From markw at illuminae.com Wed Jan 2 14:33:49 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 02 Jan 2008 11:33:49 -0800 Subject: [MOBY-dev] Manuscript and Moby 2 funding Message-ID: Hi all, I've just re-submitted the revised manuscript to Briefings in Bioinformatics. After discussing with the editor how best to respond to the contradictory requests of the reviewers, I have simply added a couple of sentences to each technical section of the manuscript describing the "biologists problem" that each component of Moby is trying to address. I also put some screenshots of a Gbrowse-Moby browsing session into the supplementary information to help the biologist visualise how Moby can be used to direct the flow of data from service to service. I'll put the final copy of the manuscript into the CVS later today. Sorry I didn't pass it around for everyone to review before resubmission, but the deadline was tight due to the holidays, and the changes were quite minor. I hope nobody minds! On another note, thank you to everyone who wrote support letters for the Genome Canada application for Moby 2.0. Sadly, we didn't get funded... but we do have funding from the Heart and Stroke Foundation and from Microsoft, so we're still alive and kicking :-) Best wishes and Happy New Year to all Mobyers! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 3 09:56:05 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 03 Jan 2008 06:56:05 -0800 Subject: [MOBY-dev] Paper Accepted! Message-ID: Hi everyone! The Moby 1.0 paper has been accepted to Briefings. Halleluja for that! Best wishes, Mark From Pieter.Neerincx at wur.nl Thu Jan 3 11:31:32 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 3 Jan 2008 17:31:32 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> Hi Mark et al., Congratulations! Too bad we can't share champagne digitally over the world wide web :) Cheers, Pi On 3-jan-2008, at 15:56, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From carole.goble at manchester.ac.uk Thu Jan 3 11:48:57 2008 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Thu, 03 Jan 2008 16:48:57 +0000 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> References: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> Message-ID: <477D11F9.1040807@manchester.ac.uk> Well done Mark! Carole > Hi Mark et al., > > Congratulations! Too bad we can't share champagne digitally over the > world wide web :) > > Cheers, > > Pi > > On 3-jan-2008, at 15:56, Mark Wilkinson wrote: > >> Hi everyone! >> >> The Moby 1.0 paper has been accepted to Briefings. >> >> Halleluja for that! >> >> Best wishes, >> >> Mark >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Thu Jan 3 11:54:29 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 03 Jan 2008 09:54:29 -0700 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> References: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> Message-ID: <477D1345.5090502@ucalgary.ca> We'll have to settle for the reference to wine in the Dutch Sailor's dialog in Moby Dick then :-) Grand snoozing to-night, maty; fat night for that. I mark this in our old Mogul's wine; it's quite as deadening to some as filliping to others. Pieter Neerincx wrote: > Hi Mark et al., > > Congratulations! Too bad we can't share champagne digitally over the > world wide web :) > > Cheers, > > Pi > > On 3-jan-2008, at 15:56, Mark Wilkinson wrote: > >> Hi everyone! >> >> The Moby 1.0 paper has been accepted to Briefings. >> >> Halleluja for that! >> >> Best wishes, >> >> Mark >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,477d0d22109501959316500! > > > From markw at illuminae.com Thu Jan 3 17:59:58 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 03 Jan 2008 14:59:58 -0800 Subject: [MOBY-dev] Question to Async service providers Message-ID: Do asynchronous services respond correctly to the Moby "ping"? If so, I'll add them into the service tester. Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 simont at hmgc.mcw.edu Thu Jan 3 23:03:21 2008 From: simont at hmgc.mcw.edu (Twigger, Simon (MCW)) Date: Thu, 3 Jan 2008 22:03:21 -0600 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> Hi Mark, That's spectacular, a great way to start the New year! best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 3, 2008, at 8:56 AM, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From simont at hmgc.mcw.edu Thu Jan 3 23:03:21 2008 From: simont at hmgc.mcw.edu (Twigger, Simon (MCW)) Date: Thu, 3 Jan 2008 22:03:21 -0600 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> Hi Mark, That's spectacular, a great way to start the New year! best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 3, 2008, at 8:56 AM, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jan 3 23:24:37 2008 From: markw at illuminae.com (mark wilkinson) Date: Fri, 4 Jan 2008 04:24:37 +0000 GMT Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> References: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> Message-ID: <1211310426-1199420748-cardhu_blackberry.rim.net-17035-@engine24-cell01> Indeed! January 3rd - that's gotta be a new record :-) What makes me even more happy is how wonderfully professional the review process was compared to the PLoS ONE story. The reviews were rapid (and there was more than one of them!), but most importantly there was constant communication and advice from the editors of the journal as to what they wanted and how they thought the reviews should be interpreted (and the edits were quite massive! More than 30% of the text was removed in the first re-write, with the guidance of the editor, before it even went out for review!). It was such a pleasure to work through this (somewhat unusual) submission with the BiB editorial team! Kudo's to them!! Mark -- Mark Wilkinson ...on the road! -----Original Message----- From: "Twigger, Simon (MCW)" Date: Thu, 3 Jan 2008 22:03:21 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Paper Accepted! Hi Mark, That's spectacular, a great way to start the New year! best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 3, 2008, at 8:56 AM, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Fri Jan 4 05:22:56 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Fri, 4 Jan 2008 11:22:56 +0100 (CET) Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <477D1345.5090502@ucalgary.ca> References: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> <477D1345.5090502@ucalgary.ca> Message-ID: <61522.89.52.129.18.1199442176.squirrel@mpizmail.mpiz-koeln.mpg.de> Didnt get a word you said ;-) But hurray... das ist einfach grossartig ! Best andreas > Grand snoozing to-night, maty; fat night for that. I mark this in > our old Mogul's wine; it's quite as deadening to some as filliping to > others. > > > > Pieter Neerincx wrote: >> Hi Mark et al., >> >> Congratulations! Too bad we can't share champagne digitally over the >> world wide web :) >> >> Cheers, >> >> Pi >> >> On 3-jan-2008, at 15:56, Mark Wilkinson wrote: >> >>> Hi everyone! >>> >>> The Moby 1.0 paper has been accepted to Briefings. >>> >>> Halleluja for that! >>> >>> Best wishes, >>> >>> Mark >>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> !DSPAM:60005,477d0d22109501959316500! >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From haase_dirk at web.de Fri Jan 4 06:55:22 2008 From: haase_dirk at web.de (Dirk Haase) Date: Fri, 04 Jan 2008 12:55:22 +0100 Subject: [MOBY-dev] Paper Accepted! Message-ID: <938304251@web.de> > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. Congratulations! And many thanks for your efforts Mark! Happy new year to all MOBYers, dirk From jmfernandez at cnio.es Fri Jan 4 07:35:11 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Fri, 04 Jan 2008 13:35:11 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <477E27FF.3000404@cnio.es> At last! Congratulations to everyone who has contributed to the MOBY API, libraries and community! Best Wishes, Jos? Mar?a Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From jmfernandez at cnio.es Fri Jan 4 07:35:11 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Fri, 04 Jan 2008 13:35:11 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <477E27FF.3000404@cnio.es> At last! Congratulations to everyone who has contributed to the MOBY API, libraries and community! Best Wishes, Jos? Mar?a Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From usadel at mpimp-golm.mpg.de Sat Jan 5 11:10:28 2008 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Sat, 5 Jan 2008 17:10:28 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <477FABF4.80102@mpimp-golm.mpg.de> Hi, congrats! 2008 is beginning nice... Cheers, Bj?rn Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From groscurt at mpiz-koeln.mpg.de Mon Jan 7 06:44:03 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 7 Jan 2008 12:44:03 +0100 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: References: Message-ID: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> Hi, I'm not sure, but I think there is something wrong in the MobyRequest - or I (again) miss something... The situation is the following: I want to call a service which has secondaries. I dont give any secondaries in the call, because I want to use the default ones the service was registered with In the method convertMOBYDataToMOBYRequest the secondaried from the service are fetched correctly MobyData[] secondaries = mobyService.getSecondaryInputs(); but then the secondaryParameters from the call are fetched and the following comparison makes me wonder if(secondaries != null && secondaries.length != secondaryParams.size()){ throw new MobyException("Service " + mobyService.getName() + " was provided " + secondaryParams.size() + " secondary input parameter(s), but takes " + secondaries.length + " (query " + queryName + ")"); } This means - if i dont provide any secondaries in my call, the method will always throw an exception, although i want that the defaults to be taken. In my opinion, it should check whether any secondaries from the call are present and if not, then use the default ones from the service. So, am I right or what did I miss ? Thanks Andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From markw at illuminae.com Mon Jan 7 18:08:03 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 07 Jan 2008 15:08:03 -0800 Subject: [MOBY-dev] Yay Funding! Message-ID: Hi all, So after last week's disappointment from Genome Canada, I got news this morning that the Canadian Institutes of Health Research have funded CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have almost $1M to invest in Moby 2 :-) Here we go!! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Mon Jan 7 17:47:27 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 07 Jan 2008 15:47:27 -0700 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> Message-ID: <4782ABFF.8030903@ucalgary.ca> Hi Andreas, I wouldn't really call it a bug, MobyRequest just didn't expect you to be lazy :-) For example, it doesn't check that you're sending primary parameters of the right data types either. This was primarily because I wanted to be able to create data envelopes and send them without consulting the ontologies if I so desired. On the other hand, I already have the secondary data, so it doesn't hurt to add those that aren't already specified in the request. I've done this now (do a cvs update), and have documented that the MobyContentInstance you pass in may be modified in this way. Regards, Paul Andreas Groscurth wrote: > Hi, > > I'm not sure, but I think there is something wrong in the MobyRequest - or I > (again) miss something... > > The situation is the following: > > I want to call a service which has secondaries. I dont give any secondaries in > the call, because I want to use the default ones the service was registered > with > > In the method convertMOBYDataToMOBYRequest the secondaried from the service > are fetched correctly > > MobyData[] secondaries = mobyService.getSecondaryInputs(); > > but then the secondaryParameters from the call are fetched and the following > comparison makes me wonder > > if(secondaries != null && secondaries.length != secondaryParams.size()){ > throw new MobyException("Service " + mobyService.getName() + " was provided > " + secondaryParams.size() + " secondary input parameter(s), but takes " + > secondaries.length + " (query " + queryName + ")"); > } > > This means - if i dont provide any secondaries in my call, the method will > always throw an exception, although i want that the defaults to be taken. > > In my opinion, it should check whether any secondaries from the call are > present and if not, then use the default ones from the service. > > So, am I right or what did I miss ? > > Thanks > Andreas > From carole.goble at manchester.ac.uk Mon Jan 7 18:17:04 2008 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Mon, 07 Jan 2008 23:17:04 +0000 Subject: [MOBY-dev] Yay Funding! In-Reply-To: References: Message-ID: <4782B2F0.4030200@manchester.ac.uk> Mark wow!!!! Well done!! Carole > Hi all, > > So after last week's disappointment from Genome Canada, I got news > this morning that the Canadian Institutes of Health Research have > funded CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have > almost $1M to invest in Moby 2 :-) > > Here we go!! > > Mark > > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee > and may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received > this communication in error, please notify the sender immediately by > reply e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From carole.goble at manchester.ac.uk Mon Jan 7 18:17:04 2008 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Mon, 07 Jan 2008 23:17:04 +0000 Subject: [MOBY-dev] Yay Funding! In-Reply-To: References: Message-ID: <4782B2F0.4030200@manchester.ac.uk> Mark wow!!!! Well done!! Carole > Hi all, > > So after last week's disappointment from Genome Canada, I got news > this morning that the Canadian Institutes of Health Research have > funded CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have > almost $1M to invest in Moby 2 :-) > > Here we go!! > > Mark > > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee > and may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received > this communication in error, please notify the sender immediately by > reply e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Jan 8 04:37:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 8 Jan 2008 10:37:55 +0100 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: <4782ABFF.8030903@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> Message-ID: <200801081037.55853.groscurt@mpiz-koeln.mpg.de> Hi Paul, thanks for the update... Although I aggree with you on the primary data issue, I wouldnt call it 'being lazy'... why are then default values at all if one is forced to send the secondaries at all ? If I'm ok with the defined default values, why should I send secondaries ? I understood the secondaries as optional parameters for which I could just use the default values. but what surprises me is, when actually does the secondaries are set to the request data ? When I see the code correctly, you fill the secondaryParams - but I cant find anything where this information is then set ? MobyDataUtils.toXMLDocument( mobyRequest, data ); seems to be where you create the xml request with the data... but where is the link between data and the parameters ? Thanks andreas On Monday 07 January 2008 23:47, Paul Gordon wrote: > Hi Andreas, > > I wouldn't really call it a bug, MobyRequest just didn't expect you to > be lazy :-) > > For example, it doesn't check that you're sending primary parameters of > the right data types either. This was primarily because I wanted to be > able to create data envelopes and send them without consulting the > ontologies if I so desired. On the other hand, I already have the > secondary data, so it doesn't hurt to add those that aren't already > specified in the request. I've done this now (do a cvs update), and > have documented that the MobyContentInstance you pass in may be modified > in this way. > > Regards, > > Paul > > Andreas Groscurth wrote: > > Hi, > > > > I'm not sure, but I think there is something wrong in the MobyRequest - > > or I (again) miss something... > > > > The situation is the following: > > > > I want to call a service which has secondaries. I dont give any > > secondaries in the call, because I want to use the default ones the > > service was registered with > > > > In the method convertMOBYDataToMOBYRequest the secondaried from the > > service are fetched correctly > > > > MobyData[] secondaries = mobyService.getSecondaryInputs(); > > > > but then the secondaryParameters from the call are fetched and the > > following comparison makes me wonder > > > > if(secondaries != null && secondaries.length != secondaryParams.size()){ > > throw new MobyException("Service " + mobyService.getName() + " was > > provided " + secondaryParams.size() + " secondary input parameter(s), > > but takes " + secondaries.length + " (query " + queryName + ")"); > > } > > > > This means - if i dont provide any secondaries in my call, the method > > will always throw an exception, although i want that the defaults to be > > taken. > > > > In my opinion, it should check whether any secondaries from the call are > > present and if not, then use the default ones from the service. > > > > So, am I right or what did I miss ? > > > > Thanks > > Andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Tue Jan 8 05:04:30 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 8 Jan 2008 11:04:30 +0100 Subject: [MOBY-dev] Yay Funding! In-Reply-To: References: Message-ID: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> Hi, so lets celebrate for that :-) But just curiosity... Did i miss Moby 1.0 ? Shouldn't be with a number also somewhere a corresponding version in the cvs ? What I miss is that someone can build any software with Moby 1.0 or what ever... the cvs is still unversioned as I can see... I would love to see different branches. Currently it can happens that with changes in the Moby API software is not working. If this had be versionized, the API could change but software could still work with Version xy. Maybe I missed something - of course its awesome to have money for Moby2... but from my point of view Moby 1 is still missing stuff (versionizing at the top) ? Are there any plans to invite some kind of versions into Moby API ? I'm really like to discuss things further, I'm just afraid that there are several issues still alive and everyone is just thinking of Moby 2. my 2 cents andreas On Tuesday 08 January 2008 00:08, Mark Wilkinson wrote: > Hi all, > > So after last week's disappointment from Genome Canada, I got news this > morning that the Canadian Institutes of Health Research have funded > CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have almost $1M to > invest in Moby 2 :-) > > Here we go!! > > Mark -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From gordonp at ucalgary.ca Tue Jan 8 10:24:48 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 08:24:48 -0700 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: <200801081037.55853.groscurt@mpiz-koeln.mpg.de> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> Message-ID: <478395C0.4040401@ucalgary.ca> > thanks for the update... Although I aggree with you on the primary data issue, > I wouldnt call it 'being lazy'... why are then default values at all if one > is forced to send the secondaries at all ? If I'm ok with the defined default > values, why should I send secondaries ? I understood the secondaries as > optional parameters for which I could just use the default values. > Well, MobyRequest never said it would fill secondaries in for you, so I don't consider it a "bug" that it didn't :-) i.e. MobyRequest does not expect to fulfill all the contract obligations of a transaction (e.g. the API user is still responsible for data type conformity), so I considered it more like a "Request For Enhancement". > but what surprises me is, when actually does the secondaries are set to the > request data ? > When I see the code correctly, you fill the secondaryParams - but I cant find > anything where this information is then set ? > > MobyDataUtils.toXMLDocument( mobyRequest, data ); > > seems to be where you create the xml request with the data... but where is the > link between data and the parameters ? > Mea culpa. Now that actually is a bug, just introduced :-) Since it was a fairly trivial modification, I had only tested that my changes didn't break anything, not that they actually worked. :-( Please do another cvs update. On the plus side, I also made the code somewhat prettier by using the Java 5 "for each" and more Generics in the main loops. From markw at illuminae.com Tue Jan 8 11:44:15 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Jan 2008 08:44:15 -0800 Subject: [MOBY-dev] Yay Funding! In-Reply-To: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> Message-ID: I've been waiting for Eddie to finish the migration to a pure-perl codebase before making the 1.0 release. I think it's done now...?? The last thing we needed to manage was the caching of RDF since RDF::Core is a painfully slow module when it comes to on-the-fly RDF creation. If Eddie confirms that we're done, I'll make the 1.0 release right away. M On Tue, 08 Jan 2008 02:04:30 -0800, Andreas Groscurth wrote: > Hi, > > so lets celebrate for that :-) > > But just curiosity... Did i miss Moby 1.0 ? Shouldn't be with a number > also > somewhere a corresponding version in the cvs ? > > What I miss is that someone can build any software with Moby 1.0 or what > ever... the cvs is still unversioned as I can see... > > I would love to see different branches. Currently it can happens that > with > changes in the Moby API software is not working. If this had be > versionized, > the API could change but software could still work with Version xy. > > Maybe I missed something - of course its awesome to have money for > Moby2... > but from my point of view Moby 1 is still missing stuff (versionizing at > the > top) ? > > Are there any plans to invite some kind of versions into Moby API ? > > I'm really like to discuss things further, I'm just afraid that there are > several issues still alive and everyone is just thinking of Moby 2. > > my 2 cents > andreas > > On Tuesday 08 January 2008 00:08, Mark Wilkinson wrote: >> Hi all, >> >> So after last week's disappointment from Genome Canada, I got news this >> morning that the Canadian Institutes of Health Research have funded >> CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have almost $1M to >> invest in Moby 2 :-) >> >> Here we go!! >> >> Mark > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Tue Jan 8 13:38:00 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 11:38:00 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <478395C0.4040401@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> Message-ID: <4783C308.3030603@ucalgary.ca> Hi all, I was talking off-list with Eddie and I think I found a problem with the current spec vis-a-vis LSIDs. Currently, there is no way to figure out a given registry what its LSID authority is. This means you can't reliably resolve metadata about objects without hardcoding the authority. For example, if I want to resolve the meta data for a service such as TrimVectorSeqs @ moby.ucalgary.ca the LSID is urn:lsid:biomoby.org:serviceinstance:moby.ucalgary.ca,TrimVectorSeqs which I can fetch and get all kinds of wonderful details about the service, including in the future things like test cases. The problem is that the biomoby.org part only works for stuff registered at the main Moby Central server. If I want to use the INB central server, there is currently no way for the registry to tell me what to put in the LSID where the "biomoby.org" normally is. I need this, for example, so that MobyService.getService(name, authority, registry) can fetch all the details of the service and create a meaningful MobyService object from RDF (as that's the direction we are heading). This is the last bit of my jMOBY code that doesn't support multiple registries, so it's serious stumbling block. My proposal is that we a new method something like the current retrieveResourceURLs method, but called retrieveResourceLSIDAuthorities. The output would look like: In this particular case, the registry is using the standard data type, namespace and service type definitions, but has its own list of service instances...such a mirror probably may not exist at the moment, but you get the point. Thoughts? -Paul From gordonp at ucalgary.ca Tue Jan 8 13:44:29 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 11:44:29 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <4783C308.3030603@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> Message-ID: <4783C48D.8050705@ucalgary.ca> Sorry, the XML should as below (no "url" attributes) > > > > > > > From markw at illuminae.com Tue Jan 8 14:14:25 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Jan 2008 11:14:25 -0800 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <4783C308.3030603@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> Message-ID: in the mobycentral.conf file there is an "lsid-authority" parameter that is set during installation. Any new "entities" created by that registry will have that value as the authority of the lsid. ...I don't see the problem...?? M On Tue, 08 Jan 2008 10:38:00 -0800, Paul Gordon wrote: > > Hi all, > > I was talking off-list with Eddie and I think I found a problem with the > current spec vis-a-vis LSIDs. Currently, there is no way to figure out > a given registry what its LSID authority is. This means you can't > reliably resolve metadata about objects without hardcoding the > authority. For example, if I want to resolve the meta data for a > service such as TrimVectorSeqs @ moby.ucalgary.ca the LSID is > > urn:lsid:biomoby.org:serviceinstance:moby.ucalgary.ca,TrimVectorSeqs > > which I can fetch and get all kinds of wonderful details about the > service, including in the future things like test cases. The problem is > that the biomoby.org part only works for stuff registered at the main > Moby Central server. If I want to use the INB central server, there is > currently no way for the registry to tell me what to put in the LSID > where the "biomoby.org" normally is. I need this, for example, so that > MobyService.getService(name, authority, registry) can fetch all the > details of the service and create a meaningful MobyService object from > RDF (as that's the direction we are heading). This is the last bit of > my jMOBY code that doesn't support multiple registries, so it's serious > stumbling block. > > My proposal is that we a new method something like the current > retrieveResourceURLs method, but called > retrieveResourceLSIDAuthorities. The output would look like: > > > > > > > > > In this particular case, the registry is using the standard data type, > namespace and service type definitions, but has its own list of service > instances...such a mirror probably may not exist at the moment, but you > get the point. > > Thoughts? > > -Paul > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Tue Jan 8 14:25:02 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 12:25:02 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> Message-ID: <4783CE0E.8010408@ucalgary.ca> But how do I get the LSID for a service without retrieving the the whole massive ServiceInstance RDF? I want the LSID in order to avoid needing to fetch and parse that file... Mark Wilkinson wrote: > in the mobycentral.conf file there is an "lsid-authority" parameter > that is set during installation. Any new "entities" created by that > registry will have that value as the authority of the lsid. > > ...I don't see the problem...?? > > M > > > > > On Tue, 08 Jan 2008 10:38:00 -0800, Paul Gordon > wrote: > >> >> Hi all, >> >> I was talking off-list with Eddie and I think I found a problem with >> the current spec vis-a-vis LSIDs. Currently, there is no way to >> figure out a given registry what its LSID authority is. This means >> you can't reliably resolve metadata about objects without hardcoding >> the authority. For example, if I want to resolve the meta data for a >> service such as TrimVectorSeqs @ moby.ucalgary.ca the LSID is >> >> urn:lsid:biomoby.org:serviceinstance:moby.ucalgary.ca,TrimVectorSeqs >> >> which I can fetch and get all kinds of wonderful details about the >> service, including in the future things like test cases. The problem >> is that the biomoby.org part only works for stuff registered at the >> main Moby Central server. If I want to use the INB central server, >> there is currently no way for the registry to tell me what to put in >> the LSID where the "biomoby.org" normally is. I need this, for >> example, so that MobyService.getService(name, authority, registry) >> can fetch all the details of the service and create a meaningful >> MobyService object from RDF (as that's the direction we are >> heading). This is the last bit of my jMOBY code that doesn't support >> multiple registries, so it's serious stumbling block. >> >> My proposal is that we a new method something like the current >> retrieveResourceURLs method, but called >> retrieveResourceLSIDAuthorities. The output would look like: >> >> >> >> >> >> >> >> >> In this particular case, the registry is using the standard data >> type, namespace and service type definitions, but has its own list of >> service instances...such a mirror probably may not exist at the >> moment, but you get the point. >> >> Thoughts? >> >> -Paul >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From markw at illuminae.com Tue Jan 8 14:25:38 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Jan 2008 11:25:38 -0800 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <4783CE0E.8010408@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> <4783CE0E.8010408@ucalgary.ca> Message-ID: findService() or it's Java equivalent M On Tue, 08 Jan 2008 11:25:02 -0800, Paul Gordon wrote: > But how do I get the LSID for a service without retrieving the the whole > massive ServiceInstance RDF? I want the LSID in order to avoid needing > to fetch and parse that file... -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Tue Jan 8 14:44:28 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 12:44:28 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> <4783CE0E.8010408@ucalgary.ca> Message-ID: <4783D29C.80505@ucalgary.ca> Right. I guess I can only supplement the findService call, not replace it, in order to fetch metadata. Makes sense if we allow entities with various authorities in the same registry... > findService() or it's Java equivalent > > M > > > > On Tue, 08 Jan 2008 11:25:02 -0800, Paul Gordon > wrote: > >> But how do I get the LSID for a service without retrieving the the >> whole massive ServiceInstance RDF? I want the LSID in order to avoid >> needing to fetch and parse that file... > > > From groscurt at mpiz-koeln.mpg.de Wed Jan 9 05:45:35 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 9 Jan 2008 11:45:35 +0100 Subject: [MOBY-dev] Moby at the ISMB2008 In-Reply-To: References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> Message-ID: <200801091145.35805.groscurt@mpiz-koeln.mpg.de> Hi, I just wondering because the ISMB2008 is going to be in Toronto... is there anything Mobyicious planned ? I know Martin was in Vienna 2007 - so are ther any plans to be present in Toronto ? Cheers andreas From martin.senger at gmail.com Wed Jan 9 06:06:09 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 9 Jan 2008 11:06:09 +0000 Subject: [MOBY-dev] Moby at the ISMB2008 In-Reply-To: <200801091145.35805.groscurt@mpiz-koeln.mpg.de> References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> <200801091145.35805.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0801090306v40ebe270k91a5cd6bed9ff84f@mail.gmail.com> I will try to go to Toronto. But not necessarily only because of BioMoby. And I will (again) focus more on BOSC (if there will be one) rather than on ISMB. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From Pieter.Neerincx at wur.nl Wed Jan 9 06:43:55 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 9 Jan 2008 12:43:55 +0100 Subject: [MOBY-dev] Moby at the ISMB2008 In-Reply-To: <200801091145.35805.groscurt@mpiz-koeln.mpg.de> References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> <200801091145.35805.groscurt@mpiz-koeln.mpg.de> Message-ID: <3B61C008-B4C6-4361-9392-CFA08B8DE940@wur.nl> Hi Devs, I will also try to be there again like Martin and if I'm there I will stay for both the BOSC and the main ISMB conference. I'm not sure though were I will be in August 2008 as my current contract as a PhD student ends in April... If I'll be there I will present at least a poster on my current research which will involve BioMOBY. I'd love to see more posters like that in Toronto, but in addition to that I'd love to see: * More BioMOBY marketing for BioMOBY users especially now the official 1.0 is out: A talk or two + a demo would be great! * A meeting for BioMOBY developers. We could do that in a parallel session, before or after the conference or on the "tutorial day" between the BOSC SIG and the main ISMB conference.... Cheers, Pi On 9-jan-2008, at 11:45, Andreas Groscurth wrote: > Hi, > > I just wondering because the ISMB2008 is going to be in Toronto... > is there > anything Mobyicious planned ? I know Martin was in Vienna 2007 - so > are ther > any plans to be present in Toronto ? > > Cheers > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Wed Jan 9 10:06:05 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 09 Jan 2008 07:06:05 -0800 Subject: [MOBY-dev] Proofs ready Message-ID: Hi all, I've received the proofs of the Moby 1.0 paper from BiB. The instructions are to not make it public, so I'm not sure I should send it out on the mailing list since the mailing list is public and the mailing list archives are indexed by Google, but I'm happy to send it individually to anyone who asks. Just let me know. Cheers all! Mark From markw at illuminae.com Wed Jan 9 10:27:12 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 09 Jan 2008 07:27:12 -0800 Subject: [MOBY-dev] "dead" services Message-ID: Hi all, Just a reminder that the list of "dead" services (those that do not respond to a ping) is being updated every few hours. The dead services on that list are pretty consistent :-) Are they really dead? or do they just not respond properly to pings? http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Cheers! Mark From edward.kawas at gmail.com Wed Jan 9 10:50:15 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Jan 2008 07:50:15 -0800 Subject: [MOBY-dev] "dead" services In-Reply-To: <4784EA1B.8090904@ucalgary.ca> References: <4784EA1B.8090904@ucalgary.ca> Message-ID: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> Hey Paul, The code that is used to ping the services is available in the cvs under moby-live/Perl/scripts and the file is called service_tester.pl. Eddie -----Original Message----- From: Paul Gordon [mailto:gordonp at .ca] Sent: January-09-08 7:37 AM To: Mark Wilkinson; Eddie Kawas Subject: Re: [MOBY-dev] "dead" services My moby.ucalgary.ca ones are alive, but listed as dead...do y'all have a test pinger I can use to debug? Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > From groscurt at mpiz-koeln.mpg.de Wed Jan 9 13:04:30 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 9 Jan 2008 19:04:30 +0100 Subject: [MOBY-dev] "dead" services In-Reply-To: References: Message-ID: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> hiho, what are the plans with the dead services ? kill them ;-) ? andreas On Wednesday 09 January 2008 16:27, Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead services on > that list are pretty consistent :-) Are they really dead? or do they > just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From gordonp at ucalgary.ca Wed Jan 9 15:23:38 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 09 Jan 2008 13:23:38 -0700 Subject: [MOBY-dev] "dead" services In-Reply-To: References: Message-ID: <47852D4A.7040109@ucalgary.ca> Hi Mark, The pinger seems to be erroneously marking some (but not all) of mine as dead. I wrote a quick pinger in Java to make sure they actually were alive. If you do a CVS update of moby-live, cd Java, ant compile, then e.g. ./build/run/run-any-client MobyPinger ReverseComplementSequence moby.ucalgary.ca It does return a blank message, as expected. But it's still on the list at http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > From markw at illuminae.com Wed Jan 9 15:24:03 2008 From: markw at illuminae.com (mark wilkinson) Date: Wed, 9 Jan 2008 20:24:03 +0000 GMT Subject: [MOBY-dev] "dead" services In-Reply-To: <47852D4A.7040109@ucalgary.ca> References: <47852D4A.7040109@ucalgary.ca> Message-ID: <911867034-1199910330-cardhu_blackberry.rim.net-8063-@engine12-cell01> Better tell Eddie... He can check what his pinger is "seeing" -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Wed, 09 Jan 2008 13:23:38 To:Core developer announcements Subject: Re: [MOBY-dev] "dead" services Hi Mark, The pinger seems to be erroneously marking some (but not all) of mine as dead. I wrote a quick pinger in Java to make sure they actually were alive. If you do a CVS update of moby-live, cd Java, ant compile, then e.g. ./build/run/run-any-client MobyPinger ReverseComplementSequence moby.ucalgary.ca It does return a blank message, as expected. But it's still on the list at http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Wed Jan 9 21:13:50 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Jan 2008 18:13:50 -0800 Subject: [MOBY-dev] "dead" services In-Reply-To: <47852D4A.7040109@ucalgary.ca> References: <47852D4A.7040109@ucalgary.ca> Message-ID: <0A7291E23C694250B7174F2980676073@OfficePC> Hey Paul, I am attaching the code that the pinger uses. Its in the cvs, but I figure that this would be easier since I added a few lines of debug code. Attached is a cgi file. Place it in the cgi-bin of an apache install. Make sure to change the #!/perl.exe part to conform to your perl location. Once that is done, hit this url: http://localhost:8080/cgi-bin/ServicePingerValidator?authority=moby.ucalgary .ca change :8080 to be whatever port you need. You will see that apparently, those services under moby.ucalgary.ca don't have output. Then you can see how I call them. I don't do anything weird! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: January-09-08 12:24 PM To: Core developer announcements Subject: Re: [MOBY-dev] "dead" services Hi Mark, The pinger seems to be erroneously marking some (but not all) of mine as dead. I wrote a quick pinger in Java to make sure they actually were alive. If you do a CVS update of moby-live, cd Java, ant compile, then e.g. ./build/run/run-any-client MobyPinger ReverseComplementSequence moby.ucalgary.ca It does return a blank message, as expected. But it's still on the list at http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Thu Jan 10 06:17:40 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 10 Jan 2008 12:17:40 +0100 Subject: [MOBY-dev] authoritative ?! In-Reply-To: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> References: <4784EA1B.8090904@ucalgary.ca> <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> Message-ID: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Hi, I just forgot... can someone tell me what the athoritative flag is meaning exactly in the ServiceRegistration Panel in Dashboard ? Awesome Andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Thu Jan 10 06:20:11 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 10 Jan 2008 12:20:11 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: Message-ID: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> And hi again, we just had the discussion here... is it recommended to use primitives as primary input ? Or are there actually only for use in secondary parameters or as part of a complex datatype ? E.g. if a service requires an email as input - give it an object with namespace 'email' or similar - or could I use String with namespace 'email' Thanks and byebye andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Thu Jan 10 06:38:11 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 12:38:11 +0100 Subject: [MOBY-dev] authoritative ?! In-Reply-To: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> References: <4784EA1B.8090904@ucalgary.ca> <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Message-ID: <1BD17253-BA58-4074-A118-21A918F37988@wur.nl> Hi Andreas, The authoritative flag specifies whether you are the local expert with the original service. There should be only one. Any services with the same name, but hosted by different authorities are considered mirrors / copies. Cheers, Pi On 10-jan-2008, at 12:17, Andreas Groscurth wrote: > Hi, > > I just forgot... can someone tell me what the authoritative flag is > meaning > exactly in the ServiceRegistration Panel in Dashboard ? > > Awesome > Andreas > > -- > Andreas Groscurth > Bioinformatics Developer > 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)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From alanrw at cs.man.ac.uk Thu Jan 10 05:42:25 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Thu, 10 Jan 2008 10:42:25 +0000 Subject: [MOBY-dev] "dead" services In-Reply-To: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> References: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> Message-ID: <4785F691.704@cs.man.ac.uk> Andreas Groscurth wrote: > hiho, > > what are the plans with the dead services ? kill them ;-) ? "dead services" aren't necessarily permanently dead. They are really just currently unresponsive. Is there a way to get the pinger to record how long a service has been dead? If it has been down for, say, months then the chances of it coming back tomorrow are probably small. OTOH if it has only been down since yesterday, it may recover soon. > andreas Alan From edward.kawas at gmail.com Thu Jan 10 09:37:47 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 10 Jan 2008 06:37:47 -0800 Subject: [MOBY-dev] "dead" services In-Reply-To: <4785F691.704@cs.man.ac.uk> References: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> <4785F691.704@cs.man.ac.uk> Message-ID: Hi, I created a web form for testing individual services or all services for any given authority. The form is available at: http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator It's in its preliminary form and may still evolve, but it is better than nothing! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Alan Williams Sent: January-10-08 2:42 AM To: Core developer announcements Subject: Re: [MOBY-dev] "dead" services Andreas Groscurth wrote: > hiho, > > what are the plans with the dead services ? kill them ;-) ? "dead services" aren't necessarily permanently dead. They are really just currently unresponsive. Is there a way to get the pinger to record how long a service has been dead? If it has been down for, say, months then the chances of it coming back tomorrow are probably small. OTOH if it has only been down since yesterday, it may recover soon. > andreas Alan _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jan 10 11:35:10 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 08:35:10 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: Hi Andreas! That's a very interesting case! Is "email" a data-type (Object) or a semantic-type (Namespace)?? It is a semantic type in the sense that all email addresses are unique, and therefore behave as identifiers... but it is often used as a data-type in that it would be associated with other information like an address and telephone number. Personally I would be tempted to make a new namespace 'emailAddress' or something like that, since semantic "precision" is the goal of these two ontologies. What did we do for URLs? ...LOL! Okay, I just went to have a look in the ontologies and we have an Object "URL" and a Namespace "URL"!!! I guess others have had the same question and made different decisions :-) I see that it is Pieter's services that consume the Object "URL" - maybe he can explain to us why he chose to make URL an object rather than a namespace. Pieter? M On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth wrote: > And hi again, > > we just had the discussion here... is it recommended to use primitives as > primary input ? Or are there actually only for use in secondary > parameters or > as part of a complex datatype ? > > E.g. if a service requires an email as input - give it an object with > namespace 'email' or similar - or could I use String with namespace > 'email' > > Thanks and byebye > andreas > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 11:37:21 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 08:37:21 -0800 Subject: [MOBY-dev] authoritative ?! In-Reply-To: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> References: <4784EA1B.8090904@ucalgary.ca> <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Message-ID: "authoritative" is a non-validated way of saying that you are the primary source/owner of the data, and that someone else providing this data would have first had to obtain it from you. Similarly for an analysis - you are the "owner" of the algorithm, or the most up-to-date version of the code. It doesn't promise anything, but it is intended to allow you to chose between providers of the same data for some loose QC. M On Thu, 10 Jan 2008 03:17:40 -0800, Andreas Groscurth wrote: > Hi, > > I just forgot... can someone tell me what the athoritative flag is > meaning > exactly in the ServiceRegistration Panel in Dashboard ? > > Awesome > Andreas > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Thu Jan 10 11:51:06 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 10 Jan 2008 09:51:06 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: <47864CFA.5060500@ucalgary.ca> I think the litmus tests would be: -might I need to subclass the identifier? -would it be useful to associate the identifier with anything besides a base object? -is it a subtype of some other identifier? The answers for email are: -no -yes (e.g. use it as the namespace for a Person object, which relates oppositely to the data-type argument by Mark) -no Sounds like a namespace to me... Mark Wilkinson wrote: > Hi Andreas! > > That's a very interesting case! Is "email" a data-type (Object) or a > semantic-type (Namespace)?? It is a semantic type in the sense that > all email addresses are unique, and therefore behave as identifiers... > but it is often used as a data-type in that it would be associated > with other information like an address and telephone number. > > Personally I would be tempted to make a new namespace 'emailAddress' > or something like that, since semantic "precision" is the goal of > these two ontologies. > > What did we do for URLs? ...LOL! Okay, I just went to have a look in > the ontologies and we have an Object "URL" and a Namespace "URL"!!! I > guess others have had the same question and made different decisions > :-) I see that it is Pieter's services that consume the Object "URL" > - maybe he can explain to us why he chose to make URL an object rather > than a namespace. > > Pieter? > > M > > > > On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth > wrote: > >> And hi again, >> >> we just had the discussion here... is it recommended to use >> primitives as >> primary input ? Or are there actually only for use in secondary >> parameters or >> as part of a complex datatype ? >> >> E.g. if a service requires an email as input - give it an object with >> namespace 'email' or similar - or could I use String with namespace >> 'email' >> >> Thanks and byebye >> andreas >> > > > From markw at illuminae.com Thu Jan 10 11:50:51 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 08:50:51 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47864CFA.5060500@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> Message-ID: Yup, me too. (same for URL...) M On Thu, 10 Jan 2008 08:51:06 -0800, Paul Gordon wrote: > I think the litmus tests would be: > -might I need to subclass the identifier? > -would it be useful to associate the identifier with anything besides a > base object? > -is it a subtype of some other identifier? > > The answers for email are: > -no > -yes (e.g. use it as the namespace for a Person object, which relates > oppositely to the data-type argument by Mark) > -no > > Sounds like a namespace to me... > > Mark Wilkinson wrote: >> Hi Andreas! >> >> That's a very interesting case! Is "email" a data-type (Object) or a >> semantic-type (Namespace)?? It is a semantic type in the sense that >> all email addresses are unique, and therefore behave as identifiers... >> but it is often used as a data-type in that it would be associated with >> other information like an address and telephone number. >> >> Personally I would be tempted to make a new namespace 'emailAddress' or >> something like that, since semantic "precision" is the goal of these >> two ontologies. >> >> What did we do for URLs? ...LOL! Okay, I just went to have a look in >> the ontologies and we have an Object "URL" and a Namespace "URL"!!! I >> guess others have had the same question and made different decisions >> :-) I see that it is Pieter's services that consume the Object "URL" - >> maybe he can explain to us why he chose to make URL an object rather >> than a namespace. >> >> Pieter? >> >> M >> >> >> >> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >> wrote: >> >>> And hi again, >>> >>> we just had the discussion here... is it recommended to use primitives >>> as >>> primary input ? Or are there actually only for use in secondary >>> parameters or >>> as part of a complex datatype ? >>> >>> E.g. if a service requires an email as input - give it an object with >>> namespace 'email' or similar - or could I use String with namespace >>> 'email' >>> >>> Thanks and byebye >>> andreas >>> >> >> >> > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 12:29:42 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 09:29:42 -0800 Subject: [MOBY-dev] Comments by tomorrow please Message-ID: Hi all, There's a 48 hour deadline for getting the proof's edited. For those of you who have requested a copy of the proofs, please send me your comments by the end of the day tomorrow. I have found quite a few edits. Thanks! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 groscurt at mpiz-koeln.mpg.de Thu Jan 10 12:26:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 10 Jan 2008 18:26:09 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47864CFA.5060500@ucalgary.ca> References: <47864CFA.5060500@ucalgary.ca> Message-ID: <200801101826.09952.groscurt@mpiz-koeln.mpg.de> Thanks to the two of you... /bow made my world clearer again *g On Thursday 10 January 2008 17:51, Paul Gordon wrote: > I think the litmus tests would be: > -might I need to subclass the identifier? > -would it be useful to associate the identifier with anything besides a > base object? > -is it a subtype of some other identifier? > > The answers for email are: > -no > -yes (e.g. use it as the namespace for a Person object, which relates > oppositely to the data-type argument by Mark) > -no > > Sounds like a namespace to me... > > Mark Wilkinson wrote: > > Hi Andreas! > > > > That's a very interesting case! Is "email" a data-type (Object) or a > > semantic-type (Namespace)?? It is a semantic type in the sense that > > all email addresses are unique, and therefore behave as identifiers... > > but it is often used as a data-type in that it would be associated > > with other information like an address and telephone number. > > > > Personally I would be tempted to make a new namespace 'emailAddress' > > or something like that, since semantic "precision" is the goal of > > these two ontologies. > > > > What did we do for URLs? ...LOL! Okay, I just went to have a look in > > the ontologies and we have an Object "URL" and a Namespace "URL"!!! I > > guess others have had the same question and made different decisions > > > > :-) I see that it is Pieter's services that consume the Object "URL" > > > > - maybe he can explain to us why he chose to make URL an object rather > > than a namespace. > > > > Pieter? > > > > M > > > > > > > > On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth > > > > wrote: > >> And hi again, > >> > >> we just had the discussion here... is it recommended to use > >> primitives as > >> primary input ? Or are there actually only for use in secondary > >> parameters or > >> as part of a complex datatype ? > >> > >> E.g. if a service requires an email as input - give it an object with > >> namespace 'email' or similar - or could I use String with namespace > >> 'email' > >> > >> Thanks and byebye > >> andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Thu Jan 10 13:07:56 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 19:07:56 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: Hi, On 10-jan-2008, at 17:35, Mark Wilkinson wrote: > Hi Andreas! > > That's a very interesting case! Is "email" a data-type (Object) or > a semantic-type (Namespace)?? It is a semantic type in the sense > that all email addresses are unique, and therefore behave as > identifiers... but it is often used as a data-type in that it would > be associated with other information like an address and telephone > number. > > Personally I would be tempted to make a new namespace > 'emailAddress' or something like that, since semantic "precision" > is the goal of these two ontologies. > > What did we do for URLs? ...LOL! Okay, I just went to have a look > in the ontologies and we have an Object "URL" and a Namespace > "URL"!!! I guess others have had the same question and made > different decisions :-) I see that it is Pieter's services that > consume the Object "URL" - maybe he can explain to us why he chose > to make URL an object rather than a namespace. > > Pieter? I've been struggling with this question as well. If you check the object ontology you'll see I also registered an Email object. Email addresses and URLs can be both a data-type (Object) and a semantic- type (Namespace), so maybe it would be best to use both. Actually I was waiting for a response of the founding father a.k.a. chief architect to clarify this one :)... We give several courses which involve BioMOBY and usually the part where the students have to: * choose whether to recycle existing objects & namespaces or design new objects & namespaces * and if they choose to design new ones, come up with the exact structure for those objects & namespaces is the most difficult part of the entire course. Cheers, Pi > M > > > > On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth > wrote: > >> And hi again, >> >> we just had the discussion here... is it recommended to use >> primitives as >> primary input ? Or are there actually only for use in secondary >> parameters or >> as part of a complex datatype ? >> >> E.g. if a service requires an email as input - give it an object with >> namespace 'email' or similar - or could I use String with >> namespace 'email' >> >> Thanks and byebye >> andreas >> > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Thu Jan 10 13:31:06 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 10:31:06 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: I agree with Paul (or did Paul agree with me??) that email and url are namespaces. Paul's argument that it doesn't make sense to sub-class an email or a url is a compelling one, which also gives me some assurance that this decision is correct. ...on the other hand, there have been several requests from people in the community to create subclasses of namespaces (e.g. NCBI-->NCBI_gi), and in the case of IRRI their need was sufficiently strong that they ended up created objects that represented their identifiers such that they could sub-class them at the object level! So there is a clear desire and apparent need to be able to categorize namespaces as well... M On Thu, 10 Jan 2008 10:07:56 -0800, Pieter Neerincx wrote: > Hi, > > On 10-jan-2008, at 17:35, Mark Wilkinson wrote: > >> Hi Andreas! >> >> That's a very interesting case! Is "email" a data-type (Object) or a >> semantic-type (Namespace)?? It is a semantic type in the sense that >> all email addresses are unique, and therefore behave as identifiers... >> but it is often used as a data-type in that it would be associated with >> other information like an address and telephone number. >> >> Personally I would be tempted to make a new namespace 'emailAddress' or >> something like that, since semantic "precision" is the goal of these >> two ontologies. >> >> What did we do for URLs? ...LOL! Okay, I just went to have a look in >> the ontologies and we have an Object "URL" and a Namespace "URL"!!! I >> guess others have had the same question and made different decisions >> :-) I see that it is Pieter's services that consume the Object "URL" - >> maybe he can explain to us why he chose to make URL an object rather >> than a namespace. >> >> Pieter? > > I've been struggling with this question as well. If you check the object > ontology you'll see I also registered an Email object. Email addresses > and URLs can be both a data-type (Object) and a semantic-type > (Namespace), so maybe it would be best to use both. Actually I was > waiting for a response of the founding father a.k.a. chief architect to > clarify this one :)... > > We give several courses which involve BioMOBY and usually the part where > the students have to: > * choose whether to recycle existing objects & namespaces or design > new objects & namespaces > * and if they choose to design new ones, come up with the exact > structure for those objects & namespaces > is the most difficult part of the entire course. > > Cheers, > > Pi > > >> M >> >> >> >> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >> wrote: >> >>> And hi again, >>> >>> we just had the discussion here... is it recommended to use primitives >>> as >>> primary input ? Or are there actually only for use in secondary >>> parameters or >>> as part of a complex datatype ? >>> >>> E.g. if a service requires an email as input - give it an object with >>> namespace 'email' or similar - or could I use String with namespace >>> 'email' >>> >>> Thanks and byebye >>> andreas >>> >> >> >> >> ---- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Thu Jan 10 13:37:42 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 19:37:42 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47864CFA.5060500@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> Message-ID: <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> Hi Paul, On 10-jan-2008, at 17:51, Paul Gordon wrote: > I think the litmus tests would be: > 1. might I need to subclass the identifier? > 2. would it be useful to associate the identifier with anything > besides a base object? > 3. is it a subtype of some other identifier? > > The answers for email are: > 1. no > 2. yes (e.g. use it as the namespace for a Person object, which > relates oppositely to the data-type argument by Mark) > 3. no The reason I initially choose to register an Email object instead of a namespace is that it would allow me to subclass it in the future. I have to admit I didn't do that yet, which would be a vote in favour of a namespace, but who knows... Same for the URLs. My answer to question 1 would be a maybe, maybe not. In addition URLs are a subtype of URIs. (Although I have to admit I didn't register them as such: URL isa URI would make sense to me) So how would you handle URLs? Object or namespace? Cheers, Pi > Sounds like a namespace to me... > > Mark Wilkinson wrote: >> Hi Andreas! >> >> That's a very interesting case! Is "email" a data-type (Object) >> or a semantic-type (Namespace)?? It is a semantic type in the >> sense that all email addresses are unique, and therefore behave as >> identifiers... but it is often used as a data-type in that it >> would be associated with other information like an address and >> telephone number. >> >> Personally I would be tempted to make a new namespace >> 'emailAddress' or something like that, since semantic "precision" >> is the goal of these two ontologies. >> >> What did we do for URLs? ...LOL! Okay, I just went to have a >> look in the ontologies and we have an Object "URL" and a Namespace >> "URL"!!! I guess others have had the same question and made >> different decisions :-) I see that it is Pieter's services that >> consume the Object "URL" - maybe he can explain to us why he chose >> to make URL an object rather than a namespace. >> >> Pieter? >> >> M >> >> >> >> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >> wrote: >> >>> And hi again, >>> >>> we just had the discussion here... is it recommended to use >>> primitives as >>> primary input ? Or are there actually only for use in secondary >>> parameters or >>> as part of a complex datatype ? >>> >>> E.g. if a service requires an email as input - give it an object >>> with >>> namespace 'email' or similar - or could I use String with >>> namespace 'email' >>> >>> Thanks and byebye >>> andreas >>> >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Thu Jan 10 13:44:52 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 10:44:52 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> Message-ID: On Thu, 10 Jan 2008 10:37:42 -0800, Pieter Neerincx wrote: > In addition URLs are a subtype of URIs. (Although I have to admit I > didn't register them as such: URL isa URI would make sense to me) So how > would you handle URLs? Object or namespace? I think we need to un-flatten the Namespace ontology, at least from the perspective of some tools (other users, like the Gene Ontology, could use the hierarchical Namespace ontology as a flat list as they always have) Let me look at the current API and see how difficult it would be to do that without breaking anything... M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Thu Jan 10 14:03:42 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 20:03:42 +0100 Subject: [MOBY-dev] MobyCentral connection lost :( In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> Message-ID: <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> Hi Chaps, I'm repeatedly getting: Connection to MOBY Central at 'http://moby.ucalgary.ca/MOBY/Central' died because: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/ mysql.sock' (2) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ Adaptor/moby/queryapi/mysql.pm line 90 ERROR ERROR ERROR Is that a MySQL problem in Calgary or am I doing something wrong? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Pieter.Neerincx at wur.nl Thu Jan 10 14:05:18 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 20:05:18 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: <22BB025F-54EE-4450-9CF9-18633BD1BC0A@wur.nl> On 10-jan-2008, at 19:31, Mark Wilkinson wrote: > I agree with Paul (or did Paul agree with me??) that email and url > are namespaces. Paul's argument that it doesn't make sense to sub- > class an email or a url is a compelling one, which also gives me > some assurance that this decision is correct. > > ...on the other hand, there have been several requests from people > in the community to create subclasses of namespaces (e.g. NCBI-- > >NCBI_gi), and in the case of IRRI their need was sufficiently > strong that they ended up created objects that represented their > identifiers such that they could sub-class them at the object > level! So there is a clear desire and apparent need to be able to > categorize namespaces as well... Yes, that would really help! :) Pi > M > > > > On Thu, 10 Jan 2008 10:07:56 -0800, Pieter Neerincx > wrote: > >> Hi, >> >> On 10-jan-2008, at 17:35, Mark Wilkinson wrote: >> >>> Hi Andreas! >>> >>> That's a very interesting case! Is "email" a data-type (Object) >>> or a semantic-type (Namespace)?? It is a semantic type in the >>> sense that all email addresses are unique, and therefore behave >>> as identifiers... but it is often used as a data-type in that it >>> would be associated with other information like an address and >>> telephone number. >>> >>> Personally I would be tempted to make a new namespace >>> 'emailAddress' or something like that, since semantic "precision" >>> is the goal of these two ontologies. >>> >>> What did we do for URLs? ...LOL! Okay, I just went to have a >>> look in the ontologies and we have an Object "URL" and a >>> Namespace "URL"!!! I guess others have had the same question and >>> made different decisions :-) I see that it is Pieter's services >>> that consume the Object "URL" - maybe he can explain to us why he >>> chose to make URL an object rather than a namespace. >>> >>> Pieter? >> >> I've been struggling with this question as well. If you check the >> object ontology you'll see I also registered an Email object. >> Email addresses and URLs can be both a data-type (Object) and a >> semantic-type (Namespace), so maybe it would be best to use both. >> Actually I was waiting for a response of the founding father >> a.k.a. chief architect to clarify this one :)... >> >> We give several courses which involve BioMOBY and usually the part >> where the students have to: >> * choose whether to recycle existing objects & namespaces or >> design new objects & namespaces >> * and if they choose to design new ones, come up with the exact >> structure for those objects & namespaces >> is the most difficult part of the entire course. >> >> Cheers, >> >> Pi >> >> >>> M >>> >>> >>> >>> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >>> wrote: >>> >>>> And hi again, >>>> >>>> we just had the discussion here... is it recommended to use >>>> primitives as >>>> primary input ? Or are there actually only for use in secondary >>>> parameters or >>>> as part of a complex datatype ? >>>> >>>> E.g. if a service requires an email as input - give it an object >>>> with >>>> namespace 'email' or similar - or could I use String with >>>> namespace 'email' >>>> >>>> Thanks and byebye >>>> andreas >>>> >>> >>> >>> >>> ---- >>> Mark Wilkinson >>> Assistant Professor, Dept. Medical Genetics >>> University of British Columbia >>> PI Bioinformatics >>> iCAPTURE Centre, St. Paul's Hospital >>> Tel: 604 682 2344 x62129 >>> Fax: 604 806 9274 >>> >>> ***CONFIDENTIALITY NOTICE*** >>> This electronic message is intended only for the use of the >>> addressee and may contain information that is privileged and >>> confidential. Any dissemination, distribution or copying of this >>> communication by unauthorized individuals is strictly prohibited. >>> If you have received this communication in error, please notify >>> the sender immediately by reply e-mail and delete the original >>> and all copies from your system. >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> 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 > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From edward.kawas at gmail.com Thu Jan 10 14:05:06 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 10 Jan 2008 11:05:06 -0800 Subject: [MOBY-dev] MobyCentral connection lost :( In-Reply-To: <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca><6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> Message-ID: <16EFBFE2806C43D2A0F27781A894ABEA@OfficePC> Hi Pieter, There seems to be something wrong with mysql. Hopefully the problem will be resolved shortly. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: January-10-08 11:04 AM To: Core developer announcements Subject: [MOBY-dev] MobyCentral connection lost :( Hi Chaps, I'm repeatedly getting: Connection to MOBY Central at 'http://moby.ucalgary.ca/MOBY/Central' died because: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/ mysql.sock' (2) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ Adaptor/moby/queryapi/mysql.pm line 90 ERROR ERROR ERROR Is that a MySQL problem in Calgary or am I doing something wrong? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jan 10 14:06:23 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 11:06:23 -0800 Subject: [MOBY-dev] MobyCentral connection lost :( In-Reply-To: <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> Message-ID: It went down a few minutes ago - looking into it. M On Thu, 10 Jan 2008 11:03:42 -0800, Pieter Neerincx wrote: > Hi Chaps, > > I'm repeatedly getting: > > Connection to MOBY Central at 'http://moby.ucalgary.ca/MOBY/Central' > died because: > DBI connect('mobycentral:localhost:3306','moby',...) failed: > Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) > at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ > Adaptor/moby/queryapi/mysql.pm line 90 > > ERROR ERROR ERROR > > Is that a MySQL problem in Calgary or am I doing something wrong? > > Cheers, > > Pi > > > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Thu Jan 10 14:10:03 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 20:10:03 +0100 Subject: [MOBY-dev] Comments by tomorrow please In-Reply-To: References: Message-ID: <7AE7220D-69ED-449F-BAD0-C04DC756AEFE@wur.nl> Hi Mark, Please send me copy too. I'll look at it immediately after squash tonight :)... Cheers, Pi On 10-jan-2008, at 18:29, Mark Wilkinson wrote: > Hi all, > > There's a 48 hour deadline for getting the proof's edited. For > those of you who have requested a copy of the proofs, please send > me your comments by the end of the day tomorrow. I have found > quite a few edits. > > Thanks! > > Mark > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Thu Jan 10 14:10:27 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 11:10:27 -0800 Subject: [MOBY-dev] Comments by tomorrow please In-Reply-To: <7AE7220D-69ED-449F-BAD0-C04DC756AEFE@wur.nl> References: <7AE7220D-69ED-449F-BAD0-C04DC756AEFE@wur.nl> Message-ID: Crap... I sent it to the dev list by mistake :-/ >> sigh<< M On Thu, 10 Jan 2008 11:10:03 -0800, Pieter Neerincx wrote: > Hi Mark, > > Please send me copy too. I'll look at it immediately after squash > tonight :)... > > Cheers, > > Pi > > On 10-jan-2008, at 18:29, Mark Wilkinson wrote: > >> Hi all, >> >> There's a 48 hour deadline for getting the proof's edited. For those >> of you who have requested a copy of the proofs, please send me your >> comments by the end of the day tomorrow. I have found quite a few >> edits. >> >> Thanks! >> >> Mark >> >> ---- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 meredith at cantab.net Thu Jan 10 14:09:47 2008 From: meredith at cantab.net (Tom Oinn) Date: Thu, 10 Jan 2008 19:09:47 +0000 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: <47866D7B.206@cantab.net> Mark Wilkinson wrote: > I agree with Paul (or did Paul agree with me??) that email and url are > namespaces. Paul's argument that it doesn't make sense to sub-class an > email or a url is a compelling one, which also gives me some assurance > that this decision is correct. There are plenty of cases where you might want to restrict the permitted semantics of a URL, most of which boil down to a restriction on what the URL can point *to*. Email addresses are different, in that they all have the same inherent content. They're not really references in the same way as URLs. It's somewhat broken in my view to have URL in moby *at all*, it would be better to have a framework where you could explicitly seperate the reference from that to which it refers. If you have a tool that accepts a URL to an image the signature of the tool is 'image', the URL part of that is the delivery mechanism and in an ideal world they wouldn't be conflated in this way. The exception would be something that took a URL as a string to, e.g. validate it according to the URL specification (in which case the type is 'url' and the carrier type is 'string value'). If you could define types in terms of their carrier mechanism (URL, SCP path, value etc) and split this out from the actual content they carry (image, person, bio-foo-object) this would make life a lot easier (and is, in a completely non-coincidental fashion, what Taverna2 does for exactly this reason). Of course that's just a 'small' change to how Moby works :) Tom From markw at illuminae.com Thu Jan 10 16:23:08 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 13:23:08 -0800 Subject: [MOBY-dev] Ignore the RSS feeds Message-ID: They appear to not be working properly right now. Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 17:53:38 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 14:53:38 -0800 Subject: [MOBY-dev] A Demonstration at ISMB? Message-ID: I wonder if it might be worth doing a demonstration at ISMB, or maybe a couple, using the various software tools we have (e.g. Taverna, MOWServ, SeaHawk). It only costs $400 if we are selected, and the deadline is further along in the year so it isn't as frantic. http://www.iscb.org/ismb2008/sub_demonstrations.php ?? Anyone interested? If not, I'm certainly going to try to get us in for teh Moby extensions to Taverna at least, but it would be good to partner with someone else who has a different Moby interface so that people can see a broader view of what can be done. It would be a good place to hand-out T-shirts too ;-) Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 17:55:48 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 14:55:48 -0800 Subject: [MOBY-dev] The 1.0 paper into the "highlights" track Message-ID: http://www.iscb.org/ismb2008/high_track.php I'll certainly be sending the 1.0 paper to the highlights track to see if we can get in there too... fingers crossed! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Thu Jan 10 22:54:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 10 Jan 2008 20:54:52 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47866D7B.206@cantab.net> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> Message-ID: <4786E88C.4070707@ucalgary.ca> > Mark Wilkinson wrote: >> I agree with Paul (or did Paul agree with me??) that email and url >> are namespaces. Paul's argument that it doesn't make sense to >> sub-class an email or a url is a compelling one, which also gives me >> some assurance that this decision is correct. Mark, I didn't actually say that URLs were a namespace -- just e-mails. I avoided talking about URLs because I knew I'd have to write a longer philosophical e-mail..like this one :-) To be correct, the namespace should actually be "smtp", as the e-mail address format that we are used to (foo at bar.tld) is specific to SMTP. Anyone remember uucp-based e-mail? This might seem pedantic, but it makes a point: the e-mail address is what is referred to in semiotics as an "index". Now for some semiotic theory. Normally, the association between a sign (e.g. the word "cow") and the entity it refers to (an actual, physical cow) is arbitrary, it's a cultural artifact. These are called symbols (gene symbols such as "adh1" are examples of this too). An index is a sign who's association with its referent is not random: the referent is unambiguously resolveable, given a retrieval protocol. A protocol and an index go hand-in-hand. An e-mail address points an SMTP client (the sign interpreter) unambiguously at a destination for a message, ergo, the e-mail address is an index for the SMTP protocol. In Moby, the protocol is the namespace (e.g. NCBI_gi), the index is the ID (e.g. 100389), and the interpreter is an NCBI-savvy Moby service that will be able to retrieve based on the index. URLs are different beasts. The fact that you can represent an e-mail address as a URL speaks to this fact (e.g. mailto:foo at bar.tld). A URL combines a protocol and an index ("protocol:index"). Technically, probably the best way to represent the URL http://www.google.com in Moby would be to have an HTTP namespace, and use the id "//www.google.com". Then you make http-savvy Moby services, registered accepting objects in the HTTP namespace. The confusion comes from the fact that the protocol+index combo can be either in the namespace/id part, or in the form of a data type. Why then do we bother having id/namepsace? Tom was on to something, but not quite. There is exactly one "carrier mechanism" in Moby: services. They know how to resolve an index combos and give you the referent back. Namespaces are exceptionally useful because they allow you to use an index with or without the things that are keyed off them. A perfect illustration this is a VirtualSequence with a namespace and id. Another good way to get a sense of the appropriateness of namespace/id is the Moby cross-reference block (CRIB). If you made E-mail a data type, you couldn't use it in the CRIB because you're not using the namespace/id combo to make the cross-reference in the only way Moby inherently knows how. My $0.02 :-) From meredith at cantab.net Fri Jan 11 03:37:11 2008 From: meredith at cantab.net (Tom Oinn) Date: Fri, 11 Jan 2008 08:37:11 +0000 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <4786E88C.4070707@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> Message-ID: <47872AB7.8060105@cantab.net> Paul Gordon wrote: > The confusion comes from the fact that the protocol+index combo can be > either in the namespace/id part, or in the form of a data type. Why > then do we bother having id/namepsace? Tom was on to something, but not > quite. There is exactly one "carrier mechanism" in Moby: services. They > know how to resolve an index combos and give you the referent back. If the above is true then can you tell me the type for an input which requires an image in PNG format pointed to by a URL? I don't think you can... There is one carrier mechanism in Moby, but this is being used to carry entities which are themselves indices into other systems. Unless I wildly misunderstand something (entirely possible I admit) there's no way to say 'URL to an image' let alone 'URL to an image of my cat'. Tom From groscurt at mpiz-koeln.mpg.de Fri Jan 11 04:00:29 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 10:00:29 +0100 Subject: [MOBY-dev] A Demonstration at ISMB? In-Reply-To: References: Message-ID: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> If this is appropiate and enough for a part of the Moby demonstration - I would like to point to my Aggregator Jabba ( http://bioinfo.mpiz-koeln.mpg.de/jabba ). I think, and support what Pieter already said, a demonstration of available cool tools would be nice to spread out more of Moby into the world.... And... WE HAVE T-SHIRTS ?! cool *g Andreas On Thursday 10 January 2008 23:53, Mark Wilkinson wrote: > I wonder if it might be worth doing a demonstration at ISMB, or maybe a > couple, using the various software tools we have (e.g. Taverna, MOWServ, > SeaHawk). > > It only costs $400 if we are selected, and the deadline is further along > in the year so it isn't as frantic. > > http://www.iscb.org/ismb2008/sub_demonstrations.php > > ?? Anyone interested? If not, I'm certainly going to try to get us in > for teh Moby extensions to Taverna at least, but it would be good to > partner with someone else who has a different Moby interface so that > people can see a broader view of what can be done. > > It would be a good place to hand-out T-shirts too ;-) > > Mark -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Fri Jan 11 05:40:20 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 11 Jan 2008 11:40:20 +0100 Subject: [MOBY-dev] A Demonstration at ISMB? In-Reply-To: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> References: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> Message-ID: <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> Hi, On 11 Jan 2008, at 10:00, Andreas Groscurth wrote: > If this is appropiate and enough for a part of the Moby > demonstration - I > would like to point to my Aggregator Jabba > ( http://bioinfo.mpiz-koeln.mpg.de/jabba ). Hey, I haven't seen this Jabba before... Shouldn't it be listed on the BioMOBY site at http://biomoby.open-bio.org/index.php/ browser_clients/ ? > I think, and support what Pieter already said, a demonstration of > available > cool tools would be nice to spread out more of Moby into the world.... > > And... WE HAVE T-SHIRTS ?! cool *g Not yet as far as I know, but it would be a really good way to make some advertisement for BioMOBY. The last two years of ISMB there were two booths that received an enormous amount of attention for a while. Those were the BMC and PLoS booths when they were handing out free t- shirts. At the PLoS booth it was so hectic, people were almost fighting over those shirts. The next few days you saw people all over the conference and city center with those shirts :) With regard to a demo, I think the $400 is bullshit. Previously they didn't charge extra for that. They started to do that last year. The conference itself is already very expensive, but well worth it. No- one who gets selected for the PloS-track, highlights-track, poster- track, etc. has to pay extra to be able to present. So why the hell would you have to for a software demo? The problem with the software demo's is that a lot of previously demoed stuff was not freely available to the scientific community. Even if it was presented by a non-profit organisation, there was quite some closed source stuff for which you had to buy a licence. Hence, they must have figured they could charge us for a demo if we are going to make money from this software. I complained about it last year and asked the organisation to charge only for closed source payware and not for open source freeware. Unfortunately they didn't change the rules, so I think a demo is a good thing to do, but as long as we can get some papers in the highlight- and/or PLoS-track, we can just show stuff there. Whether the audience is looking at a beamer with a static PowerPoint slide with a screenshot of Taverna/MOWServ/SeaHawk or whether this is Taverna/MOWServ/SeaHawk live on a beamer is not that much different anyway. Then there is off course also the BOSC as SIG in the two days preceding the main ISMB conference. Since the BOSC is organised by the OBF and BioMOBY is an OBF project we should be able to get some substantial airtime there as well :). Getting charged extra while we spend our time to make this stuff freely available to the scientific community really feels to me like a slap into my face. Maybe some are fine with this, but I don't like spanking, so I'd rather spend the money on shirts... Cheers, Pi > Andreas > > On Thursday 10 January 2008 23:53, Mark Wilkinson wrote: >> I wonder if it might be worth doing a demonstration at ISMB, or >> maybe a >> couple, using the various software tools we have (e.g. Taverna, >> MOWServ, >> SeaHawk). >> >> It only costs $400 if we are selected, and the deadline is further >> along >> in the year so it isn't as frantic. >> >> http://www.iscb.org/ismb2008/sub_demonstrations.php >> >> ?? Anyone interested? If not, I'm certainly going to try to get >> us in >> for teh Moby extensions to Taverna at least, but it would be good to >> partner with someone else who has a different Moby interface so that >> people can see a broader view of what can be done. >> >> It would be a good place to hand-out T-shirts too ;-) >> >> Mark > > -- > Andreas Groscurth > Bioinformatics Developer > 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)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From Pieter.Neerincx at wur.nl Fri Jan 11 06:54:50 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 11 Jan 2008 12:54:50 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <4786E88C.4070707@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> Message-ID: <89EB1BFF-9C90-4C42-A573-96EB32C251AB@wur.nl> Hi Paul, You are a good advocate for the moby id/namepsace combo and I think they should be used more often. There are too many services that don't use namespace restriction where they should and I have too admit I'm guilty too. I still have some questions left though.... and I think designing good BioMOBY objects and namespaces is anything but trivial :(. On 11 Jan 2008, at 04:54, Paul Gordon wrote: > >> Mark Wilkinson wrote: >>> I agree with Paul (or did Paul agree with me??) that email and >>> url are namespaces. Paul's argument that it doesn't make sense >>> to sub-class an email or a url is a compelling one, which also >>> gives me some assurance that this decision is correct. > Mark, I didn't actually say that URLs were a namespace -- just e- > mails. I avoided talking about URLs because I knew I'd have to > write a longer philosophical e-mail..like this one :-) > > To be correct, the namespace should actually be "smtp", as the e- > mail address format that we are used to (foo at bar.tld) is specific > to SMTP. That is just for sending the e-mail. E-mail addresses are just as specific for protocols used to retrieve e-mail. So I don't see why the namespace should be smtp and not for example pop3 or imap? > Anyone remember uucp-based e-mail? This might seem pedantic, but > it makes a point: the e-mail address is what is referred to in > semiotics as an "index". Now for some semiotic theory. Normally, > the association between a sign (e.g. the word "cow") and the entity > it refers to (an actual, physical cow) is arbitrary, it's a > cultural artifact. These are called symbols (gene symbols such as > "adh1" are examples of this too). An index is a sign who's > association with its referent is not random: the referent is > unambiguously resolveable, given a retrieval protocol. A protocol > and an index go hand-in-hand. An e-mail address points an SMTP > client (the sign interpreter) unambiguously at a destination for a > message, ergo, the e-mail address is an index for the SMTP > protocol. In Moby, the protocol is the namespace (e.g. NCBI_gi), > the index is the ID (e.g. 100389), and the interpreter is an NCBI- > savvy Moby service that will be able to retrieve based on the index. > > URLs are different beasts. The fact that you can represent an e- > mail address as a URL speaks to this fact (e.g. > mailto:foo at bar.tld). A URL combines a protocol and an index > ("protocol:index"). Technically, probably the best way to > represent the URL http://www.google.com in Moby would be to have an > HTTP namespace, and use the id "//www.google.com". Then you make > http-savvy Moby services, registered accepting objects in the HTTP > namespace. Hmmm... yes, but then an e-mail address id namespace combo is now . Maybe it could be solved if we can subclass the namespace ontology. Then you could have some generic mail_protocol namespace and smtp isa mail_protocol, pop3 isa mail_protocol, etc. > The confusion comes from the fact that the protocol+index combo can > be either in the namespace/id part, or in the form of a data type. > Why then do we bother having id/namepsace? Tom was on to > something, but not quite. There is exactly one "carrier mechanism" > in Moby: services. They know how to resolve an index combos and > give you the referent back. > > Namespaces are exceptionally useful because they allow you to use > an index with or without the things that are keyed off them. A > perfect illustration this is a VirtualSequence with a namespace and > id. Another good way to get a sense of the appropriateness of > namespace/id is the Moby cross-reference block (CRIB). If you made > E-mail a data type, you couldn't use it in the CRIB because you're > not using the namespace/id combo to make the cross-reference in the > only way Moby inherently knows how. You would have to use the email namespace for the CRIB, but that doesn't mean you can not have it as a data-type too. Think of the following example: VirtualEmail isa Object AnnotatedEmail isa VirtualEmail AnnotatedEmail has Object with articleName alias AnnotatedEmail has String with articleName real_name That would look something like this: Prof.Dr. Foo Bar You can still use a CRIB to point to this thing using: ... Description ... or using a lightweight CRIB: After all VirtualEmail isa Object, right? Cheers, Pi > My $0.02 :-) > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From groscurt at mpiz-koeln.mpg.de Fri Jan 11 07:36:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 13:36:55 +0100 Subject: [MOBY-dev] Service deployment on tomcat and axis2 In-Reply-To: <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> References: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> Message-ID: <200801111336.55473.groscurt@mpiz-koeln.mpg.de> hi, i try to deploy a Web Service on tomcat and axis2, but i fail... does anyone has any experiences with that ? Axis2 has a new structure and e.g. dont use the AdminServlet to deploy services. I created a aar file containing the skeleton and the sample class with its package structure by my own, because as I can see, there is no ant task for that or any other moby structure to handle an aar file.... I also added the META-INF/services.xml into the archive and copied the archive into axis2/WEB-INF/services I then copied the biomoby-datatypes.jar, jmoby.jar and jmoby-other.jar into the lib directory of axis2/WEB-INF Validating this via the axis web interface it complaint that it misses alltools and jdom. So I copied them also into the lib directory. Then I get the the following error: Error: org.apache.axis2.deployment.DeploymentException: The following error occurred during schema generation: 2 at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:389) at org.apache.axis2.deployment.repository.util.ArchiveReader.buildServiceGroup(ArchiveReader.java:95) at org.apache.axis2.deployment.repository.util.ArchiveReader.processServiceGroup(ArchiveReader.java:172) at org.apache.axis2.deployment.ServiceDeployer.deploy(ServiceDeployer.java:78) at org.apache.axis2.deployment.repository.util.DeploymentFileData.deploy(DeploymentFileData.java:137) at org.apache.axis2.deployment.DeploymentEngine.doDeploy(DeploymentEngine.java:571) at org.apache.axis2.deployment.repository.util.WSInfoList.update(WSInfoList.java:141) at org.apache.axis2.deployment.RepositoryListener.update(RepositoryListener.java:318) at org.apache.axis2.deployment.RepositoryListener.checkServices(RepositoryListener.java:220) at org.apache.axis2.deployment.DeploymentEngine.loadServices(DeploymentEngine.java:118) at org.apache.axis2.deployment.WarBasedAxisConfigurator.loadServices(WarBasedAxisConfigurator.java:272) at org.apache.axis2.context.ConfigurationContextFactory.createConfigurationContext(ConfigurationContextFactory.java:78) at org.apache.axis2.transport.http.AxisServlet.initConfigContext(AxisServlet.java:500) at org.apache.axis2.transport.http.AxisServlet.init(AxisServlet.java:420) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:825) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:714) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1138) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java:700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) Caused by: org.apache.axis2.deployment.DeploymentException: The following error occurred during schema generation: 2 at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:354) ... 39 more Caused by: java.lang.ArrayIndexOutOfBoundsException: 2 at org.apache.axis2.description.java2wsdl.DefaultSchemaGenerator.processMethods(DefaultSchemaGenerator.java:275) at org.apache.axis2.description.java2wsdl.DefaultSchemaGenerator.generateSchema(DefaultSchemaGenerator.java:181) at org.apache.axis2.deployment.util.Utils.fillAxisService(Utils.java:352) at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:350) ... 39 more Has anyone any experience with axis2 and can tell me how do to that ? or what went wrong ? Thanks andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From martin.senger at gmail.com Fri Jan 11 08:27:00 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 11 Jan 2008 13:27:00 +0000 Subject: [MOBY-dev] Service deployment on tomcat and axis2 In-Reply-To: <200801111336.55473.groscurt@mpiz-koeln.mpg.de> References: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> <200801111336.55473.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0801110527n33710eaas197e490e6c5912d1@mail.gmail.com> My understanding is that axis2 supports by default lit-doc style of web services (it may not even support the rpc-encoded one, but that I am not sure). BioMoby still uses the rpc-encoded style. You can either tweak axis 2 to produce this style, or you cannot use axis2. Lats June, we have agreed to work on broadening the protocols used. I expect some progress on it during the next month Biohackathon in Japan. Just my 2 c's. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Jan 11 08:51:14 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 11 Jan 2008 06:51:14 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47872AB7.8060105@cantab.net> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> <47872AB7.8060105@cantab.net> Message-ID: <47877452.4000100@ucalgary.ca> Hi Tom, No, you shouldn't be able to (unless you guarantee that you know how to decode every URL type ever possible, including prospero, gopher, ftp, etc., since that's the contract you're making). The way you'd do it should be like how VirtualSequences are specifed: Then you make the text description of the VirtualPNGInage something that tells the user that it's a placeholder. You're correct that there is no systematic way in Moby, but there is a convention. Virtually nothing about data types is systematic in Moby, since it relies on someone to interpret the ontology terms by reading the term descriptions (which makes it infinitely simpler than OWL). Cheers, Paul P.S. I'm not generally a fan of namespace inheritance, but if we did it, an application that fits the bill for you would be to have URN -> URI -> URL -> httpURL ->PNGhttpURL. I fear that people will abuse an inherited namespace and say "I take NCBI IDs", when in fact they only take certain children. Inheritance just doesn't work the same way for most ID systems as it does for data types, because the retrieval protocol for a namespace is not generally both universal and non extensible. In the case of PNGhttpURL, it does not extend the httpURL retrieval protocol, so you're okay, but suppose if I register a new namespace as a child of NCBI_IDs. Because there is no universal protocol to retrieve things from the NCBI (at least for argument's sake), I've broken your service. People will start passing my new DB's IDs into your service, but you don't know how to fetch them. The contract for a namespace signature is fundamentally different from a data type contract, because of the retrieval phase. Tom Oinn wrote: > Paul Gordon wrote: > >> The confusion comes from the fact that the protocol+index combo can >> be either in the namespace/id part, or in the form of a data type. >> Why then do we bother having id/namepsace? Tom was on to something, >> but not quite. There is exactly one "carrier mechanism" in Moby: >> services. They know how to resolve an index combos and give you the >> referent back. > > If the above is true then can you tell me the type for an input which > requires an image in PNG format pointed to by a URL? I don't think you > can... > > There is one carrier mechanism in Moby, but this is being used to > carry entities which are themselves indices into other systems. Unless > I wildly misunderstand something (entirely possible I admit) there's > no way to say 'URL to an image' let alone 'URL to an image of my cat'. > > Tom > > From groscurt at mpiz-koeln.mpg.de Fri Jan 11 09:12:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 15:12:51 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47877452.4000100@ucalgary.ca> References: <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> Message-ID: <200801111512.51646.groscurt@mpiz-koeln.mpg.de> Hi, > i bet even this will confuse most of the people... In such cases I remember my boss at Bayer CropScience when we discussed about the 3th form of database normalisation... he just laughed and said "nice in theory and in university. but just horrible in practice". I think we must not tend to be too geeky and try to define everything in a correct way... There are 'normal' people out there how wants to use it ! So - I prefere a sloopy definition which is actually useable and can be told to service implementors ! cheers andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Fri Jan 11 09:14:50 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 15:14:50 +0100 Subject: [MOBY-dev] Service deployment on tomcat and axis2 In-Reply-To: <4d93f07c0801110527n33710eaas197e490e6c5912d1@mail.gmail.com> References: <200801111336.55473.groscurt@mpiz-koeln.mpg.de> <4d93f07c0801110527n33710eaas197e490e6c5912d1@mail.gmail.com> Message-ID: <200801111514.50623.groscurt@mpiz-koeln.mpg.de> thanks martin, I believe your answer if there is no other comment about that ;-) So I will see what can happen during the sessions in Japan. We have a workshop here in March and therefore I tried to set up the system with axis2... I guess its better to tell the participants to use axis1 cheers andreas On Friday 11 January 2008 14:27, Martin Senger wrote: > My understanding is that axis2 supports by default lit-doc style of web > services (it may not even support the rpc-encoded one, but that I am not > sure). BioMoby still uses the rpc-encoded style. You can either tweak axis > 2 to produce this style, or you cannot use axis2. > > Lats June, we have agreed to work on broadening the protocols used. I > expect some progress on it during the next month Biohackathon in Japan. > > Just my 2 c's. > Cheers, > Martin -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From meredith at cantab.net Fri Jan 11 09:18:34 2008 From: meredith at cantab.net (Tom Oinn) Date: Fri, 11 Jan 2008 14:18:34 +0000 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47877452.4000100@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> Message-ID: <47877ABA.7090503@cantab.net> Paul Gordon wrote: > Hi Tom, > > No, you shouldn't be able to (unless you guarantee that you know how to > decode every URL type ever possible, including prospero, gopher, ftp, > etc., since that's the contract you're making). True, but that's splitting hairs - the problem still exists if I explicitly say 'HTTP URL'. > P.S. I'm not generally a fan of namespace inheritance, but if we did it, > an application that fits the bill for you would be to have URN -> URI -> > URL -> httpURL ->PNGhttpURL. My point was that the above is inherently broken. It's a multi-axial classification (transport, content) shoehorned into a single heirarchy and, like the GO, ends up with an utter mess. The mess comes when I *do* want to allow multiple URL types (most toolkits will quite happily handle all the common ones) and you end up with a cut and paste heirarchy full of structural duplication (and thence errors over time) because of the failure to differentiate these two axes of classification. I should be able to specify the content (an image) required or produced by the service independantly from the delivery or consumption mechanism. If I were a user searching for services which accepted an image (in this case) I would definitely expect to see ones that accepted a URL to an image - the mechanics of providing the appropriate access mechanism are a different concern entirely. I don't think you can sensibly do this in moby at the moment but it would be fairly high on my wishlist, especially because Taverna2 is designed to take advantage of multiple alternative reference systems to optimise network usage. If a future moby could handle this sensibly workflows would run much faster and with much less load on both your network and your services. Tom From gordonp at ucalgary.ca Fri Jan 11 10:23:21 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 11 Jan 2008 08:23:21 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <200801111512.51646.groscurt@mpiz-koeln.mpg.de> References: <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> <200801111512.51646.groscurt@mpiz-koeln.mpg.de> Message-ID: <478789E9.8090705@ucalgary.ca> Hi all, I believe, for reasons that I've outlined before, that namespace inheritance is generally a very bad idea. I can see what Tom and Andreas are getting in terms of practicality of protocol + content type specification, but strongly stand by the fact that the protocol/namespace equivalence should be the mechanism in Moby. Now the question is how to combine the namespace and the data type in a service signature if that service is a retrieval service. The VirtualPNGImage method is currently the only way, but the Virtual idea is usable for any object. So we'd need to be able to add an attribute saying "I'm virtual". e.g. And we'd have to add to the service signature a mechanism for saying "I'll accept a PNGImage, or a virtual one that is in the http, ftp or scp namespaces". Of course, by default, a service will only accept real objects as they do know. You'd have explicitly register the fact that you take virtual data. My $0.02 Paul From gordonp at ucalgary.ca Fri Jan 11 13:43:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 11 Jan 2008 11:43:52 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <478789E9.8090705@ucalgary.ca> References: <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> <200801111512.51646.groscurt@mpiz-koeln.mpg.de> <478789E9.8090705@ucalgary.ca> Message-ID: <4787B8E8.5000503@ucalgary.ca> Any takers? Paul Gordon wrote: > Hi all, > > I believe, for reasons that I've outlined before, that namespace > inheritance is generally a very bad idea. I can see what Tom and > Andreas are getting in terms of practicality of protocol + content > type specification, but strongly stand by the fact that the > protocol/namespace equivalence should be the mechanism in Moby. Now > the question is how to combine the namespace and the data type in a > service signature if that service is a retrieval service. The > VirtualPNGImage method is currently the only way, but the Virtual idea > is usable for any object. So we'd need to be able to add an attribute > saying "I'm virtual". e.g. > > virtual="yes"/> > > And we'd have to add to the service signature a mechanism for saying > "I'll accept a PNGImage, or a virtual one that is in the http, ftp or > scp namespaces". Of course, by default, a service will only accept > real objects as they do know. You'd have explicitly register the fact > that you take virtual data. > > My $0.02 > > Paul > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478787ef10950176725398! > > > From markw at illuminae.com Sun Jan 13 11:02:50 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 13 Jan 2008 08:02:50 -0800 Subject: [MOBY-dev] RSS feeds should be working properly again now Message-ID: I just checked the cron log and it looks like the RSS feeds updated properly last night. I've also fixed the code that was producing incorrect links in the feed information. If you notice anything odd please let me know, Cheers all! Mark From groscurt at mpiz-koeln.mpg.de Mon Jan 14 07:39:13 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 13:39:13 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> References: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Message-ID: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> Hiho, I cannot load MobyCentral into Taverna: Error creating BiomobyScavenger for http://moby.ucalgary.ca/moby/MOBY-Central.pl org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not create the Datatype ontology node: Error creating Datatype tree: null at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:64) at org.biomoby.client.taverna.plugin.BiomobyScavengerHelper.getDefaults(BiomobyScavengerHelper.java:140) at org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool$ScavengerHelperDefaultsThread.run(ScavengerHelperThreadPool.java:166) Caused by: org.biomoby.shared.MobyException: Error creating Datatype tree: null at org.biomoby.client.taverna.plugin.BiomobyScavengerWorker.getDataTypes(BiomobyScavengerWorker.java:318) at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:61) ... 