From markw at illuminae.com Wed Feb 1 13:39:09 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Feb 2006 10:39:09 -0800 Subject: [MOBY-l] MOBY Central going down in 10 minutes for upgrade Message-ID: <1138819149.4897.17.camel@bioinfo.icapture.ubc.ca> Just a heads-up that MOBY Central will be offline for a few minutes, after which all of the LSID's will have been updated to include version numbers. We'll see how many people scream... ;-) I've just made a complete backup of the database, so we can roll-back to today if something goes terribly wrong! Mark -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Feb 1 14:39:54 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Feb 2006 11:39:54 -0800 Subject: [MOBY-l] Update, followed by roll-back Message-ID: <1138822794.4897.47.camel@bioinfo.icapture.ubc.ca> Hi again, The database update went ~well, but it seems there are still some places where the code doesn't like LSID versions. I didn't see these problems in my testing, and the test suite passes after the lsid update, but the results of gbrowse_moby service search were not identical before and after the update, so there's something wrong. I've rolled-back for the moment ("drop database mobycentral" is the most frightening line I have ever typed!). I'll send out another warning before I try again. Cheers all! Let me know if you notice anything strange - the rollback had some...er... peculiarities... but I think it is OK. M -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Feb 1 17:42:33 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Feb 2006 14:42:33 -0800 Subject: [MOBY-l] MOBY LSID's now versioned in the public MOBY Central Message-ID: <1138833753.6489.4.camel@bioinfo.icapture.ubc.ca> Hi everyone, Just a heads-up that, in the public registry, the LSID's for object types, service types, namespaces, and service instances now have the "version" field included as a timestamp of the objects creation date in GMT. The starting timestamp for all existing LSIDs is 2001-09-21T16-00-00Z The MOBY Central code is also updated to add versions to any entities being added to the registry or to the ontologies, and as far as I can tell it is all working properly. Please let me know ASAP if you notice anything unusual after this change. Thanks! M -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Wed Feb 1 18:00:39 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 01 Feb 2006 15:00:39 -0800 Subject: [MOBY-l] NB for anyone subscribed to teh MOBY RSS feeds In-Reply-To: <1138833753.6489.4.camel@bioinfo.icapture.ubc.ca> References: <1138833753.6489.4.camel@bioinfo.icapture.ubc.ca> Message-ID: <1138834839.6634.5.camel@bioinfo.icapture.ubc.ca> Anyone subscribing to the MOBY registry RSS feeds will get bombed shortly, since the RSS feed is using LSID's to determine which services, objects, etc are newly added. Since we've just modified all of the LSIDs, they are ALL going to look new when that cron job runs!! M On Wed, 2006-02-01 at 14:42 -0800, Mark Wilkinson wrote: > Hi everyone, > > Just a heads-up that, in the public registry, the LSID's for object > types, service types, namespaces, and service instances now have the > "version" field included as a timestamp of the objects creation date in > GMT. The starting timestamp for all existing LSIDs is > 2001-09-21T16-00-00Z > > The MOBY Central code is also updated to add versions to any entities > being added to the registry or to the ontologies, and as far as I can > tell it is all working properly. > > Please let me know ASAP if you notice anything unusual after this > change. > > Thanks! > > M > -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From Chad.Clites at usd.edu Thu Feb 2 10:30:08 2006 From: Chad.Clites at usd.edu (Chad Clites) Date: Thu, 02 Feb 2006 09:30:08 -0600 Subject: [MOBY-l] command line queries Message-ID: <91641291ae6e.91ae6e916412@usd.edu> I have been working with the BaseCmdLineClient trying to get a feel for how things work, and I am having trouble with the HASA, HAS, and ISA queries. I am assuming it is because I am supplying an incorrect query parameter. Given the command: run-cmdline-client -od2 ISA I am putting in, as data-types, simple queries such as "NucleotideSequence" or "Protien". It runs the search, and simply returns me to the command prompt. I am not getting an error message, so I am assuming at this point my query paramter is wrong, and that it is simply being swallowed. So then my next assumption would be that I have a fundamental misunderstanding of what a is. According to the MapPrimitiveDataTypes API, NucleotideSequence is a valid data type name. What am I missing? Regards, Chad Clites From senger at ebi.ac.uk Thu Feb 2 19:50:15 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 3 Feb 2006 00:50:15 +0000 (GMT) Subject: [MOBY-l] command line queries In-Reply-To: <91641291ae6e.91ae6e916412@usd.edu> Message-ID: Mark, I vaguely remember that we might have had already discussion about the method 'Relationship' but perhaps you can refresh my memory. As far as I see Chad is right, the method does not seem to work. This is the XML sent to registry: NucleotideSequence ISA 1 But I am getting back an empty answer: Do you see where is the problem? 