From senger at ebi.ac.uk Tue Dec 6 16:25:46 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 6 Dec 2005 21:25:46 +0000 (GMT) Subject: [MOBY-dev] XML Schema vs Biomoby In-Reply-To: Message-ID: >> Well.... the blame game is not useful. Our use of XML is a valid one, >> and XML Schema is not capable of representing it. End of story. >> > You are wrong. End of story. > During last several days, we have exchanged several messages with Mark about the message above and above the role of XML Schema in Biomoby. There are mainly two points: Point one is that I was told that "you are wrong" is not a proper choice of wording in English. Well, I can always improve my English but not being an English-native speaker I will never be sure. Saying that, however, does not prevent me to regret using such phrase. Sorry, Mark. Point two is probably much more interesting for the biomoby developers. We all know, and there were never doubts about it, that Biomoby XML messages are valid XML messages. But they cannot be expressed using XML Schema. Two reasons for that. One is (the one I was talking about): the Biomoby messages are changing from call to call (a service *must* expect to get more specialized message anytime). The other one (the one Mark had in mind) is that even one single message cannot be fully described by XML Schema. Eddie gave me an example and - as far as I know - he is working now on a full list of such cases. The important message for me is: isn't it now a time to talk again (I am saying 'again' because I started already a lobbying for that in Vancouver) about why Biomoby services protocol is not compliant with the XML schema, and what could be done to make it compliant? I know about recent email exchange between Richard and Mark, referring also to the work Ben has done, talking where to put syntax and where to put semantics in the Biomoby messages. All of this is very promising and in good directions, seems to me. It seems to me that perhaps now is a good time to talk about it. Are we ready for that? Perhaps Eddie's list of incompatibility and Richard/Marks comments may help to start the discussion. Perhaps changing fundamentaly biomoby messages does not need to be so painful now when we have libraries for service providers for both main languages (Perl, Java). With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From joecker at mpiz-koeln.mpg.de Wed Dec 7 03:02:22 2005 From: joecker at mpiz-koeln.mpg.de (Anika Joecker) Date: Wed, 7 Dec 2005 09:02:22 +0100 Subject: [MOBY-dev] Hello Message-ID: <200512070902.22904.joecker@mpiz-koeln.mpg.de> Hello! I`m a new phd-student in the group of Heiko Schoof at the MPIZ in Cologne. My work will include webservices to improve functional annotations. So one of my tasks is the implementation of webservices and the registration of them in MOBY. I hope during my work I will help to improve MOBY. Greetings, Anika From joecker at mpiz-koeln.mpg.de Wed Dec 7 03:09:25 2005 From: joecker at mpiz-koeln.mpg.de (Anika Joecker) Date: Wed, 7 Dec 2005 09:09:25 +0100 Subject: [MOBY-dev] Dump of mobyrelationship Message-ID: <200512070909.25554.joecker@mpiz-koeln.mpg.de> Yesterday I tried to install MOBY. Unfortunatly the dump of the mysql database mobyrelationship contains only an create statement, but no data to fill the table. I hope someone can help me by sending a new dump-file. Greetings, Anika From markw at illuminae.com Wed Dec 7 19:49:38 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 07 Dec 2005 16:49:38 -0800 Subject: [MOBY-dev] [moby] Dump of mobyrelationship In-Reply-To: <200512070909.25554.joecker@mpiz-koeln.mpg.de> References: <200512070909.25554.joecker@mpiz-koeln.mpg.de> Message-ID: <1134002978.15999.22.camel@bioinfo.icapture.ubc.ca> Sorry about that - if you do a CVS update you will find a mobyrelationship.data file in the moby-live/Database folder along with all the others. M On Wed, 2005-12-07 at 09:09 +0100, Anika Joecker wrote: > Yesterday I tried to install MOBY. Unfortunatly the dump of the mysql database > mobyrelationship contains only an create statement, but no data to fill the > table. I hope someone can help me by sending a new dump-file. > > Greetings, > Anika > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From m.anacleto at cgiar.org Thu Dec 8 11:06:55 2005 From: m.anacleto at cgiar.org (Anacleto, Mylah Rystie (IRRI)) Date: Fri, 9 Dec 2005 00:06:55 +0800 Subject: [MOBY-dev] setting up a MOBY central registry Message-ID: Hi, I am setting up a custom MOBY central registry and am at the step of testing my installation. I would like to seek your help, I get this error: # perl testMOBYClientCentral_v05.pl TESTING MOBY CLIENT with URL: http://localhost:8080/cgi-bin/MOBY-Central.pl URI: http://localhost:8080/MOBY/Central Proxy: No Proxy Server Pseudo-hashes are deprecated at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. Can't coerce array into hash at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. Thank you. Mylah ----------- Computer Programmer Biometrics and Bioinformatics Unit International Rice research Institute Los Banos, Laguna, Philippines phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Thu Dec 8 11:50:13 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Dec 2005 08:50:13 -0800 Subject: [MOBY-dev] [moby] setting up a MOBY central registry In-Reply-To: References: Message-ID: <1134060613.17652.28.camel@bioinfo.icapture.ubc.ca> Hi Mylah, I need to deprecate that test script because it is out of date. Please use the "make test" command as part of your regular make/make install process to test your installation (note that you will have to do a "make install" prior to "make test" in order to ensure that the test is using the most updated libraries) M On Fri, 2005-12-09 at 00:06 +0800, Anacleto, Mylah Rystie (IRRI) wrote: > Hi, > > I am setting up a custom MOBY central registry and am at the step of testing my installation. I would like to seek your help, I get this error: > > # perl testMOBYClientCentral_v05.pl > TESTING MOBY CLIENT with > URL: http://localhost:8080/cgi-bin/MOBY-Central.pl > URI: http://localhost:8080/MOBY/Central > Proxy: No Proxy Server > > Pseudo-hashes are deprecated at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. > Can't coerce array into hash at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. > > Thank you. > > Mylah > > ----------- > Computer Programmer > Biometrics and Bioinformatics Unit > International Rice research Institute > Los Banos, Laguna, Philippines > phone: +63-2-580-5600 (ext.2324) > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From m.anacleto at cgiar.org Thu Dec 8 12:20:59 2005 From: m.anacleto at cgiar.org (Anacleto, Mylah Rystie (IRRI)) Date: Fri, 9 Dec 2005 01:20:59 +0800 Subject: [MOBY-dev] [moby] setting up a MOBY central registry Message-ID: Dear Mark, Thank you for your fast reply. I got errors in make test, am pasting it below. I will also look at the database... There is nothing to edit in OntologyServer.cgi? please confirm... Mylah # make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Central...................................ok t/Client-Central............................ok 1/0 This is the MOBY Client Central test suite. by default this connects to the server at mobycentral.icapture.ubc.ca (or whatever the default server is set to in the code) If you want to test a different server you must set the following ENVIRONEMNT VARABLES: MOBY_SERVER='http://your.server.name/path/to/mobycentral.pl' MOBY_URI='http://your.server.name/MOBY/Central' t/Client-Central............................ok 2/0 For the following tests I will be using the server at: http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl t/Client-Central............................ok 6/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR # Looks like your test died just after 6. t/Client-Central............................