeNode( 'articleName' ); > > my $articleName = $attr ? $attr->getValue : ""; > > > > > > Here you are one solution in this particular problem: > > > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > > 'articleName' ); > > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > > my $articleName = $attr ? $attr->getValue : ""; > > > > > > > > (but I think this is one of more problems regarding MOBY namespaces) > > > > Best Regards, > > Jos?. > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Mar 22 12:41:35 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Mar 2007 09:41:35 -0700 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <46024D2D.5070502@cnio.es> References: <46024D2D.5070502@cnio.es> Message-ID: <004c01c76ca0$f5481ea0$6800a8c0@notebook> The code that I used to test getting any attribute regardless of the prefix is the below. Notice that id is prefixed while namespace is not ... --------------------- use XML::LibXML; my $xml =< EOF my $p = XML::LibXML->new; my $doc = $p->parse_string( $xml ); my $root = $doc->getDocumentElement; $root = $root->getElementsByLocalName('Object')->item(0); print "The XML:\n$xml\n"; print "Getting information for inner element 'Object'\n"; print "\tnamespace: '" .$root->getAttributeNS("", "namespace") . "'\n"; print "\tid: '" .$root->getAttributeNS("", "id") . "'\n"; ---------------------------------- Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Jose Manuel Rodriguez > Sent: Thursday, March 22, 2007 2:32 AM > To: Core developer announcements > Subject: [MOBY-dev] Problems using serviceInputParser method when the > mobyservice receives multiple Simple inputs > > Hi everyone, > > I am executing a MOBY services in Perl which needs multiple Simple inputs. > To extract the MOBY messages, when the service are called, I am using > the "serviceInputParser" but I have seen that the returned hashref which > contains the Simple inputs is wrong. I mean, the hashref > > ,whose structure is "$inputs->{$queryID}->{articleName}", > > has always empty articleName value. That means the articleName of Simple > Object is not obtained correctly. (if we have multiple simple inputs in > one mobyData, the hashref returned by "serviceInputParser" will contain > the last MOBY Object). > > > > I have been checking the code and I have seen in the method > "createFromDOM" from "MOBY::Client::SimpleArticle" file that the > 'articleNames' attribute is not extracted when this belongs to the > namespace of "moby". > > > my $attr = $dom->getAttributeNode( 'articleName' ); > my $articleName = $attr ? $attr->getValue : ""; > > > Here you are one solution in this particular problem: > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > 'articleName' ); > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > my $articleName = $attr ? $attr->getValue : ""; > > > > (but I think this is one of more problems regarding MOBY namespaces) > > Best Regards, > Jos?. > > -- > 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 > Adress: C/. Melchor Fernandez 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 martin.senger at gmail.com Thu Mar 22 12:53:17 2007 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 22 Mar 2007 16:53:17 +0000 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method whenthe mobyservice receives multiple Simple inputs In-Reply-To: <003f01c76ca0$1ced0110$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es> <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> <003f01c76ca0$1ced0110$6800a8c0@notebook> Message-ID: <4d93f07c0703220953x2b719085ib2b2eab929f1feb0@mail.gmail.com> This is how I do it in Perl/Moses code: # return a value of an attribute named $name from an $element (an # XML::LibXML type); try both with and without namespaces; return # undef if no such sttribute found sub getXMLAttribute { my ($self, $element, $name) = @_; return $element->getAttribute ($name) || $element->getAttributeNS (MOBY_XML_NS, $name); } Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Thu Mar 22 13:35:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 22 Mar 2007 11:35:49 -0600 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method whenthe mobyservice receives multiple Simple inputs In-Reply-To: <4d93f07c0703220953x2b719085ib2b2eab929f1feb0@mail.gmail.com> References: <46024D2D.5070502@cnio.es> <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> <003f01c76ca0$1ced0110$6800a8c0@notebook> <4d93f07c0703220953x2b719085ib2b2eab929f1feb0@mail.gmail.com> Message-ID: <4602BE75.8030909@ucalgary.ca> This is the logic used in jMOBY's MobyPrefixResolver class too. Great minds think alike :-) One caveat related to Eddie's earlier code (I don't know if it's applicable in the Perl implementation) is that a null namespace, and an empty string namespace are different beasts in the XML DOM, and depend on if the parser is in namespace-aware mode. > This is how I do it in Perl/Moses code: > > # return a value of an attribute named $name from an $element (an > # XML::LibXML type); try both with and without namespaces; return > # undef if no such sttribute found > sub getXMLAttribute { > my ($self, $element, $name) = @_; > return > $element->getAttribute ($name) || > $element->getAttributeNS (MOBY_XML_NS, $name); > } > > Martin > > > From jmrodriguez at cnio.es Fri Mar 23 06:46:59 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Fri, 23 Mar 2007 11:46:59 +0100 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <004c01c76ca0$f5481ea0$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> Message-ID: <4603B023.7020409@cnio.es> Hi Eddie, I have been looking for the reason why sometimes works or not...The difference is XML::LibXML library. Here I am going to show you results from both "getAttributeNode" and "getAttributeNodeNS" methods depending on different versions of XML::LibXML: The input XML is : 20060215121817 20060215121816 true XML::LibXML version 1.58: Getting information for inner element 'Simple' articleName: 'end' # getAttributeNode("articleName") Now MOBY libraries use this method WE HAVE RESULT articleName NS empty: '' # getAttributeNodeNS("", "articleName") articleName NS: 'end' # getAttributeNodeNS("http://www.biomoby.org/moby", "articleName") Getting information for inner element 'Simple' articleName: 'start' articleName NS empty: '' articleName NS: '' The same script using XML::LibXML version 1.62: Getting information for inner element 'Simple' articleName: '' # DIFFERENT RESULT!!!!!!!!! articleName NS empty: '' articleName NS: 'end' Getting information for inner element 'Simple' articleName: 'start' articleName NS empty: 'start' articleName NS: '' So, we see different results depending on XML::LibXML version but thinking which is the correct one because maybe the problem is on LibXML libraries not on MOBY. I have run the same methods with Java libraries whose results are: java version "1.5.0_08": Getting information for inner element 'Simple' articleName: '' articleName NS empty: '' articleName NS: 'end' Getting information for inner element 'Simple' articleName: 'start' articleName NS empty: 'start' articleName NS: '' The same results than version 1.62. In any case, in my opinion we have to control the XML libraries using better methods as (getAttributeNodeNS("http://www.biomoby.org/moby", "articleName")). Other question I have is we are obligate to add namespaces within MOBY xml's or not. The MOBY standard says something about that... Best Regards, Jos?. SP: If you want I can send you the scripts :) Edward Kawas wrote: > The code that I used to test getting any attribute regardless of the prefix > is the below. Notice that id is prefixed while namespace is not ... > > --------------------- > use XML::LibXML; > > my $xml =< > > > > > > > > > > EOF > my $p = XML::LibXML->new; > my $doc = $p->parse_string( $xml ); > my $root = $doc->getDocumentElement; > $root = $root->getElementsByLocalName('Object')->item(0); > > print "The XML:\n$xml\n"; > print "Getting information for inner element 'Object'\n"; > print "\tnamespace: '" .$root->getAttributeNS("", "namespace") . "'\n"; > print "\tid: '" .$root->getAttributeNS("", "id") . "'\n"; > ---------------------------------- > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Jose Manuel Rodriguez >> Sent: Thursday, March 22, 2007 2:32 AM >> To: Core developer announcements >> Subject: [MOBY-dev] Problems using serviceInputParser method when the >> mobyservice receives multiple Simple inputs >> >> Hi everyone, >> >> I am executing a MOBY services in Perl which needs multiple Simple inputs. >> To extract the MOBY messages, when the service are called, I am using >> the "serviceInputParser" but I have seen that the returned hashref which >> contains the Simple inputs is wrong. I mean, the hashref >> >> ,whose structure is "$inputs->{$queryID}->{articleName}", >> >> has always empty articleName value. That means the articleName of Simple >> Object is not obtained correctly. (if we have multiple simple inputs in >> one mobyData, the hashref returned by "serviceInputParser" will contain >> the last MOBY Object). >> >> >> >> I have been checking the code and I have seen in the method >> "createFromDOM" from "MOBY::Client::SimpleArticle" file that the >> 'articleNames' attribute is not extracted when this belongs to the >> namespace of "moby". >> >> >> my $attr = $dom->getAttributeNode( 'articleName' ); >> my $articleName = $attr ? $attr->getValue : ""; >> >> >> Here you are one solution in this particular problem: >> >> my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', >> 'articleName' ); >> $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; >> my $articleName = $attr ? $attr->getValue : ""; >> >> >> >> (but I think this is one of more problems regarding MOBY namespaces) >> >> Best Regards, >> Jos?. >> >> -- >> 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 >> Adress: C/. Melchor Fernandez 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 >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- 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 Adress: C/. Melchor Fernandez 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 Fri Mar 23 09:50:53 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 23 Mar 2007 06:50:53 -0700 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <4603B023.7020409@cnio.es> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> Message-ID: <000f01c76d52$46d8d5f0$6800a8c0@notebook> > Other question I have is we are obligate to add namespaces within MOBY > xml's or not. The MOBY standard says something about that... I don't believe that it is necessary. Eddie From markw at illuminae.com Fri Mar 23 11:49:46 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 23 Mar 2007 15:49:46 +0000 GMT Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <000f01c76d52$46d8d5f0$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook><4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook> Message-ID: <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> The attribute is necessary, but it can have a null ("") value -- Mark Wilkinson ...on the road! -----Original Message----- From: "Edward Kawas" Date: Fri, 23 Mar 2007 06:50:53 To:"'Core developer announcements'" Subject: Re: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs > Other question I have is we are obligate to add namespaces within MOBY > xml's or not. The MOBY standard says something about that... I don't believe that it is necessary. Eddie _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jmrodriguez at cnio.es Fri Mar 23 13:59:15 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Fri, 23 Mar 2007 18:59:15 +0100 Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook><4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook> <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> Message-ID: <46041573.7010108@cnio.es> Maybe I don't have explain me OK (sorry for that) The main idea that I am trying to advise is the form to call LibXML methods in MOBY library (Perl), they do not work on new versions of XML::LibXML. Specifically: In the package => MOBY::Client::SimpleArticle.pm In the method => createFromDOM code => my $attr = $dom->getAttributeNode( 'articleName' ); my $articleName = $attr ? $attr->getValue : ""; This above code (the actual one) don't work on 1.62 version of LibXML. We should use the next code: my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', 'articleName' ); $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; my $articleName = $attr ? $attr->getValue : ""; Good weekend, Jos?. mark wilkinson wrote: > The attribute is necessary, but it can have a null ("") value > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: "Edward Kawas" > Date: Fri, 23 Mar 2007 06:50:53 > To:"'Core developer announcements'" > Subject: Re: [MOBY-dev] Problems using serviceInputParser method when the > mobyservice receives multiple Simple inputs > > >> Other question I have is we are obligate to add namespaces within MOBY >> xml's or not. The MOBY standard says something about that... >> > > I don't believe that it is necessary. > > Eddie > > _______________________________________________ > 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 > > -- 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 Fernandez 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 Fri Mar 23 14:39:32 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 23 Mar 2007 11:39:32 -0700 Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <46041573.7010108@cnio.es> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook><4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook><1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> <46041573.7010108@cnio.es> Message-ID: <004901c76d7a$999ba2e0$6800a8c0@notebook> Hi Jose, If I were you, I would look at the Perl moses code located in the cvs: moby-live/Java/src/Perl The way that Perl Moses does things is the best way to go about things. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Jose Manuel Rodriguez > Sent: Friday, March 23, 2007 10:59 AM > To: markw at illuminae.com; Core developer announcements > Subject: Re: [MOBY-dev] Problems using serviceInputParser method when > themobyservice receives multiple Simple inputs > > Maybe I don't have explain me OK (sorry for that) > > The main idea that I am trying to advise is the form to call LibXML > methods in MOBY library (Perl), they do not work on new versions of > XML::LibXML. > > Specifically: > > In the package => MOBY::Client::SimpleArticle.pm > In the method => createFromDOM > code => > > my $attr = $dom->getAttributeNode( 'articleName' ); > my $articleName = $attr ? $attr->getValue : ""; > > > This above code (the actual one) don't work on 1.62 version of LibXML. > > We should use the next code: > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > 'articleName' ); > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > my $articleName = $attr ? $attr->getValue : ""; > > > Good weekend, > Jos?. > > > > mark wilkinson wrote: > > The attribute is necessary, but it can have a null ("") value > > > > > > -- > > Mark Wilkinson > > ...on the road! > > > > > > -----Original Message----- > > From: "Edward Kawas" > > Date: Fri, 23 Mar 2007 06:50:53 > > To:"'Core developer announcements'" > > Subject: Re: [MOBY-dev] Problems using serviceInputParser method when > the > > mobyservice receives multiple Simple inputs > > > > > >> Other question I have is we are obligate to add namespaces within MOBY > >> xml's or not. The MOBY standard says something about that... > >> > > > > I don't believe that it is necessary. > > > > Eddie > > > > _______________________________________________ > > 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 > > > > > > > -- > 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 Fernandez 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 martin.senger at gmail.com Fri Mar 23 15:14:33 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 23 Mar 2007 19:14:33 +0000 Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <004901c76d7a$999ba2e0$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook> <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> <46041573.7010108@cnio.es> <004901c76d7a$999ba2e0$6800a8c0@notebook> Message-ID: <4d93f07c0703231214h61974716rbcbbabbef1cc829a@mail.gmail.com> > If I were you, I would look at the Perl moses code located in the cvs: > moby-live/Java/src/Perl ...and this is the documentation to it: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/PerlMoses.html Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Fri Mar 23 13:29:02 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 23 Mar 2007 09:29:02 -0800 Subject: [MOBY-dev] [moby] Re: Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <4603B023.7020409@cnio.es> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> Message-ID: <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> On Fri, 2007-03-23 at 11:46 +0100, Jose Manuel Rodriguez wrote: > Other question I have is we are obligate to add namespaces within MOBY > xml's or not. The MOBY standard says something about that... I apologize for my earlier response - interestingly, all of that XML in the message did not render *at all* in my cell-phone emailer, so this last sentence is the only one that made sense to me when I was reading it on my phone. Now that I am on my regular computer I can see the whole message and it makes much more sense! The issue of whether or not to use a namespace really is an issue of what is correct/incorrect XML. The Perl libraries will auto-add the xmlns:moby to the various headers, so the namespace is going to be defined in messages that come from Perl services for sure. You also have to anticipate that some providers will add the moby: prefix into their mobyData Objects, so there's no way you can write services that do not handle namespaced XML, even if you don't generate namespaces in your own response XML. I recall seeing some disagreement on the various newsgroups about whether XML attributes (as opposed to XML tags) had to be namespaced, or whether the namespace of the tag was assumed to also be the namespace of the attribute... does anyone know definitively what the answer to this is? M From gordonp at ucalgary.ca Fri Mar 23 18:37:22 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 23 Mar 2007 16:37:22 -0600 Subject: [MOBY-dev] [moby] Re: Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> Message-ID: <460456A2.5060407@ucalgary.ca> Please refer to: http://www.w3.org/TR/REC-xml-names/#defaulting Essentially, unprefixed attributes inherit the namespace of the element they are in, not the default namespace. So it boils down to one of Jose's original question I think: "Other question I have is we are obligate to add namespaces within MOBY xml's or not." I know that currently the service providers are giving a mixed bag, that's why I check both. I don't remember anything from the MOBY spec about requiring a DNASequence tag, for example to be in the MOBY namespace (perhaps because previously we didn't have a super tight schema to describe valid MOBY objects!). > I recall seeing some disagreement on the various newsgroups about > whether XML attributes (as opposed to XML tags) had to be namespaced, or > whether the namespace of the tag was assumed to also be the namespace of > the attribute... does anyone know definitively what the answer to this > is? > > M > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,460451f121086182051815! > > > > From gcomesana at cnio.es Mon Mar 26 09:36:27 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Comesa=C3=B1a=2EGuillermo=22?=) Date: Mon, 26 Mar 2007 15:36:27 +0200 Subject: [MOBY-dev] question from the newbie In-Reply-To: <460456A2.5060407@ucalgary.ca> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> <460456A2.5060407@ucalgary.ca> Message-ID: <4607CC5B.5060907@cnio.es> hi everybody and sorry for the inconvenience in the BaseCmdClient i've found "It does create data input only with one Simple or one Collection. This would be easy to rectify but the command-line options would become too cumbersome. But still I may do it later." Does this mean that it is just possible to send one parameter from this command line tool to call the service? what is going on if the testing service needs more than one parameter? Regards. **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From martin.senger at gmail.com Mon Mar 26 09:59:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 26 Mar 2007 14:59:29 +0100 Subject: [MOBY-dev] question from the newbie In-Reply-To: <4607CC5B.5060907@cnio.es> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> <460456A2.5060407@ucalgary.ca> <4607CC5B.5060907@cnio.es> Message-ID: <4d93f07c0703260659m73578cbfq28b6ed6bf5fbc39f@mail.gmail.com> > Does this mean that it is just possible to send one parameter from this > command line tool to call the service? what is going on if the testing > service needs more than one parameter? Use Dashboard instead. Its "Simple Client" panel can do much more. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From jmrodriguez at cnio.es Mon Mar 26 09:51:36 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Mon, 26 Mar 2007 15:51:36 +0200 Subject: [MOBY-dev] [moby] Re: Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> Message-ID: <4607CFE8.1080507@cnio.es> Mark Wilkinson wrote: > I recall seeing some disagreement on the various newsgroups about > whether XML attributes (as opposed to XML tags) had to be namespaced, or > whether the namespace of the tag was assumed to also be the namespace of > the attribute... does anyone know definitively what the answer to this > is? > > Hi Mark, Maybe this could help you http://www.w3.org/TR/2006/REC-xml-names-20060816/#uniqAttrs Cheers, Jos?. > M > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- 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 Fernandez 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 markw at illuminae.com Mon Mar 26 19:53:44 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 26 Mar 2007 15:53:44 -0800 Subject: [MOBY-dev] Draft of the BioMoby 1.0 manuscript added to the CVS Message-ID: Hi all, I've completed a draft of the BioMoby 1.0 manuscript and have just uploaded it into the CVS (moby-live/Docs/BioMoby_1_0_version_6.pdf). Please let me know if I have missed anyone's name who should be included in the BioMoby consortium membership list, or if you see your name there and would prefer that it be removed. I welcome any and all comments! Best wishes! Mark From gcomesana at cnio.es Tue Mar 27 08:22:45 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Comesa=C3=B1a=2EGuillermo=22?=) Date: Tue, 27 Mar 2007 14:22:45 +0200 Subject: [MOBY-dev] dashboard In-Reply-To: References: Message-ID: <46090C95.1050904@cnio.es> hi there has dashboard any kind of cache with local classes?? how can i remove that cache capability? i am testing a local class with dashboard and it uses the same class version even i recompile the class. When the class is recompiled it is placed in the proper location for dashboard. Similarly, i am using log4j for logging and debuggin issues and the log gets updated, but the logging output is the same as if the class werent changed. any suggestion about this??? zanx & regards **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 martin.senger at gmail.com Tue Mar 27 09:03:55 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Mar 2007 14:03:55 +0100 Subject: [MOBY-dev] dashboard In-Reply-To: <46090C95.1050904@cnio.es> References: <46090C95.1050904@cnio.es> Message-ID: <4d93f07c0703270603u44b3634du424ff05ade36b49e@mail.gmail.com> > has dashboard any kind of cache with local classes?? There is special class loader in Dashboard. Which means, once a class is loaded it is loaded, and the class loader involved does not check if there is a newer version. how can i remove that cache capability? Just restart the Dashboard. But if you need to do a lot of testing cycles, restarting the dashboard would be boring and perhaps slow. In which case I would recommend to use the command-line client (script run-cmdline-client, invoking MobyCmdLineClient). I know you already asked how to make this client to work with multiple inputs. The way to do it is to create a service input in XML using dashboard (during testing the input usually does not change much, and if yes you still can edit directly the XML file; for testing purposes it is fine), and then call the command-line client with the following arguments: -scall You get back just raw XML - but again, for testing purposes it may be good enough. Or, even perhaps better (I forgot about it) is to use a specific command-line client for calling services. This will give you help (and there is a detailed documentation on Moses pages): build/run/run-service -help Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Tue Mar 27 17:39:27 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 27 Mar 2007 13:39:27 -0800 Subject: [MOBY-dev] revised manuscript now in CVS Message-ID: Thanks to all who read and commented on the Moby 1.0 manuscript so quickly! I've made the first set of suggested revisions, and the new manuscript is uploaded (version 7)to the CVS in the /Docs folder. Since we can't track changes using the binary PDF format, perhaps send your suggestions/edits to the mailing list so that everyone can see them and comment on them. Cheers! Mark From gcomesana at cnio.es Wed Mar 28 09:42:08 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Guillermo_Comesa=C3=B1a=2E=22?=) Date: Wed, 28 Mar 2007 15:42:08 +0200 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: References: Message-ID: <460A70B0.2080906@cnio.es> Hi everybody and sorry for possible troubles... ...but, does somebody know to say why can i get this following: 27816 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27822 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27825 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27829 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27832 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. (...) I have as many lines with this warning as LogEvent objects and I get it after locally executing my service with me at mymachine$ run-service -service getLogReport -mobye $ENDPOINT -mobyuri $MOBY_URI -class JLogReport -xml testlog.xml -showxml -outxml The class JLogReport implements the service generated as skeleton in JLogReportSkel and my dashboard yielded the LogEvent class. Previously to all those "moby warnings" the output of the service is apparently ok as you can see in the following output snippet F4D83E00-B50D-11DA-9DE7-EA517071BF93 runPhylipNeighbor 193.146.190.95 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z 701 3790E176-B512-11DA-9F9D-E262AE5C699A runPhylipNeighbor 193.146.190.95 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z 701 (...) E0A58A54-B43C-11DA-8ED1-CC6B69DB9358 getAminoAcidSequence 150.244.85.114 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z 0 any suggestion, idea, something...? Cheers in advance w i l l y **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 Mar 28 09:47:05 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 28 Mar 2007 06:47:05 -0700 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A70B0.2080906@cnio.es> References: <460A70B0.2080906@cnio.es> Message-ID: <002401c7713f$93038bf0$6800a8c0@notebook> Have you generated the datatypes first? Anytime you see the ignoring unknown element ... that means it cant find the datatype definition. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of "Guillermo Comesa??a." > Sent: Wednesday, March 28, 2007 6:42 AM > To: Core developer announcements > Subject: [MOBY-dev] JMoby bug or lack of knowledge > > > Hi everybody and sorry for possible troubles... > ...but, does somebody know to say why can i get this following: > > 27816 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27822 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27825 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27829 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27832 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > (...) > > I have as many lines with this warning as LogEvent objects and I get it > after locally executing my service with > > me at mymachine$ run-service -service getLogReport -mobye $ENDPOINT > -mobyuri $MOBY_URI -class JLogReport -xml testlog.xml -showxml -outxml > > The class JLogReport implements the service generated as skeleton in > JLogReportSkel and my dashboard yielded the LogEvent class. Previously > to all those "moby warnings" the output of the service is apparently ok > as you can see in the following output snippet > > > > > > > > > moby:articleName="id">F4D83E00-B50D-11DA-9DE7-EA517071BF93 > moby:articleName="serviceName">runPhylipNeighbor > moby:articleName="ip">193.146.190.95 > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="status">701 > > > > > moby:articleName="id">3790E176-B512-11DA-9F9D-E262AE5C699A > moby:articleName="serviceName">runPhylipNeighbor > moby:articleName="ip">193.146.190.95 > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="status">701 > > > (...) > > > moby:articleName="id">E0A58A54-B43C-11DA-8ED1-CC6B69DB9358 > moby:articleName="serviceName">getAminoAcidSequence > moby:articleName="ip">150.244.85.114 > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="status">0 > > > > > > > > any suggestion, idea, something...? > Cheers in advance > > w i l l y > > > **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 martin.senger at gmail.com Wed Mar 28 09:52:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 14:52:29 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <002401c7713f$93038bf0$6800a8c0@notebook> References: <460A70B0.2080906@cnio.es> <002401c7713f$93038bf0$6800a8c0@notebook> Message-ID: <4d93f07c0703280652o3ff1925frdc0bacbe6f08129b@mail.gmail.com> > Have you generated the datatypes first? Anytime you see the ignoring > unknown > element ... that means it cant find the datatype definition. One cannot beat Eddie on the speed, he is too fast :-) Let me just say that what he said was exactly what I wanted to say... I can just add that you can generate data types either from the command-line, or from Dashboard. And it is a one-time job, you do not need to repeat it again and again (unless you register a new data type). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Mar 28 09:58:26 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 14:58:26 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A70B0.2080906@cnio.es> References: <460A70B0.2080906@cnio.es> Message-ID: <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> ...and I can also add that you should not use the same article name twice in the same message - the 'end' is twice in one LogEvent: 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Wed Mar 28 10:37:48 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 28 Mar 2007 08:37:48 -0600 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> Message-ID: <460A7DBC.6090501@ucalgary.ca> Actually, you should be able to, if the "end" member's relationship is HAS (as opposed to HAS-A), no? > ...and I can also add that you should not use the same article name twice in > the same message - the 'end' is twice in one LogEvent: > > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > > Martin > > From gordonp at ucalgary.ca Wed Mar 28 10:43:13 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 28 Mar 2007 08:43:13 -0600 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A7DBC.6090501@ucalgary.ca> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> Message-ID: <460A7F01.7010901@ucalgary.ca> On second thought, it may be legal depending on how the data type is defined (which we don't know, since it's not registered), but of course, two end times probably doesn't make much logical sense :-) > Actually, you should be able to, if the "end" member's relationship is > HAS (as opposed to HAS-A), no? > >> ...and I can also add that you should not use the same article name twice in >> the same message - the 'end' is twice in one LogEvent: >> >> > moby:articleName="end">2006-03-24T06:19:50Z >> > moby:articleName="end">2006-03-24T06:19:50Z >> >> Martin >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,460a7c9b21086281354797! > > > > From martin.senger at gmail.com Wed Mar 28 11:05:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 16:05:29 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A7DBC.6090501@ucalgary.ca> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> Message-ID: <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> > Actually, you should be able to, if the "end" member's relationship is > HAS (as opposed to HAS-A), no? Of course, Paul is right. (I was more concentrating on a "probable logic" of two ends :-)) M. -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gcomesana at cnio.es Wed Mar 28 11:28:35 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Guillermo_Comesa=C3=B1a=2E=22?=) Date: Wed, 28 Mar 2007 17:28:35 +0200 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> Message-ID: <460A89A3.6080803@cnio.es> Cheers everybody for the help. However, nothing was useful for me so far. Apparently in my code everything is ok, the only calls to set both dates (start and end) is as follows: try { if (startLine != null) { aux = buildDate(startLine[3]).getTime(); aDate.setValue (sdf.format(aux)); logger.debug("startline iso8601: " + sdf.format (aux)); logger.debug("startLine->aDate.getValue(): "+aDate.getValue()); logEv.set_start (aDate); } if (endLine != null) { aux = buildDate(endLine[3]).getTime(); aDate.setValue(sdf.format (aux)); logger.debug("endline iso8601: " + sdf.format (aux)); logger.debug("endline->aDate.getValue(): "+aDate.getValue()); logEv.set_end (aDate); } } catch (MobyException ex) { logger.debug (ex.getMessage()); } where the set_start (MobyDateTime) and set_end (MobyDateTime) are methods of LogEvent class/datatype whose implementation is: (...) /** An article name for a member of this object. */ public static final String ARTICLE_NAME_START = "start"; protected MobyDateTime start; /** An article name for a member of this object. */ public static final String ARTICLE_NAME_END = "end"; protected MobyDateTime end; (...) /************************************************************************** * Set a new value to the member (child) 'start'. It also * adds there its registered "article name".

* * @param value to be stored *************************************************************************/ public void set_start (MobyDateTime value) { // add a correct article name if (value != null) value.setName (ARTICLE_NAME_START); start = value; } public MobyDateTime getMoby_start() { return start; } /************************************************************************** * Set a new value to the member (child) 'end'. It also * adds there its registered "article name".

* * @param value to be stored *************************************************************************/ public void set_end (MobyDateTime value) { // add a correct article name if (value != null) value.setName (ARTICLE_NAME_END); end = value; } public MobyDateTime getMoby_end() { return end; } and, finally, the definition of the registered datatype is: Name: LogEvent Auth: mmb.pcb.ub.es Desc: Encapsulates all the log messages launched for a service call Contact: moby-services at mmb.pcb.ub.es LSID: urn:lsid:biomoby.org:objectclass:LogEvent:2007-03-17T20-00-34Z ID: null Parents: Object Children (only those registered here): id (HASA) => String serviceName (HASA) => String ip (HASA) => String start (HASA) => DateTime end (HASA) => DateTime status (HASA) => Integer timeCPU (HASA) => Float numberCPUs (HASA) => Integer inputSize (HASA) => Integer outputSize (HASA) => Integer isTest (HASA) => Boolean which is registered in http://moby-dev.inab.org/MOBY/Central and i have generated the datatypes (again, but it was to be sure in the case of the LogEvent datatypes was bad yielded before...) so, any suggestion to the issue of the two ends in the xml and the warning??? cheers again and sorry for this huge and boring mail... w i l l y ps: i guess the warning can be debt to this method in class LogEvent: public org.jdom.Element toXML() { org.jdom.Element elem_I_am_sorry_that_this_produces_a_warning = super.toXML(); elem_I_am_sorry_that_this_produces_a_warning.setName (DATA_TYPE_NAME); if (the_id != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (the_id.toXML()); if (serviceName != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (serviceName.toXML()); if (ip != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (ip.toXML()); if (start != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (start.toXML()); if (end != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (end.toXML()); if (status != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (status.toXML()); if (timeCPU != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (timeCPU.toXML()); if (numberCPUs != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (numberCPUs.toXML()); if (inputSize != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (inputSize.toXML()); if (outputSize != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (outputSize.toXML()); if (isTest != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (isTest.toXML()); return elem_I_am_sorry_that_this_produces_a_warning; } **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 martin.senger at gmail.com Wed Mar 28 11:42:49 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 16:42:49 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A89A3.6080803@cnio.es> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> <460A89A3.6080803@cnio.es> Message-ID: <4d93f07c0703280842x4f75f30bw1e6c213df74f3243@mail.gmail.com> It would help if you either register your data type in the Canadian Moby Central (you may/should use the testing Moby Central there) or if you give me the URL and URI of your register (if it is publicly accessible). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 28 11:00:46 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Mar 2007 17:00:46 +0200 Subject: [MOBY-dev] Changes in the service retrieval API ? Message-ID: <200703281700.47035.groscurt@mpiz-koeln.mpg.de> Hi everyone, I'm using the getServiceNamesByAuthorityAsXML(), which does a SOAP call for retrieveServiceNames, to retrieve all services from the MOBY Central. Afterwards I want to have the full information of some services and therefore I use the method findService with a service found with the method above as parameter. With some services it happens that I it does not find any services with the findService method ! E.g. service runNCBIBlastp from inb.bsc.es is returned by calling getServiceNamesByAuthorityAsXML(). But calling findService with this service later on returns an empty service. Has something changed in den API of these methodes ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From edward.kawas at gmail.com Wed Mar 28 11:52:00 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 28 Mar 2007 08:52:00 -0700 Subject: [MOBY-dev] Changes in the service retrieval API ? In-Reply-To: <200703281700.47035.groscurt@mpiz-koeln.mpg.de> References: <200703281700.47035.groscurt@mpiz-koeln.mpg.de> Message-ID: <004901c77151$06002170$6800a8c0@notebook> Hi Andreas, I think that the services that you are looking for are async services. When you perform a findservice call with jmoby it defaults to moby services. If you change the category to moby-async, I bet it will work. I usually set the category string to be the empty string and this works for me. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: Wednesday, March 28, 2007 8:01 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Changes in the service retrieval API ? > > Hi everyone, > > I'm using the getServiceNamesByAuthorityAsXML(), which does a SOAP call > for > retrieveServiceNames, to retrieve all services from the MOBY Central. > > Afterwards I want to have the full information of some services and > therefore > I use the method findService with a service found with the method above as > parameter. > > With some services it happens that I it does not find any services with > the > findService method ! > > E.g. service runNCBIBlastp from inb.bsc.es is returned by calling > getServiceNamesByAuthorityAsXML(). But calling findService with this > service > later on returns an empty service. > > Has something changed in den API of these methodes ? > > Thanks > Andreas > > -- > Andreas Groscurth > Diplom Bioinformatik - PhD Student > Max Planck Institute for Plant Breeding Research > Carl-von-Linn?-Weg 10 > 50829 Cologne > Germany > E-mail: ? ?groscurt at mpiz-koeln.mpg.de > Phone: ? ?+49(0)221-5062-447 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gcomesana at cnio.es Wed Mar 28 11:55:25 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Guillermo_Comesa=C3=B1a=2E=22?=) Date: Wed, 28 Mar 2007 17:55:25 +0200 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <4d93f07c0703280842x4f75f30bw1e6c213df74f3243@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> <460A89A3.6080803@cnio.es> <4d93f07c0703280842x4f75f30bw1e6c213df74f3243@mail.gmail.com> Message-ID: <460A8FED.7080206@cnio.es> > It would help if you either register your data type in the Canadian Moby > Central (you may/should use the testing Moby Central there) or if you > give me the URL and URI of your register (if it is publicly accessible). yeah, no problem. url endpoint: http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl uri: http://moby-dev.inab.org/MOBY/Central i guess this is an absolutely silly problem, but i just started to work with jmoby platform few days ago and i'm not proficiency enough at this time and, as i told you before, i dont have any help here (if i had, i would be bothering my mates :) cheers > Martin w i l l y **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 gordonp at ucalgary.ca Wed Mar 28 15:28:27 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 28 Mar 2007 13:28:27 -0600 Subject: [MOBY-dev] Asynchronous services In-Reply-To: <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> Message-ID: <460AC1DB.5010204@ucalgary.ca> Hi all, Is there a stable, working asynchronous service that I can use for unit testing new asynchronous client code in Java? From martin.senger at gmail.com Fri Mar 2 00:11:12 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Mar 2007 00:11:12 +0000 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: References: Message-ID: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> > Is there an equivalent to the MOBY::Async::Service module in Java? I will be looking into in during March and April (with a definitive target date to be fully completed before I meet with Mark and few others in Vancouver in June). I will be looking how to make async services in Moses, both Java and Perl Moses. (BTW - and out of the topic - why do we still have two Perl versions?) Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From edward.kawas at gmail.com Fri Mar 2 00:16:35 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 1 Mar 2007 16:16:35 -0800 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> References: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> Message-ID: <00a001c75c60$0a7e1780$6900a8c0@notebook> Hey Martin, I have been working on a java client, recently. I must say that I have given up on using any third party libraries that advertise support for wsrf. It may be that I am a really bad programmer, but I couldn't figure out how to those libraries to work. The prototype that I got working today uses the java SOAP api and http posts. 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: Thursday, March 01, 2007 4:11 PM To: Core developer announcements Subject: Re: [MOBY-dev] MOBY::Async::Service in Java? > Is there an equivalent to the MOBY::Async::Service module in Java? I will be looking into in during March and April (with a definitive target date to be fully completed before I meet with Mark and few others in Vancouver in June). I will be looking how to make async services in Moses, both Java and Perl Moses. (BTW - and out of the topic - why do we still have two Perl versions?) 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 martin.senger at gmail.com Fri Mar 2 00:20:54 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 2 Mar 2007 00:20:54 +0000 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: <00a001c75c60$0a7e1780$6900a8c0@notebook> References: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> <00a001c75c60$0a7e1780$6900a8c0@notebook> Message-ID: <4d93f07c0703011620i10f2f5c4jd934908e4bbc027d@mail.gmail.com> > The prototype that I got working today uses the java SOAP api and http > posts. Thanks, Eddie. I will use your expertise when I dive into it myself. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From ivanp at mmb.pcb.ub.es Fri Mar 2 00:25:30 2007 From: ivanp at mmb.pcb.ub.es (=?ISO-8859-1?Q?Iv=E1n_P=E1rraga_Garc=EDa?=) Date: Fri, 02 Mar 2007 01:25:30 +0100 Subject: [MOBY-dev] MOBY::Async::Service in Java? In-Reply-To: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> References: <4d93f07c0703011611l517b601eta736f6102802ff56@mail.gmail.com> Message-ID: <45E76EFA.2070802@mmb.pcb.ub.es> Hi, If you need somebody providing Java async services, just let me know it. I'll be happy to check any version/prototype. Iv?n Martin Senger escribi?: >> Is there an equivalent to the MOBY::Async::Service module in Java? >> > > > I will be looking into in during March and April (with a definitive target > date to be fully completed before I meet with Mark and few others in > Vancouver in June). I will be looking how to make async services in Moses, > both Java and Perl Moses. (BTW - and out of the topic - why do we still have > two Perl versions?) > > Martin > > -- ------------------------------------------------ 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 Thu Mar 8 16:51:57 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Mar 2007 08:51:57 -0800 Subject: [MOBY-dev] Who is "jmrc"? Message-ID: Hiya, Just going through the commits log to get the authorship list for the MOBY 1.0 manuscript, but I can't figure out who "jmrc" is? Anyone know? Mark From markw at illuminae.com Thu Mar 8 17:08:31 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Mar 2007 09:08:31 -0800 Subject: [MOBY-dev] Who is "jmrc"? In-Reply-To: References: Message-ID: Nix that - I got it from the /etc/passwd file. It's Jose :-) M On Thu, 08 Mar 2007 08:51:57 -0800, Mark Wilkinson wrote: > Hiya, > > Just going through the commits log to get the authorship list for the > MOBY > 1.0 manuscript, but I can't figure out who "jmrc" is? > > Anyone know? > > Mark > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From markw at illuminae.com Thu Mar 8 17:08:31 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Mar 2007 09:08:31 -0800 Subject: [MOBY-dev] Who is "jmrc"? In-Reply-To: References: Message-ID: Nix that - I got it from the /etc/passwd file. It's Jose :-) M On Thu, 08 Mar 2007 08:51:57 -0800, Mark Wilkinson wrote: > Hiya, > > Just going through the commits log to get the authorship list for the > MOBY > 1.0 manuscript, but I can't figure out who "jmrc" is? > > Anyone know? > > Mark > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital ***CONFIDENTIALITY NOTICE*** This electronic message is intended only for the use of the addressee and may contain information that is privileged and confidential. Any dissemination, distribution or copying of this communication by unauthorized individuals is strictly prohibited. If you have received this communication in error, please notify the sender immediately by reply e-mail and delete the original and all copies from your system. From markw at illuminae.com Fri Mar 9 01:44:07 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 9 Mar 2007 01:44:07 +0000 GMT Subject: [MOBY-dev] The Moby 1.0 paper authorship Message-ID: <1627174959-1173404654-cardhu_blackberry.rim.net-26838-@engine09-cell01> Hi all moby dev'ers! I'm just doing the final edit of the moby 1.0 manuscript - I'll commit it to the CVS (as a PDF) in a day or two for comment from you all. The target journal is PLoS Computational Biology (unless anyone can suggest a better open-access forum for this work?) My question to you is regarding authorship. Almost everyone on this list is a co-author. Would you prefer to be individually named (as was done with the 1.0 release of BioPerl) or would you prefer to be called "The BioMoby Consortium" (as was done for the Gene Ontology's Nature paper)? I'm ambivalent, so if the wider community has any preference please let me know. Cheers all! Mark -- Mark Wilkinson ...on the road! From darin.london at duke.edu Tue Mar 6 16:03:59 2007 From: darin.london at duke.edu (Darin London) Date: Tue, 06 Mar 2007 11:03:59 -0500 Subject: [MOBY-dev] Announcing BOSC 2007 Message-ID: <45ED90EF.7030000@duke.edu> The BOSC Organizing Committee are proud to announce BOSC 2007, occurring in Vienna, Austria on July 19th, 20th. The conference this year promises to be exciting, as the BOSC developers attempt to define and solve currently intractable problems in Bioinformatics. Please refer to the following website for complete information, and requests for submissions. Thank you, and we hope to see you in Vienna. http://open-bio.org/wiki/BOSC_2007 The BOSC organizing Committee Please pass this email on to anyone that would be interested. From gordonp at ucalgary.ca Fri Mar 9 14:57:37 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 09 Mar 2007 07:57:37 -0700 Subject: [MOBY-dev] The Moby 1.0 paper authorship In-Reply-To: <1627174959-1173404654-cardhu_blackberry.rim.net-26838-@engine09-cell01> References: <1627174959-1173404654-cardhu_blackberry.rim.net-26838-@engine09-cell01> Message-ID: <45F175E1.6060406@ucalgary.ca> The question is, how long is the list? 30-40 authors is not uncommon for genome papers, for example. More than 50 is probably unreasonable, in which case you'd want to go the Consortium root... > Hi all moby dev'ers! > > I'm just doing the final edit of the moby 1.0 manuscript - I'll commit it to the CVS (as a PDF) in a day or two for comment from you all. The target journal is PLoS Computational Biology (unless anyone can suggest a better open-access forum for this work?) > > My question to you is regarding authorship. Almost everyone on this list is a co-author. Would you prefer to be individually named (as was done with the 1.0 release of BioPerl) or would you prefer to be called "The BioMoby Consortium" (as was done for the Gene Ontology's Nature paper)? > > I'm ambivalent, so if the wider community has any preference please let me know. > > Cheers all! > > Mark > > > > > -- > Mark Wilkinson > ...on the road! > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From enrique.deandres at pcm.uam.es Thu Mar 15 11:45:07 2007 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 15 Mar 2007 12:45:07 +0100 Subject: [MOBY-dev] Bug in MOBY::Client::SimpleArticle and MOBY::Client::CollectionArticle? Message-ID: <45F931C3.4030608@pcm.uam.es> Hello, I think I have detected a bug in MOBY/Client/SimpleArticle.pm. At the subroutine createFromDOM (line 277), when getting the articleName, it doesn't take into account the moby namespace (while MOBY::Client::Service adds the moby namespace to the articleName attribute): my $attr = $dom->getAttributeNode( 'articleName' ); It happens the same in MOBY/Client/CollectionArticle.pm (line 265). Thanks, Enrique. -- 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 enrique.deandres at pcm.uam.es Thu Mar 15 14:40:48 2007 From: enrique.deandres at pcm.uam.es (Enrique de Andres Saiz) Date: Thu, 15 Mar 2007 15:40:48 +0100 Subject: [MOBY-dev] Bug in MOBY::Client::SimpleArticle andMOBY::Client::CollectionArticle? In-Reply-To: <45F931C3.4030608@pcm.uam.es> References: <45F931C3.4030608@pcm.uam.es> Message-ID: <45F95AF0.4090207@pcm.uam.es> I think it is not a bug... it works well. I'm sorry for the alert, but there was something working wrong in my code and I thought that it was the reason. Sorry again. Enrique. Enrique de Andres Saiz wrote: > Hello, > > I think I have detected a bug in MOBY/Client/SimpleArticle.pm. At the > subroutine createFromDOM (line 277), when getting the articleName, it > doesn't take into account the moby namespace (while > MOBY::Client::Service adds the moby namespace to the articleName attribute): > > my $attr = $dom->getAttributeNode( 'articleName' ); > > It happens the same in MOBY/Client/CollectionArticle.pm (line 265). > > Thanks, > Enrique. > > -- Enrique de Andres Saiz Unidad de Bioinform?tica (INB GNHC-1) Parque Cientifico de Madrid Ctra. de Colmenar, Km. 15. Campus UAM, Cantoblanco - Pabellon C 28049 Madrid Tel. (+34) 91 497 3448 Fax. (+34) 91 497 3471 http://www.fpcm.es http://www.inab.org From jmrodriguez at cnio.es Thu Mar 22 09:32:29 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Thu, 22 Mar 2007 10:32:29 +0100 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs Message-ID: <46024D2D.5070502@cnio.es> Hi everyone, I am executing a MOBY services in Perl which needs multiple Simple inputs. To extract the MOBY messages, when the service are called, I am using the "serviceInputParser" but I have seen that the returned hashref which contains the Simple inputs is wrong. I mean, the hashref ,whose structure is "$inputs->{$queryID}->{articleName}", has always empty articleName value. That means the