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 nsutanto at purdue.edu Wed Feb 8 14:54:33 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Wed, 8 Feb 2006 14:54:33 -0500 Subject: [MOBY-l] question from begineer Message-ID: <1139428473.43ea4c793e49f@webmail.purdue.edu> Hi, I'm currently senior in computer engineering and doing some research about biomoby. I just got a little confuse about how to start this. I have cgi that I wrote in Perl Script and want to put it in the Moby data hosts & services, and want to make a simple client that can request to that service. How do I do that? Thanks a lot for any help. -Nicholas. From markw at illuminae.com Wed Feb 8 16:45:09 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Wed, 08 Feb 2006 13:45:09 -0800 Subject: [MOBY-l] [moby] question from begineer In-Reply-To: <1139428473.43ea4c793e49f@webmail.purdue.edu> References: <1139428473.43ea4c793e49f@webmail.purdue.edu> Message-ID: <1139435110.2184.5.camel@bioinfo.icapture.ubc.ca> Hi Nicholas, First of all - WELCOME! It's nice to see a new name in the MOBY list :-) Okay, the best way to get started is by following a tutorial. There are several of them around the Web - one day I will take the time to collect the links to all of them on our new website - however, there is one available to you on the main MOBY pages: http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial If you have checked-out the CVS of the moby-live code, you should first do an update since I just edited the example code today. Then go to the moby-live/Perl/scripts folder. In that folder is a file called Services.cgi and that shows you what a typical Perl daemon looks like. In the ./scripts/Services folder you will find two examples of MOBY service modules. The first one - HelloWorld.pm - is about as simple as a service can get, and shows you the basic scaffold for how to put a service together. The other file - LocalServices.pm - contains all of the code for all of the services that I am running from my own server here in Vancouver. Some of these are quite complex, but they will give you examples of most common MOBYesque messages. So... hopefully that will get you started. Please just send a message to this mailing list if you run into problems. There are lots of people around who can help! :-) Best wishes! Mark On Wed, 2006-02-08 at 14:54 -0500, Nicholas Sutanto wrote: > Hi, > > I'm currently senior in computer engineering and doing some research about > biomoby. > I just got a little confuse about how to start this. > I have cgi that I wrote in Perl Script and want to put it in the Moby data > hosts & services, and want to make a simple client that can request to that > service. > How do I do that? > > Thanks a lot for any help. > > -Nicholas. > > > > > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From Chad.Clites at usd.edu Fri Feb 10 09:21:19 2006 From: Chad.Clites at usd.edu (Chad Clites) Date: Fri, 10 Feb 2006 08:21:19 -0600 Subject: [MOBY-l] command line queries Message-ID: <11a13d711a1f17.11a1f1711a13d7@usd.edu> I apologize if I sound like a pest, but has there been any progress on this? Is there something I can do to help? Regards, Chad Clites From senger at ebi.ac.uk Fri Feb 10 09:35:18 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Fri, 10 Feb 2006 14:35:18 +0000 (GMT) Subject: [MOBY-l] command line queries In-Reply-To: <11a13d711a1f17.11a1f1711a13d7@usd.edu> Message-ID: > I apologize if I sound like a pest, but has there been any progress on > this? Is there something I can do to help? > I should apologize. Mark made changes - and let me test them and answer some questions - but I have it still on my table. I will make it this weeend. But the main bug was fixed - you may use it even now. 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 nsutanto at purdue.edu Tue Feb 14 22:18:57 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Tue, 14 Feb 2006 22:18:57 -0500 Subject: [MOBY-l] [moby] question from begineer In-Reply-To: <1139435110.2184.5.camel@bioinfo.icapture.ubc.ca> References: <1139428473.43ea4c793e49f@webmail.purdue.edu> <1139435110.2184.5.camel@bioinfo.icapture.ubc.ca> Message-ID: <1139973537.43f29da17a370@webmail.purdue.edu> Hello... I have several questions.. In the biomoby.org at MOBY Downloads section, there is 09/16/2004: Latest Code Release and CVS Repository. Which one should I download to use? Is the one from CVS stable enough? Also, I have myfile.cgi. I want to use BioMoby to access this file, and make simple client that call myfile.cgi from biomoby. Could you give me some direction to start? How do I run simple 'echo' program.. or hello world? I'm sorry.., I'm just really confused how bio-moby works.., how to compile it and make it work.. Best Regards, Nicholas Sutanto. From edward.kawas at gmail.com Wed Feb 15 12:13:31 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 15 Feb 2006 09:13:31 -0800 Subject: [MOBY-l] [moby] question from begineer In-Reply-To: <1139973537.43f29da17a370@webmail.purdue.edu> Message-ID: <000f01c63253$26985670$6500a8c0@notebook> Hi, Are you interested in making clients (writing services that use the moby framework) or hosting a registry? Eddie > -----Original Message----- > From: moby-l-bounces at biomoby.org > [mailto:moby-l-bounces at biomoby.org] On Behalf Of Nicholas Sutanto > Sent: Tuesday, February 14, 2006 7:19 PM > To: moby-l at biomoby.org > Subject: Re: [MOBY-l] [moby] question from begineer > > Hello... > > I have several questions.. > > In the biomoby.org at MOBY Downloads section, there is > 09/16/2004: Latest Code Release and CVS Repository. > > Which one should I download to use? Is the one from CVS stable enough? > > Also, I have myfile.cgi. I want to use BioMoby to access this > file, and make simple client that call myfile.cgi from > biomoby. Could you give me some direction to start? How do I > run simple 'echo' program.. or hello world? > > I'm sorry.., I'm just really confused how bio-moby works.., > how to compile it and make it work.. > > Best Regards, > Nicholas Sutanto. > > > > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l From nsutanto at purdue.edu Wed Feb 15 14:13:23 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Wed, 15 Feb 2006 14:13:23 -0500 Subject: [MOBY-l] error when do make test In-Reply-To: <000f01c63253$26985670$6500a8c0@notebook> References: <000f01c63253$26985670$6500a8c0@notebook> Message-ID: <1140030803.43f37d537d852@webmail.purdue.edu> Hello, I just downloaded the biomoby tarball from the CVS reprository (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby), and tried to install it here to my system. So I went to moby/moby-live/Perl folder, and do "perl Makefile.PL PREFIX=/MyInstallationFolder". Then, I do make. But it seems that it's failing when i did the make test. I copied and pasted the error message in the bottom of this email. Do you guys can give me any clue why this happen? Maybe I miss something? I did the same thing with the latest code release version (09/16/2004).., but it seems I can install it without this problem. Thanks a lot, Nicholas. alhagib 86 % make test PERL_DL_NONLAZY=1 /p/perl/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Central...................................