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-CollectionArticle..................ok t/Client-OntologyServer.....................ok 1/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR BEGIN failed--compilation aborted at t/Client-OntologyServer.t line 48. # Looks like your test died just after 1. t/Client-OntologyServer.....................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-Registration.......................ok t/Client-SecondaryArticle...................ok t/Client-Service............................ok 2/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR END failed--call queue aborted. # Looks like your test died just after 2. t/Client-Service............................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-ServiceInstance....................ok t/Client-SimpleArticle......................ok t/CommonSubs................................ok 2/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR BEGIN failed--compilation aborted at t/CommonSubs.t line 41. # Looks like your test died just after 2. t/CommonSubs................................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Config....................................skipped all skipped: Required only for local MOBY Central t/CrossReference............................ok t/dbConnect.................................ok t/lsid-authority-ClassResolver..............ok t/lsid-authority-dbConnect..................ok t/lsid-authority-Error......................ok t/lsid-authority-NamespaceResolver..........ok t/lsid-authority-PredicateResolver..........ok t/lsid-authority-RDFConfigure...............ok t/lsid-authority-RelationshipResolver.......ok t/lsid-authority-ServiceInstanceResolver....skipped all skipped: Skip until apparent namespace pollution fixed in ServiceInstanceResolver t/lsid-authority-ServiceResolver............ok t/Template..................................skipped all skipped: This is just a template Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/Client-Central.t 255 65280 6 0 0.00% ?? t/Client-OntologyServer.t 255 65280 1 0 0.00% ?? t/Client-Service.t 255 65280 2 0 0.00% ?? t/CommonSubs.t 255 65280 2 0 0.00% ?? 3 tests skipped. Failed 4/23 test scripts, 82.61% okay. 0/118 subtests failed, 100.00% okay. make: *** [test_dynamic] Error 255 -----Original Message----- From: moby-dev-bounces at biomoby.org on behalf of Mark Wilkinson Sent: Fri 12/9/2005 12:50 AM To: Core developer announcements Subject: Re: [MOBY-dev] [moby] setting up a MOBY central registry Hi Mylah, I need to deprecate that test script because it is out of date. Please use the "make test" command as part of your regular make/make install process to test your installation (note that you will have to do a "make install" prior to "make test" in order to ensure that the test is using the most updated libraries) M -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/ms-tnef Size: 4378 bytes Desc: not available Url : http://biomoby.org/pipermail/moby-dev/attachments/20051209/bb4f0967/attachment.bin From markw at illuminae.com Thu Dec 8 12:28:28 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Dec 2005 09:28:28 -0800 Subject: [MOBY-dev] [moby] setting up a MOBY central registry In-Reply-To: References: Message-ID: <1134062908.17652.49.camel@bioinfo.icapture.ubc.ca> I would say, based on the messages you are getting, that your MOBY configuration file doesn't exist :-) You may need to restart your server to get that environment variable into the Apache process... M On Fri, 2005-12-09 at 01:20 +0800, Anacleto, Mylah Rystie (IRRI) wrote: > Dear Mark, > > Thank you for your fast reply. > > I got errors in make test, am pasting it below. I will also look at the database... > > There is nothing to edit in OntologyServer.cgi? please confirm... > > Mylah > > > # make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/Central...................................ok > t/Client-Central............................ok 1/0 > > > This is the MOBY Client Central test suite. > > by default this connects to the server at mobycentral.icapture.ubc.ca > (or whatever the default server is set to in the code) > > If you want to test a different server you must set the following > ENVIRONEMNT VARABLES: > > MOBY_SERVER='http://your.server.name/path/to/mobycentral.pl' > MOBY_URI='http://your.server.name/MOBY/Central' > > > t/Client-Central............................ok 2/0 > > For the following tests I will be using the server at: > http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl > > > t/Client-Central............................ok 6/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > # Looks like your test died just after 6. > t/Client-Central............................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Client-CollectionArticle..................ok > t/Client-OntologyServer.....................ok 1/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > BEGIN failed--compilation aborted at t/Client-OntologyServer.t line 48. > # Looks like your test died just after 1. > t/Client-OntologyServer.....................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Client-Registration.......................ok > t/Client-SecondaryArticle...................ok > t/Client-Service............................ok 2/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > END failed--call queue aborted. > # Looks like your test died just after 2. > t/Client-Service............................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Client-ServiceInstance....................ok > t/Client-SimpleArticle......................ok > t/CommonSubs................................ok 2/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > BEGIN failed--compilation aborted at t/CommonSubs.t line 41. > # Looks like your test died just after 2. > t/CommonSubs................................