articleName of Simple Object is not obtained correctly. (if we have multiple simple inputs in one mobyData, the hashref returned by "serviceInputParser" will contain the last MOBY Object). I have been checking the code and I have seen in the method "createFromDOM" from "MOBY::Client::SimpleArticle" file that the 'articleNames' attribute is not extracted when this belongs to the namespace of "moby". my $attr = $dom->getAttributeNode( 'articleName' ); my $articleName = $attr ? $attr->getValue : ""; Here you are one solution in this particular problem: my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', 'articleName' ); $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; my $articleName = $attr ? $attr->getValue : ""; (but I think this is one of more problems regarding MOBY namespaces) Best Regards, Jos?. -- 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 Adress: C/. Melchor Fernandez 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 markw at illuminae.com Thu Mar 22 15:53:10 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 22 Mar 2007 07:53:10 -0800 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <46024D2D.5070502@cnio.es> References: <46024D2D.5070502@cnio.es> Message-ID: <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> Hi Jose, please go ahead and fix this in the CVS. It's interesting that there is no attribute-equivalent to getElementsByLocalName, where "local" means whatever namespace you are currently in... M On Thu, 2007-03-22 at 10:32 +0100, Jose Manuel Rodriguez wrote: > Hi everyone, > > I am executing a MOBY services in Perl which needs multiple Simple inputs. > To extract the MOBY messages, when the service are called, I am using > the "serviceInputParser" but I have seen that the returned hashref which > contains the Simple inputs is wrong. I mean, the hashref > > ,whose structure is "$inputs->{$queryID}->{articleName}", > > has always empty articleName value. That means the articleName of Simple > Object is not obtained correctly. (if we have multiple simple inputs in > one mobyData, the hashref returned by "serviceInputParser" will contain > the last MOBY Object). > > > > I have been checking the code and I have seen in the method > "createFromDOM" from "MOBY::Client::SimpleArticle" file that the > 'articleNames' attribute is not extracted when this belongs to the > namespace of "moby". > > > my $attr = $dom->getAttributeNode( 'articleName' ); > my $articleName = $attr ? $attr->getValue : ""; > > > Here you are one solution in this particular problem: > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > 'articleName' ); > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > my $articleName = $attr ? $attr->getValue : ""; > > > > (but I think this is one of more problems regarding MOBY namespaces) > > Best Regards, > Jos?. > From edward.kawas at gmail.com Thu Mar 22 16:35:33 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Mar 2007 09:35:33 -0700 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method whenthe mobyservice receives multiple Simple inputs In-Reply-To: <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> References: <46024D2D.5070502@cnio.es> <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> Message-ID: <003f01c76ca0$1ced0110$6800a8c0@notebook> To get an attribute regardless of the prefix, use: getAttributeNS("", "articleName") This seems to work on my machine. Does it work for you Jose? Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Mark Wilkinson > Sent: Thursday, March 22, 2007 8:53 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] Problems using serviceInputParser method > whenthe mobyservice receives multiple Simple inputs > > Hi Jose, > > please go ahead and fix this in the CVS. > > It's interesting that there is no attribute-equivalent to > getElementsByLocalName, where "local" means whatever namespace you are > currently in... > > M > > > > > > On Thu, 2007-03-22 at 10:32 +0100, Jose Manuel Rodriguez wrote: > > Hi everyone, > > > > I am executing a MOBY services in Perl which needs multiple Simple > inputs. > > To extract the MOBY messages, when the service are called, I am using > > the "serviceInputParser" but I have seen that the returned hashref which > > contains the Simple inputs is wrong. I mean, the hashref > > > > ,whose structure is "$inputs->{$queryID}->{articleName}", > > > > has always empty articleName value. That means the articleName of Simple > > Object is not obtained correctly. (if we have multiple simple inputs in > > one mobyData, the hashref returned by "serviceInputParser" will contain > > the last MOBY Object). > > > > > > > > I have been checking the code and I have seen in the method > > "createFromDOM" from "MOBY::Client::SimpleArticle" file that the > > 'articleNames' attribute is not extracted when this belongs to the > > namespace of "moby". > > > > > > my $attr = $dom->getAttributeNode( 'articleName' ); > > my $articleName = $attr ? $attr->getValue : ""; > > > > > > Here you are one solution in this particular problem: > > > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > > 'articleName' ); > > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > > my $articleName = $attr ? $attr->getValue : ""; > > > > > > > > (but I think this is one of more problems regarding MOBY namespaces) > > > > Best Regards, > > Jos?. > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Thu Mar 22 16:41:35 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 22 Mar 2007 09:41:35 -0700 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <46024D2D.5070502@cnio.es> References: <46024D2D.5070502@cnio.es> Message-ID: <004c01c76ca0$f5481ea0$6800a8c0@notebook> The code that I used to test getting any attribute regardless of the prefix is the below. Notice that id is prefixed while namespace is not ... --------------------- use XML::LibXML; my $xml =< EOF my $p = XML::LibXML->new; my $doc = $p->parse_string( $xml ); my $root = $doc->getDocumentElement; $root = $root->getElementsByLocalName('Object')->item(0); print "The XML:\n$xml\n"; print "Getting information for inner element 'Object'\n"; print "\tnamespace: '" .$root->getAttributeNS("", "namespace") . "'\n"; print "\tid: '" .$root->getAttributeNS("", "id") . "'\n"; ---------------------------------- Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Jose Manuel Rodriguez > Sent: Thursday, March 22, 2007 2:32 AM > To: Core developer announcements > Subject: [MOBY-dev] Problems using serviceInputParser method when the > mobyservice receives multiple Simple inputs > > Hi everyone, > > I am executing a MOBY services in Perl which needs multiple Simple inputs. > To extract the MOBY messages, when the service are called, I am using > the "serviceInputParser" but I have seen that the returned hashref which > contains the Simple inputs is wrong. I mean, the hashref > > ,whose structure is "$inputs->{$queryID}->{articleName}", > > has always empty articleName value. That means the articleName of Simple > Object is not obtained correctly. (if we have multiple simple inputs in > one mobyData, the hashref returned by "serviceInputParser" will contain > the last MOBY Object). > > > > I have been checking the code and I have seen in the method > "createFromDOM" from "MOBY::Client::SimpleArticle" file that the > 'articleNames' attribute is not extracted when this belongs to the > namespace of "moby". > > > my $attr = $dom->getAttributeNode( 'articleName' ); > my $articleName = $attr ? $attr->getValue : ""; > > > Here you are one solution in this particular problem: > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > 'articleName' ); > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > my $articleName = $attr ? $attr->getValue : ""; > > > > (but I think this is one of more problems regarding MOBY namespaces) > > Best Regards, > Jos?. > > -- > 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 > Adress: C/. Melchor Fernandez 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 martin.senger at gmail.com Thu Mar 22 16:53:17 2007 From: martin.senger at gmail.com (Martin Senger) Date: Thu, 22 Mar 2007 16:53:17 +0000 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method whenthe mobyservice receives multiple Simple inputs In-Reply-To: <003f01c76ca0$1ced0110$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es> <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> <003f01c76ca0$1ced0110$6800a8c0@notebook> Message-ID: <4d93f07c0703220953x2b719085ib2b2eab929f1feb0@mail.gmail.com> This is how I do it in Perl/Moses code: # return a value of an attribute named $name from an $element (an # XML::LibXML type); try both with and without namespaces; return # undef if no such sttribute found sub getXMLAttribute { my ($self, $element, $name) = @_; return $element->getAttribute ($name) || $element->getAttributeNS (MOBY_XML_NS, $name); } Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Thu Mar 22 17:35:49 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 22 Mar 2007 11:35:49 -0600 Subject: [MOBY-dev] [moby] Problems using serviceInputParser method whenthe mobyservice receives multiple Simple inputs In-Reply-To: <4d93f07c0703220953x2b719085ib2b2eab929f1feb0@mail.gmail.com> References: <46024D2D.5070502@cnio.es> <1174578790.7277.52.camel@bioinfo.icapture.ubc.ca> <003f01c76ca0$1ced0110$6800a8c0@notebook> <4d93f07c0703220953x2b719085ib2b2eab929f1feb0@mail.gmail.com> Message-ID: <4602BE75.8030909@ucalgary.ca> This is the logic used in jMOBY's MobyPrefixResolver class too. Great minds think alike :-) One caveat related to Eddie's earlier code (I don't know if it's applicable in the Perl implementation) is that a null namespace, and an empty string namespace are different beasts in the XML DOM, and depend on if the parser is in namespace-aware mode. > This is how I do it in Perl/Moses code: > > # return a value of an attribute named $name from an $element (an > # XML::LibXML type); try both with and without namespaces; return > # undef if no such sttribute found > sub getXMLAttribute { > my ($self, $element, $name) = @_; > return > $element->getAttribute ($name) || > $element->getAttributeNS (MOBY_XML_NS, $name); > } > > Martin > > > From jmrodriguez at cnio.es Fri Mar 23 10:46:59 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Fri, 23 Mar 2007 11:46:59 +0100 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <004c01c76ca0$f5481ea0$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> Message-ID: <4603B023.7020409@cnio.es> Hi Eddie, I have been looking for the reason why sometimes works or not...The difference is XML::LibXML library. Here I am going to show you results from both "getAttributeNode" and "getAttributeNodeNS" methods depending on different versions of XML::LibXML: The input XML is : 20060215121817 20060215121816 true XML::LibXML version 1.58: Getting information for inner element 'Simple' articleName: 'end' # getAttributeNode("articleName") Now MOBY libraries use this method WE HAVE RESULT articleName NS empty: '' # getAttributeNodeNS("", "articleName") articleName NS: 'end' # getAttributeNodeNS("http://www.biomoby.org/moby", "articleName") Getting information for inner element 'Simple' articleName: 'start' articleName NS empty: '' articleName NS: '' The same script using XML::LibXML version 1.62: Getting information for inner element 'Simple' articleName: '' # DIFFERENT RESULT!!!!!!!!! articleName NS empty: '' articleName NS: 'end' Getting information for inner element 'Simple' articleName: 'start' articleName NS empty: 'start' articleName NS: '' So, we see different results depending on XML::LibXML version but thinking which is the correct one because maybe the problem is on LibXML libraries not on MOBY. I have run the same methods with Java libraries whose results are: java version "1.5.0_08": Getting information for inner element 'Simple' articleName: '' articleName NS empty: '' articleName NS: 'end' Getting information for inner element 'Simple' articleName: 'start' articleName NS empty: 'start' articleName NS: '' The same results than version 1.62. In any case, in my opinion we have to control the XML libraries using better methods as (getAttributeNodeNS("http://www.biomoby.org/moby", "articleName")). Other question I have is we are obligate to add namespaces within MOBY xml's or not. The MOBY standard says something about that... Best Regards, Jos?. SP: If you want I can send you the scripts :) Edward Kawas wrote: > The code that I used to test getting any attribute regardless of the prefix > is the below. Notice that id is prefixed while namespace is not ... > > --------------------- > use XML::LibXML; > > my $xml =< > > > > > > > > > > EOF > my $p = XML::LibXML->new; > my $doc = $p->parse_string( $xml ); > my $root = $doc->getDocumentElement; > $root = $root->getElementsByLocalName('Object')->item(0); > > print "The XML:\n$xml\n"; > print "Getting information for inner element 'Object'\n"; > print "\tnamespace: '" .$root->getAttributeNS("", "namespace") . "'\n"; > print "\tid: '" .