# Failed test (t/Central.t at line 26) # Tried to use 'MOBY::Central'. t/Central...................................NOK 1# Error: Can't locate DBD/mysql.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/OntologyServer.pm line 70. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/OntologyServer.pm line 70. # Compilation failed in require at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/Central.pm line 14. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/Central.pm line 14. # Compilation failed in require at (eval 1) line 2. # Failed test (t/Central.t at line 57) t/Central...................................NOK 2# MOBY::Central->can('Registration') failed # MOBY::Central->can('registerObjectClass') failed # MOBY::Central->can('_registerObjectPayload') failed # MOBY::Central->can('deregisterObjectClass') failed # MOBY::Central->can('_deregisterObjectPayload') failed # MOBY::Central->can('_testObjectTypeAgainstPrimitives') failed # MOBY::Central->can('registerServiceType') failed # MOBY::Central->can('_registerServiceTypePayload') failed # MOBY::Central->can('deregisterServiceType') failed # MOBY::Central->can('_deregisterServiceTypePayload') failed # MOBY::Central->can('retrieveNamespaces') failed # MOBY::Central->can('_registerNamespacePayload') failed # MOBY::Central->can('deregisterNamespace') failed # MOBY::Central->can('_deregisterNamespacePayload') failed # MOBY::Central->can('registerService') failed # MOBY::Central->can('_registerServicePayload') failed # MOBY::Central->can('_getServiceInstanceRDF') failed # MOBY::Central->can('_registerArticles') failed # MOBY::Central->can('deregisterService') failed # MOBY::Central->can('_deregisterServicePayload') failed # MOBY::Central->can('findService') failed # MOBY::Central->can('_findServicePayload') failed # MOBY::Central->can('_extractObjectTypes') failed # MOBY::Central->can('registerServiceWSDL') failed # MOBY::Central->can('_extract_ids') failed # MOBY::Central->can('_searchForServicesWithArticle') failed # MOBY::Central->can('_searchForSimple') failed # MOBY::Central->can('_searchForCollection') failed # MOBY::Central->can('_extractObjectTypesAndNamespaces') failed # MOBY::Central->can('retrieveService') failed # MOBY::Central->can('_retrieveServicePayload') failed # MOBY::Central->can('retrieveResourceURLs') failed # MOBY::Central->can('retrieveServiceProviders') failed # MOBY::Central->can('retrieveServiceNames') failed # MOBY::Central->can('retrieveServiceTypes') failed # MOBY::Central->can('retrieveRelationshipTypes') failed # MOBY::Central->can('retrieveObjectNames') failed # MOBY::Central->can('retrieveObjectDefinition') failed # MOBY::Central->can('retrieveNamespaces') failed # MOBY::Central->can('retrieveObject') failed # MOBY::Central->can('_retrieveObjectPayload') failed # MOBY::Central->can('Relationships') failed # MOBY::Central->can('DUMP_MySQL') failed # MOBY::Central->can('_ISAPayload') failed # MOBY::Central failed to implement full API # Looks like you failed 2 tests of 2. t/Central...................................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-2 Failed 2/2 tests, 0.00% okay t/Client-Central............................ok t/Client-CollectionArticle..................ok t/Client-OntologyServer.....................ok t/Client-Registration.......................ok t/Client-SecondaryArticle...................ok t/Client-Service............................ok t/Client-ServiceInstance....................ok t/Client-SimpleArticle......................ok t/CommonSubs................................ok t/Config....................................skipped all skipped: Required only for local MOBY Central t/CrossReference............................ok t/dbConnect.................................# Failed test (t/dbConnect.t at line 18) # Tried to use 'MOBY::lsid::authority::dbConnect'. t/dbConnect.................................NOK 1# Error: Can't locate DBD/mysql.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/dbConnect.pm line 17. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/dbConnect.pm line 17. # Compilation failed in require at (eval 1) line 2. # Failed test (t/dbConnect.t at line 25) # MOBY::lsid::authority::dbConnect->can('dbConnect') failed # API not correctly implemented t/dbConnect.................................NOK 2# Looks like you failed 2 tests of 2. t/dbConnect.................................dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-2 Failed 2/2 tests, 0.00% okay t/lsid-authority-ClassResolver..............# Failed test (t/lsid-authority-ClassResolver.t at line 18) # Tried to use 'MOBY::lsid::authority::ClassResolver'. t/lsid-authority-ClassResolver..............NOK 1# Error: Can't locate XML/DOM.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/ClassResolver.pm line 5. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/ClassResolver.pm line 5. # Compilation failed in require at (eval 1) line 2. # Failed test (t/lsid-authority-ClassResolver.t at line 25) # MOBY::lsid::authority::ClassResolver->can('resolve_classtype') failed # Didn't implement full API t/lsid-authority-ClassResolver..............NOK 2# Looks like you failed 2 tests of 2. t/lsid-authority-ClassResolver..............dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-2 Failed 2/2 tests, 0.00% okay t/lsid-authority-dbConnect..................