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Config....................................skipped > all skipped: Required only for local MOBY Central > t/CrossReference............................ok > t/dbConnect.................................ok > t/lsid-authority-ClassResolver..............ok > t/lsid-authority-dbConnect..................ok > t/lsid-authority-Error......................ok > t/lsid-authority-NamespaceResolver..........ok > t/lsid-authority-PredicateResolver..........ok > t/lsid-authority-RDFConfigure...............ok > t/lsid-authority-RelationshipResolver.......ok > t/lsid-authority-ServiceInstanceResolver....skipped > all skipped: Skip until apparent namespace pollution fixed in ServiceInstanceResolver > t/lsid-authority-ServiceResolver............ok > t/Template..................................skipped > all skipped: This is just a template > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > t/Client-Central.t 255 65280 6 0 0.00% ?? > t/Client-OntologyServer.t 255 65280 1 0 0.00% ?? > t/Client-Service.t 255 65280 2 0 0.00% ?? > t/CommonSubs.t 255 65280 2 0 0.00% ?? > 3 tests skipped. > Failed 4/23 test scripts, 82.61% okay. 0/118 subtests failed, 100.00% okay. > make: *** [test_dynamic] Error 255 > > > -----Original Message----- > From: moby-dev-bounces at biomoby.org on behalf of Mark Wilkinson > Sent: Fri 12/9/2005 12:50 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] setting up a MOBY central registry > > Hi Mylah, > > I need to deprecate that test script because it is out of date. Please > use the "make test" command as part of your regular make/make install > process to test your installation (note that you will have to do a "make > install" prior to "make test" in order to ensure that the test is using > the most updated libraries) > > M > > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From markw at illuminae.com Fri Dec 9 14:45:44 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 09 Dec 2005 11:45:44 -0800 Subject: [MOBY-dev] RFC 1913 & 1914 Message-ID: <1134157544.23245.108.camel@bioinfo.icapture.ubc.ca> I'd like to propose RFC 1913 and 1914 - specification for LSID's and the content of Metadata returned by LSID metadata resolution for MOBY entities. http://biomoby.open-bio.org/index.php/for-developers/moby_extensions M -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From rebecca.ernst at gsf.de Mon Dec 12 11:07:11 2005 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Mon, 12 Dec 2005 17:07:11 +0100 Subject: [MOBY-dev] deregistration of one service deletes many other services! Message-ID: <439DA02F.1060402@gsf.de> Hi Mark! finally I found the problem which killed most of the Planet Central registry! The symptom was this: when I ran the registration skript aiming to delete one (named!) service I ended up with about 140 services deleted and only 24 left in the registry. So I had a look at the database (table service_instance) and compared the services which were left compared to the ones that were deleted. It turned out that the ones left had a lsid whereas the ones that were deleted had no lsid. I am currently updating all service_instances by hand nevertheless I think it is worth changing the call so it leaves the other services where they are. I think the call should only affect the service I explicitly named. I could imagine that other people also have old registries where the service_instances do not contain lsids. In my case a lucky accident caused that I made a database dump one day before this happend :-) , otherwise many services would have been lost forever. Cheers, Rebecca -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From markw at illuminae.com Wed Dec 14 22:35:42 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 14 Dec 2005 19:35:42 -0800 Subject: [MOBY-dev] RFC 1863 - Error handling in MOBY Message-ID: <43A0E48E.6080508@illuminae.com> Oops! We didn't close this RFC. I think it's safe to say this one passed! M From senger at ebi.ac.uk Fri Dec 16 04:52:40 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 16 Dec 2005 09:52:40 +0000 (GMT) Subject: [MOBY-dev] what is the status of id and namespace for primitive types Message-ID: Mark, Could you please refresh my memory what is the status (meaning: should they be used or not, and if yes, what they mean) of 'id' and 'namespace' attributes in the primitive types? The places I am asking for are indicated by question marks in the following example: 123 aaa Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Fri Dec 16 10:53:48 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 16 Dec 2005 07:53:48 -0800 Subject: [MOBY-dev] what is the status of id and namespace for primitive types In-Reply-To: References: Message-ID: <43A2E30C.4060607@illuminae.com> If the Integer and String are distinctly and independantly identifiable entities outside of their context in the DNASequence object, then they should carry their own namespace and id values. Otherwise these attributes have null values, and only the "identifiable" object has a namespace and ID. M Martin Senger wrote: >Mark, > Could you please refresh my memory what is the status (meaning: should >they be used or not, and if yes, what they mean) of 'id' and 'namespace' >attributes in the primitive types? The places I am asking for are >indicated by question marks in the following example: > > > 123 > aaa > > > Thanks, > Martin > > > From senger at ebi.ac.uk Mon Dec 19 05:03:33 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 19 Dec 2005 10:03:33 +0000 (GMT) Subject: [MOBY-dev] RFC #1863 Error Handling in MOBY-S In-Reply-To: <43388019.9040308@cnb.uam.es> Message-ID: David, I am trying now to incorporate the agreed changes (regarding the error handling) into Moses-generated services. But - as often with me - I cannot find the latest version of the error handling. Could you please send it (or a URL) to me. Thanks. Eddie, Mark, or whoever can do it, Could you please add it to the Moby API page - because the error handling is now part of the Moby API, isn't it? Thanks and regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From dgpisano at cnb.uam.es Mon Dec 19 05:41:50 2005 From: dgpisano at cnb.uam.es (=?ISO-8859-1?Q?David_Gonz=E1lez_Pisano?=) Date: Mon, 19 Dec 2005 11:41:50 +0100 Subject: [MOBY-dev] RFC #1863 Error Handling in MOBY-S In-Reply-To: References: Message-ID: <43A68E6E.4090201@cnb.uam.es> Hi Martin, Latest version submitted is available in Bugzilla at http://bugzilla.open-bio.org/attachment.cgi?id=246 David Martin Senger escribi?: >David, > I am trying now to incorporate the agreed changes (regarding the error >handling) into Moses-generated services. But - as often with me - I cannot >find the latest version of the error handling. Could you please send it >(or a URL) to me. Thanks. > >Eddie, Mark, or whoever can do it, > Could you please add it to the Moby API page - because the error >handling is now part of the Moby API, isn't it? > > Thanks and regards, > Martin > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: dgpisano.vcf Type: text/x-vcard Size: 338 bytes Desc: not available Url : http://biomoby.org/pipermail/moby-dev/attachments/20051219/61ddce4c/dgpisano.vcf From francis_gibbons at hms.harvard.edu Mon Dec 19 09:12:08 2005 From: francis_gibbons at hms.harvard.edu (Frank Gibbons) Date: Mon, 19 Dec 2005 09:12:08 -0500 Subject: [MOBY-dev] RFC #1863 Error Handling in MOBY-S In-Reply-To: References: <43388019.9040308@cnb.uam.es> Message-ID: <5.2.1.1.2.20051219091153.010b0bd0@email.med.harvard.edu> I'm integrating this right now. -Frank At 05:03 AM 12/19/2005, you wrote: >David, > I am trying now to incorporate the agreed changes (regarding the error >handling) into Moses-generated services. But - as often with me - I cannot >find the latest version of the error handling. Could you please send it >(or a URL) to me. Thanks. > >Eddie, Mark, or whoever can do it, > Could you please add it to the Moby API page - because the error >handling is now part of the Moby API, isn't it? > > Thanks and regards, > Martin > >-- >Martin Senger > email: martin.senger at gmail.com > skype: martinsenger >consulting for: > International Rice Research Institute > Biometrics and Bioinformatics Unit > DAPO BOX 7777, Metro Manila > Philippines, phone: +63-2-580-5600 (ext.2324) > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From akerhornou at imim.es Tue Dec 20 11:13:47 2005 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Tue, 20 Dec 2005 17:13:47 +0100 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna Message-ID: <43A82DBB.8000506@imim.es> Hi I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone have a look at this ? /Creating biomoby scavenger : 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' ... Failed: Connection timed out [Ljava.lang.StackTraceElement;@10e98d8 org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not retrieve and or process RDF document for BioMoby Objects at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:189) at org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoaderThread.run(ScavengerTree.java:327) Caused by: java.lang.NullPointerException at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:185) ... 