2 more Should this be a temp problem or is it something going wrong here ? merci andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From alanrw at cs.man.ac.uk Mon Jan 14 07:54:00 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Mon, 14 Jan 2008 12:54:00 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> References: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> <200801141339.13888.groscurt@mpiz-koeln.mpg.de> Message-ID: <478B5B68.1070202@cs.man.ac.uk> Andreas Groscurth wrote: > Hiho, Hello, > I cannot load MobyCentral into Taverna: > Error creating BiomobyScavenger for > http://moby.ucalgary.ca/moby/MOBY-Central.pl > org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not > create the Datatype ontology node: Error creating Datatype tree: null [snip] > > Should this be a temp problem or is it something going wrong here ? Which version of Taverna are you running? If it is 1.7, does it happen when the activity palette or the old service panel is showing? > merci > andreas Alan From groscurt at mpiz-koeln.mpg.de Mon Jan 14 08:08:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 14:08:09 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B5B68.1070202@cs.man.ac.uk> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> Message-ID: <200801141408.10120.groscurt@mpiz-koeln.mpg.de> On Monday 14 January 2008 13:54, Alan Williams wrote: > Andreas Groscurth wrote: > > Hiho, > > Hello, > > > I cannot load MobyCentral into Taverna: > > Error creating BiomobyScavenger for > > http://moby.ucalgary.ca/moby/MOBY-Central.pl > > org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could > > not create the Datatype ontology node: Error creating Datatype tree: null > > [snip] > > > Should this be a temp problem or is it something going wrong here ? > > Which version of Taverna are you running? If it is 1.7, does it happen > when the activity palette or the old service panel is showing? its a fresh downloaded 1.7 - and it happens while starting the application. It loads all scavenger but BioMoby best andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Mon Jan 14 08:08:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 14:08:56 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B5B68.1070202@cs.man.ac.uk> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> Message-ID: <200801141408.57057.groscurt@mpiz-koeln.mpg.de> ah sorry... its the old service panel... the default one which appears when taverna starts On Monday 14 January 2008 13:54, Alan Williams wrote: > Andreas Groscurth wrote: > > Hiho, > > Hello, > > > I cannot load MobyCentral into Taverna: > > Error creating BiomobyScavenger for > > http://moby.ucalgary.ca/moby/MOBY-Central.pl > > org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could > > not create the Datatype ontology node: Error creating Datatype tree: null > > [snip] > > > Should this be a temp problem or is it something going wrong here ? > > Which version of Taverna are you running? If it is 1.7, does it happen > when the activity palette or the old service panel is showing? > > > merci > > andreas > > Alan > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From alanrw at cs.man.ac.uk Mon Jan 14 08:31:35 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Mon, 14 Jan 2008 13:31:35 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <200801141408.57057.groscurt@mpiz-koeln.mpg.de> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> <200801141408.57057.groscurt@mpiz-koeln.mpg.de> Message-ID: <478B6437.1050005@cs.man.ac.uk> Andreas Groscurth wrote: > ah sorry... its the old service panel... the default one which appears when > taverna starts I've checked and I get the same error. I've forwarded your message to Tom Oinn who's wearing the Taverna Support Hat this week. Alan From meredith at cantab.net Mon Jan 14 08:54:42 2008 From: meredith at cantab.net (Tom Oinn) Date: Mon, 14 Jan 2008 13:54:42 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B6437.1050005@cs.man.ac.uk> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> <200801141408.57057.groscurt@mpiz-koeln.mpg.de> <478B6437.1050005@cs.man.ac.uk> Message-ID: <478B69A2.50802@cantab.net> Alan Williams wrote: > Andreas Groscurth wrote: >> ah sorry... its the old service panel... the default one which appears >> when taverna starts > > I've checked and I get the same error. I've forwarded your message to > Tom Oinn who's wearing the Taverna Support Hat this week. Sounds like a problem with the moby code that builds the object tree? It's a bit hard for me to debug seeing as this is code written by the moby guys... Looks like it's done when loading the default scavengers, so maybe the scavenger you've got set is wrong or out of date? Tom From ssoiland at cs.man.ac.uk Mon Jan 14 09:06:44 2008 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Mon, 14 Jan 2008 14:06:44 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B69A2.50802@cantab.net> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> <200801141408.57057.groscurt@mpiz-koeln.mpg.de> <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> Message-ID: <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> On Jan 14, 2008 1:54 PM, Tom Oinn wrote: > Sounds like a problem with the moby code that builds the object tree? > It's a bit hard for me to debug seeing as this is code written by the > moby guys... Looks like it's done when loading the default scavengers, > so maybe the scavenger you've got set is wrong or out of date? No, it's something changed in the data.. the line that fails with a NullPointerException is: fillSubTree(root, hashmap.get("Object").getChildren(), hashmap, REGISTRY_URL); by debugging and inspecting I find that the keys are more like http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/Object - so that if I replace the above line to use that it works, except that the scavenger tree below "Object" will now be with full URLs such as http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/AlignedSequences This seems to be correct corresponding to http58.47.47moby46ucalgary46ca47moby47MOBY45Central46pl/datatype_rdf/DATATYPES.rdf in my moby-cache directory. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From groscurt at mpiz-koeln.mpg.de Mon Jan 14 09:37:06 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 15:37:06 +0100 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <478B69A2.50802@cantab.net> References: <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> Message-ID: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> is not reachable since this morning german time... ?! best andas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From markw at illuminae.com Mon Jan 14 10:05:45 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 14 Jan 2008 07:05:45 -0800 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> References: <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> <200801141537.06989.groscurt@mpiz-koeln.mpg.de> Message-ID: the Open-Bio server went down. It's back up again now M On Mon, 14 Jan 2008 06:37:06 -0800, Andreas Groscurth wrote: > is not reachable since this morning german time... > > ?! > > best > andas > From edward.kawas at gmail.com Mon Jan 14 10:11:52 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 14 Jan 2008 07:11:52 -0800 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de><478B5B68.1070202@cs.man.ac.uk><200801141408.57057.groscurt@mpiz-koeln.mpg.de><478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> Message-ID: <4BB3042E8A6240E7B2818D940C9BB2C1@OfficePC> If you try now, it should work. Before trying, make sure to delete the .taverna-1.7.0/moby-cache/ directory first though. Let me know if you still encounter problems. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland Sent: January-14-08 6:07 AM To: tmo at ebi.ac.uk; Core developer announcements Subject: Re: [MOBY-dev] Error while loading Moby into Taverna On Jan 14, 2008 1:54 PM, Tom Oinn wrote: > Sounds like a problem with the moby code that builds the object tree? > It's a bit hard for me to debug seeing as this is code written by the > moby guys... Looks like it's done when loading the default scavengers, > so maybe the scavenger you've got set is wrong or out of date? No, it's something changed in the data.. the line that fails with a NullPointerException is: fillSubTree(root, hashmap.get("Object").getChildren(), hashmap, REGISTRY_URL); by debugging and inspecting I find that the keys are more like http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/Object - so that if I replace the above line to use that it works, except that the scavenger tree below "Object" will now be with full URLs such as http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/AlignedSequences This seems to be correct corresponding to http58.47.47moby46ucalgary46ca47moby47MOBY45Central46pl/datatype_rdf/DATATYP ES.rdf in my moby-cache directory. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Mon Jan 14 10:16:27 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 14 Jan 2008 16:16:27 +0100 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> References: <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> <200801141537.06989.groscurt@mpiz-koeln.mpg.de> Message-ID: It's fine overhere (now)... Cheers, Pi On 14-jan-2008, at 15:37, Andreas Groscurth wrote: > is not reachable since this morning german time... > > ?! > > best > andas > > -- > Andreas Groscurth > Bioinformatics Developer > 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)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From groscurt at mpiz-koeln.mpg.de Mon Jan 14 10:28:00 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 16:28:00 +0100 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> References: <478B69A2.50802@cantab.net> <200801141537.06989.groscurt@mpiz-koeln.mpg.de> Message-ID: <200801141628.01054.groscurt@mpiz-koeln.mpg.de> its a conspiracy... after sending the mail... i could connect... to my defense... some people in France also had the problem andreas On Monday 14 January 2008 15:37, Andreas Groscurth wrote: > is not reachable since this morning german time... > > ?! > > best > andas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From dmitry.repchevski at bsc.es Mon Jan 14 13:04:02 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 14 Jan 2008 19:04:02 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). Message-ID: <478BA412.60809@bsc.es> Hello everybody! Two months ago I posted a Moby API developed here is Spain and still have no any opinion about it. Please take a look into http://inb.bsc.es/java/index.html Regards, Dmitry From groscurt at mpiz-koeln.mpg.de Tue Jan 15 03:05:20 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 15 Jan 2008 09:05:20 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <4BB3042E8A6240E7B2818D940C9BB2C1@OfficePC> References: <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> <4BB3042E8A6240E7B2818D940C9BB2C1@OfficePC> Message-ID: <200801150905.20810.groscurt@mpiz-koeln.mpg.de> works fine... thanks On Monday 14 January 2008 16:11, Edward Kawas wrote: > If you try now, it should work. > > Before trying, make sure to delete the .taverna-1.7.0/moby-cache/ directory > first though. > > Let me know if you still encounter problems. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland > Sent: January-14-08 6:07 AM > To: tmo at ebi.ac.uk; Core developer announcements > Subject: Re: [MOBY-dev] Error while loading Moby into Taverna > > On Jan 14, 2008 1:54 PM, Tom Oinn wrote: > > Sounds like a problem with the moby code that builds the object tree? > > It's a bit hard for me to debug seeing as this is code written by the > > moby guys... Looks like it's done when loading the default scavengers, > > so maybe the scavenger you've got set is wrong or out of date? > > No, it's something changed in the data.. the line that fails with a > NullPointerException is: > > fillSubTree(root, > hashmap.get("Object").getChildren(), hashmap, > REGISTRY_URL); > > by debugging and inspecting I find that the keys are more like > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/Object - so that if I > replace the above line to use that it works, except that the scavenger > tree below "Object" will now be with full URLs such as > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/AlignedSequences > > This seems to be correct corresponding to > http58.47.47moby46ucalgary46ca47moby47MOBY45Central46pl/datatype_rdf/DATATY >P ES.rdf > in my moby-cache directory. -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Tue Jan 15 06:38:28 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 15 Jan 2008 12:38:28 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478BA412.60809@bsc.es> References: <478BA412.60809@bsc.es> Message-ID: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> Hi Dimitry, The reason you hadn't heard from me yet, is that I'm Perl programmer and I'm not very fluent in Java (yet). With regard to the "bug in PERL Moby API (not sure about JMoby...) when it rejects "non-moby" prefixes, which is definitly goes against XML specification where prefix is defined as an alias for a namespace" I absolutely agree that this ugly. As far as I know the XML::LibXML library that shouldn't be necessary though, so I'll have look if it's fixable... Cheers, Pi On 14 Jan 2008, at 19:04, Dmitry Repchevsky wrote: > Hello everybody! > > Two months ago I posted a Moby API developed here is Spain and > still have no any opinion about it. > Please take a look into http://inb.bsc.es/java/index.html > > Regards, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From dmitry.repchevski at bsc.es Tue Jan 15 07:43:02 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 15 Jan 2008 13:43:02 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> Message-ID: <478CAA56.20300@bsc.es> > I'm Perl programmer and I'm not very fluent in Java (yet). Yeah, I have the same problem I'm a Java programmer and illiterate in Perl (forever :D). As far as I saw/guess Perl uses XSL template to transform a Moby message and it fails... Cheers, Dmitry From edward.kawas at gmail.com Tue Jan 15 09:29:55 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Jan 2008 06:29:55 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478CAA56.20300@bsc.es> References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> <478CAA56.20300@bsc.es> Message-ID: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Glancing over the module MOBY::Central, I cant seem to find a place where the prefix 'moby' is hard coded. Do you have an example call where you know that is the case? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-15-08 4:43 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). > I'm Perl programmer and I'm not very fluent in Java (yet). Yeah, I have the same problem I'm a Java programmer and illiterate in Perl (forever :D). As far as I saw/guess Perl uses XSL template to transform a Moby message and it fails... Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Tue Jan 15 10:09:57 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 15 Jan 2008 16:09:57 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> <478CAA56.20300@bsc.es> <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Message-ID: Hi, Dimitry mentions an XSL template to transform a Moby message... Sounds to me like the alternative libs to parse large pieces of XML. As far as I know the older/original/default BioMoby Perl libs don't use XSLs to transform XML or do they? Cheers, Pi On 15-jan-2008, at 15:29, Edward Kawas wrote: > Glancing over the module MOBY::Central, I cant seem to find a place > where > the prefix 'moby' is hard coded. Do you have an example call where > you know > that is the case? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry > Repchevsky > Sent: January-15-08 4:43 AM > To: moby-dev at lists.open-bio.org > Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). > >> I'm Perl programmer and I'm not very fluent in Java (yet). > > Yeah, I have the same problem I'm a Java programmer and illiterate in > Perl (forever :D). > As far as I saw/guess Perl uses XSL template to transform a Moby > message > and it fails... > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From dmitry.repchevski at bsc.es Tue Jan 15 10:11:49 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 15 Jan 2008 16:11:49 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> References: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Message-ID: <478CCD35.5080600@bsc.es> Hello Edward, Here is the Moby message without "moby" prefix: ************************************************ ************************************************ it gives me: ************************************************ soap:Server Undefined namespace prefix xmlXPathCompiledEval: evaluation failed ************************************************ The XSLT transformation was my guess (looking into parseMobyMessage.xsl file in Perl directory)... Cheers; Dmitry From edward.kawas at gmail.com Tue Jan 15 10:12:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Jan 2008 07:12:41 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl><478CAA56.20300@bsc.es> <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Message-ID: <45D5E527185D4CBFBCA47560BFBA9161@OfficePC> No they don't. There is a template in the library somewhere, but as far as I know, it isn't used at all. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: January-15-08 7:10 AM To: Core developer announcements Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). Hi, Dimitry mentions an XSL template to transform a Moby message... Sounds to me like the alternative libs to parse large pieces of XML. As far as I know the older/original/default BioMoby Perl libs don't use XSLs to transform XML or do they? Cheers, Pi On 15-jan-2008, at 15:29, Edward Kawas wrote: > Glancing over the module MOBY::Central, I cant seem to find a place > where > the prefix 'moby' is hard coded. Do you have an example call where > you know > that is the case? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry > Repchevsky > Sent: January-15-08 4:43 AM > To: moby-dev at lists.open-bio.org > Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). > >> I'm Perl programmer and I'm not very fluent in Java (yet). > > Yeah, I have the same problem I'm a Java programmer and illiterate in > Perl (forever :D). > As far as I saw/guess Perl uses XSL template to transform a Moby > message > and it fails... > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Jan 15 10:14:58 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Jan 2008 07:14:58 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478CCD35.5080600@bsc.es> References: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> <478CCD35.5080600@bsc.es> Message-ID: <781E110FCF014865A11AD2A0168E3418@OfficePC> So it's the message sent to services. I think the problem then is the common subs module, because I believe that it looks for prefixes. As an aside, the perl moses services should not have this problem. I will look into common subs and see if I can make a module that uses LibXML. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-15-08 7:12 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). Hello Edward, Here is the Moby message without "moby" prefix: ************************************************ ************************************************ it gives me: ************************************************ soap:Server Undefined namespace prefix xmlXPathCompiledEval: evaluation failed ************************************************ The XSLT transformation was my guess (looking into parseMobyMessage.xsl file in Perl directory)... Cheers; Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Tue Jan 15 17:41:24 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 15 Jan 2008 15:41:24 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478BA412.60809@bsc.es> References: <478BA412.60809@bsc.es> Message-ID: <478D3694.5050004@ucalgary.ca> Hi Dmitry, At a conceptual level, it makes sense to be able to use a standard WS framework to access Moby Central and services. After all, that's why we decided to use SOAP in the first place, wasn't it? Currently from my side, Seahawk and MobyServlet need Axis because MobyRequest uses Axis. I actually made a version of MobyRequest that uses javax.xml.ws* instead, but haven't committed it because the update to Java version 6 is going to be a major pain on jMOBY. Version 5 and version 6 don't like to live together in jMOBY (for a long list of reasons I won't get into here), so we'll need to start a new branch if we wanted to start using Java 6 in jMOBY. I'd also suggest that even with your own marshalling/unmarshalling, you could easily reuse the existing API classes for data instances that users are familiar with... Regards, Paul Dmitry Repchevsky wrote: > Hello everybody! > > Two months ago I posted a Moby API developed here is Spain and still > have no any opinion about it. > Please take a look into http://inb.bsc.es/java/index.html > > Regards, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478ba926109502617632743! > > > From dmitry.repchevski at bsc.es Wed Jan 16 06:44:53 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 12:44:53 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478D3694.5050004@ucalgary.ca> References: <478D3694.5050004@ucalgary.ca> Message-ID: <478DEE35.9000509@bsc.es> Hello Paul, Thank you for giving your opinion. I appreciate it and have some comments/questions > I actually made a version of MobyRequest that uses javax.xml.ws* So how you handle famous "soap-encoding"? I mean that Axis 1.x is the only API which handle Moby on a server side so far. As I commented in various occasions Moby clients ignore WSDL file and name parameters differently. Another JAX-RPC API (SUN, JBoss) failed with Moby requests. > Version 5 and version 6 don't like to live together in jMOBY Actually JAX-WS can be installed apart to use with JDK5. JEE5 specification uses JDK5, but makes JAX-WS obligatory. If fact this is what I'm doing using JBoss 4.2.2 (JDK5 + JBoss-WS/JAXB). > I'd also suggest that even with your own > marshalling/unmarshalling, you could easily reuse the existing API > classes for data instances that users are familiar with... I think I didn't explain in well. There is no "my own marshalling/unmarshalling". The generated classes are the JAXB annotated Java classes. There is no "marshalling/unmarshalling" in these classes. On the over side MoSeS generated datatype classes explicitly contain marshalling method ("public org.jdom.Element toXML()") which makes them jdom dependant. Moreover, standard Java webservices architecture JAX-WS (used in JDK6/JEE) uses JAXB to parse webservices parameters, so once you wish to go further and use STANDARD webservices in Java (not soap-encoding) you are doomed to use JAXB o stick with parsing it yourself forever. By now Moby is using the latter case (I don't try to explain you the obvious, but to clarify my vision), so all webservices looks like: String runSomeService(String mobyXML); // all the parsing is done manually inside the service. Now let's think: MobyMessage runSomeService(MobyMessage request); // here the parsing is done through the JAX-WS My vision is that all Moby Datatypes must have a schema representation. My generated classes being completely Moby compatible are in fact JAXB classes, so one can easy obtain the schema through schemagen. WSDL 2.0 has support for ontologies using RDF for ontology hierarchy and XML Schema for the format description. I am pretty sure that some of the next JAX-WS (maybe JEE7) will support it The JAXB generated classes has the same hierarchy structure as MoSeS ones (both generated from the same ontology). Let's look into example: ****************************************** JAXB version ******************************************** @XmlRootElement(name="AnnotatedDomain") @XmlType(name="AnnotatedDomain") public class AnnotatedDomain extends Domain { public List getBasicAnnotation() { return getAttributes("basicAnnotation"); } public void addBasicAnnotation(BasicAnnotation basicAnnotation) { putAttribute("basicAnnotation", basicAnnotation); } } ****************************************** MoSeS version ******************************************* public class AnnotatedDomain extends Domain { private static final String DATA_TYPE_NAME = "AnnotatedDomain"; public static final String ARTICLE_NAME_BASICANNOTATION = "BasicAnnotation"; protected java.util.Vector BasicAnnotation = new java.util.Vector(); public void set_BasicAnnotation (BasicAnnotation value) { // add an article name if (value != null) value.setName (ARTICLE_NAME_BASICANNOTATION); this.BasicAnnotation.addElement (value); } public void set_BasicAnnotation (BasicAnnotation[] value) { this.BasicAnnotation = new java.util.Vector(); for (int i = 0; i < value.length; i++) set_BasicAnnotation (value[i]); } public BasicAnnotation[] getMoby_BasicAnnotation() { BasicAnnotation[] result_I_am_sorry_that_this_produces_a_warning = new BasicAnnotation [ BasicAnnotation.size() ]; BasicAnnotation.copyInto (result_I_am_sorry_that_this_produces_a_warning); return result_I_am_sorry_that_this_produces_a_warning; } public int size_BasicAnnotation() { return BasicAnnotation.size(); } 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); for (java.util.Enumeration en = BasicAnnotation.elements(); en.hasMoreElements(); ) elem_I_am_sorry_that_this_produces_a_warning.addContent ( ((BasicAnnotation)en.nextElement()).toXML() ); return elem_I_am_sorry_that_this_produces_a_warning; } public String toString() { StringBuffer buf_I_am_sorry_that_this_produces_a_warning = new StringBuffer(); buf_I_am_sorry_that_this_produces_a_warning.append (super.toString()); for (java.util.Enumeration en = BasicAnnotation.elements(); en.hasMoreElements(); ) buf_I_am_sorry_that_this_produces_a_warning.append ( ((BasicAnnotation)en.nextElement()).format (1) ); return new String (buf_I_am_sorry_that_this_produces_a_warning); } } *********************************************************************************************************** As you can see the difference is: 1) >private static final String DATA_TYPE_NAME = "AnnotatedDomain"; @XmlRootElement(name="AnnotatedDomain") @XmlType(name="AnnotatedDomain") 2) >public void set_BasicAnnotation (BasicAnnotation value) public void addBasicAnnotation(BasicAnnotation basicAnnotation) 3) >public BasicAnnotation[] getMoby_BasicAnnotation() public List getBasicAnnotation() 4) >public void set_BasicAnnotation (BasicAnnotation[] value) // NOT IMPLEMENTED 5) >public org.jdom.Element toXML() // NO NEED TO IMPLEMENT 6) >public String toString() // IMLEMENTED IN THE TOP_LEVEL CLASS As you can see there is almost no difference in both classes. Using List instead of an array - gives a possibility to add BasicAnnotation in it. Slightly different get/set method names. Appreciate any further comments. Dmitry From gordonp at ucalgary.ca Wed Jan 16 09:53:45 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 07:53:45 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478DEE35.9000509@bsc.es> References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> Message-ID: <478E1A79.2020806@ucalgary.ca> > So how you handle famous "soap-encoding"? > I mean that Axis 1.x is the only API which handle Moby on a server > side so far. > As I commented in various occasions Moby clients ignore WSDL file and > name parameters differently. > Another JAX-RPC API (SUN, JBoss) failed with Moby requests. I create the "data" tag manually in the SOAPMesssage. Only takes a couple of lines, the rest is standard use of Service and Dispatch. >> Version 5 and version 6 don't like to live together in jMOBY > Actually JAX-WS can be installed apart to use with JDK5. > JEE5 specification uses JDK5, but makes JAX-WS obligatory. If fact > this is what I'm doing using JBoss 4.2.2 (JDK5 + JBoss-WS/JAXB). I know, but I can't create the data tag using a QName with the version of JAX-WS on the Sun Web site. The Java SE6 version allows me to (this is needed to declare the xsd namespace, since createName does not stupidly allow manual declarations in the xmlns namespace). It's funny how javax.xml.ws doesn't work the same in both versions...if you can figure out how to declare a namespace manually in a SOAPMessage without QName, let me know! >> I'd also suggest that even with your own marshalling/unmarshalling, >> you could easily reuse the existing API classes for data instances >> that users are familiar with... > I think I didn't explain in well. There is no "my own > marshalling/unmarshalling". The generated classes are the JAXB > annotated Java classes. Okay, but when you work without the data types, JAXB creates an AnyMobyObject? Or how does that get created? Could it use the org.biomoby.shared.data classes instead? Sorry, I'm not familiar with how that datatype-less way works... > > My vision is that all Moby Datatypes must have a schema representation. As far as I can recall, this is not possible (others can correct me if I'm wrong, or these have been solved) . The main sticking points were that if an object is a Moby Primitive in a has relationship, it cannot be represented in XML schema. Also, I think that the fact that we must be able to accept subclasses of declared classes, even if we don't know about them, causes another problem. > My generated classes being completely Moby compatible are in fact JAXB > classes, so one can easy obtain the schema through schemagen. > The JAXB generated classes has the same hierarchy structure as MoSeS > ones (both generated from the same ontology). I don't actually use MoSeS, so I don't have much to add here. The generator code is Martin's domain of expertise, so I'll let him comment on that if he likes. :-) Regards, Paul From dmitry.repchevski at bsc.es Wed Jan 16 10:57:20 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 16:57:20 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E1A79.2020806@ucalgary.ca> References: <478E1A79.2020806@ucalgary.ca> Message-ID: <478E2960.7090902@bsc.es> Hello, I will try to answer the questions as deep as I can. > I know, but I can't create the data tag using a QName with the version > of JAX-WS on the Sun Web site. The Java SE6 version allows me to (this > is needed to declare the xsd namespace, since createName does not > stupidly allow manual declarations in the xmlns namespace). It's funny > how javax.xml.ws doesn't work the same in both versions...if you can > figure out how to declare a namespace manually in a SOAPMessage without > QName, let me know! I use the same method!!! Look into AbstractMobyEndpoint.createSoapMessage(). ********************************** env.addNamespaceDeclaration("xsd", "http://www.w3.org/2001/XMLSchema"); ********************************** is this what you mean? > Okay, but when you work without the data types, JAXB creates an > AnyMobyObject? Exactly. When JAXB can not find appropriate datatype it passes it as an Element (look into MobySimple.setJaxbObject()). So I marshall/unmarshall it into AnyMobyObject. This way you can use same API to work both with AnyMobyObject or datatypes objects (and can mix it). ALL the data stored in top-level class (MobyObject) so you can work with it without using get/set methods. This way "datatypes" are only getters/setters for the "attributes". you can either call List list = annotatedDomain.getBasicAnnotation(); or List list = mobyObject.getAttributes("basicAnnotation"); in latter case list would contain BasicAnnotation or AnyMobyObject depending if datatype was found by jaxb. For example in demo application I make drag and drop of OBJECTS (from right panel). If you put datatypes.jar in CLASSPATH so actual object will be the "real" one (for example PDB_Text), if not - it will be "AnyMobyObject". > >/ My vision is that all Moby Datatypes must have a schema representation. > /As far as I can recall, this is not possible (others can correct me if > I'm wrong, or these have been solved) . Well since JAXB MUST generate schema from valid JAXB classes... Another thing is how good the schema would be (I'm not the greatest schema specialist :-)) Just look into the schema for the AnnotatedDomain class: ******************* ******************* > The main sticking points were > that if an object is a Moby Primitive in a has relationship, it cannot > be represented in XML schema. Don't get this one... ? > Also, I think that the fact that we must > be able to accept subclasses of declared classes, even if we don't know > about them, causes another problem. JAXB can do it... It's called type substitution. I don't like the way it works... I my case it substituted by AnyMobyObject. Technically it's possible to implement some heuristic BEFORE parsing to it. I could look into known objects (To have this information I implemented a custom classloader for Jaxb loaded classes) and if there is some that matches by parameters... not sure how to do it yet... Regards, Dmitry From markw at illuminae.com Wed Jan 16 11:00:31 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Jan 2008 08:00:31 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E1A79.2020806@ucalgary.ca> References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: >> My vision is that all Moby Datatypes must have a schema representation. > As far as I can recall, this is not possible You are correct, Paul. It is not possible to define the structure of MOBY Objects in XML schema (for some of the same reasons that it is impossible to define RDF-XML documents in XML Schema) There's a belief "out there" that all XML documents can be represented in XML schema, and I've been attacked by audience members during presentations and workshops when I say this isn't true... but it isn't true!! The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML can be "defined by" an OWL ontology (please don't attack me for saying it that way - I KNOW that this is backwards from the way OWL and RDF actually work!). The resulting flexibility in document structure cannot be handled by XML Schema. It sucks for us, since we want to use WSDL... but it's a painful reality. Mark From markw at illuminae.com Wed Jan 16 11:07:29 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Jan 2008 08:07:29 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: ...unless there has been some new changes in XML Schema that I missed! I admit I haven't looked at it since my conversation with a guy from the W3C XML Schema working group, who confirmed to me that, in his opinion, it couldn't be done... I took that as "the word of God" at the time, but that was probably two years ago, maybe longer... Mark On Wed, 16 Jan 2008 08:00:31 -0800, Mark Wilkinson wrote: > >>> My vision is that all Moby Datatypes must have a schema representation. >> As far as I can recall, this is not possible > > > You are correct, Paul. It is not possible to define the structure of > MOBY Objects in XML schema (for some of the same reasons that it is > impossible to define RDF-XML documents in XML Schema) > > There's a belief "out there" that all XML documents can be represented > in XML schema, and I've been attacked by audience members during > presentations and workshops when I say this isn't true... but it isn't > true!! > > The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML > can be "defined by" an OWL ontology (please don't attack me for saying > it that way - I KNOW that this is backwards from the way OWL and RDF > actually work!). The resulting flexibility in document structure cannot > be handled by XML Schema. > > It sucks for us, since we want to use WSDL... but it's a painful reality. > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Jan 16 11:16:33 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 09:16:33 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: <478E2DE1.1020605@ucalgary.ca> As I see it, it would be nice to use standard WSDL stuff as much as possible, but we will always need to do some manipulation in the standard stack because you simply can't express everything we need in XML Schema. That's what Dmitry's running into. That being said, getting rid of Axis would be great, and doable now that Eddie defined a WSDL for Moby Central (which Dmitry's using). I'd like to see an implementation of the Central interface that doesn't use Axis, for purely selfish reasons...it adds a lot of weight to the Seahawk applet :-) Also, I get funny ClassFormatErrors when trying to use Axis in Java SE6 (version 6 is much more pedantic about class file structure), but that could be overcome I suppose by recompiling the Axis from source... Mark Wilkinson wrote: > >>> My vision is that all Moby Datatypes must have a schema representation. >> As far as I can recall, this is not possible > > > You are correct, Paul. It is not possible to define the structure of > MOBY Objects in XML schema (for some of the same reasons that it is > impossible to define RDF-XML documents in XML Schema) > > There's a belief "out there" that all XML documents can be represented > in XML schema, and I've been attacked by audience members during > presentations and workshops when I say this isn't true... but it isn't > true!! > > The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML > can be "defined by" an OWL ontology (please don't attack me for saying > it that way - I KNOW that this is backwards from the way OWL and RDF > actually work!). The resulting flexibility in document structure > cannot be handled by XML Schema. > > It sucks for us, since we want to use WSDL... but it's a painful reality. > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478e2823109501033230397! > > > From dmitry.repchevski at bsc.es Wed Jan 16 11:45:52 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 17:45:52 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: Message-ID: <478E34C0.3060504@bsc.es> Hello Mark, I understand what you say. For ANY valid XML document appropriate schema CAN be generated... But it doesn't mean that you can generate a schema that match a different set of XMLs. Well, maybe you can, but the schema itself could be unusable... > The resulting flexibility in document structure cannot be handled > by XML Schema. Well the schema is not good in defining relationships, but it's definitely possible. > It sucks for us, since we want to use WSDL... but it's a painful reality. I'm not sure... I'm looking to it from Java point of view... lets say we have C extends B extends A. If we pass B as a parameter to the webservice two things happens. We would have Schemas for B/A in WSDL and Java method that accepts B. Something like call(B b). Now imagine JAXB got "C" it's unknown to it so it can't parse it (it CAN parse it if we implicitly add it into the JAXBContext), so we need to know it A PRIORY. It is can be done by regenerating all the classes while creating the context (takes a lot of time). I discussed this in forums and the problem is that you can't change the context once it is created. by now they proposed an ugly (IMHO) hack with @SeeAlso annotation when you can accept B, but tell JAXB that there is also a "C" to take into account... again it doesn't help too much. Fortunately (!) in WSDL 2 it's possible to mix RDF with XML Schema - XML Schema specify the data format and RDF a relationship, so (as far as I understand) it should work automatically - when you find something that you don't understand - you look into the RDF to find a substitute... I know AXIS 2.0 claims to support it, but I always prefer JCP specifications (somehow those are that goes into JEE). Best regards, Dmitry From dmitry.repchevski at bsc.es Wed Jan 16 11:56:16 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 17:56:16 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E2DE1.1020605@ucalgary.ca> References: <478E2DE1.1020605@ucalgary.ca> Message-ID: <478E3730.8050708@bsc.es> Hello Paul > As I see it, it would be nice to use standard WSDL stuff as much as > possible, but we will always need to do some manipulation in the > standard stack because you simply can't express everything we need in > XML Schema. Well this is definitly not the case for the registry... Just look into the MobyRegisty API (http://inb.bsc.es/java/moby_registry.html) The only hack I'm using is the soap-encoding (MobyCore) - the rest are plain JAXB classes. By the way, could we start migrating to the document encoding from the Moby Central? ;-) I think it would be not such a pain as with Moby Services? Regards, Dmitry From markw at illuminae.com Wed Jan 16 11:59:16 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Jan 2008 08:59:16 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3730.8050708@bsc.es> References: <478E2DE1.1020605@ucalgary.ca> <478E3730.8050708@bsc.es> Message-ID: On Wed, 16 Jan 2008 08:56:16 -0800, Dmitry Repchevsky wrote: > By the way, could we start migrating to the document encoding from the > Moby Central? ;-) I think it would be not such a pain as with Moby > Services? I have just hired Jason Stewart as a private subcontractor to do the necessary code updates to SOAP::Lite that will allow this migration to happen. Hopefully by next month we'll be able to handle document-encoded messages in SOAP::Lite. This has been the limitation so far... Mark From jmfernandez at cnio.es Wed Jan 16 11:51:40 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Wed, 16 Jan 2008 17:51:40 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: <478E361C.80008@cnio.es> Hi everybody, although you cannot have an XML schema for MOBY messaging taking into account the whole ontology (unless you regenerate it each time the ontology is changed), you can create an XML schema which at least can be used to validate the fixed part of MOBY messages, using xsd:any in those places where you can put a MOBY object. Some years ago I wrote such schema, but I never checked it... Perhaps it can be useful for someone, so I'm including it in this message. Best Regards, Jos? Mar?a Mark Wilkinson wrote: > ...unless there has been some new changes in XML Schema that I missed! > I admit I haven't looked at it since my conversation with a guy from the > W3C XML Schema working group, who confirmed to me that, in his opinion, > it couldn't be done... I took that as "the word of God" at the time, but > that was probably two years ago, maybe longer... > > Mark > > > > On Wed, 16 Jan 2008 08:00:31 -0800, Mark Wilkinson > wrote: > >> >>>> My vision is that all Moby Datatypes must have a schema representation. >>> As far as I can recall, this is not possible >> >> >> You are correct, Paul. It is not possible to define the structure of >> MOBY Objects in XML schema (for some of the same reasons that it is >> impossible to define RDF-XML documents in XML Schema) >> >> There's a belief "out there" that all XML documents can be represented >> in XML schema, and I've been attacked by audience members during >> presentations and workshops when I say this isn't true... but it isn't >> true!! >> >> The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML >> can be "defined by" an OWL ontology (please don't attack me for saying >> it that way - I KNOW that this is backwards from the way OWL and RDF >> actually work!). The resulting flexibility in document structure >> cannot be handled by XML Schema. >> >> It sucks for us, since we want to use WSDL... but it's a painful reality. >> >> Mark >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: mobyServicesSchema.xsd Type: text/xml Size: 4738 bytes Desc: not available URL: From dmitry.repchevski at bsc.es Wed Jan 16 12:14:00 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 18:14:00 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: Message-ID: <478E3B58.9080403@bsc.es> > > Hopefully by next month we'll be able to handle document-encoded > messages in SOAP::Lite. This has been the limitation so far... So finally we would be able to do something like this? @WebMethod MobyMessage runXXXService(MobyMessage message); :-) As Jos? Mar?a pointed out: > although you cannot have an XML schema for MOBY messaging taking into account > the whole ontology (unless you regenerate it each time the ontology is > changed), you can create an XML schema which at least can be used to validate > the fixed part of MOBY messages, using xsd:any in those places where you can > put a MOBY object. This is exactly what I have done with MobyCore (but being more fluent with Java than XML using JAXB directly). in schema it looks like: while in java code: @XmlAnyElement(lax = true) Cheers, Dmitry From gordonp at ucalgary.ca Wed Jan 16 12:18:39 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 10:18:39 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3730.8050708@bsc.es> References: <478E2DE1.1020605@ucalgary.ca> <478E3730.8050708@bsc.es> Message-ID: <478E3C6F.3050809@ucalgary.ca> >> As I see it, it would be nice to use standard WSDL stuff as much as >> possible, but we will always need to do some manipulation in the >> standard stack because you simply can't express everything we need in >> XML Schema. > Well this is definitly not the case for the registry... That's what I said: Central is okay, it's the service calls that need modifications... By the way, I'm trying to figure out if I can avoid the endorsed lib issue in Java 5 for JAXB 2.1 somehow...that's the only sticking point left for MobyRequest to use JAX-WS in a standard Java 5... From dmitry.repchevski at bsc.es Wed Jan 16 12:25:23 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 18:25:23 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3C6F.3050809@ucalgary.ca> References: <478E3C6F.3050809@ucalgary.ca> Message-ID: <478E3E03.6000403@bsc.es> > > I'm trying to figure out if I can avoid the endorsed lib issue in Java > 5 for JAXB 2.1 somehow Why do you need "endorsed" for Java5? Java5 has no any JAXB implementation in it. Just use it as any other libraries. Dmitry From gordonp at ucalgary.ca Wed Jan 16 12:47:05 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 10:47:05 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3E03.6000403@bsc.es> References: <478E3C6F.3050809@ucalgary.ca> <478E3E03.6000403@bsc.es> Message-ID: <478E4319.1070709@ucalgary.ca> >> I'm trying to figure out if I can avoid the endorsed lib issue in >> Java 5 for JAXB 2.1 somehow > > Why do you need "endorsed" for Java5? Java5 has no any JAXB > implementation in it. Just use it as any other libraries. Ah yes, sorry, I meant Java6. I'm installing update4, which should hopefully avoid the issue I get with update 3: java.lang.LinkageError: JAXB 2.0 API is being loaded from the bootstrap classloader, but this RI (from jar:file:/export/home/gordonp/projects/moby-live/Java/lib/jaxb-impl.jar!/com/sun/xml/bind/v2/model/impl/ModelBuilder.class) needs 2.1 API. Use the endorsed directory mechanism to place jaxb-api.jar in the bootstrap classloader. (See http://java.sun.com/j2se/1.5.0/docs/guide/standards/) From dmitry.repchevski at bsc.es Wed Jan 16 12:56:23 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 18:56:23 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4319.1070709@ucalgary.ca> References: <478E4319.1070709@ucalgary.ca> Message-ID: <478E4547.9090704@bsc.es> > > Ah yes, sorry, I meant Java6. I'm installing update4, which should > hopefully avoid the issue I get with update 3: Yeah, I understand your pain... :-) There is a way - using custom classloader. One of the JAXB developers posted it in his blog. The bad thing that in this case you will have two versions of JAXB loaded... Fortunately we have 6u4 which works just fine (at least in my demo http://inb.bsc.es/java/demo/demo.html :-)). Cheers, Dmitry From gordonp at ucalgary.ca Wed Jan 16 13:04:02 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 11:04:02 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4547.9090704@bsc.es> References: <478E4319.1070709@ucalgary.ca> <478E4547.9090704@bsc.es> Message-ID: <478E4712.5050200@ucalgary.ca> Indeed, update 4 works beautifully for me...I can now go Axis-free in MobyRequest (except for there being no Central implementation without Axis... hint hint). ;-) Dmitry Repchevsky wrote: >> >> Ah yes, sorry, I meant Java6. I'm installing update4, which should >> hopefully avoid the issue I get with update 3: > > Yeah, I understand your pain... :-) > There is a way - using custom classloader. One of the JAXB developers > posted it in his blog. > The bad thing that in this case you will have two versions of JAXB > loaded... > > Fortunately we have 6u4 which works just fine (at least in my demo > http://inb.bsc.es/java/demo/demo.html :-)). > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478e433e10950260988970! > > > From dmitry.repchevski at bsc.es Wed Jan 16 13:18:06 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 19:18:06 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4712.5050200@ucalgary.ca> References: <478E4712.5050200@ucalgary.ca> Message-ID: <478E4A5E.9090103@bsc.es> > > Indeed, update 4 works beautifully for me...I can now go Axis-free in > MobyRequest (except for there being no Central implementation without > Axis... hint hint). ;-) God damn, what you mean by "no Central implementation without Axis"? Java Moby Central implementation? I think Java implementation is abandoned... My MobyRegistry (client for Moby Central) do everything with Moby Central. It implements all operations I found in http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/CentralRegistry.html My demo uses it to find the services... MobyGenerator uses it to obtain the ontology and service descriptions. Can you please be more specific? Dmitry From gordonp at ucalgary.ca Wed Jan 16 13:53:54 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 11:53:54 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4A5E.9090103@bsc.es> References: <478E4712.5050200@ucalgary.ca> <478E4A5E.9090103@bsc.es> Message-ID: <478E52C2.3060407@ucalgary.ca> Sorry, I meant something implementing org.biomoby.shared.Central, since things are much easier to be adopted if they use the existing jMoby interface definitions. There's no one class bringing all the operations together from org.biomoby.shared.jaxb.registry is there, or am I missing something obvious? > Java Moby Central implementation? I think Java implementation is > abandoned... > My MobyRegistry (client for Moby Central) do everything with Moby > Central. It implements all operations I found in > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/CentralRegistry.html > > > My demo uses it to find the services... MobyGenerator uses it to > obtain the ontology and service descriptions. > > Can you please be more specific? > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478e4856109504651529! > > > From dmitry.repchevski at bsc.es Wed Jan 16 14:23:05 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 20:23:05 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E52C2.3060407@ucalgary.ca> References: <478E52C2.3060407@ucalgary.ca> Message-ID: <478E5999.4010809@bsc.es> > > Sorry, I meant something implementing org.biomoby.shared.Central, since > things are much easier to be adopted if they use the existing jMoby > interface definitions. There's no one class bringing all the operations > together from org.biomoby.shared.jaxb.registry is there, or am I missing > something obvious? Yeah! I understand. You have the point. In MobyRegistry I have es.inb.biomoby.registry.model.CentralDigestFactory with the comment: * Utility class which is not in the main package because it's not clear yet the entire * architecture of the registry package... The problem is that Moby Central contains many objects that are _almost_ identical. Since I am using JAXB classes I had to choose between having several copies or having (if possible) one class shared between operations (messages). The latter is not always possible so to be coherent I encapsulated such objects inside operations (but there are obvious cases like RetrieveResourceURLs.class which is shared). I thought to implement some upper layer API to manage it all (something I done in CentralDigestFactory which is definitely shouldn't be in this jar...) but the question is: Should it be based on JAXB based classes? If yes, which one I have to select (in case I have different for different operations)? If no (which I do not like), I'll finish having even more duplications between JAXB (for XML) and API versions... I think the first way is better - select the JAXB classes (like org.biomoby.shared.jaxb.registry.FindServiceOperation.Services.Service). put it outside the FindServiceOperation in some model package. Next question is the functionality itself... most of the functionality is implemented inside xxxOperation itself. Just look: FindServiceOperation endpoint = new FindServiceOperation("http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl"); FindService request = new FindService("getEntryFromPDB", "inb.bsc.es"); Services response = endpoint.call(request); for (Service service : response.getServices()) { ... I understand in JMoby there is a cache... I always prefer cache + background cache update... In two words I'm open to here your suggestions and ready to implement it. Regards, Dmitry From markw at illuminae.com Mon Jan 21 18:58:29 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 21 Jan 2008 15:58:29 -0800 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC Message-ID: Hi everyone, Has anyone else looked at the INB proposal for mirroring of services? I think it's really nice, personally! I had a couple of small questions and concerns, but it really doesn't seem like an overly disruptive change, and apparently they already have it working at INB, so the codebase to support it already exists. I think we should vote on the issue soon, as the INB folks have been very, VERY patient! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Tue Jan 22 06:00:25 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 22 Jan 2008 12:00:25 +0100 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC In-Reply-To: References: Message-ID: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> Hi, I searched my mail archive and the website, but I can not find this RFC.... Was it that long ago? Anyway, can someone please send us pointer where to find this RFC? Thanks, Pi On 22-jan-2008, at 0:58, Mark Wilkinson wrote: > Hi everyone, > > Has anyone else looked at the INB proposal for mirroring of > services? I think it's really nice, personally! I had a couple of > small questions and concerns, but it really doesn't seem like an > overly disruptive change, and apparently they already have it > working at INB, so the codebase to support it already exists. > > I think we should vote on the issue soon, as the INB folks have > been very, VERY patient! > > M > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Tue Jan 22 09:42:01 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Tue, 22 Jan 2008 15:42:01 +0100 Subject: [MOBY-dev] Test Registry and RDF Message-ID: <479600B9.7000807@toulouse.inra.fr> Bonjour a tous, When I register a Service into the test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), the RDF file that I get as a response is empty (only the root tag is presentin the XML file, no content). Does anyone else have this problem ? Moreover, I do not know if there's a link with this problem, but deregistration in test central is problematic too ... I use the Perl API. Merci, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Tue Jan 22 10:00:21 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 07:00:21 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <479600B9.7000807@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> Message-ID: <4796051b.05358c0a.0df9.ffffd78e@mx.google.com> Hi Sebastien, I am not sure, but perhaps the test registry is using the old codebase and so things might not be working as they should. I will look into it and give you a definitive answer with hopefully everything then working as it should. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-22-08 6:42 AM To: Core developer announcements Subject: [MOBY-dev] Test Registry and RDF Bonjour a tous, When I register a Service into the test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), the RDF file that I get as a response is empty (only the root tag is presentin the XML file, no content). Does anyone else have this problem ? Moreover, I do not know if there's a link with this problem, but deregistration in test central is problematic too ... I use the Perl API. Merci, Sebastien From dmitry.repchevski at bsc.es Tue Jan 22 10:05:36 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 22 Jan 2008 16:05:36 +0100 Subject: [MOBY-dev] documentation error (?) registerServiceType Message-ID: <47960640.1080007@bsc.es> Hello! I found the error (?) in Moby documentation The Registry operation registerServiceType id "defined" as *********************************************** Input XML NewServiceType your_name at contact.address.com your.URI.here ExistingServiceType ExistingServiceType *********************************************** But in the schema (registerServiceType.xsd) the is defined as: *********************************************** *********************************************** So something is wrong here. If schema is ok - the xml should look like: *********************************************** *********************************************** Taking into account the the only type supported is "ISA" (?) that has no much sense... As well as using "articleName" for the parent serviceType. Can someone clarify it tu me, please? Thank you in advance, Dmitry From edward.kawas at gmail.com Tue Jan 22 10:12:55 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 07:12:55 -0800 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960640.1080007@bsc.es> References: <47960640.1080007@bsc.es> Message-ID: <47960810.22578c0a.23c1.0dbd@mx.google.com> The API is correct. I had an error in the schema. I just committed a fix. Thanks for pointing it out. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-22-08 7:06 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] documentation error (?) registerServiceType Hello! I found the error (?) in Moby documentation The Registry operation registerServiceType id "defined" as *********************************************** Input XML NewServiceType your_name at contact.address.com your.URI.here ExistingServiceType ExistingServiceType *********************************************** But in the schema (registerServiceType.xsd) the is defined as: *********************************************** *********************************************** So something is wrong here. If schema is ok - the xml should look like: *********************************************** *********************************************** Taking into account the the only type supported is "ISA" (?) that has no much sense... As well as using "articleName" for the parent serviceType. Can someone clarify it tu me, please? Thank you in advance, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jan 22 10:30:50 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 22 Jan 2008 16:30:50 +0100 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960810.22578c0a.23c1.0dbd@mx.google.com> References: <47960810.22578c0a.23c1.0dbd@mx.google.com> Message-ID: <47960C2A.5090301@bsc.es> Ok, but anyway *************************************** ExistingServiceType ExistingServiceType *************************************** Shouldn't it be relationshipType="ISA" (is it possible to specify anything else?) Cheers, Dmitry From edward.kawas at gmail.com Tue Jan 22 10:33:33 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 07:33:33 -0800 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960C2A.5090301@bsc.es> References: <47960810.22578c0a.23c1.0dbd@mx.google.com> <47960C2A.5090301@bsc.es> Message-ID: <47960ce2.22528c0a.4717.5c12@mx.google.com> It can only be ISA, but I believe that the doc mentions it this way so that in the future, if things were to change and the type could be HAS, HASA, etc it wouldn't be a huge change (I think - Mark will have to either confirm or deny ...) Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-22-08 7:31 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] documentation error (?) registerServiceType Ok, but anyway *************************************** ExistingServiceType ExistingServiceType *************************************** Shouldn't it be relationshipType="ISA" (is it possible to specify anything else?) Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Jan 22 11:29:37 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 22 Jan 2008 08:29:37 -0800 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960ce2.22528c0a.4717.5c12@mx.google.com> References: <47960810.22578c0a.23c1.0dbd@mx.google.com> <47960C2A.5090301@bsc.es> <47960ce2.22528c0a.4717.5c12@mx.google.com> Message-ID: Well... I don't think we were necessarily anticipating "HAS" and "HASA" relationships, but it was left purposely open. There are (at least at the level of the Moby databases) three relationship ontologies - one for Objects, one for Services, and one for Namespaces. So you're right, there is no choice other than ISA, because there is only one term in the Service Relationships ontology - ISA. So in that regard, the documentation is correct - what goes in that space is a Service Relationships Ontology Term :-) The idea was that the ontologies could grow independently of each other to reflect more complexity if it were determined to be necessary. It is necessary... but it has never happened. M On Tue, 22 Jan 2008 07:33:33 -0800, Edward Kawas wrote: > It can only be ISA, but I believe that the doc mentions it this way so > that > in the future, if things were to change and the type could be HAS, HASA, > etc > it wouldn't be a huge change (I think - Mark will have to either confirm > or > deny ...) > > Eddie > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry > Repchevsky > Sent: January-22-08 7:31 AM > To: moby-dev at lists.open-bio.org > Subject: Re: [MOBY-dev] documentation error (?) registerServiceType > > Ok, but anyway > > *************************************** > > > ExistingServiceType > ExistingServiceType > > > *************************************** > > Shouldn't it be relationshipType="ISA" (is it possible to specify > anything else?) > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Jan 22 11:34:16 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 08:34:16 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <479600B9.7000807@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> Message-ID: <47961b1d.0d528c0a.6572.5e28@mx.google.com> Okay, I tracked it down to a configuration problem and have since fixed it (hopefully!). So please try again. If there are any services that you need RDF for that are hosted on the test registry, please go to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will be able to generate RDF for those services. Let me know if things are better, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-22-08 6:42 AM To: Core developer announcements Subject: [MOBY-dev] Test Registry and RDF Bonjour a tous, When I register a Service into the test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), the RDF file that I get as a response is empty (only the root tag is presentin the XML file, no content). Does anyone else have this problem ? Moreover, I do not know if there's a link with this problem, but deregistration in test central is problematic too ... I use the Perl API. Merci, Sebastien From markw at illuminae.com Tue Jan 22 12:12:07 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 22 Jan 2008 09:12:07 -0800 Subject: [MOBY-dev] UC Davis News & Information :: Grant for Workflow Software Message-ID: Interesting... From serr at ac.uma.es Tue Jan 22 13:29:55 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 22 Jan 2008 19:29:55 +0100 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC In-Reply-To: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> References: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> Message-ID: <47963623.7090208@ac.uma.es> Hello to all the mobiers, In this link http://chirimoyo.ac.uma.es/proposals/BioMOBY_Mirroring.pdf you can find the INB proposal for mirroring services. It describes the new functions and the changes needed in the functions that already exist in the API of BioMOBY. The proposal also includes different options for managing the mirrors using RDF files. We would appreciate comments and suggestions, in particular how to deal with the RDF data. We have implemented the described functionality in the MOBYCentral perl code. This code will be made available, and in a few days we will provide a new link with a small tutorial about how to use the client side library. Best regards, Sergio. Pieter Neerincx wrote: > Hi, > > I searched my mail archive and the website, but I can not find this > RFC.... Was it that long ago? Anyway, can someone please send us > pointer where to find this RFC? > > Thanks, > > Pi > > On 22-jan-2008, at 0:58, Mark Wilkinson wrote: > >> Hi everyone, >> >> Has anyone else looked at the INB proposal for mirroring of services? >> I think it's really nice, personally! I had a couple of small >> questions and concerns, but it really doesn't seem like an overly >> disruptive change, and apparently they already have it working at >> INB, so the codebase to support it already exists. >> >> I think we should vote on the issue soon, as the INB folks have been >> very, VERY patient! >> >> M >> >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From Sebastien.Carrere at toulouse.inra.fr Wed Jan 23 04:22:54 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 23 Jan 2008 10:22:54 +0100 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <47961b1d.0d528c0a.6572.5e28@mx.google.com> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> Message-ID: <4797076E.5080100@toulouse.inra.fr> The RDF file seems to be okay now using test registry. However, the deregistering procedure is always problematic: "Failed with status:500 Server closed connection without sending any data back" Sebastien Edward Kawas wrote: > Okay, I tracked it down to a configuration problem and have since fixed it > (hopefully!). So please try again. If there are any services that you need > RDF for that are hosted on the test registry, please go to > http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will be able > to generate RDF for those services. > > Let me know if things are better, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: January-22-08 6:42 AM > To: Core developer announcements > Subject: [MOBY-dev] Test Registry and RDF > > Bonjour a tous, > > > When I register a Service into the test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), > the RDF file that I get as a response is empty (only the root tag is > presentin the XML file, no content). > > Does anyone else have this problem ? > > Moreover, I do not know if there's a link with this problem, but > deregistration in test central is problematic too ... > > I use the Perl API. > > Merci, > > Sebastien > > > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Jan 23 09:52:49 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 23 Jan 2008 06:52:49 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <4797076E.5080100@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> Message-ID: <479754db.05358c0a.0e2a.15c2@mx.google.com> What service are you trying to deregister and how are you trying to do it? If you are trying to use RDF, can you send it to me so I can try? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-23-08 1:23 AM To: Core developer announcements Subject: Re: [MOBY-dev] Test Registry and RDF The RDF file seems to be okay now using test registry. However, the deregistering procedure is always problematic: "Failed with status:500 Server closed connection without sending any data back" Sebastien Edward Kawas wrote: > Okay, I tracked it down to a configuration problem and have since > fixed it (hopefully!). So please try again. If there are any services > that you need RDF for that are hosted on the test registry, please go > to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will > be able to generate RDF for those services. > > Let me know if things are better, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien > Carrere > Sent: January-22-08 6:42 AM > To: Core developer announcements > Subject: [MOBY-dev] Test Registry and RDF > > Bonjour a tous, > > > When I register a Service into the test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), > the RDF file that I get as a response is empty (only the root tag is > presentin the XML file, no content). > > Does anyone else have this problem ? > > Moreover, I do not know if there's a link with this problem, but > deregistration in test central is problematic too ... > > I use the Perl API. > > Merci, > > Sebastien > > > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Sebastien.Carrere at toulouse.inra.fr Wed Jan 23 11:38:34 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 23 Jan 2008 17:38:34 +0100 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <479754db.05358c0a.0e2a.15c2@mx.google.com> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> Message-ID: <47976D8A.70404@toulouse.inra.fr> Bonjour Eddie, I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. I use the registerService procedure from MOBY::Client::Central (v 1.152) with the signature http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmoby/rdf/BlastSwissProt.rdf corresponding to an empty RDF file. What's really strange, is that when I call for the first time the deregistring protocol, the service seems not to be removed from registry. If I try a second time, the service is removed. Nevertheless, the two times I have the timeout message ... Merci, Sebastien Edward Kawas wrote: > What service are you trying to deregister and how are you trying to do it? > > If you are trying to use RDF, can you send it to me so I can try? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: January-23-08 1:23 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > > The RDF file seems to be okay now using test registry. > > However, the deregistering procedure is always problematic: > "Failed with status:500 Server closed connection without sending any data > back" > > Sebastien > > > > Edward Kawas wrote: > >> Okay, I tracked it down to a configuration problem and have since >> fixed it (hopefully!). So please try again. If there are any services >> that you need RDF for that are hosted on the test registry, please go >> to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will >> be able to generate RDF for those services. >> >> Let me know if things are better, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-22-08 6:42 AM >> To: Core developer announcements >> Subject: [MOBY-dev] Test Registry and RDF >> >> Bonjour a tous, >> >> >> When I register a Service into the test registry >> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), >> the RDF file that I get as a response is empty (only the root tag is >> presentin the XML file, no content). >> >> Does anyone else have this problem ? >> >> Moreover, I do not know if there's a link with this problem, but >> deregistration in test central is problematic too ... >> >> I use the Perl API. >> >> Merci, >> >> Sebastien >> >> >> >> >> >> >> >> _______________________________________________ >> 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 > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Jan 23 12:02:26 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 23 Jan 2008 09:02:26 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <47976D8A.70404@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> <47976D8A.70404@toulouse.inra.fr> Message-ID: <4797733d.0ebb720a.6974.1d68@mx.google.com> One quick question, when you say opencentral, are you talking about the test registry or another different registry? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-23-08 8:39 AM To: Core developer announcements Subject: Re: [MOBY-dev] Test Registry and RDF Bonjour Eddie, I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. I use the registerService procedure from MOBY::Client::Central (v 1.152) with the signature http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmoby/rdf /BlastSwissProt.rdf corresponding to an empty RDF file. What's really strange, is that when I call for the first time the deregistring protocol, the service seems not to be removed from registry. If I try a second time, the service is removed. Nevertheless, the two times I have the timeout message ... Merci, Sebastien Edward Kawas wrote: > What service are you trying to deregister and how are you trying to do it? > > If you are trying to use RDF, can you send it to me so I can try? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien > Carrere > Sent: January-23-08 1:23 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > > The RDF file seems to be okay now using test registry. > > However, the deregistering procedure is always problematic: > "Failed with status:500 Server closed connection without sending any > data back" > > Sebastien > > > > Edward Kawas wrote: > >> Okay, I tracked it down to a configuration problem and have since >> fixed it (hopefully!). So please try again. If there are any services >> that you need RDF for that are hosted on the test registry, please go >> to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you >> will be able to generate RDF for those services. >> >> Let me know if things are better, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-22-08 6:42 AM >> To: Core developer announcements >> Subject: [MOBY-dev] Test Registry and RDF >> >> Bonjour a tous, >> >> >> When I register a Service into the test registry >> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), >> the RDF file that I get as a response is empty (only the root tag is >> presentin the XML file, no content). >> >> Does anyone else have this problem ? >> >> Moreover, I do not know if there's a link with this problem, but >> deregistration in test central is problematic too ... >> >> I use the Perl API. >> >> Merci, >> >> Sebastien >> >> >> >> >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From sylvie.huchet at enst-bretagne.fr Wed Jan 23 11:05:09 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Wed, 23 Jan 2008 17:05:09 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <476AC872.70408@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> Message-ID: <479765B5.8060802@enst-bretagne.fr> Hi Paul, It seems that MobyRequest does not handle both synchronous and asynchronous calls tranparently... The invokeService() method that can be called for asynchronous calls does not defines any handler to manage asynchronous calls. And thus the performAsyncSOAPRequest method does not return any result. In addition, the asynchronous part of the invokeService does not initialize the contentsXML which leads to a NullPointerException. Regards, Sylvie. Paul Gordon a ?crit : > Hi Sylvie, > > The current class that implements asynchronous service calls is > MobyRequest (via AsyncClient). You can find both synchronous and > asynchronous services by setting the Service category to the empty > string ("") before calling CentralImpl. As Martin mentions below, the > mechanism currently used to run asynchronous services will change next > year (so there will probably be other ways to call async services > introduced), but the MobyRequest API will not need to change. > MobyRequest handles both synchronous and asynchronous calls transparently. > > Regards, > > Paul > > Martin Senger wrote: > >>> I'd like to know how asynchronous services (category moby-async) can be >>> called >>> using the java API >>> >> >> >> >> It is on the to-do list. A good opportunity to implement it will be the >> second week of February where several BioMoby developers meet at the >> Biohackaton in Japan. I hope to use this event to remove most of the >> items >> from my long-standing moby-to-do list. I am sorry for the delay. >> >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From Sebastien.Carrere at toulouse.inra.fr Wed Jan 23 12:16:13 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 23 Jan 2008 18:16:13 +0100 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <4797733d.0ebb720a.6974.1d68@mx.google.com> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> <47976D8A.70404@toulouse.inra.fr> <4797733d.0ebb720a.6974.1d68@mx.google.com> Message-ID: <4797765D.207@toulouse.inra.fr> Yes sorry, I speak about the Test registry: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl Sebastien Edward Kawas wrote: > One quick question, when you say opencentral, are you talking about the test > registry or another different registry? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: January-23-08 8:39 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > Bonjour Eddie, > > I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. > I use the registerService procedure from MOBY::Client::Central (v 1.152) > with the signature > http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmoby/rdf > /BlastSwissProt.rdf > corresponding to an empty RDF file. > > What's really strange, is that when I call for the first time the > deregistring protocol, the service seems not to be removed from registry. > If I try a second time, the service is removed. > > Nevertheless, the two times I have the timeout message ... > > > Merci, > > Sebastien > > > Edward Kawas wrote: > >> What service are you trying to deregister and how are you trying to do it? >> >> If you are trying to use RDF, can you send it to me so I can try? >> >> Thanks, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-23-08 1:23 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Test Registry and RDF >> >> >> The RDF file seems to be okay now using test registry. >> >> However, the deregistering procedure is always problematic: >> "Failed with status:500 Server closed connection without sending any >> data back" >> >> Sebastien >> >> >> >> Edward Kawas wrote: >> >> >>> Okay, I tracked it down to a configuration problem and have since >>> fixed it (hopefully!). So please try again. If there are any services >>> that you need RDF for that are hosted on the test registry, please go >>> to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you >>> will be able to generate RDF for those services. >>> >>> Let me know if things are better, >>> >>> Eddie >>> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >>> Carrere >>> Sent: January-22-08 6:42 AM >>> To: Core developer announcements >>> Subject: [MOBY-dev] Test Registry and RDF >>> >>> Bonjour a tous, >>> >>> >>> When I register a Service into the test registry >>> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), >>> the RDF file that I get as a response is empty (only the root tag is >>> presentin the XML file, no content). >>> >>> Does anyone else have this problem ? >>> >>> Moreover, I do not know if there's a link with this problem, but >>> deregistration in test central is problematic too ... >>> >>> I use the Perl API. >>> >>> Merci, >>> >>> Sebastien >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Jan 23 12:22:18 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 23 Jan 2008 09:22:18 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <4797765D.207@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> <47976D8A.70404@toulouse.inra.fr> <4797733d.0ebb720a.6974.1d68@mx.google.com> <4797765D.207@toulouse.inra.fr> Message-ID: <479777e3.25d7720a.7c14.1fe3@mx.google.com> So I have been playing around with the agent, registering my own service (using dashboard) that has a signatureURL. When I place an empty rdf document like the one that you have at my signatureURL location, and call register service with just the signatureURL filled in, the process does take a while (not sure why ... could be the server) but it does complete on its first try. The only thing that I can think of to solve the timeouts, is explicitly putting a longer timeout interval in the soap call in MOBY::Client::Central. This is assuming that the timeout that you are seeing is a result of the client and not the server. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-23-08 9:16 AM To: Core developer announcements Subject: Re: [MOBY-dev] Test Registry and RDF Yes sorry, I speak about the Test registry: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl Sebastien Edward Kawas wrote: > One quick question, when you say opencentral, are you talking about > the test registry or another different registry? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien > Carrere > Sent: January-23-08 8:39 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > Bonjour Eddie, > > I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. > I use the registerService procedure from MOBY::Client::Central (v > 1.152) with the signature > http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmo > by/rdf > /BlastSwissProt.rdf > corresponding to an empty RDF file. > > What's really strange, is that when I call for the first time the > deregistring protocol, the service seems not to be removed from registry. > If I try a second time, the service is removed. > > Nevertheless, the two times I have the timeout message ... > > > Merci, > > Sebastien > > > Edward Kawas wrote: > >> What service are you trying to deregister and how are you trying to do it? >> >> If you are trying to use RDF, can you send it to me so I can try? >> >> Thanks, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-23-08 1:23 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Test Registry and RDF >> >> >> The RDF file seems to be okay now using test registry. >> >> However, the deregistering procedure is always problematic: >> "Failed with status:500 Server closed connection without sending any >> data back" >> >> Sebastien >> >> >> >> Edward Kawas wrote: >> >> >>> Okay, I tracked it down to a configuration problem and have since >>> fixed it (hopefully!). So please try again. If there are any >>> services that you need RDF for that are hosted on the test registry, >>> please go to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi >>> and you will be able to generate RDF for those services. >>> >>> Let me know if things are better, >>> >>> Eddie >>> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >>> Carrere >>> Sent: January-22-08 6:42 AM >>> To: Core developer announcements >>> Subject: [MOBY-dev] Test Registry and RDF >>> >>> Bonjour a tous, >>> >>> >>> When I register a Service into the test registry >>> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl) >>> , the RDF file that I get as a response is empty (only the root tag >>> is presentin the XML file, no content). >>> >>> Does anyone else have this problem ? >>> >>> Moreover, I do not know if there's a link with this problem, but >>> deregistration in test central is problematic too ... >>> >>> I use the Perl API. >>> >>> Merci, >>> >>> Sebastien >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Wed Jan 23 14:05:40 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 23 Jan 2008 12:05:40 -0700 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <479765B5.8060802@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> Message-ID: <47979004.1050609@ucalgary.ca> Bonjour Sylvie, Thanks for pointing this out. The handler is null as it's supposed to be, but the lack of a StringBuffer was indeed the culprit. This has been fixed, and I'm adding a unit test for this (I'd always called asynchronous services asynchronously( or sync ones either syncly or asyncly), and so didn't catch this before).. Paul Sylvie Huchet wrote: > Hi Paul, > > It seems that MobyRequest does not handle both synchronous and asynchronous > calls tranparently... > > The invokeService() method that can be called for asynchronous calls does not > defines any handler to manage asynchronous calls. And thus the > performAsyncSOAPRequest method does not return any result. > In addition, the asynchronous part of the invokeService does not initialize the > contentsXML which leads to a NullPointerException. > > Regards, > Sylvie. > > > Paul Gordon a ?crit : > >> Hi Sylvie, >> >> The current class that implements asynchronous service calls is >> MobyRequest (via AsyncClient). You can find both synchronous and >> asynchronous services by setting the Service category to the empty >> string ("") before calling CentralImpl. As Martin mentions below, the >> mechanism currently used to run asynchronous services will change next >> year (so there will probably be other ways to call async services >> introduced), but the MobyRequest API will not need to change. >> MobyRequest handles both synchronous and asynchronous calls transparently. >> >> Regards, >> >> Paul >> >> Martin Senger wrote: >> >> >>>> I'd like to know how asynchronous services (category moby-async) can be >>>> called >>>> using the java API >>>> >>>> >>> >>> It is on the to-do list. A good opportunity to implement it will be the >>> second week of February where several BioMoby developers meet at the >>> Biohackaton in Japan. I hope to use this event to remove most of the >>> items >>> from my long-standing moby-to-do list. I am sorry for the delay. >>> >>> Martin >>> >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> > > > !DSPAM:60005,47977310109501808032233! > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47977310109501808032233! > From markw at illuminae.com Wed Jan 23 16:09:36 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 23 Jan 2008 13:09:36 -0800 Subject: [MOBY-dev] Second Proofs of the manuscript now available Message-ID: Again, I wont post to the mailing list due to copyright issues, but I'll immediately send it to anyone who requests it. I'm sending it to those who requested the last version just to save time. Comments ASAP ASAP ASAP please! Best wishes all, Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Wed Jan 23 16:20:46 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 23 Jan 2008 13:20:46 -0800 Subject: [MOBY-dev] Second Proofs of the manuscript now available In-Reply-To: References: Message-ID: They have given us 24 hours to check and correct the proofs, so ASAP means REALLY FAST!! :) Mark On Wed, 23 Jan 2008 13:09:36 -0800, Mark Wilkinson wrote: > Again, I wont post to the mailing list due to copyright issues, but I'll > immediately send it to anyone who requests it. I'm sending it to those > who requested the last version just to save time. > > Comments ASAP ASAP ASAP please! > > Best wishes all, > > Mark > > > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 sylvie.huchet at enst-bretagne.fr Thu Jan 24 03:51:08 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Thu, 24 Jan 2008 09:51:08 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <47979004.1050609@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> Message-ID: <4798517C.1070104@enst-bretagne.fr> Bonjour Paul, Thanks for the update, but this is not enough. If the handler has to be null, the code of performAsyncSOAPRequest must be modified to get the data : The data is got back only if the following test : "if(newDataAvailable.size() > 0 && handler != null)" is true, which is never the case. Regards, Sylvie. Paul Gordon a ?crit : > Bonjour Sylvie, > > Thanks for pointing this out. The handler is null as it's supposed to > be, but the lack of a StringBuffer was indeed the culprit. This has > been fixed, and I'm adding a unit test for this (I'd always called > asynchronous services asynchronously( or sync ones either syncly or > asyncly), and so didn't catch this before).. > > > > Paul > > Sylvie Huchet wrote: > >> Hi Paul, >> >> It seems that MobyRequest does not handle both synchronous and >> asynchronous >> calls tranparently... >> >> The invokeService() method that can be called for asynchronous calls >> does not >> defines any handler to manage asynchronous calls. And thus the >> performAsyncSOAPRequest method does not return any result. >> In addition, the asynchronous part of the invokeService does not >> initialize the >> contentsXML which leads to a NullPointerException. >> >> Regards, >> Sylvie. >> >> >> Paul Gordon a ?crit : >> >> >>> Hi Sylvie, >>> >>> The current class that implements asynchronous service calls is >>> MobyRequest (via AsyncClient). You can find both synchronous and >>> asynchronous services by setting the Service category to the empty >>> string ("") before calling CentralImpl. As Martin mentions below, the >>> mechanism currently used to run asynchronous services will change next >>> year (so there will probably be other ways to call async services >>> introduced), but the MobyRequest API will not need to change. >>> MobyRequest handles both synchronous and asynchronous calls >>> transparently. >>> >>> Regards, >>> >>> Paul >>> >>> Martin Senger wrote: >>> >>> >>> >>>>> I'd like to know how asynchronous services (category moby-async) >>>>> can be >>>>> called >>>>> using the java API >>>>> >>>> >>>> >>>> It is on the to-do list. A good opportunity to implement it will be the >>>> second week of February where several BioMoby developers meet at the >>>> Biohackaton in Japan. I hope to use this event to remove most of the >>>> items >>>> from my long-standing moby-to-do list. I am sorry for the delay. >>>> >>>> Martin >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> >> >> >> !DSPAM:60005,47977310109501808032233! >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> !DSPAM:60005,47977310109501808032233! >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From groscurt at mpiz-koeln.mpg.de Fri Jan 25 03:40:20 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 25 Jan 2008 09:40:20 +0100 Subject: [MOBY-dev] Compiling error in MobySaveDialog In-Reply-To: <4798517C.1070104@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> Message-ID: <200801250940.20763.groscurt@mpiz-koeln.mpg.de> Hi, i just checked out moby and run the gather task and included all downloaded libs in the eclipse project. One error remains in the ca.ucalcary.seahawk.gui.MobySaveDialog "The type com.sun.star.lang.XEventListener cannot be resolved. It is indirectly referenced from required .class files? It seems one lib is missing - could this be added to the jar archive which is downloaded by the gather task ? Thanks andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From gordonp at ucalgary.ca Fri Jan 25 08:28:14 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 25 Jan 2008 06:28:14 -0700 Subject: [MOBY-dev] Compiling error in MobySaveDialog In-Reply-To: <200801250940.20763.groscurt@mpiz-koeln.mpg.de> References: <476A8DAD.1060208@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> <200801250940.20763.groscurt@mpiz-koeln.mpg.de> Message-ID: <4799E3EE.30106@ucalgary.ca> Hi Andreas, I'll get on that for you. The standard JDK doesn't need the JAR the compile, but obviously Eclipse does some extra dependency checking. Regards, Paul Andreas Groscurth wrote: > Hi, > > i just checked out moby and run the gather task and included all downloaded > libs in the eclipse project. > > One error remains in the ca.ucalcary.seahawk.gui.MobySaveDialog > > "The type com.sun.star.lang.XEventListener cannot be resolved. It is > indirectly referenced from required .class files? > > It seems one lib is missing - could this be added to the jar archive which is > downloaded by the gather task ? > > Thanks > andreas > > From gordonp at ucalgary.ca Sat Jan 26 13:03:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Sat, 26 Jan 2008 11:03:52 -0700 Subject: [MOBY-dev] Compiling error in MobySaveDialog In-Reply-To: <200801250940.20763.groscurt@mpiz-koeln.mpg.de> References: <476A8DAD.1060208@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> <200801250940.20763.groscurt@mpiz-koeln.mpg.de> Message-ID: <479B7608.1000300@ucalgary.ca> Hi Andreas, I've added extra libraries to the CVS now. Do a CVS update, then a build.sh and you be good to go... Regards, Paul Andreas Groscurth wrote: > Hi, > > i just checked out moby and run the gather task and included all downloaded > libs in the eclipse project. > > One error remains in the ca.ucalcary.seahawk.gui.MobySaveDialog > > "The type com.sun.star.lang.XEventListener cannot be resolved. It is > indirectly referenced from required .class files? > > It seems one lib is missing - could this be added to the jar archive which is > downloaded by the gather task ? > > Thanks > andreas > > From gordonp at ucalgary.ca Sat Jan 26 13:06:15 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Sat, 26 Jan 2008 11:06:15 -0700 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <4798517C.1070104@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> Message-ID: <479B7697.80202@ucalgary.ca> Hi Sylvie, Yes, sorry about that. I've moved the "handler != null" deeper into the function so that synchronous calls actually pickup the results too. It's in CVS now. Do you have a particular service of interest that I can use as a test case? Regards, Paul Sylvie Huchet wrote: > Bonjour Paul, > > Thanks for the update, but this is not enough. > If the handler has to be null, the code of performAsyncSOAPRequest must be > modified to get the data : The data is got back only if the following test : > "if(newDataAvailable.size() > 0 && handler != null)" is true, which is never the > case. > > Regards, > Sylvie. > > Paul Gordon a ?crit : > >> Bonjour Sylvie, >> >> Thanks for pointing this out. The handler is null as it's supposed to >> be, but the lack of a StringBuffer was indeed the culprit. This has >> been fixed, and I'm adding a unit test for this (I'd always called >> asynchronous services asynchronously( or sync ones either syncly or >> asyncly), and so didn't catch this before).. >> >> >> >> Paul >> >> Sylvie Huchet wrote: >> >> >>> Hi Paul, >>> >>> It seems that MobyRequest does not handle both synchronous and >>> asynchronous >>> calls tranparently... >>> >>> The invokeService() method that can be called for asynchronous calls >>> does not >>> defines any handler to manage asynchronous calls. And thus the >>> performAsyncSOAPRequest method does not return any result. >>> In addition, the asynchronous part of the invokeService does not >>> initialize the >>> contentsXML which leads to a NullPointerException. >>> >>> Regards, >>> Sylvie. >>> >>> >>> Paul Gordon a ?crit : >>> >>> >>> >>>> Hi Sylvie, >>>> >>>> The current class that implements asynchronous service calls is >>>> MobyRequest (via AsyncClient). You can find both synchronous and >>>> asynchronous services by setting the Service category to the empty >>>> string ("") before calling CentralImpl. As Martin mentions below, the >>>> mechanism currently used to run asynchronous services will change next >>>> year (so there will probably be other ways to call async services >>>> introduced), but the MobyRequest API will not need to change. >>>> MobyRequest handles both synchronous and asynchronous calls >>>> transparently. >>>> >>>> Regards, >>>> >>>> Paul >>>> >>>> Martin Senger wrote: >>>> >>>> >>>> >>>> >>>>>> I'd like to know how asynchronous services (category moby-async) >>>>>> can be >>>>>> called >>>>>> using the java API >>>>>> >>>>>> >>>>> It is on the to-do list. A good opportunity to implement it will be the >>>>> second week of February where several BioMoby developers meet at the >>>>> Biohackaton in Japan. I hope to use this event to remove most of the >>>>> items >>>>> from my long-standing moby-to-do list. I am sorry for the delay. >>>>> >>>>> Martin >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> !DSPAM:60005,47977310109501808032233! >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> > > > !DSPAM:60005,47984f74109501894423288! > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47984f74109501894423288! > From sylvie.huchet at enst-bretagne.fr Mon Jan 28 06:22:16 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Mon, 28 Jan 2008 12:22:16 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <479B7697.80202@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> <479B7697.80202@ucalgary.ca> Message-ID: <479DBAE8.50806@enst-bretagne.fr> Hi Paul, Thank you for the modification. A service to test it could be inb.bsc.es#runPhylipDnapenny. Regards, Sylvie. Paul Gordon a ?crit : > Hi Sylvie, > > Yes, sorry about that. I've moved the "handler != null" deeper into the > function so that synchronous calls actually pickup the results too. > It's in CVS now. Do you have a particular service of interest that I can > use as a test case? > > Regards, > > Paul > > Sylvie Huchet wrote: > >> Bonjour Paul, >> >> Thanks for the update, but this is not enough. >> If the handler has to be null, the code of performAsyncSOAPRequest >> must be >> modified to get the data : The data is got back only if the following >> test : >> "if(newDataAvailable.size() > 0 && handler != null)" is true, which is >> never the >> case. >> >> Regards, >> Sylvie. >> >> Paul Gordon a ?crit : >> >> >>> Bonjour Sylvie, >>> >>> Thanks for pointing this out. The handler is null as it's supposed to >>> be, but the lack of a StringBuffer was indeed the culprit. This has >>> been fixed, and I'm adding a unit test for this (I'd always called >>> asynchronous services asynchronously( or sync ones either syncly or >>> asyncly), and so didn't catch this before).. >>> >>> >>> >>> Paul >>> >>> Sylvie Huchet wrote: >>> >>> >>> >>>> Hi Paul, >>>> >>>> It seems that MobyRequest does not handle both synchronous and >>>> asynchronous >>>> calls tranparently... >>>> >>>> The invokeService() method that can be called for asynchronous calls >>>> does not >>>> defines any handler to manage asynchronous calls. And thus the >>>> performAsyncSOAPRequest method does not return any result. >>>> In addition, the asynchronous part of the invokeService does not >>>> initialize the >>>> contentsXML which leads to a NullPointerException. >>>> >>>> Regards, >>>> Sylvie. >>>> >>>> >>>> Paul Gordon a ?crit : >>>> >>>> >>>> >>>> >>>>> Hi Sylvie, >>>>> >>>>> The current class that implements asynchronous service calls is >>>>> MobyRequest (via AsyncClient). You can find both synchronous and >>>>> asynchronous services by setting the Service category to the empty >>>>> string ("") before calling CentralImpl. As Martin mentions below, the >>>>> mechanism currently used to run asynchronous services will change next >>>>> year (so there will probably be other ways to call async services >>>>> introduced), but the MobyRequest API will not need to change. >>>>> MobyRequest handles both synchronous and asynchronous calls >>>>> transparently. >>>>> >>>>> Regards, >>>>> >>>>> Paul >>>>> >>>>> Martin Senger wrote: >>>>> >>>>> >>>>> >>>>> >>>>>>> I'd like to know how asynchronous services (category moby-async) >>>>>>> can be >>>>>>> called >>>>>>> using the java API >>>>>>> >>>>>> >>>>>> It is on the to-do list. A good opportunity to implement it will >>>>>> be the >>>>>> second week of February where several BioMoby developers meet at the >>>>>> Biohackaton in Japan. I hope to use this event to remove most of the >>>>>> items >>>>>> from my long-standing moby-to-do list. I am sorry for the delay. >>>>>> >>>>>> Martin >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> !DSPAM:60005,47977310109501808032233! >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> >> >> >> !DSPAM:60005,47984f74109501894423288! >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> !DSPAM:60005,47984f74109501894423288! >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From simont at hmgc.mcw.edu Mon Jan 28 23:45:25 2008 From: simont at hmgc.mcw.edu (Twigger, Simon (MCW)) Date: Mon, 28 Jan 2008 22:45:25 -0600 Subject: [MOBY-dev] UC Davis News & Information :: Grant for Workflow Software In-Reply-To: References: Message-ID: <3A38C930-28BC-47D3-BFA5-5E28C02C2F32@hmgc.mcw.edu> I came across this video on the Kepler workflow project this evening while browsing SciVee, I think it was from 2006 so perhaps a little out of date these days. http://www.scivee.tv/node/3452 S. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 22, 2008, at 11:12 AM, Mark Wilkinson wrote: > > > Interesting... > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Jan 29 10:34:42 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 29 Jan 2008 16:34:42 +0100 Subject: [MOBY-dev] BioMoby Tutorial Update In-Reply-To: <478BA3D7.6050206@avignon.inra.fr> References: <478BA3D7.6050206@avignon.inra.fr> Message-ID: <200801291634.43553.groscurt@mpiz-koeln.mpg.de> Hi all, I just wanted to inform you that I updated our BioMoby Java tutorial and added some new fenzy flash movies :-) Actually I just recorded myself doing all steps and converted them into flash movies. So you can directly see what steps have to be done how, starting from checking out BioMoby from CVS, setting up eclipse and how to register, implement and deploy a Web Service. The movies are splitted into several files for each topic and for each topic there is also a text version available. You are kind of my guinea pigs - if you have time please have a look at the tutorial and the movies. Is everything understandable, is something missing, something hard to follow - please let me know. You can find it at http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step Thanks Andreas PS: Things I will add soon: - how to implement a service with more complex objects (like AminoAcidSequence) - how to set up a system for creating secure Web Services -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From dmitry.repchevski at bsc.es Tue Jan 29 14:33:14 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 29 Jan 2008 20:33:14 +0100 Subject: [MOBY-dev] Apache http 1.1 problem Message-ID: <479F7F7A.4030306@bsc.es> Hello everybody, I am facing a problem with several servers (central and service endpoints). The problem is with messages that use http 1.1 chunked messages. Some endpoints (like http://inb.bsc.es/cgi-bin/brokerRetrieval/mobydev.cgi) demand to put "Content-Length" header (otherwise return 411 error) even do not use it (chunked message). Another (for example http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl) just reject the messages (411). Does anyone faced this problem? I'm sure this must be something with Apache configuration... Cheers, Dmitry From markw at illuminae.com Thu Jan 31 14:23:09 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 31 Jan 2008 11:23:09 -0800 Subject: [MOBY-dev] Fwd: Your article has been published in Briefings in Bioinformatics In-Reply-To: <20080131104248.4E82E2DEA19@marz.stanford.edu> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> Message-ID: ------- Forwarded message ------- From: bib-tfl at highwire.stanford.edu To: markw at illuminae.com Cc: bib at oxfordjournals.org Subject: Your article has been published in Briefings in Bioinformatics Date: Thu, 31 Jan 2008 02:42:49 -0800 Dear Author I am pleased to inform you that Oxford Journals has published your article in Briefings in Bioinformatics. Here are the free-access links to your online article: Abstract: http://bib.oxfordjournals.org/cgi/content/abstract/bbn003? ijkey=7jMqiO6BpntmxyT&keytype=ref Full Text: http://bib.oxfordjournals.org/cgi/content/full/bbn003? ijkey=7jMqiO6BpntmxyT&keytype=ref PDF: http://bib.oxfordjournals.org/cgi/reprint/bbn003? ijkey=7jMqiO6BpntmxyT&keytype=ref The full citation for your article is: Interoperability with Moby 1.0--It's better than sharing your toothbrush! The BioMoby Consortium Briefings in Bioinformatics 2008; doi: 10.1093/bib/bbn003 This is the final published version of your article and it can be cited using the DOI given above (for more information on DOIs see http://www.doi.org). Please see below for additional information and the conditions of use for the links. You can view information about how your article has been accessed on your Article Data Webpage, a new service for Oxford Journals? authors. View the latest online usage figures, track citations, and register for relevant journal alerts. Visit the page regularly to see how your article is used over a period of time. Thank you for publishing with Oxford Journals and I hope to be of service to you again soon. Best wishes, Briefings in Bioinformatics Production Editor E-mail: bib at oxfordjournals.org Visit Briefings in Bioinformatics Online Additional information (please read) Sending a free-access URL There are several advantages to providing you with a free-access link to your article instead of a PDF file, including: ? Access to both the HTML and PDF versions of an article (where available). ? You (and your co-authors) plus any users of your own personal/institutional web sites will get free access to the finally published and authoritative version of the article that is available from our site whether or not they are a subscriber to the journal; ? 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For those wishing to make commercial use of the article, please direct them to journals.permissions at oxfordjournals.org for permissions information or see the website. Advance Access articles Please note that the URLs given here are for the Advance Access version of your paper. Once the article appears in a paginated issue the link will automatically take you to the latest version. To be alerted when the page numbers are available, please register for our electronic table of contents (eTOC) alerting service. From markw at illuminae.com Wed Jan 2 19:33:49 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 02 Jan 2008 11:33:49 -0800 Subject: [MOBY-dev] Manuscript and Moby 2 funding Message-ID: Hi all, I've just re-submitted the revised manuscript to Briefings in Bioinformatics. After discussing with the editor how best to respond to the contradictory requests of the reviewers, I have simply added a couple of sentences to each technical section of the manuscript describing the "biologists problem" that each component of Moby is trying to address. I also put some screenshots of a Gbrowse-Moby browsing session into the supplementary information to help the biologist visualise how Moby can be used to direct the flow of data from service to service. I'll put the final copy of the manuscript into the CVS later today. Sorry I didn't pass it around for everyone to review before resubmission, but the deadline was tight due to the holidays, and the changes were quite minor. I hope nobody minds! On another note, thank you to everyone who wrote support letters for the Genome Canada application for Moby 2.0. Sadly, we didn't get funded... but we do have funding from the Heart and Stroke Foundation and from Microsoft, so we're still alive and kicking :-) Best wishes and Happy New Year to all Mobyers! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 3 14:56:05 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 03 Jan 2008 06:56:05 -0800 Subject: [MOBY-dev] Paper Accepted! Message-ID: Hi everyone! The Moby 1.0 paper has been accepted to Briefings. Halleluja for that! Best wishes, Mark From Pieter.Neerincx at wur.nl Thu Jan 3 16:31:32 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 3 Jan 2008 17:31:32 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> Hi Mark et al., Congratulations! Too bad we can't share champagne digitally over the world wide web :) Cheers, Pi On 3-jan-2008, at 15:56, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From carole.goble at manchester.ac.uk Thu Jan 3 16:48:57 2008 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Thu, 03 Jan 2008 16:48:57 +0000 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> References: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> Message-ID: <477D11F9.1040807@manchester.ac.uk> Well done Mark! Carole > Hi Mark et al., > > Congratulations! Too bad we can't share champagne digitally over the > world wide web :) > > Cheers, > > Pi > > On 3-jan-2008, at 15:56, Mark Wilkinson wrote: > >> Hi everyone! >> >> The Moby 1.0 paper has been accepted to Briefings. >> >> Halleluja for that! >> >> Best wishes, >> >> Mark >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Thu Jan 3 16:54:29 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 03 Jan 2008 09:54:29 -0700 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> References: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> Message-ID: <477D1345.5090502@ucalgary.ca> We'll have to settle for the reference to wine in the Dutch Sailor's dialog in Moby Dick then :-) Grand snoozing to-night, maty; fat night for that. I mark this in our old Mogul's wine; it's quite as deadening to some as filliping to others. Pieter Neerincx wrote: > Hi Mark et al., > > Congratulations! Too bad we can't share champagne digitally over the > world wide web :) > > Cheers, > > Pi > > On 3-jan-2008, at 15:56, Mark Wilkinson wrote: > >> Hi everyone! >> >> The Moby 1.0 paper has been accepted to Briefings. >> >> Halleluja for that! >> >> Best wishes, >> >> Mark >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,477d0d22109501959316500! > > > From markw at illuminae.com Thu Jan 3 22:59:58 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 03 Jan 2008 14:59:58 -0800 Subject: [MOBY-dev] Question to Async service providers Message-ID: Do asynchronous services respond correctly to the Moby "ping"? If so, I'll add them into the service tester. Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 simont at hmgc.mcw.edu Fri Jan 4 04:03:21 2008 From: simont at hmgc.mcw.edu (Twigger, Simon (MCW)) Date: Thu, 3 Jan 2008 22:03:21 -0600 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> Hi Mark, That's spectacular, a great way to start the New year! best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 3, 2008, at 8:56 AM, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From simont at hmgc.mcw.edu Fri Jan 4 04:03:21 2008 From: simont at hmgc.mcw.edu (Twigger, Simon (MCW)) Date: Thu, 3 Jan 2008 22:03:21 -0600 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> Hi Mark, That's spectacular, a great way to start the New year! best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 3, 2008, at 8:56 AM, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Fri Jan 4 04:24:37 2008 From: markw at illuminae.com (mark wilkinson) Date: Fri, 4 Jan 2008 04:24:37 +0000 GMT Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> References: <796B0EC7-D9D9-4022-A7C5-E6BB084FC0A3@hmgc.mcw.edu> Message-ID: <1211310426-1199420748-cardhu_blackberry.rim.net-17035-@engine24-cell01> Indeed! January 3rd - that's gotta be a new record :-) What makes me even more happy is how wonderfully professional the review process was compared to the PLoS ONE story. The reviews were rapid (and there was more than one of them!), but most importantly there was constant communication and advice from the editors of the journal as to what they wanted and how they thought the reviews should be interpreted (and the edits were quite massive! More than 30% of the text was removed in the first re-write, with the guidance of the editor, before it even went out for review!). It was such a pleasure to work through this (somewhat unusual) submission with the BiB editorial team! Kudo's to them!! Mark -- Mark Wilkinson ...on the road! -----Original Message----- From: "Twigger, Simon (MCW)" Date: Thu, 3 Jan 2008 22:03:21 To:Core developer announcements Cc:mobydev Subject: Re: [MOBY-dev] Paper Accepted! Hi Mark, That's spectacular, a great way to start the New year! best, Simon. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 3, 2008, at 8:56 AM, Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Fri Jan 4 10:22:56 2008 From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de) Date: Fri, 4 Jan 2008 11:22:56 +0100 (CET) Subject: [MOBY-dev] Paper Accepted! In-Reply-To: <477D1345.5090502@ucalgary.ca> References: <5006D316-946B-4D19-B14A-2D2995A2CE6A@wur.nl> <477D1345.5090502@ucalgary.ca> Message-ID: <61522.89.52.129.18.1199442176.squirrel@mpizmail.mpiz-koeln.mpg.de> Didnt get a word you said ;-) But hurray... das ist einfach grossartig ! Best andreas > Grand snoozing to-night, maty; fat night for that. I mark this in > our old Mogul's wine; it's quite as deadening to some as filliping to > others. > > > > Pieter Neerincx wrote: >> Hi Mark et al., >> >> Congratulations! Too bad we can't share champagne digitally over the >> world wide web :) >> >> Cheers, >> >> Pi >> >> On 3-jan-2008, at 15:56, Mark Wilkinson wrote: >> >>> Hi everyone! >>> >>> The Moby 1.0 paper has been accepted to Briefings. >>> >>> Halleluja for that! >>> >>> Best wishes, >>> >>> Mark >>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> !DSPAM:60005,477d0d22109501959316500! >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From haase_dirk at web.de Fri Jan 4 11:55:22 2008 From: haase_dirk at web.de (Dirk Haase) Date: Fri, 04 Jan 2008 12:55:22 +0100 Subject: [MOBY-dev] Paper Accepted! Message-ID: <938304251@web.de> > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. Congratulations! And many thanks for your efforts Mark! Happy new year to all MOBYers, dirk From jmfernandez at cnio.es Fri Jan 4 12:35:11 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Fri, 04 Jan 2008 13:35:11 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <477E27FF.3000404@cnio.es> At last! Congratulations to everyone who has contributed to the MOBY API, libraries and community! Best Wishes, Jos? Mar?a Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From jmfernandez at cnio.es Fri Jan 4 12:35:11 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Fri, 04 Jan 2008 13:35:11 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <477E27FF.3000404@cnio.es> At last! Congratulations to everyone who has contributed to the MOBY API, libraries and community! Best Wishes, Jos? Mar?a Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. From usadel at mpimp-golm.mpg.de Sat Jan 5 16:10:28 2008 From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=) Date: Sat, 5 Jan 2008 17:10:28 +0100 Subject: [MOBY-dev] Paper Accepted! In-Reply-To: References: Message-ID: <477FABF4.80102@mpimp-golm.mpg.de> Hi, congrats! 2008 is beginning nice... Cheers, Bj?rn Mark Wilkinson wrote: > Hi everyone! > > The Moby 1.0 paper has been accepted to Briefings. > > Halleluja for that! > > Best wishes, > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From groscurt at mpiz-koeln.mpg.de Mon Jan 7 11:44:03 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 7 Jan 2008 12:44:03 +0100 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: References: Message-ID: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> Hi, I'm not sure, but I think there is something wrong in the MobyRequest - or I (again) miss something... The situation is the following: I want to call a service which has secondaries. I dont give any secondaries in the call, because I want to use the default ones the service was registered with In the method convertMOBYDataToMOBYRequest the secondaried from the service are fetched correctly MobyData[] secondaries = mobyService.getSecondaryInputs(); but then the secondaryParameters from the call are fetched and the following comparison makes me wonder if(secondaries != null && secondaries.length != secondaryParams.size()){ throw new MobyException("Service " + mobyService.getName() + " was provided " + secondaryParams.size() + " secondary input parameter(s), but takes " + secondaries.length + " (query " + queryName + ")"); } This means - if i dont provide any secondaries in my call, the method will always throw an exception, although i want that the defaults to be taken. In my opinion, it should check whether any secondaries from the call are present and if not, then use the default ones from the service. So, am I right or what did I miss ? Thanks Andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From markw at illuminae.com Mon Jan 7 23:08:03 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 07 Jan 2008 15:08:03 -0800 Subject: [MOBY-dev] Yay Funding! Message-ID: Hi all, So after last week's disappointment from Genome Canada, I got news this morning that the Canadian Institutes of Health Research have funded CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have almost $1M to invest in Moby 2 :-) Here we go!! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Mon Jan 7 22:47:27 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Mon, 07 Jan 2008 15:47:27 -0700 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> Message-ID: <4782ABFF.8030903@ucalgary.ca> Hi Andreas, I wouldn't really call it a bug, MobyRequest just didn't expect you to be lazy :-) For example, it doesn't check that you're sending primary parameters of the right data types either. This was primarily because I wanted to be able to create data envelopes and send them without consulting the ontologies if I so desired. On the other hand, I already have the secondary data, so it doesn't hurt to add those that aren't already specified in the request. I've done this now (do a cvs update), and have documented that the MobyContentInstance you pass in may be modified in this way. Regards, Paul Andreas Groscurth wrote: > Hi, > > I'm not sure, but I think there is something wrong in the MobyRequest - or I > (again) miss something... > > The situation is the following: > > I want to call a service which has secondaries. I dont give any secondaries in > the call, because I want to use the default ones the service was registered > with > > In the method convertMOBYDataToMOBYRequest the secondaried from the service > are fetched correctly > > MobyData[] secondaries = mobyService.getSecondaryInputs(); > > but then the secondaryParameters from the call are fetched and the following > comparison makes me wonder > > if(secondaries != null && secondaries.length != secondaryParams.size()){ > throw new MobyException("Service " + mobyService.getName() + " was provided > " + secondaryParams.size() + " secondary input parameter(s), but takes " + > secondaries.length + " (query " + queryName + ")"); > } > > This means - if i dont provide any secondaries in my call, the method will > always throw an exception, although i want that the defaults to be taken. > > In my opinion, it should check whether any secondaries from the call are > present and if not, then use the default ones from the service. > > So, am I right or what did I miss ? > > Thanks > Andreas > From carole.goble at manchester.ac.uk Mon Jan 7 23:17:04 2008 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Mon, 07 Jan 2008 23:17:04 +0000 Subject: [MOBY-dev] Yay Funding! In-Reply-To: References: Message-ID: <4782B2F0.4030200@manchester.ac.uk> Mark wow!!!! Well done!! Carole > Hi all, > > So after last week's disappointment from Genome Canada, I got news > this morning that the Canadian Institutes of Health Research have > funded CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have > almost $1M to invest in Moby 2 :-) > > Here we go!! > > Mark > > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee > and may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received > this communication in error, please notify the sender immediately by > reply e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From carole.goble at manchester.ac.uk Mon Jan 7 23:17:04 2008 From: carole.goble at manchester.ac.uk (Carole Goble) Date: Mon, 07 Jan 2008 23:17:04 +0000 Subject: [MOBY-dev] Yay Funding! In-Reply-To: References: Message-ID: <4782B2F0.4030200@manchester.ac.uk> Mark wow!!!! Well done!! Carole > Hi all, > > So after last week's disappointment from Genome Canada, I got news > this morning that the Canadian Institutes of Health Research have > funded CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have > almost $1M to invest in Moby 2 :-) > > Here we go!! > > Mark > > > > ---- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the addressee > and may contain information that is privileged and confidential. Any > dissemination, distribution or copying of this communication by > unauthorized individuals is strictly prohibited. If you have received > this communication in error, please notify the sender immediately by > reply e-mail and delete the original and all copies from your system. > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Jan 8 09:37:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 8 Jan 2008 10:37:55 +0100 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: <4782ABFF.8030903@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> Message-ID: <200801081037.55853.groscurt@mpiz-koeln.mpg.de> Hi Paul, thanks for the update... Although I aggree with you on the primary data issue, I wouldnt call it 'being lazy'... why are then default values at all if one is forced to send the secondaries at all ? If I'm ok with the defined default values, why should I send secondaries ? I understood the secondaries as optional parameters for which I could just use the default values. but what surprises me is, when actually does the secondaries are set to the request data ? When I see the code correctly, you fill the secondaryParams - but I cant find anything where this information is then set ? MobyDataUtils.toXMLDocument( mobyRequest, data ); seems to be where you create the xml request with the data... but where is the link between data and the parameters ? Thanks andreas On Monday 07 January 2008 23:47, Paul Gordon wrote: > Hi Andreas, > > I wouldn't really call it a bug, MobyRequest just didn't expect you to > be lazy :-) > > For example, it doesn't check that you're sending primary parameters of > the right data types either. This was primarily because I wanted to be > able to create data envelopes and send them without consulting the > ontologies if I so desired. On the other hand, I already have the > secondary data, so it doesn't hurt to add those that aren't already > specified in the request. I've done this now (do a cvs update), and > have documented that the MobyContentInstance you pass in may be modified > in this way. > > Regards, > > Paul > > Andreas Groscurth wrote: > > Hi, > > > > I'm not sure, but I think there is something wrong in the MobyRequest - > > or I (again) miss something... > > > > The situation is the following: > > > > I want to call a service which has secondaries. I dont give any > > secondaries in the call, because I want to use the default ones the > > service was registered with > > > > In the method convertMOBYDataToMOBYRequest the secondaried from the > > service are fetched correctly > > > > MobyData[] secondaries = mobyService.getSecondaryInputs(); > > > > but then the secondaryParameters from the call are fetched and the > > following comparison makes me wonder > > > > if(secondaries != null && secondaries.length != secondaryParams.size()){ > > throw new MobyException("Service " + mobyService.getName() + " was > > provided " + secondaryParams.size() + " secondary input parameter(s), > > but takes " + secondaries.length + " (query " + queryName + ")"); > > } > > > > This means - if i dont provide any secondaries in my call, the method > > will always throw an exception, although i want that the defaults to be > > taken. > > > > In my opinion, it should check whether any secondaries from the call are > > present and if not, then use the default ones from the service. > > > > So, am I right or what did I miss ? > > > > Thanks > > Andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Tue Jan 8 10:04:30 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 8 Jan 2008 11:04:30 +0100 Subject: [MOBY-dev] Yay Funding! In-Reply-To: References: Message-ID: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> Hi, so lets celebrate for that :-) But just curiosity... Did i miss Moby 1.0 ? Shouldn't be with a number also somewhere a corresponding version in the cvs ? What I miss is that someone can build any software with Moby 1.0 or what ever... the cvs is still unversioned as I can see... I would love to see different branches. Currently it can happens that with changes in the Moby API software is not working. If this had be versionized, the API could change but software could still work with Version xy. Maybe I missed something - of course its awesome to have money for Moby2... but from my point of view Moby 1 is still missing stuff (versionizing at the top) ? Are there any plans to invite some kind of versions into Moby API ? I'm really like to discuss things further, I'm just afraid that there are several issues still alive and everyone is just thinking of Moby 2. my 2 cents andreas On Tuesday 08 January 2008 00:08, Mark Wilkinson wrote: > Hi all, > > So after last week's disappointment from Genome Canada, I got news this > morning that the Canadian Institutes of Health Research have funded > CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have almost $1M to > invest in Moby 2 :-) > > Here we go!! > > Mark -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From gordonp at ucalgary.ca Tue Jan 8 15:24:48 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 08:24:48 -0700 Subject: [MOBY-dev] Bug in MobyRequest ? In-Reply-To: <200801081037.55853.groscurt@mpiz-koeln.mpg.de> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> Message-ID: <478395C0.4040401@ucalgary.ca> > thanks for the update... Although I aggree with you on the primary data issue, > I wouldnt call it 'being lazy'... why are then default values at all if one > is forced to send the secondaries at all ? If I'm ok with the defined default > values, why should I send secondaries ? I understood the secondaries as > optional parameters for which I could just use the default values. > Well, MobyRequest never said it would fill secondaries in for you, so I don't consider it a "bug" that it didn't :-) i.e. MobyRequest does not expect to fulfill all the contract obligations of a transaction (e.g. the API user is still responsible for data type conformity), so I considered it more like a "Request For Enhancement". > but what surprises me is, when actually does the secondaries are set to the > request data ? > When I see the code correctly, you fill the secondaryParams - but I cant find > anything where this information is then set ? > > MobyDataUtils.toXMLDocument( mobyRequest, data ); > > seems to be where you create the xml request with the data... but where is the > link between data and the parameters ? > Mea culpa. Now that actually is a bug, just introduced :-) Since it was a fairly trivial modification, I had only tested that my changes didn't break anything, not that they actually worked. :-( Please do another cvs update. On the plus side, I also made the code somewhat prettier by using the Java 5 "for each" and more Generics in the main loops. From markw at illuminae.com Tue Jan 8 16:44:15 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Jan 2008 08:44:15 -0800 Subject: [MOBY-dev] Yay Funding! In-Reply-To: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> Message-ID: I've been waiting for Eddie to finish the migration to a pure-perl codebase before making the 1.0 release. I think it's done now...?? The last thing we needed to manage was the caching of RDF since RDF::Core is a painfully slow module when it comes to on-the-fly RDF creation. If Eddie confirms that we're done, I'll make the 1.0 release right away. M On Tue, 08 Jan 2008 02:04:30 -0800, Andreas Groscurth wrote: > Hi, > > so lets celebrate for that :-) > > But just curiosity... Did i miss Moby 1.0 ? Shouldn't be with a number > also > somewhere a corresponding version in the cvs ? > > What I miss is that someone can build any software with Moby 1.0 or what > ever... the cvs is still unversioned as I can see... > > I would love to see different branches. Currently it can happens that > with > changes in the Moby API software is not working. If this had be > versionized, > the API could change but software could still work with Version xy. > > Maybe I missed something - of course its awesome to have money for > Moby2... > but from my point of view Moby 1 is still missing stuff (versionizing at > the > top) ? > > Are there any plans to invite some kind of versions into Moby API ? > > I'm really like to discuss things further, I'm just afraid that there are > several issues still alive and everyone is just thinking of Moby 2. > > my 2 cents > andreas > > On Tuesday 08 January 2008 00:08, Mark Wilkinson wrote: >> Hi all, >> >> So after last week's disappointment from Genome Canada, I got news this >> morning that the Canadian Institutes of Health Research have funded >> CardioSHARE (a.k.a. Moby 2.0) for $500,000!!! We now have almost $1M to >> invest in Moby 2 :-) >> >> Here we go!! >> >> Mark > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Tue Jan 8 18:38:00 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 11:38:00 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <478395C0.4040401@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> Message-ID: <4783C308.3030603@ucalgary.ca> Hi all, I was talking off-list with Eddie and I think I found a problem with the current spec vis-a-vis LSIDs. Currently, there is no way to figure out a given registry what its LSID authority is. This means you can't reliably resolve metadata about objects without hardcoding the authority. For example, if I want to resolve the meta data for a service such as TrimVectorSeqs @ moby.ucalgary.ca the LSID is urn:lsid:biomoby.org:serviceinstance:moby.ucalgary.ca,TrimVectorSeqs which I can fetch and get all kinds of wonderful details about the service, including in the future things like test cases. The problem is that the biomoby.org part only works for stuff registered at the main Moby Central server. If I want to use the INB central server, there is currently no way for the registry to tell me what to put in the LSID where the "biomoby.org" normally is. I need this, for example, so that MobyService.getService(name, authority, registry) can fetch all the details of the service and create a meaningful MobyService object from RDF (as that's the direction we are heading). This is the last bit of my jMOBY code that doesn't support multiple registries, so it's serious stumbling block. My proposal is that we a new method something like the current retrieveResourceURLs method, but called retrieveResourceLSIDAuthorities. The output would look like: In this particular case, the registry is using the standard data type, namespace and service type definitions, but has its own list of service instances...such a mirror probably may not exist at the moment, but you get the point. Thoughts? -Paul From gordonp at ucalgary.ca Tue Jan 8 18:44:29 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 11:44:29 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <4783C308.3030603@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> Message-ID: <4783C48D.8050705@ucalgary.ca> Sorry, the XML should as below (no "url" attributes) > > > > > > > From markw at illuminae.com Tue Jan 8 19:14:25 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Jan 2008 11:14:25 -0800 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <4783C308.3030603@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> Message-ID: in the mobycentral.conf file there is an "lsid-authority" parameter that is set during installation. Any new "entities" created by that registry will have that value as the authority of the lsid. ...I don't see the problem...?? M On Tue, 08 Jan 2008 10:38:00 -0800, Paul Gordon wrote: > > Hi all, > > I was talking off-list with Eddie and I think I found a problem with the > current spec vis-a-vis LSIDs. Currently, there is no way to figure out > a given registry what its LSID authority is. This means you can't > reliably resolve metadata about objects without hardcoding the > authority. For example, if I want to resolve the meta data for a > service such as TrimVectorSeqs @ moby.ucalgary.ca the LSID is > > urn:lsid:biomoby.org:serviceinstance:moby.ucalgary.ca,TrimVectorSeqs > > which I can fetch and get all kinds of wonderful details about the > service, including in the future things like test cases. The problem is > that the biomoby.org part only works for stuff registered at the main > Moby Central server. If I want to use the INB central server, there is > currently no way for the registry to tell me what to put in the LSID > where the "biomoby.org" normally is. I need this, for example, so that > MobyService.getService(name, authority, registry) can fetch all the > details of the service and create a meaningful MobyService object from > RDF (as that's the direction we are heading). This is the last bit of > my jMOBY code that doesn't support multiple registries, so it's serious > stumbling block. > > My proposal is that we a new method something like the current > retrieveResourceURLs method, but called > retrieveResourceLSIDAuthorities. The output would look like: > > > > > > > > > In this particular case, the registry is using the standard data type, > namespace and service type definitions, but has its own list of service > instances...such a mirror probably may not exist at the moment, but you > get the point. > > Thoughts? > > -Paul > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Tue Jan 8 19:25:02 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 12:25:02 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> Message-ID: <4783CE0E.8010408@ucalgary.ca> But how do I get the LSID for a service without retrieving the the whole massive ServiceInstance RDF? I want the LSID in order to avoid needing to fetch and parse that file... Mark Wilkinson wrote: > in the mobycentral.conf file there is an "lsid-authority" parameter > that is set during installation. Any new "entities" created by that > registry will have that value as the authority of the lsid. > > ...I don't see the problem...?? > > M > > > > > On Tue, 08 Jan 2008 10:38:00 -0800, Paul Gordon > wrote: > >> >> Hi all, >> >> I was talking off-list with Eddie and I think I found a problem with >> the current spec vis-a-vis LSIDs. Currently, there is no way to >> figure out a given registry what its LSID authority is. This means >> you can't reliably resolve metadata about objects without hardcoding >> the authority. For example, if I want to resolve the meta data for a >> service such as TrimVectorSeqs @ moby.ucalgary.ca the LSID is >> >> urn:lsid:biomoby.org:serviceinstance:moby.ucalgary.ca,TrimVectorSeqs >> >> which I can fetch and get all kinds of wonderful details about the >> service, including in the future things like test cases. The problem >> is that the biomoby.org part only works for stuff registered at the >> main Moby Central server. If I want to use the INB central server, >> there is currently no way for the registry to tell me what to put in >> the LSID where the "biomoby.org" normally is. I need this, for >> example, so that MobyService.getService(name, authority, registry) >> can fetch all the details of the service and create a meaningful >> MobyService object from RDF (as that's the direction we are >> heading). This is the last bit of my jMOBY code that doesn't support >> multiple registries, so it's serious stumbling block. >> >> My proposal is that we a new method something like the current >> retrieveResourceURLs method, but called >> retrieveResourceLSIDAuthorities. The output would look like: >> >> >> >> >> >> >> >> >> In this particular case, the registry is using the standard data >> type, namespace and service type definitions, but has its own list of >> service instances...such a mirror probably may not exist at the >> moment, but you get the point. >> >> Thoughts? >> >> -Paul >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > From markw at illuminae.com Tue Jan 8 19:25:38 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 08 Jan 2008 11:25:38 -0800 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: <4783CE0E.8010408@ucalgary.ca> References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> <4783CE0E.8010408@ucalgary.ca> Message-ID: findService() or it's Java equivalent M On Tue, 08 Jan 2008 11:25:02 -0800, Paul Gordon wrote: > But how do I get the LSID for a service without retrieving the the whole > massive ServiceInstance RDF? I want the LSID in order to avoid needing > to fetch and parse that file... -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Tue Jan 8 19:44:28 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 08 Jan 2008 12:44:28 -0700 Subject: [MOBY-dev] A need for Moby 1.0.0.1? In-Reply-To: References: <200801071244.03574.groscurt@mpiz-koeln.mpg.de> <4782ABFF.8030903@ucalgary.ca> <200801081037.55853.groscurt@mpiz-koeln.mpg.de> <478395C0.4040401@ucalgary.ca> <4783C308.3030603@ucalgary.ca> <4783CE0E.8010408@ucalgary.ca> Message-ID: <4783D29C.80505@ucalgary.ca> Right. I guess I can only supplement the findService call, not replace it, in order to fetch metadata. Makes sense if we allow entities with various authorities in the same registry... > findService() or it's Java equivalent > > M > > > > On Tue, 08 Jan 2008 11:25:02 -0800, Paul Gordon > wrote: > >> But how do I get the LSID for a service without retrieving the the >> whole massive ServiceInstance RDF? I want the LSID in order to avoid >> needing to fetch and parse that file... > > > From groscurt at mpiz-koeln.mpg.de Wed Jan 9 10:45:35 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 9 Jan 2008 11:45:35 +0100 Subject: [MOBY-dev] Moby at the ISMB2008 In-Reply-To: References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> Message-ID: <200801091145.35805.groscurt@mpiz-koeln.mpg.de> Hi, I just wondering because the ISMB2008 is going to be in Toronto... is there anything Mobyicious planned ? I know Martin was in Vienna 2007 - so are ther any plans to be present in Toronto ? Cheers andreas From martin.senger at gmail.com Wed Jan 9 11:06:09 2008 From: martin.senger at gmail.com (Martin Senger) Date: Wed, 9 Jan 2008 11:06:09 +0000 Subject: [MOBY-dev] Moby at the ISMB2008 In-Reply-To: <200801091145.35805.groscurt@mpiz-koeln.mpg.de> References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> <200801091145.35805.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0801090306v40ebe270k91a5cd6bed9ff84f@mail.gmail.com> I will try to go to Toronto. But not necessarily only because of BioMoby. And I will (again) focus more on BOSC (if there will be one) rather than on ISMB. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From Pieter.Neerincx at wur.nl Wed Jan 9 11:43:55 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Wed, 9 Jan 2008 12:43:55 +0100 Subject: [MOBY-dev] Moby at the ISMB2008 In-Reply-To: <200801091145.35805.groscurt@mpiz-koeln.mpg.de> References: <200801081104.31082.groscurt@mpiz-koeln.mpg.de> <200801091145.35805.groscurt@mpiz-koeln.mpg.de> Message-ID: <3B61C008-B4C6-4361-9392-CFA08B8DE940@wur.nl> Hi Devs, I will also try to be there again like Martin and if I'm there I will stay for both the BOSC and the main ISMB conference. I'm not sure though were I will be in August 2008 as my current contract as a PhD student ends in April... If I'll be there I will present at least a poster on my current research which will involve BioMOBY. I'd love to see more posters like that in Toronto, but in addition to that I'd love to see: * More BioMOBY marketing for BioMOBY users especially now the official 1.0 is out: A talk or two + a demo would be great! * A meeting for BioMOBY developers. We could do that in a parallel session, before or after the conference or on the "tutorial day" between the BOSC SIG and the main ISMB conference.... Cheers, Pi On 9-jan-2008, at 11:45, Andreas Groscurth wrote: > Hi, > > I just wondering because the ISMB2008 is going to be in Toronto... > is there > anything Mobyicious planned ? I know Martin was in Vienna 2007 - so > are ther > any plans to be present in Toronto ? > > Cheers > andreas > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Wed Jan 9 15:06:05 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 09 Jan 2008 07:06:05 -0800 Subject: [MOBY-dev] Proofs ready Message-ID: Hi all, I've received the proofs of the Moby 1.0 paper from BiB. The instructions are to not make it public, so I'm not sure I should send it out on the mailing list since the mailing list is public and the mailing list archives are indexed by Google, but I'm happy to send it individually to anyone who asks. Just let me know. Cheers all! Mark From markw at illuminae.com Wed Jan 9 15:27:12 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 09 Jan 2008 07:27:12 -0800 Subject: [MOBY-dev] "dead" services Message-ID: Hi all, Just a reminder that the list of "dead" services (those that do not respond to a ping) is being updated every few hours. The dead services on that list are pretty consistent :-) Are they really dead? or do they just not respond properly to pings? http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Cheers! Mark From edward.kawas at gmail.com Wed Jan 9 15:50:15 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Jan 2008 07:50:15 -0800 Subject: [MOBY-dev] "dead" services In-Reply-To: <4784EA1B.8090904@ucalgary.ca> References: <4784EA1B.8090904@ucalgary.ca> Message-ID: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> Hey Paul, The code that is used to ping the services is available in the cvs under moby-live/Perl/scripts and the file is called service_tester.pl. Eddie -----Original Message----- From: Paul Gordon [mailto:gordonp at .ca] Sent: January-09-08 7:37 AM To: Mark Wilkinson; Eddie Kawas Subject: Re: [MOBY-dev] "dead" services My moby.ucalgary.ca ones are alive, but listed as dead...do y'all have a test pinger I can use to debug? Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > From groscurt at mpiz-koeln.mpg.de Wed Jan 9 18:04:30 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Wed, 9 Jan 2008 19:04:30 +0100 Subject: [MOBY-dev] "dead" services In-Reply-To: References: Message-ID: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> hiho, what are the plans with the dead services ? kill them ;-) ? andreas On Wednesday 09 January 2008 16:27, Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead services on > that list are pretty consistent :-) Are they really dead? or do they > just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From gordonp at ucalgary.ca Wed Jan 9 20:23:38 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 09 Jan 2008 13:23:38 -0700 Subject: [MOBY-dev] "dead" services In-Reply-To: References: Message-ID: <47852D4A.7040109@ucalgary.ca> Hi Mark, The pinger seems to be erroneously marking some (but not all) of mine as dead. I wrote a quick pinger in Java to make sure they actually were alive. If you do a CVS update of moby-live, cd Java, ant compile, then e.g. ./build/run/run-any-client MobyPinger ReverseComplementSequence moby.ucalgary.ca It does return a blank message, as expected. But it's still on the list at http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > From markw at illuminae.com Wed Jan 9 20:24:03 2008 From: markw at illuminae.com (mark wilkinson) Date: Wed, 9 Jan 2008 20:24:03 +0000 GMT Subject: [MOBY-dev] "dead" services In-Reply-To: <47852D4A.7040109@ucalgary.ca> References: <47852D4A.7040109@ucalgary.ca> Message-ID: <911867034-1199910330-cardhu_blackberry.rim.net-8063-@engine12-cell01> Better tell Eddie... He can check what his pinger is "seeing" -- Mark Wilkinson ...on the road! -----Original Message----- From: Paul Gordon Date: Wed, 09 Jan 2008 13:23:38 To:Core developer announcements Subject: Re: [MOBY-dev] "dead" services Hi Mark, The pinger seems to be erroneously marking some (but not all) of mine as dead. I wrote a quick pinger in Java to make sure they actually were alive. If you do a CVS update of moby-live, cd Java, ant compile, then e.g. ./build/run/run-any-client MobyPinger ReverseComplementSequence moby.ucalgary.ca It does return a blank message, as expected. But it's still on the list at http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > _______________________________________________ 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 Jan 10 02:13:50 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 9 Jan 2008 18:13:50 -0800 Subject: [MOBY-dev] "dead" services In-Reply-To: <47852D4A.7040109@ucalgary.ca> References: <47852D4A.7040109@ucalgary.ca> Message-ID: <0A7291E23C694250B7174F2980676073@OfficePC> Hey Paul, I am attaching the code that the pinger uses. Its in the cvs, but I figure that this would be easier since I added a few lines of debug code. Attached is a cgi file. Place it in the cgi-bin of an apache install. Make sure to change the #!/perl.exe part to conform to your perl location. Once that is done, hit this url: http://localhost:8080/cgi-bin/ServicePingerValidator?authority=moby.ucalgary .ca change :8080 to be whatever port you need. You will see that apparently, those services under moby.ucalgary.ca don't have output. Then you can see how I call them. I don't do anything weird! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Paul Gordon Sent: January-09-08 12:24 PM To: Core developer announcements Subject: Re: [MOBY-dev] "dead" services Hi Mark, The pinger seems to be erroneously marking some (but not all) of mine as dead. I wrote a quick pinger in Java to make sure they actually were alive. If you do a CVS update of moby-live, cd Java, ant compile, then e.g. ./build/run/run-any-client MobyPinger ReverseComplementSequence moby.ucalgary.ca It does return a blank message, as expected. But it's still on the list at http://moby.ucalgary.ca/moby/ValidateService?getDeadServices Mark Wilkinson wrote: > Hi all, > > Just a reminder that the list of "dead" services (those that do not > respond to a ping) is being updated every few hours. The dead > services on that list are pretty consistent :-) Are they really > dead? or do they just not respond properly to pings? > > http://moby.ucalgary.ca/moby/ValidateService?getDeadServices > > Cheers! > > Mark > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,4784e5d410950124281630! > > > _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Thu Jan 10 11:17:40 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 10 Jan 2008 12:17:40 +0100 Subject: [MOBY-dev] authoritative ?! In-Reply-To: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> References: <4784EA1B.8090904@ucalgary.ca> <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> Message-ID: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Hi, I just forgot... can someone tell me what the athoritative flag is meaning exactly in the ServiceRegistration Panel in Dashboard ? Awesome Andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Thu Jan 10 11:20:11 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 10 Jan 2008 12:20:11 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: Message-ID: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> And hi again, we just had the discussion here... is it recommended to use primitives as primary input ? Or are there actually only for use in secondary parameters or as part of a complex datatype ? E.g. if a service requires an email as input - give it an object with namespace 'email' or similar - or could I use String with namespace 'email' Thanks and byebye andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Thu Jan 10 11:38:11 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 12:38:11 +0100 Subject: [MOBY-dev] authoritative ?! In-Reply-To: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> References: <4784EA1B.8090904@ucalgary.ca> <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Message-ID: <1BD17253-BA58-4074-A118-21A918F37988@wur.nl> Hi Andreas, The authoritative flag specifies whether you are the local expert with the original service. There should be only one. Any services with the same name, but hosted by different authorities are considered mirrors / copies. Cheers, Pi On 10-jan-2008, at 12:17, Andreas Groscurth wrote: > Hi, > > I just forgot... can someone tell me what the authoritative flag is > meaning > exactly in the ServiceRegistration Panel in Dashboard ? > > Awesome > Andreas > > -- > Andreas Groscurth > Bioinformatics Developer > 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)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From alanrw at cs.man.ac.uk Thu Jan 10 10:42:25 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Thu, 10 Jan 2008 10:42:25 +0000 Subject: [MOBY-dev] "dead" services In-Reply-To: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> References: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> Message-ID: <4785F691.704@cs.man.ac.uk> Andreas Groscurth wrote: > hiho, > > what are the plans with the dead services ? kill them ;-) ? "dead services" aren't necessarily permanently dead. They are really just currently unresponsive. Is there a way to get the pinger to record how long a service has been dead? If it has been down for, say, months then the chances of it coming back tomorrow are probably small. OTOH if it has only been down since yesterday, it may recover soon. > andreas Alan From edward.kawas at gmail.com Thu Jan 10 14:37:47 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 10 Jan 2008 06:37:47 -0800 Subject: [MOBY-dev] "dead" services In-Reply-To: <4785F691.704@cs.man.ac.uk> References: <200801091904.30554.groscurt@mpiz-koeln.mpg.de> <4785F691.704@cs.man.ac.uk> Message-ID: Hi, I created a web form for testing individual services or all services for any given authority. The form is available at: http://moby.ucalgary.ca/cgi-bin/ServicePingerValidator It's in its preliminary form and may still evolve, but it is better than nothing! Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Alan Williams Sent: January-10-08 2:42 AM To: Core developer announcements Subject: Re: [MOBY-dev] "dead" services Andreas Groscurth wrote: > hiho, > > what are the plans with the dead services ? kill them ;-) ? "dead services" aren't necessarily permanently dead. They are really just currently unresponsive. Is there a way to get the pinger to record how long a service has been dead? If it has been down for, say, months then the chances of it coming back tomorrow are probably small. OTOH if it has only been down since yesterday, it may recover soon. > andreas Alan _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jan 10 16:35:10 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 08:35:10 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: Hi Andreas! That's a very interesting case! Is "email" a data-type (Object) or a semantic-type (Namespace)?? It is a semantic type in the sense that all email addresses are unique, and therefore behave as identifiers... but it is often used as a data-type in that it would be associated with other information like an address and telephone number. Personally I would be tempted to make a new namespace 'emailAddress' or something like that, since semantic "precision" is the goal of these two ontologies. What did we do for URLs? ...LOL! Okay, I just went to have a look in the ontologies and we have an Object "URL" and a Namespace "URL"!!! I guess others have had the same question and made different decisions :-) I see that it is Pieter's services that consume the Object "URL" - maybe he can explain to us why he chose to make URL an object rather than a namespace. Pieter? M On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth wrote: > And hi again, > > we just had the discussion here... is it recommended to use primitives as > primary input ? Or are there actually only for use in secondary > parameters or > as part of a complex datatype ? > > E.g. if a service requires an email as input - give it an object with > namespace 'email' or similar - or could I use String with namespace > 'email' > > Thanks and byebye > andreas > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 16:37:21 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 08:37:21 -0800 Subject: [MOBY-dev] authoritative ?! In-Reply-To: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> References: <4784EA1B.8090904@ucalgary.ca> <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Message-ID: "authoritative" is a non-validated way of saying that you are the primary source/owner of the data, and that someone else providing this data would have first had to obtain it from you. Similarly for an analysis - you are the "owner" of the algorithm, or the most up-to-date version of the code. It doesn't promise anything, but it is intended to allow you to chose between providers of the same data for some loose QC. M On Thu, 10 Jan 2008 03:17:40 -0800, Andreas Groscurth wrote: > Hi, > > I just forgot... can someone tell me what the athoritative flag is > meaning > exactly in the ServiceRegistration Panel in Dashboard ? > > Awesome > Andreas > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Thu Jan 10 16:51:06 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 10 Jan 2008 09:51:06 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: <47864CFA.5060500@ucalgary.ca> I think the litmus tests would be: -might I need to subclass the identifier? -would it be useful to associate the identifier with anything besides a base object? -is it a subtype of some other identifier? The answers for email are: -no -yes (e.g. use it as the namespace for a Person object, which relates oppositely to the data-type argument by Mark) -no Sounds like a namespace to me... Mark Wilkinson wrote: > Hi Andreas! > > That's a very interesting case! Is "email" a data-type (Object) or a > semantic-type (Namespace)?? It is a semantic type in the sense that > all email addresses are unique, and therefore behave as identifiers... > but it is often used as a data-type in that it would be associated > with other information like an address and telephone number. > > Personally I would be tempted to make a new namespace 'emailAddress' > or something like that, since semantic "precision" is the goal of > these two ontologies. > > What did we do for URLs? ...LOL! Okay, I just went to have a look in > the ontologies and we have an Object "URL" and a Namespace "URL"!!! I > guess others have had the same question and made different decisions > :-) I see that it is Pieter's services that consume the Object "URL" > - maybe he can explain to us why he chose to make URL an object rather > than a namespace. > > Pieter? > > M > > > > On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth > wrote: > >> And hi again, >> >> we just had the discussion here... is it recommended to use >> primitives as >> primary input ? Or are there actually only for use in secondary >> parameters or >> as part of a complex datatype ? >> >> E.g. if a service requires an email as input - give it an object with >> namespace 'email' or similar - or could I use String with namespace >> 'email' >> >> Thanks and byebye >> andreas >> > > > From markw at illuminae.com Thu Jan 10 16:50:51 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 08:50:51 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47864CFA.5060500@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> Message-ID: Yup, me too. (same for URL...) M On Thu, 10 Jan 2008 08:51:06 -0800, Paul Gordon wrote: > I think the litmus tests would be: > -might I need to subclass the identifier? > -would it be useful to associate the identifier with anything besides a > base object? > -is it a subtype of some other identifier? > > The answers for email are: > -no > -yes (e.g. use it as the namespace for a Person object, which relates > oppositely to the data-type argument by Mark) > -no > > Sounds like a namespace to me... > > Mark Wilkinson wrote: >> Hi Andreas! >> >> That's a very interesting case! Is "email" a data-type (Object) or a >> semantic-type (Namespace)?? It is a semantic type in the sense that >> all email addresses are unique, and therefore behave as identifiers... >> but it is often used as a data-type in that it would be associated with >> other information like an address and telephone number. >> >> Personally I would be tempted to make a new namespace 'emailAddress' or >> something like that, since semantic "precision" is the goal of these >> two ontologies. >> >> What did we do for URLs? ...LOL! Okay, I just went to have a look in >> the ontologies and we have an Object "URL" and a Namespace "URL"!!! I >> guess others have had the same question and made different decisions >> :-) I see that it is Pieter's services that consume the Object "URL" - >> maybe he can explain to us why he chose to make URL an object rather >> than a namespace. >> >> Pieter? >> >> M >> >> >> >> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >> wrote: >> >>> And hi again, >>> >>> we just had the discussion here... is it recommended to use primitives >>> as >>> primary input ? Or are there actually only for use in secondary >>> parameters or >>> as part of a complex datatype ? >>> >>> E.g. if a service requires an email as input - give it an object with >>> namespace 'email' or similar - or could I use String with namespace >>> 'email' >>> >>> Thanks and byebye >>> andreas >>> >> >> >> > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 17:29:42 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 09:29:42 -0800 Subject: [MOBY-dev] Comments by tomorrow please Message-ID: Hi all, There's a 48 hour deadline for getting the proof's edited. For those of you who have requested a copy of the proofs, please send me your comments by the end of the day tomorrow. I have found quite a few edits. Thanks! Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 groscurt at mpiz-koeln.mpg.de Thu Jan 10 17:26:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Thu, 10 Jan 2008 18:26:09 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47864CFA.5060500@ucalgary.ca> References: <47864CFA.5060500@ucalgary.ca> Message-ID: <200801101826.09952.groscurt@mpiz-koeln.mpg.de> Thanks to the two of you... /bow made my world clearer again *g On Thursday 10 January 2008 17:51, Paul Gordon wrote: > I think the litmus tests would be: > -might I need to subclass the identifier? > -would it be useful to associate the identifier with anything besides a > base object? > -is it a subtype of some other identifier? > > The answers for email are: > -no > -yes (e.g. use it as the namespace for a Person object, which relates > oppositely to the data-type argument by Mark) > -no > > Sounds like a namespace to me... > > Mark Wilkinson wrote: > > Hi Andreas! > > > > That's a very interesting case! Is "email" a data-type (Object) or a > > semantic-type (Namespace)?? It is a semantic type in the sense that > > all email addresses are unique, and therefore behave as identifiers... > > but it is often used as a data-type in that it would be associated > > with other information like an address and telephone number. > > > > Personally I would be tempted to make a new namespace 'emailAddress' > > or something like that, since semantic "precision" is the goal of > > these two ontologies. > > > > What did we do for URLs? ...LOL! Okay, I just went to have a look in > > the ontologies and we have an Object "URL" and a Namespace "URL"!!! I > > guess others have had the same question and made different decisions > > > > :-) I see that it is Pieter's services that consume the Object "URL" > > > > - maybe he can explain to us why he chose to make URL an object rather > > than a namespace. > > > > Pieter? > > > > M > > > > > > > > On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth > > > > wrote: > >> And hi again, > >> > >> we just had the discussion here... is it recommended to use > >> primitives as > >> primary input ? Or are there actually only for use in secondary > >> parameters or > >> as part of a complex datatype ? > >> > >> E.g. if a service requires an email as input - give it an object with > >> namespace 'email' or similar - or could I use String with namespace > >> 'email' > >> > >> Thanks and byebye > >> andreas > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Thu Jan 10 18:07:56 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 19:07:56 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: Hi, On 10-jan-2008, at 17:35, Mark Wilkinson wrote: > Hi Andreas! > > That's a very interesting case! Is "email" a data-type (Object) or > a semantic-type (Namespace)?? It is a semantic type in the sense > that all email addresses are unique, and therefore behave as > identifiers... but it is often used as a data-type in that it would > be associated with other information like an address and telephone > number. > > Personally I would be tempted to make a new namespace > 'emailAddress' or something like that, since semantic "precision" > is the goal of these two ontologies. > > What did we do for URLs? ...LOL! Okay, I just went to have a look > in the ontologies and we have an Object "URL" and a Namespace > "URL"!!! I guess others have had the same question and made > different decisions :-) I see that it is Pieter's services that > consume the Object "URL" - maybe he can explain to us why he chose > to make URL an object rather than a namespace. > > Pieter? I've been struggling with this question as well. If you check the object ontology you'll see I also registered an Email object. Email addresses and URLs can be both a data-type (Object) and a semantic- type (Namespace), so maybe it would be best to use both. Actually I was waiting for a response of the founding father a.k.a. chief architect to clarify this one :)... We give several courses which involve BioMOBY and usually the part where the students have to: * choose whether to recycle existing objects & namespaces or design new objects & namespaces * and if they choose to design new ones, come up with the exact structure for those objects & namespaces is the most difficult part of the entire course. Cheers, Pi > M > > > > On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth > wrote: > >> And hi again, >> >> we just had the discussion here... is it recommended to use >> primitives as >> primary input ? Or are there actually only for use in secondary >> parameters or >> as part of a complex datatype ? >> >> E.g. if a service requires an email as input - give it an object with >> namespace 'email' or similar - or could I use String with >> namespace 'email' >> >> Thanks and byebye >> andreas >> > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Thu Jan 10 18:31:06 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 10:31:06 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: I agree with Paul (or did Paul agree with me??) that email and url are namespaces. Paul's argument that it doesn't make sense to sub-class an email or a url is a compelling one, which also gives me some assurance that this decision is correct. ...on the other hand, there have been several requests from people in the community to create subclasses of namespaces (e.g. NCBI-->NCBI_gi), and in the case of IRRI their need was sufficiently strong that they ended up created objects that represented their identifiers such that they could sub-class them at the object level! So there is a clear desire and apparent need to be able to categorize namespaces as well... M On Thu, 10 Jan 2008 10:07:56 -0800, Pieter Neerincx wrote: > Hi, > > On 10-jan-2008, at 17:35, Mark Wilkinson wrote: > >> Hi Andreas! >> >> That's a very interesting case! Is "email" a data-type (Object) or a >> semantic-type (Namespace)?? It is a semantic type in the sense that >> all email addresses are unique, and therefore behave as identifiers... >> but it is often used as a data-type in that it would be associated with >> other information like an address and telephone number. >> >> Personally I would be tempted to make a new namespace 'emailAddress' or >> something like that, since semantic "precision" is the goal of these >> two ontologies. >> >> What did we do for URLs? ...LOL! Okay, I just went to have a look in >> the ontologies and we have an Object "URL" and a Namespace "URL"!!! I >> guess others have had the same question and made different decisions >> :-) I see that it is Pieter's services that consume the Object "URL" - >> maybe he can explain to us why he chose to make URL an object rather >> than a namespace. >> >> Pieter? > > I've been struggling with this question as well. If you check the object > ontology you'll see I also registered an Email object. Email addresses > and URLs can be both a data-type (Object) and a semantic-type > (Namespace), so maybe it would be best to use both. Actually I was > waiting for a response of the founding father a.k.a. chief architect to > clarify this one :)... > > We give several courses which involve BioMOBY and usually the part where > the students have to: > * choose whether to recycle existing objects & namespaces or design > new objects & namespaces > * and if they choose to design new ones, come up with the exact > structure for those objects & namespaces > is the most difficult part of the entire course. > > Cheers, > > Pi > > >> M >> >> >> >> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >> wrote: >> >>> And hi again, >>> >>> we just had the discussion here... is it recommended to use primitives >>> as >>> primary input ? Or are there actually only for use in secondary >>> parameters or >>> as part of a complex datatype ? >>> >>> E.g. if a service requires an email as input - give it an object with >>> namespace 'email' or similar - or could I use String with namespace >>> 'email' >>> >>> Thanks and byebye >>> andreas >>> >> >> >> >> ---- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Thu Jan 10 18:37:42 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 19:37:42 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47864CFA.5060500@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> Message-ID: <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> Hi Paul, On 10-jan-2008, at 17:51, Paul Gordon wrote: > I think the litmus tests would be: > 1. might I need to subclass the identifier? > 2. would it be useful to associate the identifier with anything > besides a base object? > 3. is it a subtype of some other identifier? > > The answers for email are: > 1. no > 2. yes (e.g. use it as the namespace for a Person object, which > relates oppositely to the data-type argument by Mark) > 3. no The reason I initially choose to register an Email object instead of a namespace is that it would allow me to subclass it in the future. I have to admit I didn't do that yet, which would be a vote in favour of a namespace, but who knows... Same for the URLs. My answer to question 1 would be a maybe, maybe not. In addition URLs are a subtype of URIs. (Although I have to admit I didn't register them as such: URL isa URI would make sense to me) So how would you handle URLs? Object or namespace? Cheers, Pi > Sounds like a namespace to me... > > Mark Wilkinson wrote: >> Hi Andreas! >> >> That's a very interesting case! Is "email" a data-type (Object) >> or a semantic-type (Namespace)?? It is a semantic type in the >> sense that all email addresses are unique, and therefore behave as >> identifiers... but it is often used as a data-type in that it >> would be associated with other information like an address and >> telephone number. >> >> Personally I would be tempted to make a new namespace >> 'emailAddress' or something like that, since semantic "precision" >> is the goal of these two ontologies. >> >> What did we do for URLs? ...LOL! Okay, I just went to have a >> look in the ontologies and we have an Object "URL" and a Namespace >> "URL"!!! I guess others have had the same question and made >> different decisions :-) I see that it is Pieter's services that >> consume the Object "URL" - maybe he can explain to us why he chose >> to make URL an object rather than a namespace. >> >> Pieter? >> >> M >> >> >> >> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >> wrote: >> >>> And hi again, >>> >>> we just had the discussion here... is it recommended to use >>> primitives as >>> primary input ? Or are there actually only for use in secondary >>> parameters or >>> as part of a complex datatype ? >>> >>> E.g. if a service requires an email as input - give it an object >>> with >>> namespace 'email' or similar - or could I use String with >>> namespace 'email' >>> >>> Thanks and byebye >>> andreas >>> >> >> >> > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Thu Jan 10 18:44:52 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 10:44:52 -0800 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> Message-ID: On Thu, 10 Jan 2008 10:37:42 -0800, Pieter Neerincx wrote: > In addition URLs are a subtype of URIs. (Although I have to admit I > didn't register them as such: URL isa URI would make sense to me) So how > would you handle URLs? Object or namespace? I think we need to un-flatten the Namespace ontology, at least from the perspective of some tools (other users, like the Gene Ontology, could use the hierarchical Namespace ontology as a flat list as they always have) Let me look at the current API and see how difficult it would be to do that without breaking anything... M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Thu Jan 10 19:03:42 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 20:03:42 +0100 Subject: [MOBY-dev] MobyCentral connection lost :( In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> Message-ID: <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> Hi Chaps, I'm repeatedly getting: Connection to MOBY Central at 'http://moby.ucalgary.ca/MOBY/Central' died because: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/ mysql.sock' (2) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ Adaptor/moby/queryapi/mysql.pm line 90 ERROR ERROR ERROR Is that a MySQL problem in Calgary or am I doing something wrong? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Pieter.Neerincx at wur.nl Thu Jan 10 19:05:18 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 20:05:18 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: <22BB025F-54EE-4450-9CF9-18633BD1BC0A@wur.nl> On 10-jan-2008, at 19:31, Mark Wilkinson wrote: > I agree with Paul (or did Paul agree with me??) that email and url > are namespaces. Paul's argument that it doesn't make sense to sub- > class an email or a url is a compelling one, which also gives me > some assurance that this decision is correct. > > ...on the other hand, there have been several requests from people > in the community to create subclasses of namespaces (e.g. NCBI-- > >NCBI_gi), and in the case of IRRI their need was sufficiently > strong that they ended up created objects that represented their > identifiers such that they could sub-class them at the object > level! So there is a clear desire and apparent need to be able to > categorize namespaces as well... Yes, that would really help! :) Pi > M > > > > On Thu, 10 Jan 2008 10:07:56 -0800, Pieter Neerincx > wrote: > >> Hi, >> >> On 10-jan-2008, at 17:35, Mark Wilkinson wrote: >> >>> Hi Andreas! >>> >>> That's a very interesting case! Is "email" a data-type (Object) >>> or a semantic-type (Namespace)?? It is a semantic type in the >>> sense that all email addresses are unique, and therefore behave >>> as identifiers... but it is often used as a data-type in that it >>> would be associated with other information like an address and >>> telephone number. >>> >>> Personally I would be tempted to make a new namespace >>> 'emailAddress' or something like that, since semantic "precision" >>> is the goal of these two ontologies. >>> >>> What did we do for URLs? ...LOL! Okay, I just went to have a >>> look in the ontologies and we have an Object "URL" and a >>> Namespace "URL"!!! I guess others have had the same question and >>> made different decisions :-) I see that it is Pieter's services >>> that consume the Object "URL" - maybe he can explain to us why he >>> chose to make URL an object rather than a namespace. >>> >>> Pieter? >> >> I've been struggling with this question as well. If you check the >> object ontology you'll see I also registered an Email object. >> Email addresses and URLs can be both a data-type (Object) and a >> semantic-type (Namespace), so maybe it would be best to use both. >> Actually I was waiting for a response of the founding father >> a.k.a. chief architect to clarify this one :)... >> >> We give several courses which involve BioMOBY and usually the part >> where the students have to: >> * choose whether to recycle existing objects & namespaces or >> design new objects & namespaces >> * and if they choose to design new ones, come up with the exact >> structure for those objects & namespaces >> is the most difficult part of the entire course. >> >> Cheers, >> >> Pi >> >> >>> M >>> >>> >>> >>> On Thu, 10 Jan 2008 03:20:11 -0800, Andreas Groscurth >>> wrote: >>> >>>> And hi again, >>>> >>>> we just had the discussion here... is it recommended to use >>>> primitives as >>>> primary input ? Or are there actually only for use in secondary >>>> parameters or >>>> as part of a complex datatype ? >>>> >>>> E.g. if a service requires an email as input - give it an object >>>> with >>>> namespace 'email' or similar - or could I use String with >>>> namespace 'email' >>>> >>>> Thanks and byebye >>>> andreas >>>> >>> >>> >>> >>> ---- >>> Mark Wilkinson >>> Assistant Professor, Dept. Medical Genetics >>> University of British Columbia >>> PI Bioinformatics >>> iCAPTURE Centre, St. Paul's Hospital >>> Tel: 604 682 2344 x62129 >>> Fax: 604 806 9274 >>> >>> ***CONFIDENTIALITY NOTICE*** >>> This electronic message is intended only for the use of the >>> addressee and may contain information that is privileged and >>> confidential. Any dissemination, distribution or copying of this >>> communication by unauthorized individuals is strictly prohibited. >>> If you have received this communication in error, please notify >>> the sender immediately by reply e-mail and delete the original >>> and all copies from your system. >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >> >> ------------------------------------------------------------- >> Wageningen University and Research centre (WUR) >> Laboratory of Bioinformatics >> Transitorium (building 312) room 1034 >> >> Dreijenlaan 3 >> 6703 HA Wageningen >> The Netherlands >> >> phone: 0317-483 039 >> fax: 0317-483 584 >> mobile: 06-143 66 783 >> mail: pieter.neerincx at wur.nl >> skype: pieter.online >> ------------------------------------------------------------ >> >> >> _______________________________________________ >> 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 > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From edward.kawas at gmail.com Thu Jan 10 19:05:06 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Thu, 10 Jan 2008 11:05:06 -0800 Subject: [MOBY-dev] MobyCentral connection lost :( In-Reply-To: <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca><6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> Message-ID: <16EFBFE2806C43D2A0F27781A894ABEA@OfficePC> Hi Pieter, There seems to be something wrong with mysql. Hopefully the problem will be resolved shortly. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: January-10-08 11:04 AM To: Core developer announcements Subject: [MOBY-dev] MobyCentral connection lost :( Hi Chaps, I'm repeatedly getting: Connection to MOBY Central at 'http://moby.ucalgary.ca/MOBY/Central' died because: DBI connect('mobycentral:localhost:3306','moby',...) failed: Can't connect to local MySQL server through socket '/tmp/ mysql.sock' (2) at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ Adaptor/moby/queryapi/mysql.pm line 90 ERROR ERROR ERROR Is that a MySQL problem in Calgary or am I doing something wrong? Cheers, Pi ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Thu Jan 10 19:06:23 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 11:06:23 -0800 Subject: [MOBY-dev] MobyCentral connection lost :( In-Reply-To: <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47864CFA.5060500@ucalgary.ca> <6068FDFC-06AD-4481-AC52-791CBACC7BF9@wur.nl> <495FCBA3-1CAD-4419-B6FA-B387A5D8F0E7@wur.nl> Message-ID: It went down a few minutes ago - looking into it. M On Thu, 10 Jan 2008 11:03:42 -0800, Pieter Neerincx wrote: > Hi Chaps, > > I'm repeatedly getting: > > Connection to MOBY Central at 'http://moby.ucalgary.ca/MOBY/Central' > died because: > DBI connect('mobycentral:localhost:3306','moby',...) failed: > Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2) > at /opt/coolstack/lib/perl5/site_perl/5.8.8/MOBY/ > Adaptor/moby/queryapi/mysql.pm line 90 > > ERROR ERROR ERROR > > Is that a MySQL problem in Calgary or am I doing something wrong? > > Cheers, > > Pi > > > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Thu Jan 10 19:10:03 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Thu, 10 Jan 2008 20:10:03 +0100 Subject: [MOBY-dev] Comments by tomorrow please In-Reply-To: References: Message-ID: <7AE7220D-69ED-449F-BAD0-C04DC756AEFE@wur.nl> Hi Mark, Please send me copy too. I'll look at it immediately after squash tonight :)... Cheers, Pi On 10-jan-2008, at 18:29, Mark Wilkinson wrote: > Hi all, > > There's a 48 hour deadline for getting the proof's edited. For > those of you who have requested a copy of the proofs, please send > me your comments by the end of the day tomorrow. I have found > quite a few edits. > > Thanks! > > Mark > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From markw at illuminae.com Thu Jan 10 19:10:27 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 11:10:27 -0800 Subject: [MOBY-dev] Comments by tomorrow please In-Reply-To: <7AE7220D-69ED-449F-BAD0-C04DC756AEFE@wur.nl> References: <7AE7220D-69ED-449F-BAD0-C04DC756AEFE@wur.nl> Message-ID: Crap... I sent it to the dev list by mistake :-/ >> sigh<< M On Thu, 10 Jan 2008 11:10:03 -0800, Pieter Neerincx wrote: > Hi Mark, > > Please send me copy too. I'll look at it immediately after squash > tonight :)... > > Cheers, > > Pi > > On 10-jan-2008, at 18:29, Mark Wilkinson wrote: > >> Hi all, >> >> There's a 48 hour deadline for getting the proof's edited. For those >> of you who have requested a copy of the proofs, please send me your >> comments by the end of the day tomorrow. I have found quite a few >> edits. >> >> Thanks! >> >> Mark >> >> ---- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > 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 Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 meredith at cantab.net Thu Jan 10 19:09:47 2008 From: meredith at cantab.net (Tom Oinn) Date: Thu, 10 Jan 2008 19:09:47 +0000 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> Message-ID: <47866D7B.206@cantab.net> Mark Wilkinson wrote: > I agree with Paul (or did Paul agree with me??) that email and url are > namespaces. Paul's argument that it doesn't make sense to sub-class an > email or a url is a compelling one, which also gives me some assurance > that this decision is correct. There are plenty of cases where you might want to restrict the permitted semantics of a URL, most of which boil down to a restriction on what the URL can point *to*. Email addresses are different, in that they all have the same inherent content. They're not really references in the same way as URLs. It's somewhat broken in my view to have URL in moby *at all*, it would be better to have a framework where you could explicitly seperate the reference from that to which it refers. If you have a tool that accepts a URL to an image the signature of the tool is 'image', the URL part of that is the delivery mechanism and in an ideal world they wouldn't be conflated in this way. The exception would be something that took a URL as a string to, e.g. validate it according to the URL specification (in which case the type is 'url' and the carrier type is 'string value'). If you could define types in terms of their carrier mechanism (URL, SCP path, value etc) and split this out from the actual content they carry (image, person, bio-foo-object) this would make life a lot easier (and is, in a completely non-coincidental fashion, what Taverna2 does for exactly this reason). Of course that's just a 'small' change to how Moby works :) Tom From markw at illuminae.com Thu Jan 10 21:23:08 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 13:23:08 -0800 Subject: [MOBY-dev] Ignore the RSS feeds Message-ID: They appear to not be working properly right now. Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 22:53:38 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 14:53:38 -0800 Subject: [MOBY-dev] A Demonstration at ISMB? Message-ID: I wonder if it might be worth doing a demonstration at ISMB, or maybe a couple, using the various software tools we have (e.g. Taverna, MOWServ, SeaHawk). It only costs $400 if we are selected, and the deadline is further along in the year so it isn't as frantic. http://www.iscb.org/ismb2008/sub_demonstrations.php ?? Anyone interested? If not, I'm certainly going to try to get us in for teh Moby extensions to Taverna at least, but it would be good to partner with someone else who has a different Moby interface so that people can see a broader view of what can be done. It would be a good place to hand-out T-shirts too ;-) Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Jan 10 22:55:48 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 10 Jan 2008 14:55:48 -0800 Subject: [MOBY-dev] The 1.0 paper into the "highlights" track Message-ID: http://www.iscb.org/ismb2008/high_track.php I'll certainly be sending the 1.0 paper to the highlights track to see if we can get in there too... fingers crossed! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 gordonp at ucalgary.ca Fri Jan 11 03:54:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Thu, 10 Jan 2008 20:54:52 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47866D7B.206@cantab.net> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> Message-ID: <4786E88C.4070707@ucalgary.ca> > Mark Wilkinson wrote: >> I agree with Paul (or did Paul agree with me??) that email and url >> are namespaces. Paul's argument that it doesn't make sense to >> sub-class an email or a url is a compelling one, which also gives me >> some assurance that this decision is correct. Mark, I didn't actually say that URLs were a namespace -- just e-mails. I avoided talking about URLs because I knew I'd have to write a longer philosophical e-mail..like this one :-) To be correct, the namespace should actually be "smtp", as the e-mail address format that we are used to (foo at bar.tld) is specific to SMTP. Anyone remember uucp-based e-mail? This might seem pedantic, but it makes a point: the e-mail address is what is referred to in semiotics as an "index". Now for some semiotic theory. Normally, the association between a sign (e.g. the word "cow") and the entity it refers to (an actual, physical cow) is arbitrary, it's a cultural artifact. These are called symbols (gene symbols such as "adh1" are examples of this too). An index is a sign who's association with its referent is not random: the referent is unambiguously resolveable, given a retrieval protocol. A protocol and an index go hand-in-hand. An e-mail address points an SMTP client (the sign interpreter) unambiguously at a destination for a message, ergo, the e-mail address is an index for the SMTP protocol. In Moby, the protocol is the namespace (e.g. NCBI_gi), the index is the ID (e.g. 100389), and the interpreter is an NCBI-savvy Moby service that will be able to retrieve based on the index. URLs are different beasts. The fact that you can represent an e-mail address as a URL speaks to this fact (e.g. mailto:foo at bar.tld). A URL combines a protocol and an index ("protocol:index"). Technically, probably the best way to represent the URL http://www.google.com in Moby would be to have an HTTP namespace, and use the id "//www.google.com". Then you make http-savvy Moby services, registered accepting objects in the HTTP namespace. The confusion comes from the fact that the protocol+index combo can be either in the namespace/id part, or in the form of a data type. Why then do we bother having id/namepsace? Tom was on to something, but not quite. There is exactly one "carrier mechanism" in Moby: services. They know how to resolve an index combos and give you the referent back. Namespaces are exceptionally useful because they allow you to use an index with or without the things that are keyed off them. A perfect illustration this is a VirtualSequence with a namespace and id. Another good way to get a sense of the appropriateness of namespace/id is the Moby cross-reference block (CRIB). If you made E-mail a data type, you couldn't use it in the CRIB because you're not using the namespace/id combo to make the cross-reference in the only way Moby inherently knows how. My $0.02 :-) From meredith at cantab.net Fri Jan 11 08:37:11 2008 From: meredith at cantab.net (Tom Oinn) Date: Fri, 11 Jan 2008 08:37:11 +0000 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <4786E88C.4070707@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> Message-ID: <47872AB7.8060105@cantab.net> Paul Gordon wrote: > The confusion comes from the fact that the protocol+index combo can be > either in the namespace/id part, or in the form of a data type. Why > then do we bother having id/namepsace? Tom was on to something, but not > quite. There is exactly one "carrier mechanism" in Moby: services. They > know how to resolve an index combos and give you the referent back. If the above is true then can you tell me the type for an input which requires an image in PNG format pointed to by a URL? I don't think you can... There is one carrier mechanism in Moby, but this is being used to carry entities which are themselves indices into other systems. Unless I wildly misunderstand something (entirely possible I admit) there's no way to say 'URL to an image' let alone 'URL to an image of my cat'. Tom From groscurt at mpiz-koeln.mpg.de Fri Jan 11 09:00:29 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 10:00:29 +0100 Subject: [MOBY-dev] A Demonstration at ISMB? In-Reply-To: References: Message-ID: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> If this is appropiate and enough for a part of the Moby demonstration - I would like to point to my Aggregator Jabba ( http://bioinfo.mpiz-koeln.mpg.de/jabba ). I think, and support what Pieter already said, a demonstration of available cool tools would be nice to spread out more of Moby into the world.... And... WE HAVE T-SHIRTS ?! cool *g Andreas On Thursday 10 January 2008 23:53, Mark Wilkinson wrote: > I wonder if it might be worth doing a demonstration at ISMB, or maybe a > couple, using the various software tools we have (e.g. Taverna, MOWServ, > SeaHawk). > > It only costs $400 if we are selected, and the deadline is further along > in the year so it isn't as frantic. > > http://www.iscb.org/ismb2008/sub_demonstrations.php > > ?? Anyone interested? If not, I'm certainly going to try to get us in > for teh Moby extensions to Taverna at least, but it would be good to > partner with someone else who has a different Moby interface so that > people can see a broader view of what can be done. > > It would be a good place to hand-out T-shirts too ;-) > > Mark -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Fri Jan 11 10:40:20 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 11 Jan 2008 11:40:20 +0100 Subject: [MOBY-dev] A Demonstration at ISMB? In-Reply-To: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> References: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> Message-ID: <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> Hi, On 11 Jan 2008, at 10:00, Andreas Groscurth wrote: > If this is appropiate and enough for a part of the Moby > demonstration - I > would like to point to my Aggregator Jabba > ( http://bioinfo.mpiz-koeln.mpg.de/jabba ). Hey, I haven't seen this Jabba before... Shouldn't it be listed on the BioMOBY site at http://biomoby.open-bio.org/index.php/ browser_clients/ ? > I think, and support what Pieter already said, a demonstration of > available > cool tools would be nice to spread out more of Moby into the world.... > > And... WE HAVE T-SHIRTS ?! cool *g Not yet as far as I know, but it would be a really good way to make some advertisement for BioMOBY. The last two years of ISMB there were two booths that received an enormous amount of attention for a while. Those were the BMC and PLoS booths when they were handing out free t- shirts. At the PLoS booth it was so hectic, people were almost fighting over those shirts. The next few days you saw people all over the conference and city center with those shirts :) With regard to a demo, I think the $400 is bullshit. Previously they didn't charge extra for that. They started to do that last year. The conference itself is already very expensive, but well worth it. No- one who gets selected for the PloS-track, highlights-track, poster- track, etc. has to pay extra to be able to present. So why the hell would you have to for a software demo? The problem with the software demo's is that a lot of previously demoed stuff was not freely available to the scientific community. Even if it was presented by a non-profit organisation, there was quite some closed source stuff for which you had to buy a licence. Hence, they must have figured they could charge us for a demo if we are going to make money from this software. I complained about it last year and asked the organisation to charge only for closed source payware and not for open source freeware. Unfortunately they didn't change the rules, so I think a demo is a good thing to do, but as long as we can get some papers in the highlight- and/or PLoS-track, we can just show stuff there. Whether the audience is looking at a beamer with a static PowerPoint slide with a screenshot of Taverna/MOWServ/SeaHawk or whether this is Taverna/MOWServ/SeaHawk live on a beamer is not that much different anyway. Then there is off course also the BOSC as SIG in the two days preceding the main ISMB conference. Since the BOSC is organised by the OBF and BioMOBY is an OBF project we should be able to get some substantial airtime there as well :). Getting charged extra while we spend our time to make this stuff freely available to the scientific community really feels to me like a slap into my face. Maybe some are fine with this, but I don't like spanking, so I'd rather spend the money on shirts... Cheers, Pi > Andreas > > On Thursday 10 January 2008 23:53, Mark Wilkinson wrote: >> I wonder if it might be worth doing a demonstration at ISMB, or >> maybe a >> couple, using the various software tools we have (e.g. Taverna, >> MOWServ, >> SeaHawk). >> >> It only costs $400 if we are selected, and the deadline is further >> along >> in the year so it isn't as frantic. >> >> http://www.iscb.org/ismb2008/sub_demonstrations.php >> >> ?? Anyone interested? If not, I'm certainly going to try to get >> us in >> for teh Moby extensions to Taverna at least, but it would be good to >> partner with someone else who has a different Moby interface so that >> people can see a broader view of what can be done. >> >> It would be a good place to hand-out T-shirts too ;-) >> >> Mark > > -- > Andreas Groscurth > Bioinformatics Developer > 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)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From Pieter.Neerincx at wur.nl Fri Jan 11 11:54:50 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Fri, 11 Jan 2008 12:54:50 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <4786E88C.4070707@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> Message-ID: <89EB1BFF-9C90-4C42-A573-96EB32C251AB@wur.nl> Hi Paul, You are a good advocate for the moby id/namepsace combo and I think they should be used more often. There are too many services that don't use namespace restriction where they should and I have too admit I'm guilty too. I still have some questions left though.... and I think designing good BioMOBY objects and namespaces is anything but trivial :(. On 11 Jan 2008, at 04:54, Paul Gordon wrote: > >> Mark Wilkinson wrote: >>> I agree with Paul (or did Paul agree with me??) that email and >>> url are namespaces. Paul's argument that it doesn't make sense >>> to sub-class an email or a url is a compelling one, which also >>> gives me some assurance that this decision is correct. > Mark, I didn't actually say that URLs were a namespace -- just e- > mails. I avoided talking about URLs because I knew I'd have to > write a longer philosophical e-mail..like this one :-) > > To be correct, the namespace should actually be "smtp", as the e- > mail address format that we are used to (foo at bar.tld) is specific > to SMTP. That is just for sending the e-mail. E-mail addresses are just as specific for protocols used to retrieve e-mail. So I don't see why the namespace should be smtp and not for example pop3 or imap? > Anyone remember uucp-based e-mail? This might seem pedantic, but > it makes a point: the e-mail address is what is referred to in > semiotics as an "index". Now for some semiotic theory. Normally, > the association between a sign (e.g. the word "cow") and the entity > it refers to (an actual, physical cow) is arbitrary, it's a > cultural artifact. These are called symbols (gene symbols such as > "adh1" are examples of this too). An index is a sign who's > association with its referent is not random: the referent is > unambiguously resolveable, given a retrieval protocol. A protocol > and an index go hand-in-hand. An e-mail address points an SMTP > client (the sign interpreter) unambiguously at a destination for a > message, ergo, the e-mail address is an index for the SMTP > protocol. In Moby, the protocol is the namespace (e.g. NCBI_gi), > the index is the ID (e.g. 100389), and the interpreter is an NCBI- > savvy Moby service that will be able to retrieve based on the index. > > URLs are different beasts. The fact that you can represent an e- > mail address as a URL speaks to this fact (e.g. > mailto:foo at bar.tld). A URL combines a protocol and an index > ("protocol:index"). Technically, probably the best way to > represent the URL http://www.google.com in Moby would be to have an > HTTP namespace, and use the id "//www.google.com". Then you make > http-savvy Moby services, registered accepting objects in the HTTP > namespace. Hmmm... yes, but then an e-mail address id namespace combo is now . Maybe it could be solved if we can subclass the namespace ontology. Then you could have some generic mail_protocol namespace and smtp isa mail_protocol, pop3 isa mail_protocol, etc. > The confusion comes from the fact that the protocol+index combo can > be either in the namespace/id part, or in the form of a data type. > Why then do we bother having id/namepsace? Tom was on to > something, but not quite. There is exactly one "carrier mechanism" > in Moby: services. They know how to resolve an index combos and > give you the referent back. > > Namespaces are exceptionally useful because they allow you to use > an index with or without the things that are keyed off them. A > perfect illustration this is a VirtualSequence with a namespace and > id. Another good way to get a sense of the appropriateness of > namespace/id is the Moby cross-reference block (CRIB). If you made > E-mail a data type, you couldn't use it in the CRIB because you're > not using the namespace/id combo to make the cross-reference in the > only way Moby inherently knows how. You would have to use the email namespace for the CRIB, but that doesn't mean you can not have it as a data-type too. Think of the following example: VirtualEmail isa Object AnnotatedEmail isa VirtualEmail AnnotatedEmail has Object with articleName alias AnnotatedEmail has String with articleName real_name That would look something like this: Prof.Dr. Foo Bar You can still use a CRIB to point to this thing using: ... Description ... or using a lightweight CRIB: After all VirtualEmail isa Object, right? Cheers, Pi > My $0.02 :-) > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From groscurt at mpiz-koeln.mpg.de Fri Jan 11 12:36:55 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 13:36:55 +0100 Subject: [MOBY-dev] Service deployment on tomcat and axis2 In-Reply-To: <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> References: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> Message-ID: <200801111336.55473.groscurt@mpiz-koeln.mpg.de> hi, i try to deploy a Web Service on tomcat and axis2, but i fail... does anyone has any experiences with that ? Axis2 has a new structure and e.g. dont use the AdminServlet to deploy services. I created a aar file containing the skeleton and the sample class with its package structure by my own, because as I can see, there is no ant task for that or any other moby structure to handle an aar file.... I also added the META-INF/services.xml into the archive and copied the archive into axis2/WEB-INF/services I then copied the biomoby-datatypes.jar, jmoby.jar and jmoby-other.jar into the lib directory of axis2/WEB-INF Validating this via the axis web interface it complaint that it misses alltools and jdom. So I copied them also into the lib directory. Then I get the the following error: Error: org.apache.axis2.deployment.DeploymentException: The following error occurred during schema generation: 2 at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:389) at org.apache.axis2.deployment.repository.util.ArchiveReader.buildServiceGroup(ArchiveReader.java:95) at org.apache.axis2.deployment.repository.util.ArchiveReader.processServiceGroup(ArchiveReader.java:172) at org.apache.axis2.deployment.ServiceDeployer.deploy(ServiceDeployer.java:78) at org.apache.axis2.deployment.repository.util.DeploymentFileData.deploy(DeploymentFileData.java:137) at org.apache.axis2.deployment.DeploymentEngine.doDeploy(DeploymentEngine.java:571) at org.apache.axis2.deployment.repository.util.WSInfoList.update(WSInfoList.java:141) at org.apache.axis2.deployment.RepositoryListener.update(RepositoryListener.java:318) at org.apache.axis2.deployment.RepositoryListener.checkServices(RepositoryListener.java:220) at org.apache.axis2.deployment.DeploymentEngine.loadServices(DeploymentEngine.java:118) at org.apache.axis2.deployment.WarBasedAxisConfigurator.loadServices(WarBasedAxisConfigurator.java:272) at org.apache.axis2.context.ConfigurationContextFactory.createConfigurationContext(ConfigurationContextFactory.java:78) at org.apache.axis2.transport.http.AxisServlet.initConfigContext(AxisServlet.java:500) at org.apache.axis2.transport.http.AxisServlet.init(AxisServlet.java:420) at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139) at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966) at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4230) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544) at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:825) at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:714) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1138) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022) at org.apache.catalina.core.StandardHost.start(StandardHost.java:736) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443) at org.apache.catalina.core.StandardService.start(StandardService.java:448) at org.apache.catalina.core.StandardServer.start(StandardServer.java:700) at org.apache.catalina.startup.Catalina.start(Catalina.java:552) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:585) at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295) at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433) Caused by: org.apache.axis2.deployment.DeploymentException: The following error occurred during schema generation: 2 at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:354) ... 39 more Caused by: java.lang.ArrayIndexOutOfBoundsException: 2 at org.apache.axis2.description.java2wsdl.DefaultSchemaGenerator.processMethods(DefaultSchemaGenerator.java:275) at org.apache.axis2.description.java2wsdl.DefaultSchemaGenerator.generateSchema(DefaultSchemaGenerator.java:181) at org.apache.axis2.deployment.util.Utils.fillAxisService(Utils.java:352) at org.apache.axis2.deployment.ServiceBuilder.populateService(ServiceBuilder.java:350) ... 39 more Has anyone any experience with axis2 and can tell me how do to that ? or what went wrong ? Thanks andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From martin.senger at gmail.com Fri Jan 11 13:27:00 2008 From: martin.senger at gmail.com (Martin Senger) Date: Fri, 11 Jan 2008 13:27:00 +0000 Subject: [MOBY-dev] Service deployment on tomcat and axis2 In-Reply-To: <200801111336.55473.groscurt@mpiz-koeln.mpg.de> References: <200801111000.29318.groscurt@mpiz-koeln.mpg.de> <814E7F04-858D-4EB9-9900-3FE8C5B6D330@wur.nl> <200801111336.55473.groscurt@mpiz-koeln.mpg.de> Message-ID: <4d93f07c0801110527n33710eaas197e490e6c5912d1@mail.gmail.com> My understanding is that axis2 supports by default lit-doc style of web services (it may not even support the rpc-encoded one, but that I am not sure). BioMoby still uses the rpc-encoded style. You can either tweak axis 2 to produce this style, or you cannot use axis2. Lats June, we have agreed to work on broadening the protocols used. I expect some progress on it during the next month Biohackathon in Japan. Just my 2 c's. Cheers, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger From gordonp at ucalgary.ca Fri Jan 11 13:51:14 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 11 Jan 2008 06:51:14 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47872AB7.8060105@cantab.net> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> <47872AB7.8060105@cantab.net> Message-ID: <47877452.4000100@ucalgary.ca> Hi Tom, No, you shouldn't be able to (unless you guarantee that you know how to decode every URL type ever possible, including prospero, gopher, ftp, etc., since that's the contract you're making). The way you'd do it should be like how VirtualSequences are specifed: Then you make the text description of the VirtualPNGInage something that tells the user that it's a placeholder. You're correct that there is no systematic way in Moby, but there is a convention. Virtually nothing about data types is systematic in Moby, since it relies on someone to interpret the ontology terms by reading the term descriptions (which makes it infinitely simpler than OWL). Cheers, Paul P.S. I'm not generally a fan of namespace inheritance, but if we did it, an application that fits the bill for you would be to have URN -> URI -> URL -> httpURL ->PNGhttpURL. I fear that people will abuse an inherited namespace and say "I take NCBI IDs", when in fact they only take certain children. Inheritance just doesn't work the same way for most ID systems as it does for data types, because the retrieval protocol for a namespace is not generally both universal and non extensible. In the case of PNGhttpURL, it does not extend the httpURL retrieval protocol, so you're okay, but suppose if I register a new namespace as a child of NCBI_IDs. Because there is no universal protocol to retrieve things from the NCBI (at least for argument's sake), I've broken your service. People will start passing my new DB's IDs into your service, but you don't know how to fetch them. The contract for a namespace signature is fundamentally different from a data type contract, because of the retrieval phase. Tom Oinn wrote: > Paul Gordon wrote: > >> The confusion comes from the fact that the protocol+index combo can >> be either in the namespace/id part, or in the form of a data type. >> Why then do we bother having id/namepsace? Tom was on to something, >> but not quite. There is exactly one "carrier mechanism" in Moby: >> services. They know how to resolve an index combos and give you the >> referent back. > > If the above is true then can you tell me the type for an input which > requires an image in PNG format pointed to by a URL? I don't think you > can... > > There is one carrier mechanism in Moby, but this is being used to > carry entities which are themselves indices into other systems. Unless > I wildly misunderstand something (entirely possible I admit) there's > no way to say 'URL to an image' let alone 'URL to an image of my cat'. > > Tom > > From groscurt at mpiz-koeln.mpg.de Fri Jan 11 14:12:51 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 15:12:51 +0100 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47877452.4000100@ucalgary.ca> References: <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> Message-ID: <200801111512.51646.groscurt@mpiz-koeln.mpg.de> Hi, > i bet even this will confuse most of the people... In such cases I remember my boss at Bayer CropScience when we discussed about the 3th form of database normalisation... he just laughed and said "nice in theory and in university. but just horrible in practice". I think we must not tend to be too geeky and try to define everything in a correct way... There are 'normal' people out there how wants to use it ! So - I prefere a sloopy definition which is actually useable and can be told to service implementors ! cheers andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Fri Jan 11 14:14:50 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 11 Jan 2008 15:14:50 +0100 Subject: [MOBY-dev] Service deployment on tomcat and axis2 In-Reply-To: <4d93f07c0801110527n33710eaas197e490e6c5912d1@mail.gmail.com> References: <200801111336.55473.groscurt@mpiz-koeln.mpg.de> <4d93f07c0801110527n33710eaas197e490e6c5912d1@mail.gmail.com> Message-ID: <200801111514.50623.groscurt@mpiz-koeln.mpg.de> thanks martin, I believe your answer if there is no other comment about that ;-) So I will see what can happen during the sessions in Japan. We have a workshop here in March and therefore I tried to set up the system with axis2... I guess its better to tell the participants to use axis1 cheers andreas On Friday 11 January 2008 14:27, Martin Senger wrote: > My understanding is that axis2 supports by default lit-doc style of web > services (it may not even support the rpc-encoded one, but that I am not > sure). BioMoby still uses the rpc-encoded style. You can either tweak axis > 2 to produce this style, or you cannot use axis2. > > Lats June, we have agreed to work on broadening the protocols used. I > expect some progress on it during the next month Biohackathon in Japan. > > Just my 2 c's. > Cheers, > Martin -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From meredith at cantab.net Fri Jan 11 14:18:34 2008 From: meredith at cantab.net (Tom Oinn) Date: Fri, 11 Jan 2008 14:18:34 +0000 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <47877452.4000100@ucalgary.ca> References: <200801101220.11982.groscurt@mpiz-koeln.mpg.de> <47866D7B.206@cantab.net> <4786E88C.4070707@ucalgary.ca> <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> Message-ID: <47877ABA.7090503@cantab.net> Paul Gordon wrote: > Hi Tom, > > No, you shouldn't be able to (unless you guarantee that you know how to > decode every URL type ever possible, including prospero, gopher, ftp, > etc., since that's the contract you're making). True, but that's splitting hairs - the problem still exists if I explicitly say 'HTTP URL'. > P.S. I'm not generally a fan of namespace inheritance, but if we did it, > an application that fits the bill for you would be to have URN -> URI -> > URL -> httpURL ->PNGhttpURL. My point was that the above is inherently broken. It's a multi-axial classification (transport, content) shoehorned into a single heirarchy and, like the GO, ends up with an utter mess. The mess comes when I *do* want to allow multiple URL types (most toolkits will quite happily handle all the common ones) and you end up with a cut and paste heirarchy full of structural duplication (and thence errors over time) because of the failure to differentiate these two axes of classification. I should be able to specify the content (an image) required or produced by the service independantly from the delivery or consumption mechanism. If I were a user searching for services which accepted an image (in this case) I would definitely expect to see ones that accepted a URL to an image - the mechanics of providing the appropriate access mechanism are a different concern entirely. I don't think you can sensibly do this in moby at the moment but it would be fairly high on my wishlist, especially because Taverna2 is designed to take advantage of multiple alternative reference systems to optimise network usage. If a future moby could handle this sensibly workflows would run much faster and with much less load on both your network and your services. Tom From gordonp at ucalgary.ca Fri Jan 11 15:23:21 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 11 Jan 2008 08:23:21 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <200801111512.51646.groscurt@mpiz-koeln.mpg.de> References: <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> <200801111512.51646.groscurt@mpiz-koeln.mpg.de> Message-ID: <478789E9.8090705@ucalgary.ca> Hi all, I believe, for reasons that I've outlined before, that namespace inheritance is generally a very bad idea. I can see what Tom and Andreas are getting in terms of practicality of protocol + content type specification, but strongly stand by the fact that the protocol/namespace equivalence should be the mechanism in Moby. Now the question is how to combine the namespace and the data type in a service signature if that service is a retrieval service. The VirtualPNGImage method is currently the only way, but the Virtual idea is usable for any object. So we'd need to be able to add an attribute saying "I'm virtual". e.g. And we'd have to add to the service signature a mechanism for saying "I'll accept a PNGImage, or a virtual one that is in the http, ftp or scp namespaces". Of course, by default, a service will only accept real objects as they do know. You'd have explicitly register the fact that you take virtual data. My $0.02 Paul From gordonp at ucalgary.ca Fri Jan 11 18:43:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 11 Jan 2008 11:43:52 -0700 Subject: [MOBY-dev] Primitives as primary input In-Reply-To: <478789E9.8090705@ucalgary.ca> References: <47872AB7.8060105@cantab.net> <47877452.4000100@ucalgary.ca> <200801111512.51646.groscurt@mpiz-koeln.mpg.de> <478789E9.8090705@ucalgary.ca> Message-ID: <4787B8E8.5000503@ucalgary.ca> Any takers? Paul Gordon wrote: > Hi all, > > I believe, for reasons that I've outlined before, that namespace > inheritance is generally a very bad idea. I can see what Tom and > Andreas are getting in terms of practicality of protocol + content > type specification, but strongly stand by the fact that the > protocol/namespace equivalence should be the mechanism in Moby. Now > the question is how to combine the namespace and the data type in a > service signature if that service is a retrieval service. The > VirtualPNGImage method is currently the only way, but the Virtual idea > is usable for any object. So we'd need to be able to add an attribute > saying "I'm virtual". e.g. > > virtual="yes"/> > > And we'd have to add to the service signature a mechanism for saying > "I'll accept a PNGImage, or a virtual one that is in the http, ftp or > scp namespaces". Of course, by default, a service will only accept > real objects as they do know. You'd have explicitly register the fact > that you take virtual data. > > My $0.02 > > Paul > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478787ef10950176725398! > > > From markw at illuminae.com Sun Jan 13 16:02:50 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Sun, 13 Jan 2008 08:02:50 -0800 Subject: [MOBY-dev] RSS feeds should be working properly again now Message-ID: I just checked the cron log and it looks like the RSS feeds updated properly last night. I've also fixed the code that was producing incorrect links in the feed information. If you notice anything odd please let me know, Cheers all! Mark From groscurt at mpiz-koeln.mpg.de Mon Jan 14 12:39:13 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 13:39:13 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <200801101217.40476.groscurt@mpiz-koeln.mpg.de> References: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> Message-ID: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> Hiho, I cannot load MobyCentral into Taverna: Error creating BiomobyScavenger for http://moby.ucalgary.ca/moby/MOBY-Central.pl org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not create the Datatype ontology node: Error creating Datatype tree: null at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:64) at org.biomoby.client.taverna.plugin.BiomobyScavengerHelper.getDefaults(BiomobyScavengerHelper.java:140) at org.embl.ebi.escience.scuflui.workbench.ScavengerHelperThreadPool$ScavengerHelperDefaultsThread.run(ScavengerHelperThreadPool.java:166) Caused by: org.biomoby.shared.MobyException: Error creating Datatype tree: null at org.biomoby.client.taverna.plugin.BiomobyScavengerWorker.getDataTypes(BiomobyScavengerWorker.java:318) at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:61) ... 