$root->getAttributeNS("", "id") . "'\n"; > ---------------------------------- > > Eddie > > >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- >> bounces at lists.open-bio.org] On Behalf Of Jose Manuel Rodriguez >> Sent: Thursday, March 22, 2007 2:32 AM >> To: Core developer announcements >> Subject: [MOBY-dev] Problems using serviceInputParser method when the >> mobyservice receives multiple Simple inputs >> >> Hi everyone, >> >> I am executing a MOBY services in Perl which needs multiple Simple inputs. >> To extract the MOBY messages, when the service are called, I am using >> the "serviceInputParser" but I have seen that the returned hashref which >> contains the Simple inputs is wrong. I mean, the hashref >> >> ,whose structure is "$inputs->{$queryID}->{articleName}", >> >> has always empty articleName value. That means the articleName of Simple >> Object is not obtained correctly. (if we have multiple simple inputs in >> one mobyData, the hashref returned by "serviceInputParser" will contain >> the last MOBY Object). >> >> >> >> I have been checking the code and I have seen in the method >> "createFromDOM" from "MOBY::Client::SimpleArticle" file that the >> 'articleNames' attribute is not extracted when this belongs to the >> namespace of "moby". >> >> >> my $attr = $dom->getAttributeNode( 'articleName' ); >> my $articleName = $attr ? $attr->getValue : ""; >> >> >> Here you are one solution in this particular problem: >> >> my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', >> 'articleName' ); >> $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; >> my $articleName = $attr ? $attr->getValue : ""; >> >> >> >> (but I think this is one of more problems regarding MOBY namespaces) >> >> Best Regards, >> Jos?. >> >> -- >> 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 >> Adress: C/. Melchor Fernandez 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 >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- 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 Adress: C/. Melchor Fernandez 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 Fri Mar 23 13:50:53 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 23 Mar 2007 06:50:53 -0700 Subject: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <4603B023.7020409@cnio.es> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> Message-ID: <000f01c76d52$46d8d5f0$6800a8c0@notebook> > Other question I have is we are obligate to add namespaces within MOBY > xml's or not. The MOBY standard says something about that... I don't believe that it is necessary. Eddie From markw at illuminae.com Fri Mar 23 15:49:46 2007 From: markw at illuminae.com (mark wilkinson) Date: Fri, 23 Mar 2007 15:49:46 +0000 GMT Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <000f01c76d52$46d8d5f0$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook><4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook> Message-ID: <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> The attribute is necessary, but it can have a null ("") value -- Mark Wilkinson ...on the road! -----Original Message----- From: "Edward Kawas" Date: Fri, 23 Mar 2007 06:50:53 To:"'Core developer announcements'" Subject: Re: [MOBY-dev] Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs > Other question I have is we are obligate to add namespaces within MOBY > xml's or not. The MOBY standard says something about that... I don't believe that it is necessary. Eddie _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From jmrodriguez at cnio.es Fri Mar 23 17:59:15 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Fri, 23 Mar 2007 18:59:15 +0100 Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook><4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook> <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> Message-ID: <46041573.7010108@cnio.es> Maybe I don't have explain me OK (sorry for that) The main idea that I am trying to advise is the form to call LibXML methods in MOBY library (Perl), they do not work on new versions of XML::LibXML. Specifically: In the package => MOBY::Client::SimpleArticle.pm In the method => createFromDOM code => my $attr = $dom->getAttributeNode( 'articleName' ); my $articleName = $attr ? $attr->getValue : ""; This above code (the actual one) don't work on 1.62 version of LibXML. We should use the next code: my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', 'articleName' ); $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; my $articleName = $attr ? $attr->getValue : ""; Good weekend, Jos?. mark wilkinson wrote: > The attribute is necessary, but it can have a null ("") value > > > -- > Mark Wilkinson > ...on the road! > > > -----Original Message----- > From: "Edward Kawas" > Date: Fri, 23 Mar 2007 06:50:53 > To:"'Core developer announcements'" > Subject: Re: [MOBY-dev] Problems using serviceInputParser method when the > mobyservice receives multiple Simple inputs > > >> Other question I have is we are obligate to add namespaces within MOBY >> xml's or not. The MOBY standard says something about that... >> > > I don't believe that it is necessary. > > Eddie > > _______________________________________________ > 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 > > -- 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 Fernandez 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 Fri Mar 23 18:39:32 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Fri, 23 Mar 2007 11:39:32 -0700 Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <46041573.7010108@cnio.es> References: <46024D2D.5070502@cnio.es><004c01c76ca0$f5481ea0$6800a8c0@notebook><4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook><1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> <46041573.7010108@cnio.es> Message-ID: <004901c76d7a$999ba2e0$6800a8c0@notebook> Hi Jose, If I were you, I would look at the Perl moses code located in the cvs: moby-live/Java/src/Perl The way that Perl Moses does things is the best way to go about things. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Jose Manuel Rodriguez > Sent: Friday, March 23, 2007 10:59 AM > To: markw at illuminae.com; Core developer announcements > Subject: Re: [MOBY-dev] Problems using serviceInputParser method when > themobyservice receives multiple Simple inputs > > Maybe I don't have explain me OK (sorry for that) > > The main idea that I am trying to advise is the form to call LibXML > methods in MOBY library (Perl), they do not work on new versions of > XML::LibXML. > > Specifically: > > In the package => MOBY::Client::SimpleArticle.pm > In the method => createFromDOM > code => > > my $attr = $dom->getAttributeNode( 'articleName' ); > my $articleName = $attr ? $attr->getValue : ""; > > > This above code (the actual one) don't work on 1.62 version of LibXML. > > We should use the next code: > > my $attr = $dom->getAttributeNodeNS( 'http://www.biomoby.org/moby', > 'articleName' ); > $attr = $dom->getAttributeNode( 'articleName' ) unless defined $attr; > my $articleName = $attr ? $attr->getValue : ""; > > > Good weekend, > Jos?. > > > > mark wilkinson wrote: > > The attribute is necessary, but it can have a null ("") value > > > > > > -- > > Mark Wilkinson > > ...on the road! > > > > > > -----Original Message----- > > From: "Edward Kawas" > > Date: Fri, 23 Mar 2007 06:50:53 > > To:"'Core developer announcements'" > > Subject: Re: [MOBY-dev] Problems using serviceInputParser method when > the > > mobyservice receives multiple Simple inputs > > > > > >> Other question I have is we are obligate to add namespaces within MOBY > >> xml's or not. The MOBY standard says something about that... > >> > > > > I don't believe that it is necessary. > > > > Eddie > > > > _______________________________________________ > > 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 > > > > > > > -- > 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 Fernandez 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 martin.senger at gmail.com Fri Mar 23 19:14:33 2007 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 23 Mar 2007 19:14:33 +0000 Subject: [MOBY-dev] Problems using serviceInputParser method when themobyservice receives multiple Simple inputs In-Reply-To: <004901c76d7a$999ba2e0$6800a8c0@notebook> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <000f01c76d52$46d8d5f0$6800a8c0@notebook> <1632543032-1174661455-cardhu_blackberry.rim.net-730-@engine20-cell01> <46041573.7010108@cnio.es> <004901c76d7a$999ba2e0$6800a8c0@notebook> Message-ID: <4d93f07c0703231214h61974716rbcbbabbef1cc829a@mail.gmail.com> > If I were you, I would look at the Perl moses code located in the cvs: > moby-live/Java/src/Perl ...and this is the documentation to it: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/PerlMoses.html Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Fri Mar 23 17:29:02 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 23 Mar 2007 09:29:02 -0800 Subject: [MOBY-dev] [moby] Re: Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <4603B023.7020409@cnio.es> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> Message-ID: <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> On Fri, 2007-03-23 at 11:46 +0100, Jose Manuel Rodriguez wrote: > Other question I have is we are obligate to add namespaces within MOBY > xml's or not. The MOBY standard says something about that... I apologize for my earlier response - interestingly, all of that XML in the message did not render *at all* in my cell-phone emailer, so this last sentence is the only one that made sense to me when I was reading it on my phone. Now that I am on my regular computer I can see the whole message and it makes much more sense! The issue of whether or not to use a namespace really is an issue of what is correct/incorrect XML. The Perl libraries will auto-add the xmlns:moby to the various headers, so the namespace is going to be defined in messages that come from Perl services for sure. You also have to anticipate that some providers will add the moby: prefix into their mobyData Objects, so there's no way you can write services that do not handle namespaced XML, even if you don't generate namespaces in your own response XML. I recall seeing some disagreement on the various newsgroups about whether XML attributes (as opposed to XML tags) had to be namespaced, or whether the namespace of the tag was assumed to also be the namespace of the attribute... does anyone know definitively what the answer to this is? M From gordonp at ucalgary.ca Fri Mar 23 22:37:22 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 23 Mar 2007 16:37:22 -0600 Subject: [MOBY-dev] [moby] Re: Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> Message-ID: <460456A2.5060407@ucalgary.ca> Please refer to: http://www.w3.org/TR/REC-xml-names/#defaulting Essentially, unprefixed attributes inherit the namespace of the element they are in, not the default namespace. So it boils down to one of Jose's original question I think: "Other question I have is we are obligate to add namespaces within MOBY xml's or not." I know that currently the service providers are giving a mixed bag, that's why I check both. I don't remember anything from the MOBY spec about requiring a DNASequence tag, for example to be in the MOBY namespace (perhaps because previously we didn't have a super tight schema to describe valid MOBY objects!). > I recall seeing some disagreement on the various newsgroups about > whether XML attributes (as opposed to XML tags) had to be namespaced, or > whether the namespace of the tag was assumed to also be the namespace of > the attribute... does anyone know definitively what the answer to this > is? > > M > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,460451f121086182051815! > > > > From gcomesana at cnio.es Mon Mar 26 13:36:27 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Comesa=C3=B1a=2EGuillermo=22?=) Date: Mon, 26 Mar 2007 15:36:27 +0200 Subject: [MOBY-dev] question from the newbie In-Reply-To: <460456A2.5060407@ucalgary.ca> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> <460456A2.5060407@ucalgary.ca> Message-ID: <4607CC5B.5060907@cnio.es> hi everybody and sorry for the inconvenience in the BaseCmdClient i've found "It does create data input only with one Simple or one Collection. This would be easy to rectify but the command-line options would become too cumbersome. But still I may do it later." Does this mean that it is just possible to send one parameter from this command line tool to call the service? what is going on if the testing service needs more than one parameter? Regards. **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From martin.senger at gmail.com Mon Mar 26 13:59:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Mon, 26 Mar 2007 14:59:29 +0100 Subject: [MOBY-dev] question from the newbie In-Reply-To: <4607CC5B.5060907@cnio.es> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> <460456A2.5060407@ucalgary.ca> <4607CC5B.5060907@cnio.es> Message-ID: <4d93f07c0703260659m73578cbfq28b6ed6bf5fbc39f@mail.gmail.com> > Does this mean that it is just possible to send one parameter from this > command line tool to call the service? what is going on if the testing > service needs more than one parameter? Use Dashboard instead. Its "Simple Client" panel can do much more. Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From jmrodriguez at cnio.es Mon Mar 26 13:51:36 2007 From: jmrodriguez at cnio.es (Jose Manuel Rodriguez) Date: Mon, 26 Mar 2007 15:51:36 +0200 Subject: [MOBY-dev] [moby] Re: Problems using serviceInputParser method when the mobyservice receives multiple Simple inputs In-Reply-To: <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> References: <46024D2D.5070502@cnio.es> <004c01c76ca0$f5481ea0$6800a8c0@notebook> <4603B023.7020409@cnio.es> <1174670942.10843.16.camel@bioinfo.icapture.ubc.ca> Message-ID: <4607CFE8.1080507@cnio.es> Mark Wilkinson wrote: > I recall seeing some disagreement on the various newsgroups about > whether XML attributes (as opposed to XML tags) had to be namespaced, or > whether the namespace of the tag was assumed to also be the namespace of > the attribute... does anyone know definitively what the answer to this > is? > > Hi Mark, Maybe this could help you http://www.w3.org/TR/2006/REC-xml-names-20060816/#uniqAttrs Cheers, Jos?. > M > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -- 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 Fernandez 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 markw at illuminae.com Mon Mar 26 23:53:44 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 26 Mar 2007 15:53:44 -0800 Subject: [MOBY-dev] Draft of the BioMoby 1.0 manuscript added to the CVS Message-ID: Hi all, I've completed a draft of the BioMoby 1.0 manuscript and have just uploaded it into the CVS (moby-live/Docs/BioMoby_1_0_version_6.pdf). Please let me know if I have missed anyone's name who should be included in the BioMoby consortium membership list, or if you see your name there and would prefer that it be removed. I welcome any and all comments! Best wishes! Mark From gcomesana at cnio.es Tue Mar 27 12:22:45 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Comesa=C3=B1a=2EGuillermo=22?=) Date: Tue, 27 Mar 2007 14:22:45 +0200 Subject: [MOBY-dev] dashboard In-Reply-To: References: Message-ID: <46090C95.1050904@cnio.es> hi there has dashboard any kind of cache with local classes?? how can i remove that cache capability? i am testing a local class with dashboard and it uses the same class version even i recompile the class. When the class is recompiled it is placed in the proper location for dashboard. Similarly, i am using log4j for logging and debuggin issues and the log gets updated, but the logging output is the same as if the class werent changed. any suggestion about this??? zanx & regards **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 martin.senger at gmail.com Tue Mar 27 13:03:55 2007 From: martin.senger at gmail.com (Martin Senger) Date: Tue, 27 Mar 2007 14:03:55 +0100 Subject: [MOBY-dev] dashboard In-Reply-To: <46090C95.1050904@cnio.es> References: <46090C95.1050904@cnio.es> Message-ID: <4d93f07c0703270603u44b3634du424ff05ade36b49e@mail.gmail.com> > has dashboard any kind of cache with local classes?? There is special class loader in Dashboard. Which means, once a class is loaded it is loaded, and the class loader involved does not check if there is a newer version. how can i remove that cache capability? Just restart the Dashboard. But if you need to do a lot of testing cycles, restarting the dashboard would be boring and perhaps slow. In which case I would recommend to use the command-line client (script run-cmdline-client, invoking MobyCmdLineClient). I know you already asked how to make this client to work with multiple inputs. The way to do it is to create a service input in XML using dashboard (during testing the input usually does not change much, and if yes you still can edit directly the XML file; for testing purposes it is fine), and then call the command-line client with the following arguments: -scall You get back just raw XML - but again, for testing purposes it may be good enough. Or, even perhaps better (I forgot about it) is to use a specific command-line client for calling services. This will give you help (and there is a detailed documentation on Moses pages): build/run/run-service -help Regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From markw at illuminae.com Tue Mar 27 21:39:27 2007 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 27 Mar 2007 13:39:27 -0800 Subject: [MOBY-dev] revised manuscript now in CVS Message-ID: Thanks to all who read and commented on the Moby 1.0 manuscript so quickly! I've made the first set of suggested revisions, and the new manuscript is uploaded (version 7)to the CVS in the /Docs folder. Since we can't track changes using the binary PDF format, perhaps send your suggestions/edits to the mailing list so that everyone can see them and comment on them. Cheers! Mark From gcomesana at cnio.es Wed Mar 28 13:42:08 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Guillermo_Comesa=C3=B1a=2E=22?=) Date: Wed, 28 Mar 2007 15:42:08 +0200 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: References: Message-ID: <460A70B0.2080906@cnio.es> Hi everybody and sorry for possible troubles... ...but, does somebody know to say why can i get this following: 27816 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27822 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27825 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27829 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. 27832 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. (...) I have as many lines with this warning as LogEvent objects and I get it after locally executing my service with me at mymachine$ run-service -service getLogReport -mobye $ENDPOINT -mobyuri $MOBY_URI -class JLogReport -xml testlog.xml -showxml -outxml The class JLogReport implements the service generated as skeleton in JLogReportSkel and my dashboard yielded the LogEvent class. Previously to all those "moby warnings" the output of the service is apparently ok as you can see in the following output snippet F4D83E00-B50D-11DA-9DE7-EA517071BF93 runPhylipNeighbor 193.146.190.95 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z 701 3790E176-B512-11DA-9F9D-E262AE5C699A runPhylipNeighbor 193.146.190.95 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z 701 (...) E0A58A54-B43C-11DA-8ED1-CC6B69DB9358 getAminoAcidSequence 150.244.85.114 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z 0 any suggestion, idea, something...? Cheers in advance w i l l y **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 Mar 28 13:47:05 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 28 Mar 2007 06:47:05 -0700 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A70B0.2080906@cnio.es> References: <460A70B0.2080906@cnio.es> Message-ID: <002401c7713f$93038bf0$6800a8c0@notebook> Have you generated the datatypes first? Anytime you see the ignoring unknown element ... that means it cant find the datatype definition. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of "Guillermo Comesa??a." > Sent: Wednesday, March 28, 2007 6:42 AM > To: Core developer announcements > Subject: [MOBY-dev] JMoby bug or lack of knowledge > > > Hi everybody and sorry for possible troubles... > ...but, does somebody know to say why can i get this following: > > 27816 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27822 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27825 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27829 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > 27832 [main] WARN MobyParser - Ignoring unknown element 'LogEvent'. > (...) > > I have as many lines with this warning as LogEvent objects and I get it > after locally executing my service with > > me at mymachine$ run-service -service getLogReport -mobye $ENDPOINT > -mobyuri $MOBY_URI -class JLogReport -xml testlog.xml -showxml -outxml > > The class JLogReport implements the service generated as skeleton in > JLogReportSkel and my dashboard yielded the LogEvent class. Previously > to all those "moby warnings" the output of the service is apparently ok > as you can see in the following output snippet > > > > > > > > > moby:articleName="id">F4D83E00-B50D-11DA-9DE7-EA517071BF93 > moby:articleName="serviceName">runPhylipNeighbor > moby:articleName="ip">193.146.190.95 > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="status">701 > > > > > moby:articleName="id">3790E176-B512-11DA-9F9D-E262AE5C699A > moby:articleName="serviceName">runPhylipNeighbor > moby:articleName="ip">193.146.190.95 > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="status">701 > > > (...) > > > moby:articleName="id">E0A58A54-B43C-11DA-8ED1-CC6B69DB9358 > moby:articleName="serviceName">getAminoAcidSequence > moby:articleName="ip">150.244.85.114 > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="status">0 > > > > > > > > any suggestion, idea, something...? > Cheers in advance > > w i l l y > > > **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 martin.senger at gmail.com Wed Mar 28 13:52:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 14:52:29 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <002401c7713f$93038bf0$6800a8c0@notebook> References: <460A70B0.2080906@cnio.es> <002401c7713f$93038bf0$6800a8c0@notebook> Message-ID: <4d93f07c0703280652o3ff1925frdc0bacbe6f08129b@mail.gmail.com> > Have you generated the datatypes first? Anytime you see the ignoring > unknown > element ... that means it cant find the datatype definition. One cannot beat Eddie on the speed, he is too fast :-) Let me just say that what he said was exactly what I wanted to say... I can just add that you can generate data types either from the command-line, or from Dashboard. And it is a one-time job, you do not need to repeat it again and again (unless you register a new data type). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From martin.senger at gmail.com Wed Mar 28 13:58:26 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 14:58:26 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A70B0.2080906@cnio.es> References: <460A70B0.2080906@cnio.es> Message-ID: <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> ...and I can also add that you should not use the same article name twice in the same message - the 'end' is twice in one LogEvent: 2006-03-24T06:19:50Z 2006-03-24T06:19:50Z Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Wed Mar 28 14:37:48 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 28 Mar 2007 08:37:48 -0600 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> Message-ID: <460A7DBC.6090501@ucalgary.ca> Actually, you should be able to, if the "end" member's relationship is HAS (as opposed to HAS-A), no? > ...and I can also add that you should not use the same article name twice in > the same message - the 'end' is twice in one LogEvent: > > moby:articleName="end">2006-03-24T06:19:50Z > moby:articleName="end">2006-03-24T06:19:50Z > > Martin > > From gordonp at ucalgary.ca Wed Mar 28 14:43:13 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 28 Mar 2007 08:43:13 -0600 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A7DBC.6090501@ucalgary.ca> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> Message-ID: <460A7F01.7010901@ucalgary.ca> On second thought, it may be legal depending on how the data type is defined (which we don't know, since it's not registered), but of course, two end times probably doesn't make much logical sense :-) > Actually, you should be able to, if the "end" member's relationship is > HAS (as opposed to HAS-A), no? > >> ...and I can also add that you should not use the same article name twice in >> the same message - the 'end' is twice in one LogEvent: >> >> > moby:articleName="end">2006-03-24T06:19:50Z >> > moby:articleName="end">2006-03-24T06:19:50Z >> >> Martin >> >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,460a7c9b21086281354797! > > > > From martin.senger at gmail.com Wed Mar 28 15:05:29 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 16:05:29 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A7DBC.6090501@ucalgary.ca> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> Message-ID: <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> > Actually, you should be able to, if the "end" member's relationship is > HAS (as opposed to HAS-A), no? Of course, Paul is right. (I was more concentrating on a "probable logic" of two ends :-)) M. -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gcomesana at cnio.es Wed Mar 28 15:28:35 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Guillermo_Comesa=C3=B1a=2E=22?=) Date: Wed, 28 Mar 2007 17:28:35 +0200 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> Message-ID: <460A89A3.6080803@cnio.es> Cheers everybody for the help. However, nothing was useful for me so far. Apparently in my code everything is ok, the only calls to set both dates (start and end) is as follows: try { if (startLine != null) { aux = buildDate(startLine[3]).getTime(); aDate.setValue (sdf.format(aux)); logger.debug("startline iso8601: " + sdf.format (aux)); logger.debug("startLine->aDate.getValue(): "+aDate.getValue()); logEv.set_start (aDate); } if (endLine != null) { aux = buildDate(endLine[3]).getTime(); aDate.setValue(sdf.format (aux)); logger.debug("endline iso8601: " + sdf.format (aux)); logger.debug("endline->aDate.getValue(): "+aDate.getValue()); logEv.set_end (aDate); } } catch (MobyException ex) { logger.debug (ex.getMessage()); } where the set_start (MobyDateTime) and set_end (MobyDateTime) are methods of LogEvent class/datatype whose implementation is: (...) /** An article name for a member of this object. */ public static final String ARTICLE_NAME_START = "start"; protected MobyDateTime start; /** An article name for a member of this object. */ public static final String ARTICLE_NAME_END = "end"; protected MobyDateTime end; (...) /************************************************************************** * Set a new value to the member (child) 'start'. It also * adds there its registered "article name".