1 more/ thanks Arnaud From edward.kawas at gmail.com Tue Dec 20 11:17:17 2005 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 20 Dec 2005 08:17:17 -0800 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <43A82DBB.8000506@imim.es> Message-ID: <000901c60580$da08a430$6500a8c0@notebook> I just loaded up Taverna and the Moby scavenger works. Perhaps you should try again. Eddie -----Original Message----- From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Arnaud Kerhornou Sent: Tuesday, December 20, 2005 8:14 AM To: taverna-users at lists.sourceforge.net; mobydev Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna Hi I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone have a look at this ? /Creating biomoby scavenger : 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' ... Failed: Connection timed out [Ljava.lang.StackTraceElement;@10e98d8 org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not retrieve and or process RDF document for BioMoby Objects at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j ava:189) at org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader Thread.run(ScavengerTree.java:327) Caused by: java.lang.NullPointerException at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j ava:185) ... 1 more/ thanks Arnaud _______________________________________________ MOBY-dev mailing list MOBY-dev at biomoby.org http://biomoby.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Dec 20 11:24:36 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Dec 2005 08:24:36 -0800 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <000901c60580$da08a430$6500a8c0@notebook> References: <000901c60580$da08a430$6500a8c0@notebook> Message-ID: <43A83044.8010508@illuminae.com> Yup... the RESOURCES script is working fine, as is the port 80 proxy... must have been a network error? M Edward Kawas wrote: >I just loaded up Taverna and the Moby scavenger works. Perhaps you should >try again. > >Eddie > >-----Original Message----- >From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On >Behalf Of Arnaud Kerhornou >Sent: Tuesday, December 20, 2005 8:14 AM >To: taverna-users at lists.sourceforge.net; mobydev >Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna > >Hi > >I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone >have a look at this ? > >/Creating biomoby scavenger : >'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' >... >Failed: Connection timed out >[Ljava.lang.StackTraceElement;@10e98d8 >org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: >Could not retrieve and or process RDF document for BioMoby Objects > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:189) > at >org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader >Thread.run(ScavengerTree.java:327) >Caused by: java.lang.NullPointerException > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:185) > ... 1 more/ > >thanks >Arnaud >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > > > > From akerhornou at imim.es Tue Dec 20 11:25:30 2005 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Tue, 20 Dec 2005 17:25:30 +0100 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <000901c60580$da08a430$6500a8c0@notebook> References: <000901c60580$da08a430$6500a8c0@notebook> Message-ID: <43A8307A.7090405@imim.es> Hi Eddie, Yes it works fine, i don't know what happened then, cheers Arnaud Edward Kawas wrote: >I just loaded up Taverna and the Moby scavenger works. Perhaps you should >try again. > >Eddie > >-----Original Message----- >From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On >Behalf Of Arnaud Kerhornou >Sent: Tuesday, December 20, 2005 8:14 AM >To: taverna-users at lists.sourceforge.net; mobydev >Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna > >Hi > >I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone >have a look at this ? > >/Creating biomoby scavenger : >'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' >... >Failed: Connection timed out >[Ljava.lang.StackTraceElement;@10e98d8 >org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: >Could not retrieve and or process RDF document for BioMoby Objects > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:189) > at >org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader >Thread.run(ScavengerTree.java:327) >Caused by: java.lang.NullPointerException > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:185) > ... 1 more/ > >thanks >Arnaud > > > From markw at illuminae.com Tue Dec 20 11:26:48 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Dec 2005 08:26:48 -0800 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <000901c60580$da08a430$6500a8c0@notebook> References: <000901c60580$da08a430$6500a8c0@notebook> Message-ID: <43A830C8.6070704@illuminae.com> Of course, an Amrerican pundit suggested yesterday that all Canadians are "retarted", so Eddie and I might just not be understanding the problem ;-) M Edward Kawas wrote: >I just loaded up Taverna and the Moby scavenger works. Perhaps you should >try again. > >Eddie > >-----Original Message----- >From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On >Behalf Of Arnaud Kerhornou >Sent: Tuesday, December 20, 2005 8:14 AM >To: taverna-users at lists.sourceforge.net; mobydev >Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna > >Hi > >I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone >have a look at this ? > >/Creating biomoby scavenger : >'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' >... >Failed: Connection timed out >[Ljava.lang.StackTraceElement;@10e98d8 >org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: >Could not retrieve and or process RDF document for BioMoby Objects > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:189) > at >org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader >Thread.run(ScavengerTree.java:327) >Caused by: java.lang.NullPointerException > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:185) > ... 