# Failed test (t/lsid-authority-dbConnect.t at line 18) t/lsid-authority-dbConnect..................NOK 1# Tried to use 'MOBY::lsid::authority::dbConnect'. # Error: Can't locate DBD/mysql.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/dbConnect.pm line 17. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/dbConnect.pm line 17. # Compilation failed in require at (eval 1) line 2. # Looks like you failed 1 tests of 1. t/lsid-authority-dbConnect..................dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay t/lsid-authority-Error......................ok t/lsid-authority-NamespaceResolver..........# Failed test (t/lsid-authority-NamespaceResolver.t at line 18) # Tried to use 'MOBY::lsid::authority::NamespaceResolver'. # Error: Can't locate XML/DOM.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/NamespaceResolver.pm line 5. t/lsid-authority-NamespaceResolver..........NOK 1# BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/NamespaceResolver.pm line 5. # Compilation failed in require at (eval 1) line 2. # Failed test (t/lsid-authority-NamespaceResolver.t at line 25) # MOBY::lsid::authority::NamespaceResolver->can('resolve_namespacetype') failed # NamespaceResolver didn't implement API correctly # Looks like you failed 2 tests of 2. t/lsid-authority-NamespaceResolver..........dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-2 Failed 2/2 tests, 0.00% okay t/lsid-authority-PredicateResolver..........# Failed test (t/lsid-authority-PredicateResolver.t at line 18) # Tried to use 'MOBY::lsid::authority::PredicateResolver'. # Error: Can't locate XML/DOM.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/PredicateResolver.pm line 5. t/lsid-authority-PredicateResolver..........NOK 1# BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/PredicateResolver.pm line 5. # Compilation failed in require at (eval 1) line 2. # Looks like you failed 1 tests of 1. t/lsid-authority-PredicateResolver..........dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay t/lsid-authority-RDFConfigure...............ok t/lsid-authority-RelationshipResolver.......# Failed test (t/lsid-authority-RelationshipResolver.t at line 18) # Tried to use 'MOBY::lsid::authority::RelationshipResolver'. t/lsid-authority-RelationshipResolver.......NOK 1# Error: Can't locate XML/DOM.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/RelationshipResolver.pm line 5. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/RelationshipResolver.pm line 5. # Compilation failed in require at (eval 1) line 2. # Failed test (t/lsid-authority-RelationshipResolver.t at line 25) # MOBY::lsid::authority::RelationshipResolver->can('resolve_relationshiptype') failed # RelationshipResolver didn't implement full API t/lsid-authority-RelationshipResolver.......NOK 2# Looks like you failed 2 tests of 2. t/lsid-authority-RelationshipResolver.......dubious Test returned status 2 (wstat 512, 0x200) DIED. FAILED tests 1-2 Failed 2/2 tests, 0.00% okay t/lsid-authority-ServiceInstanceResolver....skipped all skipped: Skip until apparent namespace pollution fixed in ServiceInstanceResolver t/lsid-authority-ServiceResolver............# Failed test (t/lsid-authority-ServiceResolver.t at line 18) # Tried to use 'MOBY::lsid::authority::ServiceResolver'. t/lsid-authority-ServiceResolver............NOK 1# Error: Can't locate XML/DOM.pm in @INC (@INC contains: /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/5.8.4 /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/ServiceResolver.pm line 5. # BEGIN failed--compilation aborted at /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/lsid/authority/ServiceResolver.pm line 5. # Compilation failed in require at (eval 1) line 2. # Looks like you failed 1 tests of 1. t/lsid-authority-ServiceResolver............dubious Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 Failed 1/1 tests, 0.00% okay t/Template..................................skipped all skipped: This is just a template Failed Test Stat Wstat Total Fail Failed List of Failed ------------------------------------------------------------------------------- t/Central.t 2 512 2 2 100.00% 1-2 t/dbConnect.t 2 512 2 2 100.00% 1-2 t/lsid-authority-ClassResolver.t 2 512 2 2 100.00% 1-2 t/lsid-authority-NamespaceResolve 2 512 2 2 100.00% 1-2 t/lsid-authority-PredicateResolve 1 256 1 1 100.00% 1 t/lsid-authority-RelationshipReso 2 512 2 2 100.00% 1-2 t/lsid-authority-ServiceResolver. 1 256 1 1 100.00% 1 t/lsid-authority-dbConnect.t 1 256 1 1 100.00% 1 3 tests skipped. Failed 8/23 test scripts, 65.22% okay. 13/380 subtests failed, 96.58% okay. *** Error code 29 make: Fatal error: Command failed for target `test_dynamic' From edward.kawas at gmail.com Wed Feb 15 15:06:10 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Wed, 15 Feb 2006 12:06:10 -0800 Subject: [MOBY-l] error when do make test In-Reply-To: <1140030803.43f37d537d852@webmail.purdue.edu> Message-ID: <001401c6326b$450f06e0$6500a8c0@notebook> Make sure that you have the following libraries installed * Bundle::CPAN * LWP * HTML::Parser with unicode support (this might have caused some of the later problems) * Bundle::DBI * SOAP::Lite * XML::DOM * DBD::mysql You can use ppm to download and install them. Eddie > -----Original Message----- > From: moby-l-bounces at biomoby.org > [mailto:moby-l-bounces at biomoby.org] On Behalf Of Nicholas Sutanto > Sent: Wednesday, February 15, 2006 11:13 AM > To: moby-l at biomoby.org > Subject: [MOBY-l] error when do make test > > Hello, > > I just downloaded the biomoby tarball from the CVS > reprository > (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot= > biomoby), and tried to install it here to my system. > > So I went to moby/moby-live/Perl folder, and do "perl > Makefile.PL PREFIX=/MyInstallationFolder". > Then, I do make. > > But it seems that it's failing when i did the make test. > I copied and pasted the error message in the bottom of this email. > > Do you guys can give me any clue why this happen? Maybe I > miss something? > > I did the same thing with the latest code release version > (09/16/2004).., but it seems I can install it without this problem. > > > Thanks a lot, > Nicholas. > > > alhagib 86 % make test > PERL_DL_NONLAZY=1 /p/perl/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/Central...................................