* * @param value to be stored *************************************************************************/ public void set_start (MobyDateTime value) { // add a correct article name if (value != null) value.setName (ARTICLE_NAME_START); start = value; } public MobyDateTime getMoby_start() { return start; } /************************************************************************** * Set a new value to the member (child) 'end'. It also * adds there its registered "article name".

* * @param value to be stored *************************************************************************/ public void set_end (MobyDateTime value) { // add a correct article name if (value != null) value.setName (ARTICLE_NAME_END); end = value; } public MobyDateTime getMoby_end() { return end; } and, finally, the definition of the registered datatype is: Name: LogEvent Auth: mmb.pcb.ub.es Desc: Encapsulates all the log messages launched for a service call Contact: moby-services at mmb.pcb.ub.es LSID: urn:lsid:biomoby.org:objectclass:LogEvent:2007-03-17T20-00-34Z ID: null Parents: Object Children (only those registered here): id (HASA) => String serviceName (HASA) => String ip (HASA) => String start (HASA) => DateTime end (HASA) => DateTime status (HASA) => Integer timeCPU (HASA) => Float numberCPUs (HASA) => Integer inputSize (HASA) => Integer outputSize (HASA) => Integer isTest (HASA) => Boolean which is registered in http://moby-dev.inab.org/MOBY/Central and i have generated the datatypes (again, but it was to be sure in the case of the LogEvent datatypes was bad yielded before...) so, any suggestion to the issue of the two ends in the xml and the warning??? cheers again and sorry for this huge and boring mail... w i l l y ps: i guess the warning can be debt to this method in class LogEvent: public org.jdom.Element toXML() { org.jdom.Element elem_I_am_sorry_that_this_produces_a_warning = super.toXML(); elem_I_am_sorry_that_this_produces_a_warning.setName (DATA_TYPE_NAME); if (the_id != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (the_id.toXML()); if (serviceName != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (serviceName.toXML()); if (ip != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (ip.toXML()); if (start != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (start.toXML()); if (end != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (end.toXML()); if (status != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (status.toXML()); if (timeCPU != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (timeCPU.toXML()); if (numberCPUs != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (numberCPUs.toXML()); if (inputSize != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (inputSize.toXML()); if (outputSize != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (outputSize.toXML()); if (isTest != null) elem_I_am_sorry_that_this_produces_a_warning.addContent (isTest.toXML()); return elem_I_am_sorry_that_this_produces_a_warning; } **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 martin.senger at gmail.com Wed Mar 28 15:42:49 2007 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 28 Mar 2007 16:42:49 +0100 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <460A89A3.6080803@cnio.es> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> <460A89A3.6080803@cnio.es> Message-ID: <4d93f07c0703280842x4f75f30bw1e6c213df74f3243@mail.gmail.com> It would help if you either register your data type in the Canadian Moby Central (you may/should use the testing Moby Central there) or if you give me the URL and URI of your register (if it is publicly accessible). Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From groscurt at mpiz-koeln.mpg.de Wed Mar 28 15:00:46 2007 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 28 Mar 2007 17:00:46 +0200 Subject: [MOBY-dev] Changes in the service retrieval API ? Message-ID: <200703281700.47035.groscurt@mpiz-koeln.mpg.de> Hi everyone, I'm using the getServiceNamesByAuthorityAsXML(), which does a SOAP call for retrieveServiceNames, to retrieve all services from the MOBY Central. Afterwards I want to have the full information of some services and therefore I use the method findService with a service found with the method above as parameter. With some services it happens that I it does not find any services with the findService method ! E.g. service runNCBIBlastp from inb.bsc.es is returned by calling getServiceNamesByAuthorityAsXML(). But calling findService with this service later on returns an empty service. Has something changed in den API of these methodes ? Thanks Andreas -- Andreas Groscurth Diplom Bioinformatik - PhD Student Max Planck Institute for Plant Breeding Research Carl-von-Linn?-Weg 10 50829 Cologne Germany E-mail: ? ?groscurt at mpiz-koeln.mpg.de Phone: ? ?+49(0)221-5062-447 From edward.kawas at gmail.com Wed Mar 28 15:52:00 2007 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 28 Mar 2007 08:52:00 -0700 Subject: [MOBY-dev] Changes in the service retrieval API ? In-Reply-To: <200703281700.47035.groscurt@mpiz-koeln.mpg.de> References: <200703281700.47035.groscurt@mpiz-koeln.mpg.de> Message-ID: <004901c77151$06002170$6800a8c0@notebook> Hi Andreas, I think that the services that you are looking for are async services. When you perform a findservice call with jmoby it defaults to moby services. If you change the category to moby-async, I bet it will work. I usually set the category string to be the empty string and this works for me. Eddie > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev- > bounces at lists.open-bio.org] On Behalf Of Andreas Groscurth > Sent: Wednesday, March 28, 2007 8:01 AM > To: moby-dev at lists.open-bio.org > Subject: [MOBY-dev] Changes in the service retrieval API ? > > Hi everyone, > > I'm using the getServiceNamesByAuthorityAsXML(), which does a SOAP call > for > retrieveServiceNames, to retrieve all services from the MOBY Central. > > Afterwards I want to have the full information of some services and > therefore > I use the method findService with a service found with the method above as > parameter. > > With some services it happens that I it does not find any services with > the > findService method ! > > E.g. service runNCBIBlastp from inb.bsc.es is returned by calling > getServiceNamesByAuthorityAsXML(). But calling findService with this > service > later on returns an empty service. > > Has something changed in den API of these methodes ? > > Thanks > Andreas > > -- > Andreas Groscurth > Diplom Bioinformatik - PhD Student > Max Planck Institute for Plant Breeding Research > Carl-von-Linn?-Weg 10 > 50829 Cologne > Germany > E-mail: ? ?groscurt at mpiz-koeln.mpg.de > Phone: ? ?+49(0)221-5062-447 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gcomesana at cnio.es Wed Mar 28 15:55:25 2007 From: gcomesana at cnio.es (=?ISO-8859-1?Q?=22Guillermo_Comesa=C3=B1a=2E=22?=) Date: Wed, 28 Mar 2007 17:55:25 +0200 Subject: [MOBY-dev] JMoby bug or lack of knowledge In-Reply-To: <4d93f07c0703280842x4f75f30bw1e6c213df74f3243@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> <460A89A3.6080803@cnio.es> <4d93f07c0703280842x4f75f30bw1e6c213df74f3243@mail.gmail.com> Message-ID: <460A8FED.7080206@cnio.es> > It would help if you either register your data type in the Canadian Moby > Central (you may/should use the testing Moby Central there) or if you > give me the URL and URI of your register (if it is publicly accessible). yeah, no problem. url endpoint: http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl uri: http://moby-dev.inab.org/MOBY/Central i guess this is an absolutely silly problem, but i just started to work with jmoby platform few days ago and i'm not proficiency enough at this time and, as i told you before, i dont have any help here (if i had, i would be bothering my mates :) cheers > Martin w i l l y **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 gordonp at ucalgary.ca Wed Mar 28 19:28:27 2007 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 28 Mar 2007 13:28:27 -0600 Subject: [MOBY-dev] Asynchronous services In-Reply-To: <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> References: <460A70B0.2080906@cnio.es> <4d93f07c0703280658i74f5519cvfa14de7ea84ff913@mail.gmail.com> <460A7DBC.6090501@ucalgary.ca> <4d93f07c0703280805l5a29ebc2vfb62c1835e716cd0@mail.gmail.com> Message-ID: <460AC1DB.5010204@ucalgary.ca> Hi all, Is there a stable, working asynchronous service that I can use for unit testing new asynchronous client code in Java?