1 more/ > >thanks >Arnaud >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > > > > From senger at ebi.ac.uk Tue Dec 6 21:25:46 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 6 Dec 2005 21:25:46 +0000 (GMT) Subject: [MOBY-dev] XML Schema vs Biomoby In-Reply-To: Message-ID: >> Well.... the blame game is not useful. Our use of XML is a valid one, >> and XML Schema is not capable of representing it. End of story. >> > You are wrong. End of story. > During last several days, we have exchanged several messages with Mark about the message above and above the role of XML Schema in Biomoby. There are mainly two points: Point one is that I was told that "you are wrong" is not a proper choice of wording in English. Well, I can always improve my English but not being an English-native speaker I will never be sure. Saying that, however, does not prevent me to regret using such phrase. Sorry, Mark. Point two is probably much more interesting for the biomoby developers. We all know, and there were never doubts about it, that Biomoby XML messages are valid XML messages. But they cannot be expressed using XML Schema. Two reasons for that. One is (the one I was talking about): the Biomoby messages are changing from call to call (a service *must* expect to get more specialized message anytime). The other one (the one Mark had in mind) is that even one single message cannot be fully described by XML Schema. Eddie gave me an example and - as far as I know - he is working now on a full list of such cases. The important message for me is: isn't it now a time to talk again (I am saying 'again' because I started already a lobbying for that in Vancouver) about why Biomoby services protocol is not compliant with the XML schema, and what could be done to make it compliant? I know about recent email exchange between Richard and Mark, referring also to the work Ben has done, talking where to put syntax and where to put semantics in the Biomoby messages. All of this is very promising and in good directions, seems to me. It seems to me that perhaps now is a good time to talk about it. Are we ready for that? Perhaps Eddie's list of incompatibility and Richard/Marks comments may help to start the discussion. Perhaps changing fundamentaly biomoby messages does not need to be so painful now when we have libraries for service providers for both main languages (Perl, Java). With regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From joecker at mpiz-koeln.mpg.de Wed Dec 7 08:02:22 2005 From: joecker at mpiz-koeln.mpg.de (Anika Joecker) Date: Wed, 7 Dec 2005 09:02:22 +0100 Subject: [MOBY-dev] Hello Message-ID: <200512070902.22904.joecker@mpiz-koeln.mpg.de> Hello! I`m a new phd-student in the group of Heiko Schoof at the MPIZ in Cologne. My work will include webservices to improve functional annotations. So one of my tasks is the implementation of webservices and the registration of them in MOBY. I hope during my work I will help to improve MOBY. Greetings, Anika From joecker at mpiz-koeln.mpg.de Wed Dec 7 08:09:25 2005 From: joecker at mpiz-koeln.mpg.de (Anika Joecker) Date: Wed, 7 Dec 2005 09:09:25 +0100 Subject: [MOBY-dev] Dump of mobyrelationship Message-ID: <200512070909.25554.joecker@mpiz-koeln.mpg.de> Yesterday I tried to install MOBY. Unfortunatly the dump of the mysql database mobyrelationship contains only an create statement, but no data to fill the table. I hope someone can help me by sending a new dump-file. Greetings, Anika From markw at illuminae.com Thu Dec 8 00:49:38 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 07 Dec 2005 16:49:38 -0800 Subject: [MOBY-dev] [moby] Dump of mobyrelationship In-Reply-To: <200512070909.25554.joecker@mpiz-koeln.mpg.de> References: <200512070909.25554.joecker@mpiz-koeln.mpg.de> Message-ID: <1134002978.15999.22.camel@bioinfo.icapture.ubc.ca> Sorry about that - if you do a CVS update you will find a mobyrelationship.data file in the moby-live/Database folder along with all the others. M On Wed, 2005-12-07 at 09:09 +0100, Anika Joecker wrote: > Yesterday I tried to install MOBY. Unfortunatly the dump of the mysql database > mobyrelationship contains only an create statement, but no data to fill the > table. I hope someone can help me by sending a new dump-file. > > Greetings, > Anika > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From m.anacleto at cgiar.org Thu Dec 8 16:06:55 2005 From: m.anacleto at cgiar.org (Anacleto, Mylah Rystie (IRRI)) Date: Fri, 9 Dec 2005 00:06:55 +0800 Subject: [MOBY-dev] setting up a MOBY central registry Message-ID: Hi, I am setting up a custom MOBY central registry and am at the step of testing my installation. I would like to seek your help, I get this error: # perl testMOBYClientCentral_v05.pl TESTING MOBY CLIENT with URL: http://localhost:8080/cgi-bin/MOBY-Central.pl URI: http://localhost:8080/MOBY/Central Proxy: No Proxy Server Pseudo-hashes are deprecated at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. Can't coerce array into hash at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. Thank you. Mylah ----------- Computer Programmer Biometrics and Bioinformatics Unit International Rice research Institute Los Banos, Laguna, Philippines phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Thu Dec 8 16:50:13 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Dec 2005 08:50:13 -0800 Subject: [MOBY-dev] [moby] setting up a MOBY central registry In-Reply-To: References: Message-ID: <1134060613.17652.28.camel@bioinfo.icapture.ubc.ca> Hi Mylah, I need to deprecate that test script because it is out of date. Please use the "make test" command as part of your regular make/make install process to test your installation (note that you will have to do a "make install" prior to "make test" in order to ensure that the test is using the most updated libraries) M On Fri, 2005-12-09 at 00:06 +0800, Anacleto, Mylah Rystie (IRRI) wrote: > Hi, > > I am setting up a custom MOBY central registry and am at the step of testing my installation. I would like to seek your help, I get this error: > > # perl testMOBYClientCentral_v05.pl > TESTING MOBY CLIENT with > URL: http://localhost:8080/cgi-bin/MOBY-Central.pl > URI: http://localhost:8080/MOBY/Central > Proxy: No Proxy Server > > Pseudo-hashes are deprecated at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. > Can't coerce array into hash at /usr/lib/perl5/site_perl/5.8.0/MOBY/Client/Central.pm line 412. > > Thank you. > > Mylah > > ----------- > Computer Programmer > Biometrics and Bioinformatics Unit > International Rice research Institute > Los Banos, Laguna, Philippines > phone: +63-2-580-5600 (ext.2324) > > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at biomoby.org > http://biomoby.org/mailman/listinfo/moby-dev -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From m.anacleto at cgiar.org Thu Dec 8 17:20:59 2005 From: m.anacleto at cgiar.org (Anacleto, Mylah Rystie (IRRI)) Date: Fri, 9 Dec 2005 01:20:59 +0800 Subject: [MOBY-dev] [moby] setting up a MOBY central registry Message-ID: Dear Mark, Thank you for your fast reply. I got errors in make test, am pasting it below. I will also look at the database... There is nothing to edit in OntologyServer.cgi? please confirm... Mylah # make test PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Central...................................ok t/Client-Central............................ok 1/0 This is the MOBY Client Central test suite. by default this connects to the server at mobycentral.icapture.ubc.ca (or whatever the default server is set to in the code) If you want to test a different server you must set the following ENVIRONEMNT VARABLES: MOBY_SERVER='http://your.server.name/path/to/mobycentral.pl' MOBY_URI='http://your.server.name/MOBY/Central' t/Client-Central............................ok 2/0 For the following tests I will be using the server at: http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl t/Client-Central............................ok 6/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR # Looks like your test died just after 6. t/Client-Central............................