# Failed test > (t/Central.t at > line 26) > # Tried to use 'MOBY::Central'. > t/Central...................................NOK 1# Error: > Can't locate > DBD/mysql.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/OntologyServer.pm > line 70. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/OntologyServer.pm > line 70. > # Compilation failed in require at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/Central.pm > line 14. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/Central.pm > line 14. > # Compilation failed in require at (eval 1) line 2. > # Failed test (t/Central.t at line 57) > t/Central...................................NOK 2# > MOBY::Central->can('Registration') failed > # MOBY::Central->can('registerObjectClass') failed > # MOBY::Central->can('_registerObjectPayload') failed > # MOBY::Central->can('deregisterObjectClass') failed > # MOBY::Central->can('_deregisterObjectPayload') failed > # MOBY::Central->can('_testObjectTypeAgainstPrimitives') failed > # MOBY::Central->can('registerServiceType') failed > # MOBY::Central->can('_registerServiceTypePayload') failed > # MOBY::Central->can('deregisterServiceType') failed > # MOBY::Central->can('_deregisterServiceTypePayload') failed > # MOBY::Central->can('retrieveNamespaces') failed > # MOBY::Central->can('_registerNamespacePayload') failed > # MOBY::Central->can('deregisterNamespace') failed > # MOBY::Central->can('_deregisterNamespacePayload') failed > # MOBY::Central->can('registerService') failed > # MOBY::Central->can('_registerServicePayload') failed > # MOBY::Central->can('_getServiceInstanceRDF') failed > # MOBY::Central->can('_registerArticles') failed > # MOBY::Central->can('deregisterService') failed > # MOBY::Central->can('_deregisterServicePayload') failed > # MOBY::Central->can('findService') failed > # MOBY::Central->can('_findServicePayload') failed > # MOBY::Central->can('_extractObjectTypes') failed > # MOBY::Central->can('registerServiceWSDL') failed > # MOBY::Central->can('_extract_ids') failed > # MOBY::Central->can('_searchForServicesWithArticle') failed > # MOBY::Central->can('_searchForSimple') failed > # MOBY::Central->can('_searchForCollection') failed > # MOBY::Central->can('_extractObjectTypesAndNamespaces') failed > # MOBY::Central->can('retrieveService') failed > # MOBY::Central->can('_retrieveServicePayload') failed > # MOBY::Central->can('retrieveResourceURLs') failed > # MOBY::Central->can('retrieveServiceProviders') failed > # MOBY::Central->can('retrieveServiceNames') failed > # MOBY::Central->can('retrieveServiceTypes') failed > # MOBY::Central->can('retrieveRelationshipTypes') failed > # MOBY::Central->can('retrieveObjectNames') failed > # MOBY::Central->can('retrieveObjectDefinition') failed > # MOBY::Central->can('retrieveNamespaces') failed > # MOBY::Central->can('retrieveObject') failed > # MOBY::Central->can('_retrieveObjectPayload') failed > # MOBY::Central->can('Relationships') failed > # MOBY::Central->can('DUMP_MySQL') failed > # MOBY::Central->can('_ISAPayload') failed > # MOBY::Central failed to implement full API # Looks like you > failed 2 tests of 2. > t/Central...................................dubious > > Test returned status 2 (wstat 512, 0x200) DIED. > FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/Client-Central............................ok > > t/Client-CollectionArticle..................ok > > t/Client-OntologyServer.....................ok > > t/Client-Registration.......................ok > > t/Client-SecondaryArticle...................ok > > t/Client-Service............................ok > > t/Client-ServiceInstance....................ok > > t/Client-SimpleArticle......................ok > > t/CommonSubs................................ok > > t/Config....................................skipped > all skipped: Required only for local MOBY Central > t/CrossReference............................ok > > t/dbConnect.................................# Failed test > (t/dbConnect.t at > line 18) > # Tried to use 'MOBY::lsid::authority::dbConnect'. > t/dbConnect.................................NOK 1# Error: > Can't locate > DBD/mysql.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/dbConnect.pm > line 17. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/dbConnect.pm > line 17. > # Compilation failed in require at (eval 1) line 2. > # Failed test (t/dbConnect.t at line 25) > # MOBY::lsid::authority::dbConnect->can('dbConnect') failed > # API not correctly implemented > t/dbConnect.................................NOK 2# Looks like > you failed 2 tests of 2. > t/dbConnect.................................dubious > > Test returned status 2 (wstat 512, 0x200) DIED. > FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/lsid-authority-ClassResolver..............# Failed test > (t/lsid-authority-ClassResolver.t at line 18) > # Tried to use 'MOBY::lsid::authority::ClassResolver'. > t/lsid-authority-ClassResolver..............NOK 1# Error: > Can't locate > XML/DOM.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/ClassResolver.pm > line 5. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/ClassResolver.pm > line 5. > # Compilation failed in require at (eval 1) line 2. > # Failed test (t/lsid-authority-ClassResolver.t at line 25) > # > MOBY::lsid::authority::ClassResolver->can('resolve_classtype') failed > # Didn't implement full API > t/lsid-authority-ClassResolver..............NOK 2# Looks like > you failed 2 tests of 2. > t/lsid-authority-ClassResolver..............dubious > > Test returned status 2 (wstat 512, 0x200) DIED. > FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/lsid-authority-dbConnect..................# Failed test > (t/lsid-authority-dbConnect.t at line 18) > t/lsid-authority-dbConnect..................NOK 1# Tried to use > 'MOBY::lsid::authority::dbConnect'. > # Error: Can't locate DBD/mysql.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/dbConnect.pm > line 17. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/dbConnect.pm > line 17. > # Compilation failed in require at (eval 1) line 2. > # Looks like you failed 1 tests of 1. > t/lsid-authority-dbConnect..................dubious > > Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > t/lsid-authority-Error......................ok > > t/lsid-authority-NamespaceResolver..........# Failed test > (t/lsid-authority-NamespaceResolver.t at line 18) > # Tried to use 'MOBY::lsid::authority::NamespaceResolver'. > # Error: Can't locate XML/DOM.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/NamespaceResolver.pm > line 5. > t/lsid-authority-NamespaceResolver..........NOK 1# BEGIN > failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/NamespaceResolver.pm > line 5. > # Compilation failed in require at (eval 1) line 2. > # Failed test (t/lsid-authority-NamespaceResolver.t at line 25) > # > MOBY::lsid::authority::NamespaceResolver->can('resolve_namespa > cetype') failed > # NamespaceResolver didn't implement API correctly # Looks > like you failed 2 tests of 2. > t/lsid-authority-NamespaceResolver..........dubious > > Test returned status 2 (wstat 512, 0x200) DIED. > FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/lsid-authority-PredicateResolver..........# Failed test > (t/lsid-authority-PredicateResolver.t at line 18) > # Tried to use 'MOBY::lsid::authority::PredicateResolver'. > # Error: Can't locate XML/DOM.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/PredicateResolver.pm > line 5. > t/lsid-authority-PredicateResolver..........NOK 1# BEGIN > failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/PredicateResolver.pm > line 5. > # Compilation failed in require at (eval 1) line 2. > # Looks like you failed 1 tests of 1. > t/lsid-authority-PredicateResolver..........dubious > > Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > t/lsid-authority-RDFConfigure...............ok > > t/lsid-authority-RelationshipResolver.......# Failed test > (t/lsid-authority-RelationshipResolver.t at line 18) > # Tried to use 'MOBY::lsid::authority::RelationshipResolver'. > t/lsid-authority-RelationshipResolver.......NOK 1# Error: > Can't locate > XML/DOM.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/RelationshipResolver.pm > line 5. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/RelationshipResolver.pm > line 5. > # Compilation failed in require at (eval 1) line 2. > # Failed test (t/lsid-authority-RelationshipResolver.t at line 25) > # > MOBY::lsid::authority::RelationshipResolver->can('resolve_rela > tionshiptype') failed # RelationshipResolver didn't implement > full API t/lsid-authority-RelationshipResolver.......NOK 2# > Looks like you failed 2 tests of 2. > t/lsid-authority-RelationshipResolver.......dubious > > Test returned status 2 (wstat 512, 0x200) DIED. > FAILED tests 1-2 > Failed 2/2 tests, 0.00% okay > t/lsid-authority-ServiceInstanceResolver....skipped > all skipped: Skip until apparent namespace pollution > fixed in ServiceInstanceResolver > t/lsid-authority-ServiceResolver............# Failed test > (t/lsid-authority-ServiceResolver.t at line 18) > # Tried to use 'MOBY::lsid::authority::ServiceResolver'. > t/lsid-authority-ServiceResolver............NOK 1# Error: > Can't locate > XML/DOM.pm in @INC (@INC contains: > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8. > 4/sun4-solaris-thread-multi > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl . > /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/5.8.4 > /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi > /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl > .) at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/ServiceResolver.pm > line 5. > # BEGIN failed--compilation aborted at > /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/bli > b/lib/MOBY/lsid/authority/ServiceResolver.pm > line 5. > # Compilation failed in require at (eval 1) line 2. > # Looks like you failed 1 tests of 1. > t/lsid-authority-ServiceResolver............dubious > > Test returned status 1 (wstat 256, 0x100) DIED. FAILED test 1 > Failed 1/1 tests, 0.00% okay > t/Template..................................skipped > all skipped: This is just a template > Failed Test Stat Wstat Total Fail > Failed List of Failed > -------------------------------------------------------------- > ----------------- > t/Central.t 2 512 2 2 100.00% 1-2 > t/dbConnect.t 2 512 2 2 100.00% 1-2 > t/lsid-authority-ClassResolver.t 2 512 2 2 100.00% 1-2 > t/lsid-authority-NamespaceResolve 2 512 2 2 100.00% 1-2 > t/lsid-authority-PredicateResolve 1 256 1 1 100.00% 1 > t/lsid-authority-RelationshipReso 2 512 2 2 100.00% 1-2 > t/lsid-authority-ServiceResolver. 