2 more Should this be a temp problem or is it something going wrong here ? merci andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From alanrw at cs.man.ac.uk Mon Jan 14 12:54:00 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Mon, 14 Jan 2008 12:54:00 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> References: <49D7A9F6C8ED4946A37E2B20F4D6E5F9@OfficePC> <200801101217.40476.groscurt@mpiz-koeln.mpg.de> <200801141339.13888.groscurt@mpiz-koeln.mpg.de> Message-ID: <478B5B68.1070202@cs.man.ac.uk> Andreas Groscurth wrote: > Hiho, Hello, > I cannot load MobyCentral into Taverna: > Error creating BiomobyScavenger for > http://moby.ucalgary.ca/moby/MOBY-Central.pl > org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not > create the Datatype ontology node: Error creating Datatype tree: null [snip] > > Should this be a temp problem or is it something going wrong here ? Which version of Taverna are you running? If it is 1.7, does it happen when the activity palette or the old service panel is showing? > merci > andreas Alan From groscurt at mpiz-koeln.mpg.de Mon Jan 14 13:08:09 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 14:08:09 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B5B68.1070202@cs.man.ac.uk> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> Message-ID: <200801141408.10120.groscurt@mpiz-koeln.mpg.de> On Monday 14 January 2008 13:54, Alan Williams wrote: > Andreas Groscurth wrote: > > Hiho, > > Hello, > > > I cannot load MobyCentral into Taverna: > > Error creating BiomobyScavenger for > > http://moby.ucalgary.ca/moby/MOBY-Central.pl > > org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could > > not create the Datatype ontology node: Error creating Datatype tree: null > > [snip] > > > Should this be a temp problem or is it something going wrong here ? > > Which version of Taverna are you running? If it is 1.7, does it happen > when the activity palette or the old service panel is showing? its a fresh downloaded 1.7 - and it happens while starting the application. It loads all scavenger but BioMoby best andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From groscurt at mpiz-koeln.mpg.de Mon Jan 14 13:08:56 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 14:08:56 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B5B68.1070202@cs.man.ac.uk> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> Message-ID: <200801141408.57057.groscurt@mpiz-koeln.mpg.de> ah sorry... its the old service panel... the default one which appears when taverna starts On Monday 14 January 2008 13:54, Alan Williams wrote: > Andreas Groscurth wrote: > > Hiho, > > Hello, > > > I cannot load MobyCentral into Taverna: > > Error creating BiomobyScavenger for > > http://moby.ucalgary.ca/moby/MOBY-Central.pl > > org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could > > not create the Datatype ontology node: Error creating Datatype tree: null > > [snip] > > > Should this be a temp problem or is it something going wrong here ? > > Which version of Taverna are you running? If it is 1.7, does it happen > when the activity palette or the old service panel is showing? > > > merci > > andreas > > Alan > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From alanrw at cs.man.ac.uk Mon Jan 14 13:31:35 2008 From: alanrw at cs.man.ac.uk (Alan Williams) Date: Mon, 14 Jan 2008 13:31:35 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <200801141408.57057.groscurt@mpiz-koeln.mpg.de> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> <200801141408.57057.groscurt@mpiz-koeln.mpg.de> Message-ID: <478B6437.1050005@cs.man.ac.uk> Andreas Groscurth wrote: > ah sorry... its the old service panel... the default one which appears when > taverna starts I've checked and I get the same error. I've forwarded your message to Tom Oinn who's wearing the Taverna Support Hat this week. Alan From meredith at cantab.net Mon Jan 14 13:54:42 2008 From: meredith at cantab.net (Tom Oinn) Date: Mon, 14 Jan 2008 13:54:42 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B6437.1050005@cs.man.ac.uk> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> <200801141408.57057.groscurt@mpiz-koeln.mpg.de> <478B6437.1050005@cs.man.ac.uk> Message-ID: <478B69A2.50802@cantab.net> Alan Williams wrote: > Andreas Groscurth wrote: >> ah sorry... its the old service panel... the default one which appears >> when taverna starts > > I've checked and I get the same error. I've forwarded your message to > Tom Oinn who's wearing the Taverna Support Hat this week. Sounds like a problem with the moby code that builds the object tree? It's a bit hard for me to debug seeing as this is code written by the moby guys... Looks like it's done when loading the default scavengers, so maybe the scavenger you've got set is wrong or out of date? Tom From ssoiland at cs.man.ac.uk Mon Jan 14 14:06:44 2008 From: ssoiland at cs.man.ac.uk (Stian Soiland) Date: Mon, 14 Jan 2008 14:06:44 +0000 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <478B69A2.50802@cantab.net> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de> <478B5B68.1070202@cs.man.ac.uk> <200801141408.57057.groscurt@mpiz-koeln.mpg.de> <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> Message-ID: <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> On Jan 14, 2008 1:54 PM, Tom Oinn wrote: > Sounds like a problem with the moby code that builds the object tree? > It's a bit hard for me to debug seeing as this is code written by the > moby guys... Looks like it's done when loading the default scavengers, > so maybe the scavenger you've got set is wrong or out of date? No, it's something changed in the data.. the line that fails with a NullPointerException is: fillSubTree(root, hashmap.get("Object").getChildren(), hashmap, REGISTRY_URL); by debugging and inspecting I find that the keys are more like http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/Object - so that if I replace the above line to use that it works, except that the scavenger tree below "Object" will now be with full URLs such as http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/AlignedSequences This seems to be correct corresponding to http58.47.47moby46ucalgary46ca47moby47MOBY45Central46pl/datatype_rdf/DATATYPES.rdf in my moby-cache directory. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ From groscurt at mpiz-koeln.mpg.de Mon Jan 14 14:37:06 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 15:37:06 +0100 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <478B69A2.50802@cantab.net> References: <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> Message-ID: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> is not reachable since this morning german time... ?! best andas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From markw at illuminae.com Mon Jan 14 15:05:45 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 14 Jan 2008 07:05:45 -0800 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> References: <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> <200801141537.06989.groscurt@mpiz-koeln.mpg.de> Message-ID: the Open-Bio server went down. It's back up again now M On Mon, 14 Jan 2008 06:37:06 -0800, Andreas Groscurth wrote: > is not reachable since this morning german time... > > ?! > > best > andas > From edward.kawas at gmail.com Mon Jan 14 15:11:52 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 14 Jan 2008 07:11:52 -0800 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> References: <200801141339.13888.groscurt@mpiz-koeln.mpg.de><478B5B68.1070202@cs.man.ac.uk><200801141408.57057.groscurt@mpiz-koeln.mpg.de><478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> Message-ID: <4BB3042E8A6240E7B2818D940C9BB2C1@OfficePC> If you try now, it should work. Before trying, make sure to delete the .taverna-1.7.0/moby-cache/ directory first though. Let me know if you still encounter problems. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland Sent: January-14-08 6:07 AM To: tmo at ebi.ac.uk; Core developer announcements Subject: Re: [MOBY-dev] Error while loading Moby into Taverna On Jan 14, 2008 1:54 PM, Tom Oinn wrote: > Sounds like a problem with the moby code that builds the object tree? > It's a bit hard for me to debug seeing as this is code written by the > moby guys... Looks like it's done when loading the default scavengers, > so maybe the scavenger you've got set is wrong or out of date? No, it's something changed in the data.. the line that fails with a NullPointerException is: fillSubTree(root, hashmap.get("Object").getChildren(), hashmap, REGISTRY_URL); by debugging and inspecting I find that the keys are more like http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/Object - so that if I replace the above line to use that it works, except that the scavenger tree below "Object" will now be with full URLs such as http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/AlignedSequences This seems to be correct corresponding to http58.47.47moby46ucalgary46ca47moby47MOBY45Central46pl/datatype_rdf/DATATYP ES.rdf in my moby-cache directory. -- Stian Soiland, myGrid team School of Computer Science The University of Manchester http://www.cs.man.ac.uk/~ssoiland/ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Mon Jan 14 15:16:27 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Mon, 14 Jan 2008 16:16:27 +0100 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> References: <478B6437.1050005@cs.man.ac.uk> <478B69A2.50802@cantab.net> <200801141537.06989.groscurt@mpiz-koeln.mpg.de> Message-ID: It's fine overhere (now)... Cheers, Pi On 14-jan-2008, at 15:37, Andreas Groscurth wrote: > is not reachable since this morning german time... > > ?! > > best > andas > > -- > Andreas Groscurth > Bioinformatics Developer > 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)221-5062-449 > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From groscurt at mpiz-koeln.mpg.de Mon Jan 14 15:28:00 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Mon, 14 Jan 2008 16:28:00 +0100 Subject: [MOBY-dev] Biomoby.org is gone In-Reply-To: <200801141537.06989.groscurt@mpiz-koeln.mpg.de> References: <478B69A2.50802@cantab.net> <200801141537.06989.groscurt@mpiz-koeln.mpg.de> Message-ID: <200801141628.01054.groscurt@mpiz-koeln.mpg.de> its a conspiracy... after sending the mail... i could connect... to my defense... some people in France also had the problem andreas On Monday 14 January 2008 15:37, Andreas Groscurth wrote: > is not reachable since this morning german time... > > ?! > > best > andas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From dmitry.repchevski at bsc.es Mon Jan 14 18:04:02 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Mon, 14 Jan 2008 19:04:02 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). Message-ID: <478BA412.60809@bsc.es> Hello everybody! Two months ago I posted a Moby API developed here is Spain and still have no any opinion about it. Please take a look into http://inb.bsc.es/java/index.html Regards, Dmitry From groscurt at mpiz-koeln.mpg.de Tue Jan 15 08:05:20 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 15 Jan 2008 09:05:20 +0100 Subject: [MOBY-dev] Error while loading Moby into Taverna In-Reply-To: <4BB3042E8A6240E7B2818D940C9BB2C1@OfficePC> References: <43abb4040801140606v12be2ae4mfd45825848042fe1@mail.gmail.com> <4BB3042E8A6240E7B2818D940C9BB2C1@OfficePC> Message-ID: <200801150905.20810.groscurt@mpiz-koeln.mpg.de> works fine... thanks On Monday 14 January 2008 16:11, Edward Kawas wrote: > If you try now, it should work. > > Before trying, make sure to delete the .taverna-1.7.0/moby-cache/ directory > first though. > > Let me know if you still encounter problems. > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Stian Soiland > Sent: January-14-08 6:07 AM > To: tmo at ebi.ac.uk; Core developer announcements > Subject: Re: [MOBY-dev] Error while loading Moby into Taverna > > On Jan 14, 2008 1:54 PM, Tom Oinn wrote: > > Sounds like a problem with the moby code that builds the object tree? > > It's a bit hard for me to debug seeing as this is code written by the > > moby guys... Looks like it's done when loading the default scavengers, > > so maybe the scavenger you've got set is wrong or out of date? > > No, it's something changed in the data.. the line that fails with a > NullPointerException is: > > fillSubTree(root, > hashmap.get("Object").getChildren(), hashmap, > REGISTRY_URL); > > by debugging and inspecting I find that the keys are more like > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/Object - so that if I > replace the above line to use that it works, except that the scavenger > tree below "Object" will now be with full URLs such as > http://moby.ucalgary.ca/RESOURCES/MOBY-S/Objects/AlignedSequences > > This seems to be correct corresponding to > http58.47.47moby46ucalgary46ca47moby47MOBY45Central46pl/datatype_rdf/DATATY >P ES.rdf > in my moby-cache directory. -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From Pieter.Neerincx at wur.nl Tue Jan 15 11:38:28 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 15 Jan 2008 12:38:28 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478BA412.60809@bsc.es> References: <478BA412.60809@bsc.es> Message-ID: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> Hi Dimitry, The reason you hadn't heard from me yet, is that I'm Perl programmer and I'm not very fluent in Java (yet). With regard to the "bug in PERL Moby API (not sure about JMoby...) when it rejects "non-moby" prefixes, which is definitly goes against XML specification where prefix is defined as an alias for a namespace" I absolutely agree that this ugly. As far as I know the XML::LibXML library that shouldn't be necessary though, so I'll have look if it's fixable... Cheers, Pi On 14 Jan 2008, at 19:04, Dmitry Repchevsky wrote: > Hello everybody! > > Two months ago I posted a Moby API developed here is Spain and > still have no any opinion about it. > Please take a look into http://inb.bsc.es/java/index.html > > Regards, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------- From dmitry.repchevski at bsc.es Tue Jan 15 12:43:02 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 15 Jan 2008 13:43:02 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> Message-ID: <478CAA56.20300@bsc.es> > I'm Perl programmer and I'm not very fluent in Java (yet). Yeah, I have the same problem I'm a Java programmer and illiterate in Perl (forever :D). As far as I saw/guess Perl uses XSL template to transform a Moby message and it fails... Cheers, Dmitry From edward.kawas at gmail.com Tue Jan 15 14:29:55 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Jan 2008 06:29:55 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478CAA56.20300@bsc.es> References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> <478CAA56.20300@bsc.es> Message-ID: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Glancing over the module MOBY::Central, I cant seem to find a place where the prefix 'moby' is hard coded. Do you have an example call where you know that is the case? Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-15-08 4:43 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). > I'm Perl programmer and I'm not very fluent in Java (yet). Yeah, I have the same problem I'm a Java programmer and illiterate in Perl (forever :D). As far as I saw/guess Perl uses XSL template to transform a Moby message and it fails... Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From Pieter.Neerincx at wur.nl Tue Jan 15 15:09:57 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 15 Jan 2008 16:09:57 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl> <478CAA56.20300@bsc.es> <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Message-ID: Hi, Dimitry mentions an XSL template to transform a Moby message... Sounds to me like the alternative libs to parse large pieces of XML. As far as I know the older/original/default BioMoby Perl libs don't use XSLs to transform XML or do they? Cheers, Pi On 15-jan-2008, at 15:29, Edward Kawas wrote: > Glancing over the module MOBY::Central, I cant seem to find a place > where > the prefix 'moby' is hard coded. Do you have an example call where > you know > that is the case? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry > Repchevsky > Sent: January-15-08 4:43 AM > To: moby-dev at lists.open-bio.org > Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). > >> I'm Perl programmer and I'm not very fluent in Java (yet). > > Yeah, I have the same problem I'm a Java programmer and illiterate in > Perl (forever :D). > As far as I saw/guess Perl uses XSL template to transform a Moby > message > and it fails... > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From dmitry.repchevski at bsc.es Tue Jan 15 15:11:49 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 15 Jan 2008 16:11:49 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> References: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Message-ID: <478CCD35.5080600@bsc.es> Hello Edward, Here is the Moby message without "moby" prefix: ************************************************ ************************************************ it gives me: ************************************************ soap:Server Undefined namespace prefix xmlXPathCompiledEval: evaluation failed ************************************************ The XSLT transformation was my guess (looking into parseMobyMessage.xsl file in Perl directory)... Cheers; Dmitry From edward.kawas at gmail.com Tue Jan 15 15:12:41 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Jan 2008 07:12:41 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <54113548-34AD-49A5-BBB5-55D3CBF59A3A@wur.nl><478CAA56.20300@bsc.es> <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> Message-ID: <45D5E527185D4CBFBCA47560BFBA9161@OfficePC> No they don't. There is a template in the library somewhere, but as far as I know, it isn't used at all. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx Sent: January-15-08 7:10 AM To: Core developer announcements Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). Hi, Dimitry mentions an XSL template to transform a Moby message... Sounds to me like the alternative libs to parse large pieces of XML. As far as I know the older/original/default BioMoby Perl libs don't use XSLs to transform XML or do they? Cheers, Pi On 15-jan-2008, at 15:29, Edward Kawas wrote: > Glancing over the module MOBY::Central, I cant seem to find a place > where > the prefix 'moby' is hard coded. Do you have an example call where > you know > that is the case? > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry > Repchevsky > Sent: January-15-08 4:43 AM > To: moby-dev at lists.open-bio.org > Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). > >> I'm Perl programmer and I'm not very fluent in Java (yet). > > Yeah, I have the same problem I'm a Java programmer and illiterate in > Perl (forever :D). > As far as I saw/guess Perl uses XSL template to transform a Moby > message > and it fails... > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Jan 15 15:14:58 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 15 Jan 2008 07:14:58 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478CCD35.5080600@bsc.es> References: <4CCFA7B4CDEC41A39A44CC71A8CFEA4F@OfficePC> <478CCD35.5080600@bsc.es> Message-ID: <781E110FCF014865A11AD2A0168E3418@OfficePC> So it's the message sent to services. I think the problem then is the common subs module, because I believe that it looks for prefixes. As an aside, the perl moses services should not have this problem. I will look into common subs and see if I can make a module that uses LibXML. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-15-08 7:12 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] JAX-WS BioMoby API (2nd round). Hello Edward, Here is the Moby message without "moby" prefix: ************************************************ ************************************************ it gives me: ************************************************ soap:Server Undefined namespace prefix xmlXPathCompiledEval: evaluation failed ************************************************ The XSLT transformation was my guess (looking into parseMobyMessage.xsl file in Perl directory)... Cheers; Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Tue Jan 15 22:41:24 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Tue, 15 Jan 2008 15:41:24 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478BA412.60809@bsc.es> References: <478BA412.60809@bsc.es> Message-ID: <478D3694.5050004@ucalgary.ca> Hi Dmitry, At a conceptual level, it makes sense to be able to use a standard WS framework to access Moby Central and services. After all, that's why we decided to use SOAP in the first place, wasn't it? Currently from my side, Seahawk and MobyServlet need Axis because MobyRequest uses Axis. I actually made a version of MobyRequest that uses javax.xml.ws* instead, but haven't committed it because the update to Java version 6 is going to be a major pain on jMOBY. Version 5 and version 6 don't like to live together in jMOBY (for a long list of reasons I won't get into here), so we'll need to start a new branch if we wanted to start using Java 6 in jMOBY. I'd also suggest that even with your own marshalling/unmarshalling, you could easily reuse the existing API classes for data instances that users are familiar with... Regards, Paul Dmitry Repchevsky wrote: > Hello everybody! > > Two months ago I posted a Moby API developed here is Spain and still > have no any opinion about it. > Please take a look into http://inb.bsc.es/java/index.html > > Regards, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478ba926109502617632743! > > > From dmitry.repchevski at bsc.es Wed Jan 16 11:44:53 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 12:44:53 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478D3694.5050004@ucalgary.ca> References: <478D3694.5050004@ucalgary.ca> Message-ID: <478DEE35.9000509@bsc.es> Hello Paul, Thank you for giving your opinion. I appreciate it and have some comments/questions > I actually made a version of MobyRequest that uses javax.xml.ws* So how you handle famous "soap-encoding"? I mean that Axis 1.x is the only API which handle Moby on a server side so far. As I commented in various occasions Moby clients ignore WSDL file and name parameters differently. Another JAX-RPC API (SUN, JBoss) failed with Moby requests. > Version 5 and version 6 don't like to live together in jMOBY Actually JAX-WS can be installed apart to use with JDK5. JEE5 specification uses JDK5, but makes JAX-WS obligatory. If fact this is what I'm doing using JBoss 4.2.2 (JDK5 + JBoss-WS/JAXB). > I'd also suggest that even with your own > marshalling/unmarshalling, you could easily reuse the existing API > classes for data instances that users are familiar with... I think I didn't explain in well. There is no "my own marshalling/unmarshalling". The generated classes are the JAXB annotated Java classes. There is no "marshalling/unmarshalling" in these classes. On the over side MoSeS generated datatype classes explicitly contain marshalling method ("public org.jdom.Element toXML()") which makes them jdom dependant. Moreover, standard Java webservices architecture JAX-WS (used in JDK6/JEE) uses JAXB to parse webservices parameters, so once you wish to go further and use STANDARD webservices in Java (not soap-encoding) you are doomed to use JAXB o stick with parsing it yourself forever. By now Moby is using the latter case (I don't try to explain you the obvious, but to clarify my vision), so all webservices looks like: String runSomeService(String mobyXML); // all the parsing is done manually inside the service. Now let's think: MobyMessage runSomeService(MobyMessage request); // here the parsing is done through the JAX-WS My vision is that all Moby Datatypes must have a schema representation. My generated classes being completely Moby compatible are in fact JAXB classes, so one can easy obtain the schema through schemagen. WSDL 2.0 has support for ontologies using RDF for ontology hierarchy and XML Schema for the format description. I am pretty sure that some of the next JAX-WS (maybe JEE7) will support it The JAXB generated classes has the same hierarchy structure as MoSeS ones (both generated from the same ontology). Let's look into example: ****************************************** JAXB version ******************************************** @XmlRootElement(name="AnnotatedDomain") @XmlType(name="AnnotatedDomain") public class AnnotatedDomain extends Domain { public List getBasicAnnotation() { return getAttributes("basicAnnotation"); } public void addBasicAnnotation(BasicAnnotation basicAnnotation) { putAttribute("basicAnnotation", basicAnnotation); } } ****************************************** MoSeS version ******************************************* public class AnnotatedDomain extends Domain { private static final String DATA_TYPE_NAME = "AnnotatedDomain"; public static final String ARTICLE_NAME_BASICANNOTATION = "BasicAnnotation"; protected java.util.Vector BasicAnnotation = new java.util.Vector(); public void set_BasicAnnotation (BasicAnnotation value) { // add an article name if (value != null) value.setName (ARTICLE_NAME_BASICANNOTATION); this.BasicAnnotation.addElement (value); } public void set_BasicAnnotation (BasicAnnotation[] value) { this.BasicAnnotation = new java.util.Vector(); for (int i = 0; i < value.length; i++) set_BasicAnnotation (value[i]); } public BasicAnnotation[] getMoby_BasicAnnotation() { BasicAnnotation[] result_I_am_sorry_that_this_produces_a_warning = new BasicAnnotation [ BasicAnnotation.size() ]; BasicAnnotation.copyInto (result_I_am_sorry_that_this_produces_a_warning); return result_I_am_sorry_that_this_produces_a_warning; } public int size_BasicAnnotation() { return BasicAnnotation.size(); } 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); for (java.util.Enumeration en = BasicAnnotation.elements(); en.hasMoreElements(); ) elem_I_am_sorry_that_this_produces_a_warning.addContent ( ((BasicAnnotation)en.nextElement()).toXML() ); return elem_I_am_sorry_that_this_produces_a_warning; } public String toString() { StringBuffer buf_I_am_sorry_that_this_produces_a_warning = new StringBuffer(); buf_I_am_sorry_that_this_produces_a_warning.append (super.toString()); for (java.util.Enumeration en = BasicAnnotation.elements(); en.hasMoreElements(); ) buf_I_am_sorry_that_this_produces_a_warning.append ( ((BasicAnnotation)en.nextElement()).format (1) ); return new String (buf_I_am_sorry_that_this_produces_a_warning); } } *********************************************************************************************************** As you can see the difference is: 1) >private static final String DATA_TYPE_NAME = "AnnotatedDomain"; @XmlRootElement(name="AnnotatedDomain") @XmlType(name="AnnotatedDomain") 2) >public void set_BasicAnnotation (BasicAnnotation value) public void addBasicAnnotation(BasicAnnotation basicAnnotation) 3) >public BasicAnnotation[] getMoby_BasicAnnotation() public List getBasicAnnotation() 4) >public void set_BasicAnnotation (BasicAnnotation[] value) // NOT IMPLEMENTED 5) >public org.jdom.Element toXML() // NO NEED TO IMPLEMENT 6) >public String toString() // IMLEMENTED IN THE TOP_LEVEL CLASS As you can see there is almost no difference in both classes. Using List instead of an array - gives a possibility to add BasicAnnotation in it. Slightly different get/set method names. Appreciate any further comments. Dmitry From gordonp at ucalgary.ca Wed Jan 16 14:53:45 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 07:53:45 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478DEE35.9000509@bsc.es> References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> Message-ID: <478E1A79.2020806@ucalgary.ca> > So how you handle famous "soap-encoding"? > I mean that Axis 1.x is the only API which handle Moby on a server > side so far. > As I commented in various occasions Moby clients ignore WSDL file and > name parameters differently. > Another JAX-RPC API (SUN, JBoss) failed with Moby requests. I create the "data" tag manually in the SOAPMesssage. Only takes a couple of lines, the rest is standard use of Service and Dispatch. >> Version 5 and version 6 don't like to live together in jMOBY > Actually JAX-WS can be installed apart to use with JDK5. > JEE5 specification uses JDK5, but makes JAX-WS obligatory. If fact > this is what I'm doing using JBoss 4.2.2 (JDK5 + JBoss-WS/JAXB). I know, but I can't create the data tag using a QName with the version of JAX-WS on the Sun Web site. The Java SE6 version allows me to (this is needed to declare the xsd namespace, since createName does not stupidly allow manual declarations in the xmlns namespace). It's funny how javax.xml.ws doesn't work the same in both versions...if you can figure out how to declare a namespace manually in a SOAPMessage without QName, let me know! >> I'd also suggest that even with your own marshalling/unmarshalling, >> you could easily reuse the existing API classes for data instances >> that users are familiar with... > I think I didn't explain in well. There is no "my own > marshalling/unmarshalling". The generated classes are the JAXB > annotated Java classes. Okay, but when you work without the data types, JAXB creates an AnyMobyObject? Or how does that get created? Could it use the org.biomoby.shared.data classes instead? Sorry, I'm not familiar with how that datatype-less way works... > > My vision is that all Moby Datatypes must have a schema representation. As far as I can recall, this is not possible (others can correct me if I'm wrong, or these have been solved) . The main sticking points were that if an object is a Moby Primitive in a has relationship, it cannot be represented in XML schema. Also, I think that the fact that we must be able to accept subclasses of declared classes, even if we don't know about them, causes another problem. > My generated classes being completely Moby compatible are in fact JAXB > classes, so one can easy obtain the schema through schemagen. > The JAXB generated classes has the same hierarchy structure as MoSeS > ones (both generated from the same ontology). I don't actually use MoSeS, so I don't have much to add here. The generator code is Martin's domain of expertise, so I'll let him comment on that if he likes. :-) Regards, Paul From dmitry.repchevski at bsc.es Wed Jan 16 15:57:20 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 16:57:20 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E1A79.2020806@ucalgary.ca> References: <478E1A79.2020806@ucalgary.ca> Message-ID: <478E2960.7090902@bsc.es> Hello, I will try to answer the questions as deep as I can. > I know, but I can't create the data tag using a QName with the version > of JAX-WS on the Sun Web site. The Java SE6 version allows me to (this > is needed to declare the xsd namespace, since createName does not > stupidly allow manual declarations in the xmlns namespace). It's funny > how javax.xml.ws doesn't work the same in both versions...if you can > figure out how to declare a namespace manually in a SOAPMessage without > QName, let me know! I use the same method!!! Look into AbstractMobyEndpoint.createSoapMessage(). ********************************** env.addNamespaceDeclaration("xsd", "http://www.w3.org/2001/XMLSchema"); ********************************** is this what you mean? > Okay, but when you work without the data types, JAXB creates an > AnyMobyObject? Exactly. When JAXB can not find appropriate datatype it passes it as an Element (look into MobySimple.setJaxbObject()). So I marshall/unmarshall it into AnyMobyObject. This way you can use same API to work both with AnyMobyObject or datatypes objects (and can mix it). ALL the data stored in top-level class (MobyObject) so you can work with it without using get/set methods. This way "datatypes" are only getters/setters for the "attributes". you can either call List list = annotatedDomain.getBasicAnnotation(); or List list = mobyObject.getAttributes("basicAnnotation"); in latter case list would contain BasicAnnotation or AnyMobyObject depending if datatype was found by jaxb. For example in demo application I make drag and drop of OBJECTS (from right panel). If you put datatypes.jar in CLASSPATH so actual object will be the "real" one (for example PDB_Text), if not - it will be "AnyMobyObject". > >/ My vision is that all Moby Datatypes must have a schema representation. > /As far as I can recall, this is not possible (others can correct me if > I'm wrong, or these have been solved) . Well since JAXB MUST generate schema from valid JAXB classes... Another thing is how good the schema would be (I'm not the greatest schema specialist :-)) Just look into the schema for the AnnotatedDomain class: ******************* ******************* > The main sticking points were > that if an object is a Moby Primitive in a has relationship, it cannot > be represented in XML schema. Don't get this one... ? > Also, I think that the fact that we must > be able to accept subclasses of declared classes, even if we don't know > about them, causes another problem. JAXB can do it... It's called type substitution. I don't like the way it works... I my case it substituted by AnyMobyObject. Technically it's possible to implement some heuristic BEFORE parsing to it. I could look into known objects (To have this information I implemented a custom classloader for Jaxb loaded classes) and if there is some that matches by parameters... not sure how to do it yet... Regards, Dmitry From markw at illuminae.com Wed Jan 16 16:00:31 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Jan 2008 08:00:31 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E1A79.2020806@ucalgary.ca> References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: >> My vision is that all Moby Datatypes must have a schema representation. > As far as I can recall, this is not possible You are correct, Paul. It is not possible to define the structure of MOBY Objects in XML schema (for some of the same reasons that it is impossible to define RDF-XML documents in XML Schema) There's a belief "out there" that all XML documents can be represented in XML schema, and I've been attacked by audience members during presentations and workshops when I say this isn't true... but it isn't true!! The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML can be "defined by" an OWL ontology (please don't attack me for saying it that way - I KNOW that this is backwards from the way OWL and RDF actually work!). The resulting flexibility in document structure cannot be handled by XML Schema. It sucks for us, since we want to use WSDL... but it's a painful reality. Mark From markw at illuminae.com Wed Jan 16 16:07:29 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Jan 2008 08:07:29 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: ...unless there has been some new changes in XML Schema that I missed! I admit I haven't looked at it since my conversation with a guy from the W3C XML Schema working group, who confirmed to me that, in his opinion, it couldn't be done... I took that as "the word of God" at the time, but that was probably two years ago, maybe longer... Mark On Wed, 16 Jan 2008 08:00:31 -0800, Mark Wilkinson wrote: > >>> My vision is that all Moby Datatypes must have a schema representation. >> As far as I can recall, this is not possible > > > You are correct, Paul. It is not possible to define the structure of > MOBY Objects in XML schema (for some of the same reasons that it is > impossible to define RDF-XML documents in XML Schema) > > There's a belief "out there" that all XML documents can be represented > in XML schema, and I've been attacked by audience members during > presentations and workshops when I say this isn't true... but it isn't > true!! > > The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML > can be "defined by" an OWL ontology (please don't attack me for saying > it that way - I KNOW that this is backwards from the way OWL and RDF > actually work!). The resulting flexibility in document structure cannot > be handled by XML Schema. > > It sucks for us, since we want to use WSDL... but it's a painful reality. > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From gordonp at ucalgary.ca Wed Jan 16 16:16:33 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 09:16:33 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: <478E2DE1.1020605@ucalgary.ca> As I see it, it would be nice to use standard WSDL stuff as much as possible, but we will always need to do some manipulation in the standard stack because you simply can't express everything we need in XML Schema. That's what Dmitry's running into. That being said, getting rid of Axis would be great, and doable now that Eddie defined a WSDL for Moby Central (which Dmitry's using). I'd like to see an implementation of the Central interface that doesn't use Axis, for purely selfish reasons...it adds a lot of weight to the Seahawk applet :-) Also, I get funny ClassFormatErrors when trying to use Axis in Java SE6 (version 6 is much more pedantic about class file structure), but that could be overcome I suppose by recompiling the Axis from source... Mark Wilkinson wrote: > >>> My vision is that all Moby Datatypes must have a schema representation. >> As far as I can recall, this is not possible > > > You are correct, Paul. It is not possible to define the structure of > MOBY Objects in XML schema (for some of the same reasons that it is > impossible to define RDF-XML documents in XML Schema) > > There's a belief "out there" that all XML documents can be represented > in XML schema, and I've been attacked by audience members during > presentations and workshops when I say this isn't true... but it isn't > true!! > > The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML > can be "defined by" an OWL ontology (please don't attack me for saying > it that way - I KNOW that this is backwards from the way OWL and RDF > actually work!). The resulting flexibility in document structure > cannot be handled by XML Schema. > > It sucks for us, since we want to use WSDL... but it's a painful reality. > > Mark > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478e2823109501033230397! > > > From dmitry.repchevski at bsc.es Wed Jan 16 16:45:52 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 17:45:52 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: Message-ID: <478E34C0.3060504@bsc.es> Hello Mark, I understand what you say. For ANY valid XML document appropriate schema CAN be generated... But it doesn't mean that you can generate a schema that match a different set of XMLs. Well, maybe you can, but the schema itself could be unusable... > The resulting flexibility in document structure cannot be handled > by XML Schema. Well the schema is not good in defining relationships, but it's definitely possible. > It sucks for us, since we want to use WSDL... but it's a painful reality. I'm not sure... I'm looking to it from Java point of view... lets say we have C extends B extends A. If we pass B as a parameter to the webservice two things happens. We would have Schemas for B/A in WSDL and Java method that accepts B. Something like call(B b). Now imagine JAXB got "C" it's unknown to it so it can't parse it (it CAN parse it if we implicitly add it into the JAXBContext), so we need to know it A PRIORY. It is can be done by regenerating all the classes while creating the context (takes a lot of time). I discussed this in forums and the problem is that you can't change the context once it is created. by now they proposed an ugly (IMHO) hack with @SeeAlso annotation when you can accept B, but tell JAXB that there is also a "C" to take into account... again it doesn't help too much. Fortunately (!) in WSDL 2 it's possible to mix RDF with XML Schema - XML Schema specify the data format and RDF a relationship, so (as far as I understand) it should work automatically - when you find something that you don't understand - you look into the RDF to find a substitute... I know AXIS 2.0 claims to support it, but I always prefer JCP specifications (somehow those are that goes into JEE). Best regards, Dmitry From dmitry.repchevski at bsc.es Wed Jan 16 16:56:16 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 17:56:16 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E2DE1.1020605@ucalgary.ca> References: <478E2DE1.1020605@ucalgary.ca> Message-ID: <478E3730.8050708@bsc.es> Hello Paul > As I see it, it would be nice to use standard WSDL stuff as much as > possible, but we will always need to do some manipulation in the > standard stack because you simply can't express everything we need in > XML Schema. Well this is definitly not the case for the registry... Just look into the MobyRegisty API (http://inb.bsc.es/java/moby_registry.html) The only hack I'm using is the soap-encoding (MobyCore) - the rest are plain JAXB classes. By the way, could we start migrating to the document encoding from the Moby Central? ;-) I think it would be not such a pain as with Moby Services? Regards, Dmitry From markw at illuminae.com Wed Jan 16 16:59:16 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 16 Jan 2008 08:59:16 -0800 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3730.8050708@bsc.es> References: <478E2DE1.1020605@ucalgary.ca> <478E3730.8050708@bsc.es> Message-ID: On Wed, 16 Jan 2008 08:56:16 -0800, Dmitry Repchevsky wrote: > By the way, could we start migrating to the document encoding from the > Moby Central? ;-) I think it would be not such a pain as with Moby > Services? I have just hired Jason Stewart as a private subcontractor to do the necessary code updates to SOAP::Lite that will allow this migration to happen. Hopefully by next month we'll be able to handle document-encoded messages in SOAP::Lite. This has been the limitation so far... Mark From jmfernandez at cnio.es Wed Jan 16 16:51:40 2008 From: jmfernandez at cnio.es (=?ISO-8859-1?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=) Date: Wed, 16 Jan 2008 17:51:40 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: <478D3694.5050004@ucalgary.ca> <478DEE35.9000509@bsc.es> <478E1A79.2020806@ucalgary.ca> Message-ID: <478E361C.80008@cnio.es> Hi everybody, although you cannot have an XML schema for MOBY messaging taking into account the whole ontology (unless you regenerate it each time the ontology is changed), you can create an XML schema which at least can be used to validate the fixed part of MOBY messages, using xsd:any in those places where you can put a MOBY object. Some years ago I wrote such schema, but I never checked it... Perhaps it can be useful for someone, so I'm including it in this message. Best Regards, Jos? Mar?a Mark Wilkinson wrote: > ...unless there has been some new changes in XML Schema that I missed! > I admit I haven't looked at it since my conversation with a guy from the > W3C XML Schema working group, who confirmed to me that, in his opinion, > it couldn't be done... I took that as "the word of God" at the time, but > that was probably two years ago, maybe longer... > > Mark > > > > On Wed, 16 Jan 2008 08:00:31 -0800, Mark Wilkinson > wrote: > >> >>>> My vision is that all Moby Datatypes must have a schema representation. >>> As far as I can recall, this is not possible >> >> >> You are correct, Paul. It is not possible to define the structure of >> MOBY Objects in XML schema (for some of the same reasons that it is >> impossible to define RDF-XML documents in XML Schema) >> >> There's a belief "out there" that all XML documents can be represented >> in XML schema, and I've been attacked by audience members during >> presentations and workshops when I say this isn't true... but it isn't >> true!! >> >> The Moby XML is "defined" by the Moby Object ontology, much as RDF-XML >> can be "defined by" an OWL ontology (please don't attack me for saying >> it that way - I KNOW that this is backwards from the way OWL and RDF >> actually work!). The resulting flexibility in document structure >> cannot be handled by XML Schema. >> >> It sucks for us, since we want to use WSDL... but it's a painful reality. >> >> Mark >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- "Premature optimization is the root of all evil." - Donald Knuth Jos? Mar?a Fern?ndez Gonz?lez Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061) e-mail: jmfernandez at cnio.es Fax: (+34) 91 224 69 76 Unidad del Instituto Nacional de Bioinform?tica Biolog?a Estructural y Biocomputaci?n Structural Biology and Biocomputing Centro Nacional de Investigaciones Oncol?gicas C.P.: 28029 Zip Code: 28029 C/. Melchor Fern?ndez Almagro, 3 Madrid (Spain) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. -------------- next part -------------- A non-text attachment was scrubbed... Name: mobyServicesSchema.xsd Type: text/xml Size: 4738 bytes Desc: not available URL: From dmitry.repchevski at bsc.es Wed Jan 16 17:14:00 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 18:14:00 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: References: Message-ID: <478E3B58.9080403@bsc.es> > > Hopefully by next month we'll be able to handle document-encoded > messages in SOAP::Lite. This has been the limitation so far... So finally we would be able to do something like this? @WebMethod MobyMessage runXXXService(MobyMessage message); :-) As Jos? Mar?a pointed out: > although you cannot have an XML schema for MOBY messaging taking into account > the whole ontology (unless you regenerate it each time the ontology is > changed), you can create an XML schema which at least can be used to validate > the fixed part of MOBY messages, using xsd:any in those places where you can > put a MOBY object. This is exactly what I have done with MobyCore (but being more fluent with Java than XML using JAXB directly). in schema it looks like: while in java code: @XmlAnyElement(lax = true) Cheers, Dmitry From gordonp at ucalgary.ca Wed Jan 16 17:18:39 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 10:18:39 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3730.8050708@bsc.es> References: <478E2DE1.1020605@ucalgary.ca> <478E3730.8050708@bsc.es> Message-ID: <478E3C6F.3050809@ucalgary.ca> >> As I see it, it would be nice to use standard WSDL stuff as much as >> possible, but we will always need to do some manipulation in the >> standard stack because you simply can't express everything we need in >> XML Schema. > Well this is definitly not the case for the registry... That's what I said: Central is okay, it's the service calls that need modifications... By the way, I'm trying to figure out if I can avoid the endorsed lib issue in Java 5 for JAXB 2.1 somehow...that's the only sticking point left for MobyRequest to use JAX-WS in a standard Java 5... From dmitry.repchevski at bsc.es Wed Jan 16 17:25:23 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 18:25:23 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3C6F.3050809@ucalgary.ca> References: <478E3C6F.3050809@ucalgary.ca> Message-ID: <478E3E03.6000403@bsc.es> > > I'm trying to figure out if I can avoid the endorsed lib issue in Java > 5 for JAXB 2.1 somehow Why do you need "endorsed" for Java5? Java5 has no any JAXB implementation in it. Just use it as any other libraries. Dmitry From gordonp at ucalgary.ca Wed Jan 16 17:47:05 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 10:47:05 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E3E03.6000403@bsc.es> References: <478E3C6F.3050809@ucalgary.ca> <478E3E03.6000403@bsc.es> Message-ID: <478E4319.1070709@ucalgary.ca> >> I'm trying to figure out if I can avoid the endorsed lib issue in >> Java 5 for JAXB 2.1 somehow > > Why do you need "endorsed" for Java5? Java5 has no any JAXB > implementation in it. Just use it as any other libraries. Ah yes, sorry, I meant Java6. I'm installing update4, which should hopefully avoid the issue I get with update 3: java.lang.LinkageError: JAXB 2.0 API is being loaded from the bootstrap classloader, but this RI (from jar:file:/export/home/gordonp/projects/moby-live/Java/lib/jaxb-impl.jar!/com/sun/xml/bind/v2/model/impl/ModelBuilder.class) needs 2.1 API. Use the endorsed directory mechanism to place jaxb-api.jar in the bootstrap classloader. (See http://java.sun.com/j2se/1.5.0/docs/guide/standards/) From dmitry.repchevski at bsc.es Wed Jan 16 17:56:23 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 18:56:23 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4319.1070709@ucalgary.ca> References: <478E4319.1070709@ucalgary.ca> Message-ID: <478E4547.9090704@bsc.es> > > Ah yes, sorry, I meant Java6. I'm installing update4, which should > hopefully avoid the issue I get with update 3: Yeah, I understand your pain... :-) There is a way - using custom classloader. One of the JAXB developers posted it in his blog. The bad thing that in this case you will have two versions of JAXB loaded... Fortunately we have 6u4 which works just fine (at least in my demo http://inb.bsc.es/java/demo/demo.html :-)). Cheers, Dmitry From gordonp at ucalgary.ca Wed Jan 16 18:04:02 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 11:04:02 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4547.9090704@bsc.es> References: <478E4319.1070709@ucalgary.ca> <478E4547.9090704@bsc.es> Message-ID: <478E4712.5050200@ucalgary.ca> Indeed, update 4 works beautifully for me...I can now go Axis-free in MobyRequest (except for there being no Central implementation without Axis... hint hint). ;-) Dmitry Repchevsky wrote: >> >> Ah yes, sorry, I meant Java6. I'm installing update4, which should >> hopefully avoid the issue I get with update 3: > > Yeah, I understand your pain... :-) > There is a way - using custom classloader. One of the JAXB developers > posted it in his blog. > The bad thing that in this case you will have two versions of JAXB > loaded... > > Fortunately we have 6u4 which works just fine (at least in my demo > http://inb.bsc.es/java/demo/demo.html :-)). > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478e433e10950260988970! > > > From dmitry.repchevski at bsc.es Wed Jan 16 18:18:06 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 19:18:06 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4712.5050200@ucalgary.ca> References: <478E4712.5050200@ucalgary.ca> Message-ID: <478E4A5E.9090103@bsc.es> > > Indeed, update 4 works beautifully for me...I can now go Axis-free in > MobyRequest (except for there being no Central implementation without > Axis... hint hint). ;-) God damn, what you mean by "no Central implementation without Axis"? Java Moby Central implementation? I think Java implementation is abandoned... My MobyRegistry (client for Moby Central) do everything with Moby Central. It implements all operations I found in http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/CentralRegistry.html My demo uses it to find the services... MobyGenerator uses it to obtain the ontology and service descriptions. Can you please be more specific? Dmitry From gordonp at ucalgary.ca Wed Jan 16 18:53:54 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 16 Jan 2008 11:53:54 -0700 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E4A5E.9090103@bsc.es> References: <478E4712.5050200@ucalgary.ca> <478E4A5E.9090103@bsc.es> Message-ID: <478E52C2.3060407@ucalgary.ca> Sorry, I meant something implementing org.biomoby.shared.Central, since things are much easier to be adopted if they use the existing jMoby interface definitions. There's no one class bringing all the operations together from org.biomoby.shared.jaxb.registry is there, or am I missing something obvious? > Java Moby Central implementation? I think Java implementation is > abandoned... > My MobyRegistry (client for Moby Central) do everything with Moby > Central. It implements all operations I found in > http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/CentralRegistry.html > > > My demo uses it to find the services... MobyGenerator uses it to > obtain the ontology and service descriptions. > > Can you please be more specific? > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > !DSPAM:60005,478e4856109504651529! > > > From dmitry.repchevski at bsc.es Wed Jan 16 19:23:05 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Wed, 16 Jan 2008 20:23:05 +0100 Subject: [MOBY-dev] JAX-WS BioMoby API (2nd round). In-Reply-To: <478E52C2.3060407@ucalgary.ca> References: <478E52C2.3060407@ucalgary.ca> Message-ID: <478E5999.4010809@bsc.es> > > Sorry, I meant something implementing org.biomoby.shared.Central, since > things are much easier to be adopted if they use the existing jMoby > interface definitions. There's no one class bringing all the operations > together from org.biomoby.shared.jaxb.registry is there, or am I missing > something obvious? Yeah! I understand. You have the point. In MobyRegistry I have es.inb.biomoby.registry.model.CentralDigestFactory with the comment: * Utility class which is not in the main package because it's not clear yet the entire * architecture of the registry package... The problem is that Moby Central contains many objects that are _almost_ identical. Since I am using JAXB classes I had to choose between having several copies or having (if possible) one class shared between operations (messages). The latter is not always possible so to be coherent I encapsulated such objects inside operations (but there are obvious cases like RetrieveResourceURLs.class which is shared). I thought to implement some upper layer API to manage it all (something I done in CentralDigestFactory which is definitely shouldn't be in this jar...) but the question is: Should it be based on JAXB based classes? If yes, which one I have to select (in case I have different for different operations)? If no (which I do not like), I'll finish having even more duplications between JAXB (for XML) and API versions... I think the first way is better - select the JAXB classes (like org.biomoby.shared.jaxb.registry.FindServiceOperation.Services.Service). put it outside the FindServiceOperation in some model package. Next question is the functionality itself... most of the functionality is implemented inside xxxOperation itself. Just look: FindServiceOperation endpoint = new FindServiceOperation("http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl"); FindService request = new FindService("getEntryFromPDB", "inb.bsc.es"); Services response = endpoint.call(request); for (Service service : response.getServices()) { ... I understand in JMoby there is a cache... I always prefer cache + background cache update... In two words I'm open to here your suggestions and ready to implement it. Regards, Dmitry From markw at illuminae.com Mon Jan 21 23:58:29 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Mon, 21 Jan 2008 15:58:29 -0800 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC Message-ID: Hi everyone, Has anyone else looked at the INB proposal for mirroring of services? I think it's really nice, personally! I had a couple of small questions and concerns, but it really doesn't seem like an overly disruptive change, and apparently they already have it working at INB, so the codebase to support it already exists. I think we should vote on the issue soon, as the INB folks have been very, VERY patient! M -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Pieter.Neerincx at wur.nl Tue Jan 22 11:00:25 2008 From: Pieter.Neerincx at wur.nl (Pieter Neerincx) Date: Tue, 22 Jan 2008 12:00:25 +0100 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC In-Reply-To: References: Message-ID: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> Hi, I searched my mail archive and the website, but I can not find this RFC.... Was it that long ago? Anyway, can someone please send us pointer where to find this RFC? Thanks, Pi On 22-jan-2008, at 0:58, Mark Wilkinson wrote: > Hi everyone, > > Has anyone else looked at the INB proposal for mirroring of > services? I think it's really nice, personally! I had a couple of > small questions and concerns, but it really doesn't seem like an > overly disruptive change, and apparently they already have it > working at INB, so the codebase to support it already exists. > > I think we should vote on the issue soon, as the INB folks have > been very, VERY patient! > > M > > > > -- > -- > Mark Wilkinson > Assistant Professor, Dept. Medical Genetics > University of British Columbia > PI Bioinformatics > iCAPTURE Centre, St. Paul's Hospital > Tel: 604 682 2344 x62129 > Fax: 604 806 9274 > > ***CONFIDENTIALITY NOTICE*** > This electronic message is intended only for the use of the > addressee and may contain information that is privileged and > confidential. Any dissemination, distribution or copying of this > communication by unauthorized individuals is strictly prohibited. > If you have received this communication in error, please notify the > sender immediately by reply e-mail and delete the original and all > copies from your system. > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > ------------------------------------------------------------- Wageningen University and Research centre (WUR) Laboratory of Bioinformatics Transitorium (building 312) room 1034 Dreijenlaan 3 6703 HA Wageningen The Netherlands phone: 0317-483 039 fax: 0317-483 584 mobile: 06-143 66 783 mail: pieter.neerincx at wur.nl skype: pieter.online ------------------------------------------------------------ From Sebastien.Carrere at toulouse.inra.fr Tue Jan 22 14:42:01 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Tue, 22 Jan 2008 15:42:01 +0100 Subject: [MOBY-dev] Test Registry and RDF Message-ID: <479600B9.7000807@toulouse.inra.fr> Bonjour a tous, When I register a Service into the test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), the RDF file that I get as a response is empty (only the root tag is presentin the XML file, no content). Does anyone else have this problem ? Moreover, I do not know if there's a link with this problem, but deregistration in test central is problematic too ... I use the Perl API. Merci, Sebastien -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Tue Jan 22 15:00:21 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 07:00:21 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <479600B9.7000807@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> Message-ID: <4796051b.05358c0a.0df9.ffffd78e@mx.google.com> Hi Sebastien, I am not sure, but perhaps the test registry is using the old codebase and so things might not be working as they should. I will look into it and give you a definitive answer with hopefully everything then working as it should. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-22-08 6:42 AM To: Core developer announcements Subject: [MOBY-dev] Test Registry and RDF Bonjour a tous, When I register a Service into the test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), the RDF file that I get as a response is empty (only the root tag is presentin the XML file, no content). Does anyone else have this problem ? Moreover, I do not know if there's a link with this problem, but deregistration in test central is problematic too ... I use the Perl API. Merci, Sebastien From dmitry.repchevski at bsc.es Tue Jan 22 15:05:36 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 22 Jan 2008 16:05:36 +0100 Subject: [MOBY-dev] documentation error (?) registerServiceType Message-ID: <47960640.1080007@bsc.es> Hello! I found the error (?) in Moby documentation The Registry operation registerServiceType id "defined" as *********************************************** Input XML NewServiceType your_name at contact.address.com your.URI.here ExistingServiceType ExistingServiceType *********************************************** But in the schema (registerServiceType.xsd) the is defined as: *********************************************** *********************************************** So something is wrong here. If schema is ok - the xml should look like: *********************************************** *********************************************** Taking into account the the only type supported is "ISA" (?) that has no much sense... As well as using "articleName" for the parent serviceType. Can someone clarify it tu me, please? Thank you in advance, Dmitry From edward.kawas at gmail.com Tue Jan 22 15:12:55 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 07:12:55 -0800 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960640.1080007@bsc.es> References: <47960640.1080007@bsc.es> Message-ID: <47960810.22578c0a.23c1.0dbd@mx.google.com> The API is correct. I had an error in the schema. I just committed a fix. Thanks for pointing it out. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-22-08 7:06 AM To: moby-dev at lists.open-bio.org Subject: [MOBY-dev] documentation error (?) registerServiceType Hello! I found the error (?) in Moby documentation The Registry operation registerServiceType id "defined" as *********************************************** Input XML NewServiceType your_name at contact.address.com your.URI.here ExistingServiceType ExistingServiceType *********************************************** But in the schema (registerServiceType.xsd) the is defined as: *********************************************** *********************************************** So something is wrong here. If schema is ok - the xml should look like: *********************************************** *********************************************** Taking into account the the only type supported is "ISA" (?) that has no much sense... As well as using "articleName" for the parent serviceType. Can someone clarify it tu me, please? Thank you in advance, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From dmitry.repchevski at bsc.es Tue Jan 22 15:30:50 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 22 Jan 2008 16:30:50 +0100 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960810.22578c0a.23c1.0dbd@mx.google.com> References: <47960810.22578c0a.23c1.0dbd@mx.google.com> Message-ID: <47960C2A.5090301@bsc.es> Ok, but anyway *************************************** ExistingServiceType ExistingServiceType *************************************** Shouldn't it be relationshipType="ISA" (is it possible to specify anything else?) Cheers, Dmitry From edward.kawas at gmail.com Tue Jan 22 15:33:33 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 07:33:33 -0800 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960C2A.5090301@bsc.es> References: <47960810.22578c0a.23c1.0dbd@mx.google.com> <47960C2A.5090301@bsc.es> Message-ID: <47960ce2.22528c0a.4717.5c12@mx.google.com> It can only be ISA, but I believe that the doc mentions it this way so that in the future, if things were to change and the type could be HAS, HASA, etc it wouldn't be a huge change (I think - Mark will have to either confirm or deny ...) Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry Repchevsky Sent: January-22-08 7:31 AM To: moby-dev at lists.open-bio.org Subject: Re: [MOBY-dev] documentation error (?) registerServiceType Ok, but anyway *************************************** ExistingServiceType ExistingServiceType *************************************** Shouldn't it be relationshipType="ISA" (is it possible to specify anything else?) Cheers, Dmitry _______________________________________________ MOBY-dev mailing list MOBY-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Jan 22 16:29:37 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 22 Jan 2008 08:29:37 -0800 Subject: [MOBY-dev] documentation error (?) registerServiceType In-Reply-To: <47960ce2.22528c0a.4717.5c12@mx.google.com> References: <47960810.22578c0a.23c1.0dbd@mx.google.com> <47960C2A.5090301@bsc.es> <47960ce2.22528c0a.4717.5c12@mx.google.com> Message-ID: Well... I don't think we were necessarily anticipating "HAS" and "HASA" relationships, but it was left purposely open. There are (at least at the level of the Moby databases) three relationship ontologies - one for Objects, one for Services, and one for Namespaces. So you're right, there is no choice other than ISA, because there is only one term in the Service Relationships ontology - ISA. So in that regard, the documentation is correct - what goes in that space is a Service Relationships Ontology Term :-) The idea was that the ontologies could grow independently of each other to reflect more complexity if it were determined to be necessary. It is necessary... but it has never happened. M On Tue, 22 Jan 2008 07:33:33 -0800, Edward Kawas wrote: > It can only be ISA, but I believe that the doc mentions it this way so > that > in the future, if things were to change and the type could be HAS, HASA, > etc > it wouldn't be a huge change (I think - Mark will have to either confirm > or > deny ...) > > Eddie > > > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Dmitry > Repchevsky > Sent: January-22-08 7:31 AM > To: moby-dev at lists.open-bio.org > Subject: Re: [MOBY-dev] documentation error (?) registerServiceType > > Ok, but anyway > > *************************************** > > > ExistingServiceType > ExistingServiceType > > > *************************************** > > Shouldn't it be relationshipType="ISA" (is it possible to specify > anything else?) > > Cheers, > > Dmitry > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From edward.kawas at gmail.com Tue Jan 22 16:34:16 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 22 Jan 2008 08:34:16 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <479600B9.7000807@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> Message-ID: <47961b1d.0d528c0a.6572.5e28@mx.google.com> Okay, I tracked it down to a configuration problem and have since fixed it (hopefully!). So please try again. If there are any services that you need RDF for that are hosted on the test registry, please go to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will be able to generate RDF for those services. Let me know if things are better, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-22-08 6:42 AM To: Core developer announcements Subject: [MOBY-dev] Test Registry and RDF Bonjour a tous, When I register a Service into the test registry (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), the RDF file that I get as a response is empty (only the root tag is presentin the XML file, no content). Does anyone else have this problem ? Moreover, I do not know if there's a link with this problem, but deregistration in test central is problematic too ... I use the Perl API. Merci, Sebastien From markw at illuminae.com Tue Jan 22 17:12:07 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 22 Jan 2008 09:12:07 -0800 Subject: [MOBY-dev] UC Davis News & Information :: Grant for Workflow Software Message-ID: Interesting... From serr at ac.uma.es Tue Jan 22 18:29:55 2008 From: serr at ac.uma.es (Sergio Ramirez Ramirez) Date: Tue, 22 Jan 2008 19:29:55 +0100 Subject: [MOBY-dev] INB Proposal for Mirroring - RFC In-Reply-To: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> References: <938F7558-E5E8-4073-B08C-A37437E46543@wur.nl> Message-ID: <47963623.7090208@ac.uma.es> Hello to all the mobiers, In this link http://chirimoyo.ac.uma.es/proposals/BioMOBY_Mirroring.pdf you can find the INB proposal for mirroring services. It describes the new functions and the changes needed in the functions that already exist in the API of BioMOBY. The proposal also includes different options for managing the mirrors using RDF files. We would appreciate comments and suggestions, in particular how to deal with the RDF data. We have implemented the described functionality in the MOBYCentral perl code. This code will be made available, and in a few days we will provide a new link with a small tutorial about how to use the client side library. Best regards, Sergio. Pieter Neerincx wrote: > Hi, > > I searched my mail archive and the website, but I can not find this > RFC.... Was it that long ago? Anyway, can someone please send us > pointer where to find this RFC? > > Thanks, > > Pi > > On 22-jan-2008, at 0:58, Mark Wilkinson wrote: > >> Hi everyone, >> >> Has anyone else looked at the INB proposal for mirroring of services? >> I think it's really nice, personally! I had a couple of small >> questions and concerns, but it really doesn't seem like an overly >> disruptive change, and apparently they already have it working at >> INB, so the codebase to support it already exists. >> >> I think we should vote on the issue soon, as the INB folks have been >> very, VERY patient! >> >> M >> >> >> >> -- >> -- >> Mark Wilkinson >> Assistant Professor, Dept. Medical Genetics >> University of British Columbia >> PI Bioinformatics >> iCAPTURE Centre, St. Paul's Hospital >> Tel: 604 682 2344 x62129 >> Fax: 604 806 9274 >> >> ***CONFIDENTIALITY NOTICE*** >> This electronic message is intended only for the use of the addressee >> and may contain information that is privileged and confidential. Any >> dissemination, distribution or copying of this communication by >> unauthorized individuals is strictly prohibited. If you have received >> this communication in error, please notify the sender immediately by >> reply e-mail and delete the original and all copies from your system. >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> > > ------------------------------------------------------------- > Wageningen University and Research centre (WUR) > Laboratory of Bioinformatics > Transitorium (building 312) room 1034 > > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > phone: 0317-483 039 > fax: 0317-483 584 > mobile: 06-143 66 783 > mail: pieter.neerincx at wur.nl > skype: pieter.online > ------------------------------------------------------------ > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -- Sergio Ram?rez Ram?rez Instituto Nacional de Bioinform?tica (INB) Integrated Bioinformatics Node (GNV-5) Dpto. de Arquitectura de Computadores Campus Universitario de Teatinos, despacho 2.3.9a 29071 M?laga (Spain) +34 95 213 3387 "Short-term decisions tend to fail in the long-term." Frank Herbert, God Emperor of Dune From Sebastien.Carrere at toulouse.inra.fr Wed Jan 23 09:22:54 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 23 Jan 2008 10:22:54 +0100 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <47961b1d.0d528c0a.6572.5e28@mx.google.com> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> Message-ID: <4797076E.5080100@toulouse.inra.fr> The RDF file seems to be okay now using test registry. However, the deregistering procedure is always problematic: "Failed with status:500 Server closed connection without sending any data back" Sebastien Edward Kawas wrote: > Okay, I tracked it down to a configuration problem and have since fixed it > (hopefully!). So please try again. If there are any services that you need > RDF for that are hosted on the test registry, please go to > http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will be able > to generate RDF for those services. > > Let me know if things are better, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: January-22-08 6:42 AM > To: Core developer announcements > Subject: [MOBY-dev] Test Registry and RDF > > Bonjour a tous, > > > When I register a Service into the test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), > the RDF file that I get as a response is empty (only the root tag is > presentin the XML file, no content). > > Does anyone else have this problem ? > > Moreover, I do not know if there's a link with this problem, but > deregistration in test central is problematic too ... > > I use the Perl API. > > Merci, > > Sebastien > > > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Jan 23 14:52:49 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 23 Jan 2008 06:52:49 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <4797076E.5080100@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> Message-ID: <479754db.05358c0a.0e2a.15c2@mx.google.com> What service are you trying to deregister and how are you trying to do it? If you are trying to use RDF, can you send it to me so I can try? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-23-08 1:23 AM To: Core developer announcements Subject: Re: [MOBY-dev] Test Registry and RDF The RDF file seems to be okay now using test registry. However, the deregistering procedure is always problematic: "Failed with status:500 Server closed connection without sending any data back" Sebastien Edward Kawas wrote: > Okay, I tracked it down to a configuration problem and have since > fixed it (hopefully!). So please try again. If there are any services > that you need RDF for that are hosted on the test registry, please go > to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will > be able to generate RDF for those services. > > Let me know if things are better, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien > Carrere > Sent: January-22-08 6:42 AM > To: Core developer announcements > Subject: [MOBY-dev] Test Registry and RDF > > Bonjour a tous, > > > When I register a Service into the test registry > (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), > the RDF file that I get as a response is empty (only the root tag is > presentin the XML file, no content). > > Does anyone else have this problem ? > > Moreover, I do not know if there's a link with this problem, but > deregistration in test central is problematic too ... > > I use the Perl API. > > Merci, > > Sebastien > > > > > > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From Sebastien.Carrere at toulouse.inra.fr Wed Jan 23 16:38:34 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 23 Jan 2008 17:38:34 +0100 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <479754db.05358c0a.0e2a.15c2@mx.google.com> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> Message-ID: <47976D8A.70404@toulouse.inra.fr> Bonjour Eddie, I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. I use the registerService procedure from MOBY::Client::Central (v 1.152) with the signature http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmoby/rdf/BlastSwissProt.rdf corresponding to an empty RDF file. What's really strange, is that when I call for the first time the deregistring protocol, the service seems not to be removed from registry. If I try a second time, the service is removed. Nevertheless, the two times I have the timeout message ... Merci, Sebastien Edward Kawas wrote: > What service are you trying to deregister and how are you trying to do it? > > If you are trying to use RDF, can you send it to me so I can try? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: January-23-08 1:23 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > > The RDF file seems to be okay now using test registry. > > However, the deregistering procedure is always problematic: > "Failed with status:500 Server closed connection without sending any data > back" > > Sebastien > > > > Edward Kawas wrote: > >> Okay, I tracked it down to a configuration problem and have since >> fixed it (hopefully!). So please try again. If there are any services >> that you need RDF for that are hosted on the test registry, please go >> to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you will >> be able to generate RDF for those services. >> >> Let me know if things are better, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-22-08 6:42 AM >> To: Core developer announcements >> Subject: [MOBY-dev] Test Registry and RDF >> >> Bonjour a tous, >> >> >> When I register a Service into the test registry >> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), >> the RDF file that I get as a response is empty (only the root tag is >> presentin the XML file, no content). >> >> Does anyone else have this problem ? >> >> Moreover, I do not know if there's a link with this problem, but >> deregistration in test central is problematic too ... >> >> I use the Perl API. >> >> Merci, >> >> Sebastien >> >> >> >> >> >> >> >> _______________________________________________ >> 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 > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Jan 23 17:02:26 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 23 Jan 2008 09:02:26 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <47976D8A.70404@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> <47976D8A.70404@toulouse.inra.fr> Message-ID: <4797733d.0ebb720a.6974.1d68@mx.google.com> One quick question, when you say opencentral, are you talking about the test registry or another different registry? Thanks, Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-23-08 8:39 AM To: Core developer announcements Subject: Re: [MOBY-dev] Test Registry and RDF Bonjour Eddie, I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. I use the registerService procedure from MOBY::Client::Central (v 1.152) with the signature http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmoby/rdf /BlastSwissProt.rdf corresponding to an empty RDF file. What's really strange, is that when I call for the first time the deregistring protocol, the service seems not to be removed from registry. If I try a second time, the service is removed. Nevertheless, the two times I have the timeout message ... Merci, Sebastien Edward Kawas wrote: > What service are you trying to deregister and how are you trying to do it? > > If you are trying to use RDF, can you send it to me so I can try? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien > Carrere > Sent: January-23-08 1:23 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > > The RDF file seems to be okay now using test registry. > > However, the deregistering procedure is always problematic: > "Failed with status:500 Server closed connection without sending any > data back" > > Sebastien > > > > Edward Kawas wrote: > >> Okay, I tracked it down to a configuration problem and have since >> fixed it (hopefully!). So please try again. If there are any services >> that you need RDF for that are hosted on the test registry, please go >> to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you >> will be able to generate RDF for those services. >> >> Let me know if things are better, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-22-08 6:42 AM >> To: Core developer announcements >> Subject: [MOBY-dev] Test Registry and RDF >> >> Bonjour a tous, >> >> >> When I register a Service into the test registry >> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), >> the RDF file that I get as a response is empty (only the root tag is >> presentin the XML file, no content). >> >> Does anyone else have this problem ? >> >> Moreover, I do not know if there's a link with this problem, but >> deregistration in test central is problematic too ... >> >> I use the Perl API. >> >> Merci, >> >> Sebastien >> >> >> >> >> >> >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From sylvie.huchet at enst-bretagne.fr Wed Jan 23 16:05:09 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Wed, 23 Jan 2008 17:05:09 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <476AC872.70408@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> Message-ID: <479765B5.8060802@enst-bretagne.fr> Hi Paul, It seems that MobyRequest does not handle both synchronous and asynchronous calls tranparently... The invokeService() method that can be called for asynchronous calls does not defines any handler to manage asynchronous calls. And thus the performAsyncSOAPRequest method does not return any result. In addition, the asynchronous part of the invokeService does not initialize the contentsXML which leads to a NullPointerException. Regards, Sylvie. Paul Gordon a ?crit : > Hi Sylvie, > > The current class that implements asynchronous service calls is > MobyRequest (via AsyncClient). You can find both synchronous and > asynchronous services by setting the Service category to the empty > string ("") before calling CentralImpl. As Martin mentions below, the > mechanism currently used to run asynchronous services will change next > year (so there will probably be other ways to call async services > introduced), but the MobyRequest API will not need to change. > MobyRequest handles both synchronous and asynchronous calls transparently. > > Regards, > > Paul > > Martin Senger wrote: > >>> I'd like to know how asynchronous services (category moby-async) can be >>> called >>> using the java API >>> >> >> >> >> It is on the to-do list. A good opportunity to implement it will be the >> second week of February where several BioMoby developers meet at the >> Biohackaton in Japan. I hope to use this event to remove most of the >> items >> from my long-standing moby-to-do list. I am sorry for the delay. >> >> Martin >> >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From Sebastien.Carrere at toulouse.inra.fr Wed Jan 23 17:16:13 2008 From: Sebastien.Carrere at toulouse.inra.fr (Sebastien Carrere) Date: Wed, 23 Jan 2008 18:16:13 +0100 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <4797733d.0ebb720a.6974.1d68@mx.google.com> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> <47976D8A.70404@toulouse.inra.fr> <4797733d.0ebb720a.6974.1d68@mx.google.com> Message-ID: <4797765D.207@toulouse.inra.fr> Yes sorry, I speak about the Test registry: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl Sebastien Edward Kawas wrote: > One quick question, when you say opencentral, are you talking about the test > registry or another different registry? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere > Sent: January-23-08 8:39 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > Bonjour Eddie, > > I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. > I use the registerService procedure from MOBY::Client::Central (v 1.152) > with the signature > http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmoby/rdf > /BlastSwissProt.rdf > corresponding to an empty RDF file. > > What's really strange, is that when I call for the first time the > deregistring protocol, the service seems not to be removed from registry. > If I try a second time, the service is removed. > > Nevertheless, the two times I have the timeout message ... > > > Merci, > > Sebastien > > > Edward Kawas wrote: > >> What service are you trying to deregister and how are you trying to do it? >> >> If you are trying to use RDF, can you send it to me so I can try? >> >> Thanks, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-23-08 1:23 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Test Registry and RDF >> >> >> The RDF file seems to be okay now using test registry. >> >> However, the deregistering procedure is always problematic: >> "Failed with status:500 Server closed connection without sending any >> data back" >> >> Sebastien >> >> >> >> Edward Kawas wrote: >> >> >>> Okay, I tracked it down to a configuration problem and have since >>> fixed it (hopefully!). So please try again. If there are any services >>> that you need RDF for that are hosted on the test registry, please go >>> to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi and you >>> will be able to generate RDF for those services. >>> >>> Let me know if things are better, >>> >>> Eddie >>> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >>> Carrere >>> Sent: January-22-08 6:42 AM >>> To: Core developer announcements >>> Subject: [MOBY-dev] Test Registry and RDF >>> >>> Bonjour a tous, >>> >>> >>> When I register a Service into the test registry >>> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl), >>> the RDF file that I get as a response is empty (only the root tag is >>> presentin the XML file, no content). >>> >>> Does anyone else have this problem ? >>> >>> Moreover, I do not know if there's a link with this problem, but >>> deregistration in test central is problematic too ... >>> >>> I use the Perl API. >>> >>> Merci, >>> >>> Sebastien >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > -------------- next part -------------- A non-text attachment was scrubbed... Name: Sebastien_Carrere.vcf Type: text/x-vcard Size: 387 bytes Desc: not available URL: From edward.kawas at gmail.com Wed Jan 23 17:22:18 2008 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 23 Jan 2008 09:22:18 -0800 Subject: [MOBY-dev] Test Registry and RDF In-Reply-To: <4797765D.207@toulouse.inra.fr> References: <479600B9.7000807@toulouse.inra.fr> <47961b1d.0d528c0a.6572.5e28@mx.google.com> <4797076E.5080100@toulouse.inra.fr> <479754db.05358c0a.0e2a.15c2@mx.google.com> <47976D8A.70404@toulouse.inra.fr> <4797733d.0ebb720a.6974.1d68@mx.google.com> <4797765D.207@toulouse.inra.fr> Message-ID: <479777e3.25d7720a.7c14.1fe3@mx.google.com> So I have been playing around with the agent, registering my own service (using dashboard) that has a signatureURL. When I place an empty rdf document like the one that you have at my signatureURL location, and call register service with just the signatureURL filled in, the process does take a while (not sure why ... could be the server) but it does complete on its first try. The only thing that I can think of to solve the timeouts, is explicitly putting a longer timeout interval in the soap call in MOBY::Client::Central. This is assuming that the timeout that you are seeing is a result of the client and not the server. Eddie -----Original Message----- From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien Carrere Sent: January-23-08 9:16 AM To: Core developer announcements Subject: Re: [MOBY-dev] Test Registry and RDF Yes sorry, I speak about the Test registry: http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl Sebastien Edward Kawas wrote: > One quick question, when you say opencentral, are you talking about > the test registry or another different registry? > > Thanks, > > Eddie > > -----Original Message----- > From: moby-dev-bounces at lists.open-bio.org > [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien > Carrere > Sent: January-23-08 8:39 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] Test Registry and RDF > > Bonjour Eddie, > > I try to suppress BlastSwissProt by carrere.toulouse.inra.fr on opencentral. > I use the registerService procedure from MOBY::Client::Central (v > 1.152) with the signature > http://lipm-bioinfo.toulouse.inra.fr/biomoby/atelier_ppv/stagef/playmo > by/rdf > /BlastSwissProt.rdf > corresponding to an empty RDF file. > > What's really strange, is that when I call for the first time the > deregistring protocol, the service seems not to be removed from registry. > If I try a second time, the service is removed. > > Nevertheless, the two times I have the timeout message ... > > > Merci, > > Sebastien > > > Edward Kawas wrote: > >> What service are you trying to deregister and how are you trying to do it? >> >> If you are trying to use RDF, can you send it to me so I can try? >> >> Thanks, >> >> Eddie >> >> -----Original Message----- >> From: moby-dev-bounces at lists.open-bio.org >> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >> Carrere >> Sent: January-23-08 1:23 AM >> To: Core developer announcements >> Subject: Re: [MOBY-dev] Test Registry and RDF >> >> >> The RDF file seems to be okay now using test registry. >> >> However, the deregistering procedure is always problematic: >> "Failed with status:500 Server closed connection without sending any >> data back" >> >> Sebastien >> >> >> >> Edward Kawas wrote: >> >> >>> Okay, I tracked it down to a configuration problem and have since >>> fixed it (hopefully!). So please try again. If there are any >>> services that you need RDF for that are hosted on the test registry, >>> please go to http://bioinfo.icapture.ubc.ca/cgi-bin/GenerateRDF.cgi >>> and you will be able to generate RDF for those services. >>> >>> Let me know if things are better, >>> >>> Eddie >>> >>> -----Original Message----- >>> From: moby-dev-bounces at lists.open-bio.org >>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Sebastien >>> Carrere >>> Sent: January-22-08 6:42 AM >>> To: Core developer announcements >>> Subject: [MOBY-dev] Test Registry and RDF >>> >>> Bonjour a tous, >>> >>> >>> When I register a Service into the test registry >>> (http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl) >>> , the RDF file that I get as a response is empty (only the root tag >>> is presentin the XML file, no content). >>> >>> Does anyone else have this problem ? >>> >>> Moreover, I do not know if there's a link with this problem, but >>> deregistration in test central is problematic too ... >>> >>> I use the Perl API. >>> >>> Merci, >>> >>> Sebastien >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> > > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > From gordonp at ucalgary.ca Wed Jan 23 19:05:40 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Wed, 23 Jan 2008 12:05:40 -0700 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <479765B5.8060802@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> Message-ID: <47979004.1050609@ucalgary.ca> Bonjour Sylvie, Thanks for pointing this out. The handler is null as it's supposed to be, but the lack of a StringBuffer was indeed the culprit. This has been fixed, and I'm adding a unit test for this (I'd always called asynchronous services asynchronously( or sync ones either syncly or asyncly), and so didn't catch this before).. Paul Sylvie Huchet wrote: > Hi Paul, > > It seems that MobyRequest does not handle both synchronous and asynchronous > calls tranparently... > > The invokeService() method that can be called for asynchronous calls does not > defines any handler to manage asynchronous calls. And thus the > performAsyncSOAPRequest method does not return any result. > In addition, the asynchronous part of the invokeService does not initialize the > contentsXML which leads to a NullPointerException. > > Regards, > Sylvie. > > > Paul Gordon a ?crit : > >> Hi Sylvie, >> >> The current class that implements asynchronous service calls is >> MobyRequest (via AsyncClient). You can find both synchronous and >> asynchronous services by setting the Service category to the empty >> string ("") before calling CentralImpl. As Martin mentions below, the >> mechanism currently used to run asynchronous services will change next >> year (so there will probably be other ways to call async services >> introduced), but the MobyRequest API will not need to change. >> MobyRequest handles both synchronous and asynchronous calls transparently. >> >> Regards, >> >> Paul >> >> Martin Senger wrote: >> >> >>>> I'd like to know how asynchronous services (category moby-async) can be >>>> called >>>> using the java API >>>> >>>> >>> >>> It is on the to-do list. A good opportunity to implement it will be the >>> second week of February where several BioMoby developers meet at the >>> Biohackaton in Japan. I hope to use this event to remove most of the >>> items >>> from my long-standing moby-to-do list. I am sorry for the delay. >>> >>> Martin >>> >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> > > > !DSPAM:60005,47977310109501808032233! > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47977310109501808032233! > From markw at illuminae.com Wed Jan 23 21:09:36 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 23 Jan 2008 13:09:36 -0800 Subject: [MOBY-dev] Second Proofs of the manuscript now available Message-ID: Again, I wont post to the mailing list due to copyright issues, but I'll immediately send it to anyone who requests it. I'm sending it to those who requested the last version just to save time. Comments ASAP ASAP ASAP please! Best wishes all, Mark -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 Wed Jan 23 21:20:46 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 23 Jan 2008 13:20:46 -0800 Subject: [MOBY-dev] Second Proofs of the manuscript now available In-Reply-To: References: Message-ID: They have given us 24 hours to check and correct the proofs, so ASAP means REALLY FAST!! :) Mark On Wed, 23 Jan 2008 13:09:36 -0800, Mark Wilkinson wrote: > Again, I wont post to the mailing list due to copyright issues, but I'll > immediately send it to anyone who requests it. I'm sending it to those > who requested the last version just to save time. > > Comments ASAP ASAP ASAP please! > > Best wishes all, > > Mark > > > -- -- Mark Wilkinson Assistant Professor, Dept. Medical Genetics University of British Columbia PI Bioinformatics iCAPTURE Centre, St. Paul's Hospital Tel: 604 682 2344 x62129 Fax: 604 806 9274 ***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 sylvie.huchet at enst-bretagne.fr Thu Jan 24 08:51:08 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Thu, 24 Jan 2008 09:51:08 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <47979004.1050609@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> Message-ID: <4798517C.1070104@enst-bretagne.fr> Bonjour Paul, Thanks for the update, but this is not enough. If the handler has to be null, the code of performAsyncSOAPRequest must be modified to get the data : The data is got back only if the following test : "if(newDataAvailable.size() > 0 && handler != null)" is true, which is never the case. Regards, Sylvie. Paul Gordon a ?crit : > Bonjour Sylvie, > > Thanks for pointing this out. The handler is null as it's supposed to > be, but the lack of a StringBuffer was indeed the culprit. This has > been fixed, and I'm adding a unit test for this (I'd always called > asynchronous services asynchronously( or sync ones either syncly or > asyncly), and so didn't catch this before).. > > > > Paul > > Sylvie Huchet wrote: > >> Hi Paul, >> >> It seems that MobyRequest does not handle both synchronous and >> asynchronous >> calls tranparently... >> >> The invokeService() method that can be called for asynchronous calls >> does not >> defines any handler to manage asynchronous calls. And thus the >> performAsyncSOAPRequest method does not return any result. >> In addition, the asynchronous part of the invokeService does not >> initialize the >> contentsXML which leads to a NullPointerException. >> >> Regards, >> Sylvie. >> >> >> Paul Gordon a ?crit : >> >> >>> Hi Sylvie, >>> >>> The current class that implements asynchronous service calls is >>> MobyRequest (via AsyncClient). You can find both synchronous and >>> asynchronous services by setting the Service category to the empty >>> string ("") before calling CentralImpl. As Martin mentions below, the >>> mechanism currently used to run asynchronous services will change next >>> year (so there will probably be other ways to call async services >>> introduced), but the MobyRequest API will not need to change. >>> MobyRequest handles both synchronous and asynchronous calls >>> transparently. >>> >>> Regards, >>> >>> Paul >>> >>> Martin Senger wrote: >>> >>> >>> >>>>> I'd like to know how asynchronous services (category moby-async) >>>>> can be >>>>> called >>>>> using the java API >>>>> >>>> >>>> >>>> It is on the to-do list. A good opportunity to implement it will be the >>>> second week of February where several BioMoby developers meet at the >>>> Biohackaton in Japan. I hope to use this event to remove most of the >>>> items >>>> from my long-standing moby-to-do list. I am sorry for the delay. >>>> >>>> Martin >>>> >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> >> >> >> !DSPAM:60005,47977310109501808032233! >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> !DSPAM:60005,47977310109501808032233! >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From groscurt at mpiz-koeln.mpg.de Fri Jan 25 08:40:20 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Fri, 25 Jan 2008 09:40:20 +0100 Subject: [MOBY-dev] Compiling error in MobySaveDialog In-Reply-To: <4798517C.1070104@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> Message-ID: <200801250940.20763.groscurt@mpiz-koeln.mpg.de> Hi, i just checked out moby and run the gather task and included all downloaded libs in the eclipse project. One error remains in the ca.ucalcary.seahawk.gui.MobySaveDialog "The type com.sun.star.lang.XEventListener cannot be resolved. It is indirectly referenced from required .class files? It seems one lib is missing - could this be added to the jar archive which is downloaded by the gather task ? Thanks andreas -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From gordonp at ucalgary.ca Fri Jan 25 13:28:14 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Fri, 25 Jan 2008 06:28:14 -0700 Subject: [MOBY-dev] Compiling error in MobySaveDialog In-Reply-To: <200801250940.20763.groscurt@mpiz-koeln.mpg.de> References: <476A8DAD.1060208@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> <200801250940.20763.groscurt@mpiz-koeln.mpg.de> Message-ID: <4799E3EE.30106@ucalgary.ca> Hi Andreas, I'll get on that for you. The standard JDK doesn't need the JAR the compile, but obviously Eclipse does some extra dependency checking. Regards, Paul Andreas Groscurth wrote: > Hi, > > i just checked out moby and run the gather task and included all downloaded > libs in the eclipse project. > > One error remains in the ca.ucalcary.seahawk.gui.MobySaveDialog > > "The type com.sun.star.lang.XEventListener cannot be resolved. It is > indirectly referenced from required .class files? > > It seems one lib is missing - could this be added to the jar archive which is > downloaded by the gather task ? > > Thanks > andreas > > From gordonp at ucalgary.ca Sat Jan 26 18:03:52 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Sat, 26 Jan 2008 11:03:52 -0700 Subject: [MOBY-dev] Compiling error in MobySaveDialog In-Reply-To: <200801250940.20763.groscurt@mpiz-koeln.mpg.de> References: <476A8DAD.1060208@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> <200801250940.20763.groscurt@mpiz-koeln.mpg.de> Message-ID: <479B7608.1000300@ucalgary.ca> Hi Andreas, I've added extra libraries to the CVS now. Do a CVS update, then a build.sh and you be good to go... Regards, Paul Andreas Groscurth wrote: > Hi, > > i just checked out moby and run the gather task and included all downloaded > libs in the eclipse project. > > One error remains in the ca.ucalcary.seahawk.gui.MobySaveDialog > > "The type com.sun.star.lang.XEventListener cannot be resolved. It is > indirectly referenced from required .class files? > > It seems one lib is missing - could this be added to the jar archive which is > downloaded by the gather task ? > > Thanks > andreas > > From gordonp at ucalgary.ca Sat Jan 26 18:06:15 2008 From: gordonp at ucalgary.ca (Paul Gordon) Date: Sat, 26 Jan 2008 11:06:15 -0700 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <4798517C.1070104@enst-bretagne.fr> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> Message-ID: <479B7697.80202@ucalgary.ca> Hi Sylvie, Yes, sorry about that. I've moved the "handler != null" deeper into the function so that synchronous calls actually pickup the results too. It's in CVS now. Do you have a particular service of interest that I can use as a test case? Regards, Paul Sylvie Huchet wrote: > Bonjour Paul, > > Thanks for the update, but this is not enough. > If the handler has to be null, the code of performAsyncSOAPRequest must be > modified to get the data : The data is got back only if the following test : > "if(newDataAvailable.size() > 0 && handler != null)" is true, which is never the > case. > > Regards, > Sylvie. > > Paul Gordon a ?crit : > >> Bonjour Sylvie, >> >> Thanks for pointing this out. The handler is null as it's supposed to >> be, but the lack of a StringBuffer was indeed the culprit. This has >> been fixed, and I'm adding a unit test for this (I'd always called >> asynchronous services asynchronously( or sync ones either syncly or >> asyncly), and so didn't catch this before).. >> >> >> >> Paul >> >> Sylvie Huchet wrote: >> >> >>> Hi Paul, >>> >>> It seems that MobyRequest does not handle both synchronous and >>> asynchronous >>> calls tranparently... >>> >>> The invokeService() method that can be called for asynchronous calls >>> does not >>> defines any handler to manage asynchronous calls. And thus the >>> performAsyncSOAPRequest method does not return any result. >>> In addition, the asynchronous part of the invokeService does not >>> initialize the >>> contentsXML which leads to a NullPointerException. >>> >>> Regards, >>> Sylvie. >>> >>> >>> Paul Gordon a ?crit : >>> >>> >>> >>>> Hi Sylvie, >>>> >>>> The current class that implements asynchronous service calls is >>>> MobyRequest (via AsyncClient). You can find both synchronous and >>>> asynchronous services by setting the Service category to the empty >>>> string ("") before calling CentralImpl. As Martin mentions below, the >>>> mechanism currently used to run asynchronous services will change next >>>> year (so there will probably be other ways to call async services >>>> introduced), but the MobyRequest API will not need to change. >>>> MobyRequest handles both synchronous and asynchronous calls >>>> transparently. >>>> >>>> Regards, >>>> >>>> Paul >>>> >>>> Martin Senger wrote: >>>> >>>> >>>> >>>> >>>>>> I'd like to know how asynchronous services (category moby-async) >>>>>> can be >>>>>> called >>>>>> using the java API >>>>>> >>>>>> >>>>> It is on the to-do list. A good opportunity to implement it will be the >>>>> second week of February where several BioMoby developers meet at the >>>>> Biohackaton in Japan. I hope to use this event to remove most of the >>>>> items >>>>> from my long-standing moby-to-do list. I am sorry for the delay. >>>>> >>>>> Martin >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> !DSPAM:60005,47977310109501808032233! >>> >>> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> > > > !DSPAM:60005,47984f74109501894423288! > > ------------------------------------------------------------------------ > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > > !DSPAM:60005,47984f74109501894423288! > From sylvie.huchet at enst-bretagne.fr Mon Jan 28 11:22:16 2008 From: sylvie.huchet at enst-bretagne.fr (Sylvie Huchet) Date: Mon, 28 Jan 2008 12:22:16 +0100 Subject: [MOBY-dev] Calling moby-async category services In-Reply-To: <479B7697.80202@ucalgary.ca> References: <476A8DAD.1060208@enst-bretagne.fr> <4d93f07c0712200917q1ed969e6m6beb047dfdcf385d@mail.gmail.com> <476AC872.70408@ucalgary.ca> <479765B5.8060802@enst-bretagne.fr> <47979004.1050609@ucalgary.ca> <4798517C.1070104@enst-bretagne.fr> <479B7697.80202@ucalgary.ca> Message-ID: <479DBAE8.50806@enst-bretagne.fr> Hi Paul, Thank you for the modification. A service to test it could be inb.bsc.es#runPhylipDnapenny. Regards, Sylvie. Paul Gordon a ?crit : > Hi Sylvie, > > Yes, sorry about that. I've moved the "handler != null" deeper into the > function so that synchronous calls actually pickup the results too. > It's in CVS now. Do you have a particular service of interest that I can > use as a test case? > > Regards, > > Paul > > Sylvie Huchet wrote: > >> Bonjour Paul, >> >> Thanks for the update, but this is not enough. >> If the handler has to be null, the code of performAsyncSOAPRequest >> must be >> modified to get the data : The data is got back only if the following >> test : >> "if(newDataAvailable.size() > 0 && handler != null)" is true, which is >> never the >> case. >> >> Regards, >> Sylvie. >> >> Paul Gordon a ?crit : >> >> >>> Bonjour Sylvie, >>> >>> Thanks for pointing this out. The handler is null as it's supposed to >>> be, but the lack of a StringBuffer was indeed the culprit. This has >>> been fixed, and I'm adding a unit test for this (I'd always called >>> asynchronous services asynchronously( or sync ones either syncly or >>> asyncly), and so didn't catch this before).. >>> >>> >>> >>> Paul >>> >>> Sylvie Huchet wrote: >>> >>> >>> >>>> Hi Paul, >>>> >>>> It seems that MobyRequest does not handle both synchronous and >>>> asynchronous >>>> calls tranparently... >>>> >>>> The invokeService() method that can be called for asynchronous calls >>>> does not >>>> defines any handler to manage asynchronous calls. And thus the >>>> performAsyncSOAPRequest method does not return any result. >>>> In addition, the asynchronous part of the invokeService does not >>>> initialize the >>>> contentsXML which leads to a NullPointerException. >>>> >>>> Regards, >>>> Sylvie. >>>> >>>> >>>> Paul Gordon a ?crit : >>>> >>>> >>>> >>>> >>>>> Hi Sylvie, >>>>> >>>>> The current class that implements asynchronous service calls is >>>>> MobyRequest (via AsyncClient). You can find both synchronous and >>>>> asynchronous services by setting the Service category to the empty >>>>> string ("") before calling CentralImpl. As Martin mentions below, the >>>>> mechanism currently used to run asynchronous services will change next >>>>> year (so there will probably be other ways to call async services >>>>> introduced), but the MobyRequest API will not need to change. >>>>> MobyRequest handles both synchronous and asynchronous calls >>>>> transparently. >>>>> >>>>> Regards, >>>>> >>>>> Paul >>>>> >>>>> Martin Senger wrote: >>>>> >>>>> >>>>> >>>>> >>>>>>> I'd like to know how asynchronous services (category moby-async) >>>>>>> can be >>>>>>> called >>>>>>> using the java API >>>>>>> >>>>>> >>>>>> It is on the to-do list. A good opportunity to implement it will >>>>>> be the >>>>>> second week of February where several BioMoby developers meet at the >>>>>> Biohackaton in Japan. I hope to use this event to remove most of the >>>>>> items >>>>>> from my long-standing moby-to-do list. I am sorry for the delay. >>>>>> >>>>>> Martin >>>>>> >>>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> !DSPAM:60005,47977310109501808032233! >>>> >>> >>> _______________________________________________ >>> MOBY-dev mailing list >>> MOBY-dev at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/moby-dev >>> >>> >>> >> >> >> >> !DSPAM:60005,47984f74109501894423288! >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev >> >> >> !DSPAM:60005,47984f74109501894423288! >> > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev > > -------------- next part -------------- A non-text attachment was scrubbed... Name: sylvie.huchet.vcf Type: text/x-vcard Size: 215 bytes Desc: not available URL: From simont at hmgc.mcw.edu Tue Jan 29 04:45:25 2008 From: simont at hmgc.mcw.edu (Twigger, Simon (MCW)) Date: Mon, 28 Jan 2008 22:45:25 -0600 Subject: [MOBY-dev] UC Davis News & Information :: Grant for Workflow Software In-Reply-To: References: Message-ID: <3A38C930-28BC-47D3-BFA5-5E28C02C2F32@hmgc.mcw.edu> I came across this video on the Kepler workflow project this evening while browsing SciVee, I think it was from 2006 so perhaps a little out of date these days. http://www.scivee.tv/node/3452 S. -- Simon N. Twigger, Ph.D. Assistant Professor, Department of Physiology Medical College of Wisconsin 8701 Watertown Plank Road, Milwaukee, WI, USA tel: 414-456-8802 fax: 414-456-6595 AIM/iChat: simontatmcw On Jan 22, 2008, at 11:12 AM, Mark Wilkinson wrote: > > > Interesting... > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev From groscurt at mpiz-koeln.mpg.de Tue Jan 29 15:34:42 2008 From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth) Date: Tue, 29 Jan 2008 16:34:42 +0100 Subject: [MOBY-dev] BioMoby Tutorial Update In-Reply-To: <478BA3D7.6050206@avignon.inra.fr> References: <478BA3D7.6050206@avignon.inra.fr> Message-ID: <200801291634.43553.groscurt@mpiz-koeln.mpg.de> Hi all, I just wanted to inform you that I updated our BioMoby Java tutorial and added some new fenzy flash movies :-) Actually I just recorded myself doing all steps and converted them into flash movies. So you can directly see what steps have to be done how, starting from checking out BioMoby from CVS, setting up eclipse and how to register, implement and deploy a Web Service. The movies are splitted into several files for each topic and for each topic there is also a text version available. You are kind of my guinea pigs - if you have time please have a look at the tutorial and the movies. Is everything understandable, is something missing, something hard to follow - please let me know. You can find it at http://bioinfo.mpiz-koeln.mpg.de/araws/documentation/help/jmoby-step-by-step Thanks Andreas PS: Things I will add soon: - how to implement a service with more complex objects (like AminoAcidSequence) - how to set up a system for creating secure Web Services -- Andreas Groscurth Bioinformatics Developer 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)221-5062-449 From dmitry.repchevski at bsc.es Tue Jan 29 19:33:14 2008 From: dmitry.repchevski at bsc.es (Dmitry Repchevsky) Date: Tue, 29 Jan 2008 20:33:14 +0100 Subject: [MOBY-dev] Apache http 1.1 problem Message-ID: <479F7F7A.4030306@bsc.es> Hello everybody, I am facing a problem with several servers (central and service endpoints). The problem is with messages that use http 1.1 chunked messages. Some endpoints (like http://inb.bsc.es/cgi-bin/brokerRetrieval/mobydev.cgi) demand to put "Content-Length" header (otherwise return 411 error) even do not use it (chunked message). Another (for example http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl) just reject the messages (411). Does anyone faced this problem? I'm sure this must be something with Apache configuration... Cheers, Dmitry From markw at illuminae.com Thu Jan 31 19:23:09 2008 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 31 Jan 2008 11:23:09 -0800 Subject: [MOBY-dev] Fwd: Your article has been published in Briefings in Bioinformatics In-Reply-To: <20080131104248.4E82E2DEA19@marz.stanford.edu> References: <20080131104248.4E82E2DEA19@marz.stanford.edu> Message-ID: ------- Forwarded message ------- From: bib-tfl at highwire.stanford.edu To: markw at illuminae.com Cc: bib at oxfordjournals.org Subject: Your article has been published in Briefings in Bioinformatics Date: Thu, 31 Jan 2008 02:42:49 -0800 Dear Author I am pleased to inform you that Oxford Journals has published your article in Briefings in Bioinformatics. 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