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-CollectionArticle..................ok t/Client-OntologyServer.....................ok 1/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR BEGIN failed--compilation aborted at t/Client-OntologyServer.t line 48. # Looks like your test died just after 1. t/Client-OntologyServer.....................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-Registration.......................ok t/Client-SecondaryArticle...................ok t/Client-Service............................ok 2/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR END failed--call queue aborted. # Looks like your test died just after 2. t/Client-Service............................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Client-ServiceInstance....................ok t/Client-SimpleArticle......................ok t/CommonSubs................................ok 2/0MOBY Configuration file doesn't exist No such file or directory ERROR ERROR ERROR BEGIN failed--compilation aborted at t/CommonSubs.t line 41. # Looks like your test died just after 2. t/CommonSubs................................dubious Test returned status 255 (wstat 65280, 0xff00) after all the subtests completed successfully t/Config....................................skipped all skipped: Required only for local MOBY Central t/CrossReference............................ok t/dbConnect.................................ok t/lsid-authority-ClassResolver..............ok t/lsid-authority-dbConnect..................ok t/lsid-authority-Error......................ok t/lsid-authority-NamespaceResolver..........ok t/lsid-authority-PredicateResolver..........ok t/lsid-authority-RDFConfigure...............ok t/lsid-authority-RelationshipResolver.......ok t/lsid-authority-ServiceInstanceResolver....skipped all skipped: Skip until apparent namespace pollution fixed in ServiceInstanceResolver t/lsid-authority-ServiceResolver............ok t/Template..................................skipped all skipped: This is just a template Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/Client-Central.t 255 65280 6 0 0.00% ?? t/Client-OntologyServer.t 255 65280 1 0 0.00% ?? t/Client-Service.t 255 65280 2 0 0.00% ?? t/CommonSubs.t 255 65280 2 0 0.00% ?? 3 tests skipped. Failed 4/23 test scripts, 82.61% okay. 0/118 subtests failed, 100.00% okay. make: *** [test_dynamic] Error 255 -----Original Message----- From: moby-dev-bounces at biomoby.org on behalf of Mark Wilkinson Sent: Fri 12/9/2005 12:50 AM To: Core developer announcements Subject: Re: [MOBY-dev] [moby] setting up a MOBY central registry Hi Mylah, I need to deprecate that test script because it is out of date. Please use the "make test" command as part of your regular make/make install process to test your installation (note that you will have to do a "make install" prior to "make test" in order to ensure that the test is using the most updated libraries) M -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4378 bytes Desc: not available URL: From markw at illuminae.com Thu Dec 8 17:28:28 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 08 Dec 2005 09:28:28 -0800 Subject: [MOBY-dev] [moby] setting up a MOBY central registry In-Reply-To: References: Message-ID: <1134062908.17652.49.camel@bioinfo.icapture.ubc.ca> I would say, based on the messages you are getting, that your MOBY configuration file doesn't exist :-) You may need to restart your server to get that environment variable into the Apache process... M On Fri, 2005-12-09 at 01:20 +0800, Anacleto, Mylah Rystie (IRRI) wrote: > Dear Mark, > > Thank you for your fast reply. > > I got errors in make test, am pasting it below. I will also look at the database... > > There is nothing to edit in OntologyServer.cgi? please confirm... > > Mylah > > > # make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/Central...................................ok > t/Client-Central............................ok 1/0 > > > This is the MOBY Client Central test suite. > > by default this connects to the server at mobycentral.icapture.ubc.ca > (or whatever the default server is set to in the code) > > If you want to test a different server you must set the following > ENVIRONEMNT VARABLES: > > MOBY_SERVER='http://your.server.name/path/to/mobycentral.pl' > MOBY_URI='http://your.server.name/MOBY/Central' > > > t/Client-Central............................ok 2/0 > > For the following tests I will be using the server at: > http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl > > > t/Client-Central............................ok 6/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > # Looks like your test died just after 6. > t/Client-Central............................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Client-CollectionArticle..................ok > t/Client-OntologyServer.....................ok 1/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > BEGIN failed--compilation aborted at t/Client-OntologyServer.t line 48. > # Looks like your test died just after 1. > t/Client-OntologyServer.....................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Client-Registration.......................ok > t/Client-SecondaryArticle...................ok > t/Client-Service............................ok 2/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > END failed--call queue aborted. > # Looks like your test died just after 2. > t/Client-Service............................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Client-ServiceInstance....................ok > t/Client-SimpleArticle......................ok > t/CommonSubs................................ok 2/0MOBY Configuration file doesn't exist No such file or directory > > ERROR ERROR ERROR > BEGIN failed--compilation aborted at t/CommonSubs.t line 41. > # Looks like your test died just after 2. > t/CommonSubs................................dubious > Test returned status 255 (wstat 65280, 0xff00) > after all the subtests completed successfully > t/Config....................................skipped > all skipped: Required only for local MOBY Central > t/CrossReference............................ok > t/dbConnect.................................ok > t/lsid-authority-ClassResolver..............ok > t/lsid-authority-dbConnect..................ok > t/lsid-authority-Error......................ok > t/lsid-authority-NamespaceResolver..........ok > t/lsid-authority-PredicateResolver..........ok > t/lsid-authority-RDFConfigure...............ok > t/lsid-authority-RelationshipResolver.......ok > t/lsid-authority-ServiceInstanceResolver....skipped > all skipped: Skip until apparent namespace pollution fixed in ServiceInstanceResolver > t/lsid-authority-ServiceResolver............ok > t/Template..................................skipped > all skipped: This is just a template > Failed Test Stat Wstat Total Fail Failed List of Failed > ------------------------------------------------------------------------------- > t/Client-Central.t 255 65280 6 0 0.00% ?? > t/Client-OntologyServer.t 255 65280 1 0 0.00% ?? > t/Client-Service.t 255 65280 2 0 0.00% ?? > t/CommonSubs.t 255 65280 2 0 0.00% ?? > 3 tests skipped. > Failed 4/23 test scripts, 82.61% okay. 0/118 subtests failed, 100.00% okay. > make: *** [test_dynamic] Error 255 > > > -----Original Message----- > From: moby-dev-bounces