1 256 1 1 100.00% 1 > t/lsid-authority-dbConnect.t 1 256 1 1 100.00% 1 > 3 tests skipped. > Failed 8/23 test scripts, 65.22% okay. 13/380 subtests > failed, 96.58% okay. > *** Error code 29 > make: Fatal error: Command failed for target `test_dynamic' > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l From nsutanto at purdue.edu Thu Feb 16 13:35:54 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Thu, 16 Feb 2006 13:35:54 -0500 Subject: [MOBY-l] error when do make test In-Reply-To: <5.2.1.1.2.20060215151504.01229aa8@email.med.harvard.edu> References: <000f01c63253$26985670$6500a8c0@notebook> <000f01c63253$26985670$6500a8c0@notebook> <5.2.1.1.2.20060215151504.01229aa8@email.med.harvard.edu> Message-ID: <43F4C60A.3020909@purdue.edu> Here is actually what I'm planning to do. I have this website: http://www.cs.purdue.edu/homes/nsutanto/bio.html. And when we do submit query, it will call "myfile.cgi". I want to make a simple client that can access "myfile.cgi" and query and have a result back to me. And I want to put "myfile.cgi" to the biomoby, and my client can call my functions from myfile.cgi through biomoby. So, how do I put "myfile.cgi" to the biomoby? Sorry if my previous question confused you all. Let me know if you guys still confuse about my goal. Thanks a lot for any help. Nicholas Sutanto. Frank Gibbons wrote: > Nicholas, > > My suggestion is to ignore these errors - it's clear that you do not > have the modules "DBD::mysql" or XML::DOM installed. Unless you are > planning to set up your own MOBY Central database, you do not need > this. But you definitely need XML::DOM, so get it from CPAN, and while > you're there, you might want to just install DBD::mysql as well. > > As Eddie mentioned earlier, it would help us a lot if you explain a > little about what your interest and ultimate goals are: set up your > own database, set up a service, etc. I'll try to fix the code so that > the tests pass for users like you, who don't have DBD::mysql. In the > meantime, you should just continue to installation and then playing > around with the dispatcher and echo-service. > > -Frank > > From markw at illuminae.com Thu Feb 16 14:42:18 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 16 Feb 2006 11:42:18 -0800 Subject: [MOBY-l] [moby] Re: error when do make test In-Reply-To: <43F4C60A.3020909@purdue.edu> References: <000f01c63253$26985670$6500a8c0@notebook> <000f01c63253$26985670$6500a8c0@notebook> <5.2.1.1.2.20060215151504.01229aa8@email.med.harvard.edu> <43F4C60A.3020909@purdue.edu> Message-ID: <1140118938.28350.85.camel@bioinfo.icapture.ubc.ca> I think you need XML::LibXML, rather than (or as well as?) XML::DOM M On Thu, 2006-02-16 at 13:35 -0500, Nicholas Sutanto wrote: > Here is actually what I'm planning to do. > > I have this website: http://www.cs.purdue.edu/homes/nsutanto/bio.html. > And when we do submit query, it will call "myfile.cgi". > > I want to make a simple client that can access "myfile.cgi" and query > and have a result back to me. And I want to put "myfile.cgi" to the > biomoby, and my client can call my functions from myfile.cgi through > biomoby. > So, how do I put "myfile.cgi" to the biomoby? > > Sorry if my previous question confused you all. > Let me know if you guys still confuse about my goal. > > Thanks a lot for any help. > Nicholas Sutanto. > > Frank Gibbons wrote: > > Nicholas, > > > > My suggestion is to ignore these errors - it's clear that you do not > > have the modules "DBD::mysql" or XML::DOM installed. Unless you are > > planning to set up your own MOBY Central database, you do not need > > this. But you definitely need XML::DOM, so get it from CPAN, and while > > you're there, you might want to just install DBD::mysql as well. > > > > As Eddie mentioned earlier, it would help us a lot if you explain a > > little about what your interest and ultimate goals are: set up your > > own database, set up a service, etc. I'll try to fix the code so that > > the tests pass for users like you, who don't have DBD::mysql. In the > > meantime, you should just continue to installation and then playing > > around with the dispatcher and echo-service. > > > > -Frank > > > > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From markw at illuminae.com Thu Feb 16 15:01:08 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 16 Feb 2006 12:01:08 -0800 Subject: [MOBY-l] [moby] Re: error when do make test In-Reply-To: <43F4C60A.3020909@purdue.edu> References: <000f01c63253$26985670$6500a8c0@notebook> <000f01c63253$26985670$6500a8c0@notebook> <5.2.1.1.2.20060215151504.01229aa8@email.med.harvard.edu> <43F4C60A.3020909@purdue.edu> Message-ID: <1140120068.28350.95.camel@bioinfo.icapture.ubc.ca> It sounds to me like what you are trying to do is wrap your web page with a BioMoby service. This isn't a particularly stable configuration to be aiming for (for all of the same reasons that screen-scraping has never been able to successfully build a semantic web!). You should probably re-think your plan and make myfile.cgi into a MOBY service directly... Nevertheless, if this is what you are committed to, here's how you would go about it: 1) set up a MOBY daemon, exactly as in the tutorial 2) set up a MOBY service exactly as in the tutorial - the service consumes an input (apparently SQL string) - the service consumes secondary parameters (e.g. BioCyc) - the service makes a Perl(?) LWP call to myfile.cgi - the service captures the HTML output from myfile.cgi - the service parses that HTML to extract the data of interest - the service re-packages that data into a MOBY object - the service returns the MOBY object to the requester 3) register that service in MOBY Central If you have not read the tutorial, I suggest you do that before you ask more questions, since I think my answers are just re-iterating what is said in those tutorials... M On Thu, 2006-02-16 at 13:35 -0500, Nicholas Sutanto wrote: > Here is actually what I'm planning to do. > > I have this website: http://www.cs.purdue.edu/homes/nsutanto/bio.html. > And when we do submit query, it will call "myfile.cgi". > > I want to make a simple client that can access "myfile.cgi" and query > and have a result back to me. And I want to put "myfile.cgi" to the > biomoby, and my client can call my functions from myfile.cgi through > biomoby. > So, how do I put "myfile.cgi" to the biomoby? > > Sorry if my previous question confused you all. > Let me know if you guys still confuse about my