at biomoby.org on behalf of Mark Wilkinson > Sent: Fri 12/9/2005 12:50 AM > To: Core developer announcements > Subject: Re: [MOBY-dev] [moby] setting up a MOBY central registry > > Hi Mylah, > > I need to deprecate that test script because it is out of date. Please > use the "make test" command as part of your regular make/make install > process to test your installation (note that you will have to do a "make > install" prior to "make test" in order to ensure that the test is using > the most updated libraries) > > M > > > -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From markw at illuminae.com Fri Dec 9 19:45:44 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 09 Dec 2005 11:45:44 -0800 Subject: [MOBY-dev] RFC 1913 & 1914 Message-ID: <1134157544.23245.108.camel@bioinfo.icapture.ubc.ca> I'd like to propose RFC 1913 and 1914 - specification for LSID's and the content of Metadata returned by LSID metadata resolution for MOBY entities. http://biomoby.open-bio.org/index.php/for-developers/moby_extensions M -- "Ontologists do it with the edges!" Mark Wilkinson Asst. Professor Dept. of Medical Genetics University of British Columbia PI in Bioinformatics iCAPTURE Centre St. Paul's Hospital Rm. 166, 1081 Burrard St. Vancouver, BC, V6Z 1Y6 tel: 604 682 2344 x62129 fax: 604 806 9274 From rebecca.ernst at gsf.de Mon Dec 12 16:07:11 2005 From: rebecca.ernst at gsf.de (Rebecca Ernst) Date: Mon, 12 Dec 2005 17:07:11 +0100 Subject: [MOBY-dev] deregistration of one service deletes many other services! Message-ID: <439DA02F.1060402@gsf.de> Hi Mark! finally I found the problem which killed most of the Planet Central registry! The symptom was this: when I ran the registration skript aiming to delete one (named!) service I ended up with about 140 services deleted and only 24 left in the registry. So I had a look at the database (table service_instance) and compared the services which were left compared to the ones that were deleted. It turned out that the ones left had a lsid whereas the ones that were deleted had no lsid. I am currently updating all service_instances by hand nevertheless I think it is worth changing the call so it leaves the other services where they are. I think the call should only affect the service I explicitly named. I could imagine that other people also have old registries where the service_instances do not contain lsids. In my case a lucky accident caused that I made a database dump one day before this happend :-) , otherwise many services would have been lost forever. Cheers, Rebecca -- Rebecca Ernst MIPS, Inst. for Bioinformatics GSF Research Center for Environment and Health Ingolstaedter Landstr. 1 85764 Neuherberg fon: +49 89 3187 3583 email: Rebecca.Ernst at gsf.de From markw at illuminae.com Thu Dec 15 03:35:42 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 14 Dec 2005 19:35:42 -0800 Subject: [MOBY-dev] RFC 1863 - Error handling in MOBY Message-ID: <43A0E48E.6080508@illuminae.com> Oops! We didn't close this RFC. I think it's safe to say this one passed! M From senger at ebi.ac.uk Fri Dec 16 09:52:40 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 16 Dec 2005 09:52:40 +0000 (GMT) Subject: [MOBY-dev] what is the status of id and namespace for primitive types Message-ID: Mark, Could you please refresh my memory what is the status (meaning: should they be used or not, and if yes, what they mean) of 'id' and 'namespace' attributes in the primitive types? The places I am asking for are indicated by question marks in the following example: 123 aaa Thanks, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From markw at illuminae.com Fri Dec 16 15:53:48 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 16 Dec 2005 07:53:48 -0800 Subject: [MOBY-dev] what is the status of id and namespace for primitive types In-Reply-To: References: Message-ID: <43A2E30C.4060607@illuminae.com> If the Integer and String are distinctly and independantly identifiable entities outside of their context in the DNASequence object, then they should carry their own namespace and id values. Otherwise these attributes have null values, and only the "identifiable" object has a namespace and ID. M Martin Senger wrote: >Mark, > Could you please refresh my memory what is the status (meaning: should >they be used or not, and if yes, what they mean) of 'id' and 'namespace' >attributes in the primitive types? The places I am asking for are >indicated by question marks in the following example: > > > 123 > aaa > > > Thanks, > Martin > > > From senger at ebi.ac.uk Mon Dec 19 10:03:33 2005 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 19 Dec 2005 10:03:33 +0000 (GMT) Subject: [MOBY-dev] RFC #1863 Error Handling in MOBY-S In-Reply-To: <43388019.9040308@cnb.uam.es> Message-ID: David, I am trying now to incorporate the agreed changes (regarding the error handling) into Moses-generated services. But - as often with me - I cannot find the latest version of the error handling. Could you please send it (or a URL) to me. Thanks. Eddie, Mark, or whoever can do it, Could you please add it to the Moby API page - because the error handling is now part of the Moby API, isn't it? Thanks and regards, Martin -- Martin Senger email: martin.senger at gmail.com skype: martinsenger consulting for: International Rice Research Institute Biometrics and Bioinformatics Unit DAPO BOX 7777, Metro Manila Philippines, phone: +63-2-580-5600 (ext.2324) From dgpisano at cnb.uam.es Mon Dec 19 10:41:50 2005 From: dgpisano at cnb.uam.es (=?ISO-8859-1?Q?David_Gonz=E1lez_Pisano?=) Date: Mon, 19 Dec 2005 11:41:50 +0100 Subject: [MOBY-dev] RFC #1863 Error Handling in MOBY-S In-Reply-To: References: Message-ID: <43A68E6E.4090201@cnb.uam.es> Hi Martin, Latest version submitted is available in Bugzilla at http://bugzilla.open-bio.org/attachment.cgi?id=246 David Martin Senger escribi?: >David, > I am trying now to incorporate the agreed changes (regarding the error >handling) into Moses-generated services. But - as often with me - I cannot >find the latest version of the error handling. Could you please send it >(or a URL) to me. Thanks. > >Eddie, Mark, or whoever can do it, > Could you please add it to the Moby API page - because the error >handling is now part of the Moby API, isn't it? > > Thanks and regards, > Martin > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: dgpisano.vcf Type: text/x-vcard Size: 338 bytes Desc: not available URL: From francis_gibbons at hms.harvard.edu Mon Dec 19 14:12:08 2005 From: francis_gibbons at hms.harvard.edu (Frank Gibbons) Date: Mon, 19 Dec 2005 09:12:08 -0500 Subject: [MOBY-dev] RFC #1863 Error Handling in MOBY-S In-Reply-To: References: <43388019.9040308@cnb.uam.es> Message-ID: <5.2.1.1.2.20051219091153.010b0bd0@email.med.harvard.edu> I'm integrating this right now. -Frank At 05:03 AM 12/19/2005, you wrote: >David, > I am trying now to incorporate the agreed changes (regarding the error >handling) into Moses-generated services. But - as often with me - I cannot >find the latest version of the error handling. Could you please send it >(or a URL) to me. Thanks. > >Eddie, Mark, or whoever can do it, > Could you please add it to the Moby API page - because the error >handling is now part of the Moby API, isn't it? > > Thanks and regards, > Martin > >-- >Martin Senger > email: martin.senger at gmail.com > skype: martinsenger >consulting for: > International Rice Research Institute > Biometrics and Bioinformatics Unit > DAPO BOX 7777, Metro Manila > Philippines, phone: +63-2-580-5600 (ext.2324) > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons From akerhornou at imim.es Tue Dec 20 16:13:47 2005 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Tue, 20 Dec 2005 17:13:47 +0100 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna Message-ID: <43A82DBB.8000506@imim.es> Hi I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone have a look at this ? /Creating biomoby scavenger : 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' ... Failed: Connection timed out [Ljava.lang.StackTraceElement;@10e98d8 org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not retrieve and or process RDF document for BioMoby Objects at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:189) at org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoaderThread.run(ScavengerTree.java:327) Caused by: java.lang.NullPointerException at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.java:185) ... 1 more/ thanks Arnaud From edward.kawas at gmail.com Tue Dec 20 16:17:17 2005 From: edward.kawas at gmail.com (Edward Kawas) Date: Tue, 20 Dec 2005 08:17:17 -0800 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <43A82DBB.8000506@imim.es> Message-ID: <000901c60580$da08a430$6500a8c0@notebook> I just loaded up Taverna and the Moby scavenger works. Perhaps you should try again. Eddie -----Original Message----- From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Arnaud Kerhornou Sent: Tuesday, December 20, 2005 8:14 AM To: taverna-users at lists.sourceforge.net; mobydev Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna Hi I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone have a look at this ? /Creating biomoby scavenger : 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' ... Failed: Connection timed out [Ljava.lang.StackTraceElement;@10e98d8 org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: Could not retrieve and or process RDF document for BioMoby Objects at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j ava:189) at org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader Thread.run(ScavengerTree.java:327) Caused by: java.lang.NullPointerException at org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j ava:185) ... 1 more/ thanks Arnaud _______________________________________________ MOBY-dev mailing list MOBY-dev at biomoby.org http://biomoby.org/mailman/listinfo/moby-dev From markw at illuminae.com Tue Dec 20 16:24:36 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Dec 2005 08:24:36 -0800 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <000901c60580$da08a430$6500a8c0@notebook> References: <000901c60580$da08a430$6500a8c0@notebook> Message-ID: <43A83044.8010508@illuminae.com> Yup... the RESOURCES script is working fine, as is the port 80 proxy... must have been a network error? M Edward Kawas wrote: >I just loaded up Taverna and the Moby scavenger works. Perhaps you should >try again. > >Eddie > >-----Original Message----- >From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On >Behalf Of Arnaud Kerhornou >Sent: Tuesday, December 20, 2005 8:14 AM >To: taverna-users at lists.sourceforge.net; mobydev >Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna > >Hi > >I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone >have a look at this ? > >/Creating biomoby scavenger : >'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' >... >Failed: Connection timed out >[Ljava.lang.StackTraceElement;@10e98d8 >org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: >Could not retrieve and or process RDF document for BioMoby Objects > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:189) > at >org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader >Thread.run(ScavengerTree.java:327) >Caused by: java.lang.NullPointerException > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:185) > ... 1 more/ > >thanks >Arnaud >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > > > > From akerhornou at imim.es Tue Dec 20 16:25:30 2005 From: akerhornou at imim.es (Arnaud Kerhornou) Date: Tue, 20 Dec 2005 17:25:30 +0100 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <000901c60580$da08a430$6500a8c0@notebook> References: <000901c60580$da08a430$6500a8c0@notebook> Message-ID: <43A8307A.7090405@imim.es> Hi Eddie, Yes it works fine, i don't know what happened then, cheers Arnaud Edward Kawas wrote: >I just loaded up Taverna and the Moby scavenger works. Perhaps you should >try again. > >Eddie > >-----Original Message----- >From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On >Behalf Of Arnaud Kerhornou >Sent: Tuesday, December 20, 2005 8:14 AM >To: taverna-users at lists.sourceforge.net; mobydev >Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna > >Hi > >I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone >have a look at this ? > >/Creating biomoby scavenger : >'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' >... >Failed: Connection timed out >[Ljava.lang.StackTraceElement;@10e98d8 >org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: >Could not retrieve and or process RDF document for BioMoby Objects > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:189) > at >org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader >Thread.run(ScavengerTree.java:327) >Caused by: java.lang.NullPointerException > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:185) > ... 1 more/ > >thanks >Arnaud > > > From markw at illuminae.com Tue Dec 20 16:26:48 2005 From: markw at illuminae.com (Mark Wilkinson) Date: Tue, 20 Dec 2005 08:26:48 -0800 Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna In-Reply-To: <000901c60580$da08a430$6500a8c0@notebook> References: <000901c60580$da08a430$6500a8c0@notebook> Message-ID: <43A830C8.6070704@illuminae.com> Of course, an Amrerican pundit suggested yesterday that all Canadians are "retarted", so Eddie and I might just not be understanding the problem ;-) M Edward Kawas wrote: >I just loaded up Taverna and the Moby scavenger works. Perhaps you should >try again. > >Eddie > >-----Original Message----- >From: moby-dev-bounces at biomoby.org [mailto:moby-dev-bounces at biomoby.org] On >Behalf Of Arnaud Kerhornou >Sent: Tuesday, December 20, 2005 8:14 AM >To: taverna-users at lists.sourceforge.net; mobydev >Subject: [MOBY-dev] Biomoby scavenger not being loaded in taverna > >Hi > >I can not load the biomoby scavenger in teverna 1.3.1 right now, can someone >have a look at this ? > >/Creating biomoby scavenger : >'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl' >... >Failed: Connection timed out >[Ljava.lang.StackTraceElement;@10e98d8 >org.embl.ebi.escience.scuflui.workbench.ScavengerCreationException: >Could not retrieve and or process RDF document for BioMoby Objects > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:189) > at >org.embl.ebi.escience.scuflui.workbench.ScavengerTree$DefaultScavengerLoader >Thread.run(ScavengerTree.java:327) >Caused by: java.lang.NullPointerException > at >org.biomoby.client.taverna.plugin.BiomobyScavenger.(BiomobyScavenger.j >ava:185) > ... 1 more/ > >thanks >Arnaud >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > >_______________________________________________ >MOBY-dev mailing list >MOBY-dev at biomoby.org >http://biomoby.org/mailman/listinfo/moby-dev > > > >