goal. > > Thanks a lot for any help. > Nicholas Sutanto. > > Frank Gibbons wrote: > > Nicholas, > > > > My suggestion is to ignore these errors - it's clear that you do not > > have the modules "DBD::mysql" or XML::DOM installed. Unless you are > > planning to set up your own MOBY Central database, you do not need > > this. But you definitely need XML::DOM, so get it from CPAN, and while > > you're there, you might want to just install DBD::mysql as well. > > > > As Eddie mentioned earlier, it would help us a lot if you explain a > > little about what your interest and ultimate goals are: set up your > > own database, set up a service, etc. I'll try to fix the code so that > > the tests pass for users like you, who don't have DBD::mysql. In the > > meantime, you should just continue to installation and then playing > > around with the dispatcher and echo-service. > > > > -Frank > > > > > > _______________________________________________ > moby-l mailing list > moby-l at biomoby.org > http://biomoby.org/mailman/listinfo/moby-l -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From simont at hmgc.mcw.edu Fri Feb 17 12:10:50 2006 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Fri, 17 Feb 2006 11:10:50 -0600 Subject: [MOBY-l] RSS feeds for objects and services Message-ID: <574F5C93-8211-4992-8F21-B5FCEFDA6FFB@hmgc.mcw.edu> I was looking at the website and noticed that the RSS feeds for the services and objects dont have anything on there. Are these meant to be a list of all current services/objects or do things appear on there only when they are new? Mark, I see the feeds are coming from your group so I was wondering if you could let me know how this is meant to work? I wasnt sure if this was broken or if they are functioning correctly and there's just nothing there. I'd quite like it to return all the current services and objects, then if I subscribe I would think that new services/objects would pop up in my newsreader as new 'stories' so I would be alerted to them. If having it return everything is unwieldy, maybe have it return the 10 newest services or objects, etc. I don't think its good that it returns nothing at all. 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 From markw at illuminae.com Fri Feb 17 14:08:47 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Fri, 17 Feb 2006 11:08:47 -0800 Subject: [MOBY-l] [moby] RSS feeds for objects and services In-Reply-To: <574F5C93-8211-4992-8F21-B5FCEFDA6FFB@hmgc.mcw.edu> References: <574F5C93-8211-4992-8F21-B5FCEFDA6FFB@hmgc.mcw.edu> Message-ID: <1140203327.754.9.camel@bioinfo.icapture.ubc.ca> On Fri, 2006-02-17 at 11:10 -0600, Twigger Simon wrote: > Are these meant to > be a list of all current services/objects or do things appear on > there only when they are new? Mark, I see the feeds are coming from > your group so I was wondering if you could let me know how this is > meant to work? The feeds are updated daily, and contain the list of services/objects registered in the previous 24 hours > I wasnt sure if this was broken or if they are functioning correctly > and there's just nothing there. I'd quite like it to return all the > current services and objects, then if I subscribe I would think that > new services/objects would pop up in my newsreader as new 'stories' > so I would be alerted to them. It does work that way, except that it works only in 4 hour blocks. I can change that behaviour if you like. It's just a matter of changing ">" to ">>" when I write to the file. Some RSS readers will be able to figure out which "stories" are old and which are new, but I'm not sure if all of them can. Some people might end up with a massive list of entities that they can't get rid of if we simply concatenate. > If having it return everything is > unwieldy, maybe have it return the 10 newest services or objects, Now that we have timestamps on our LSID's it would be possible to do this, though it is a bit more effort (a.k.a. will take longer for me to code-up). The only way to determine which things were new so far has been to do a diff against the dump of the previous day - if there were no new services, the feed was blank. In principle, it would be possible now to work out which services are the most recent by examining the LSID timestamp, and publish those ones to the feed. M -- -- ...his last words were 'Hey guys! Watch this!' -- 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 "For most of this century we have viewed communications as a conduit, a pipe between physical locations on the planet. What's happened now is that the conduit has become so big and interesting that communication has become more than a conduit, it has become a destination in its own right..." Paul Saffo - Director, Institute for the Future From simont at hmgc.mcw.edu Mon Feb 20 11:52:35 2006 From: simont at hmgc.mcw.edu (Twigger Simon) Date: Mon, 20 Feb 2006 10:52:35 -0600 Subject: [MOBY-l] [moby] RSS feeds for objects and services In-Reply-To: <1140203327.754.9.camel@bioinfo.icapture.ubc.ca> References: <574F5C93-8211-4992-8F21-B5FCEFDA6FFB@hmgc.mcw.edu> <1140203327.754.9.camel@bioinfo.icapture.ubc.ca> Message-ID: Hi Mark, THe timestamp will be good - I was wondering if you could just do a select on the database to get all services ordered by registration date and then use LIMIT 10 to get the first 10 off the top of the list, ie the 10 most recently registered. The LSID timestamp would probably do the trick here. The query could be set up to run every hour to create the RSS file, etc. so it would have a reasonable refresh rate but not too burdensome. This would be nice in that it will always show something to people. However, if someone registers more than 10 services/objects then they wont all make the cut so there may be a good case for the 'new in the last 24 hours' feed too, I think we just need to label it better so people understand that it's for a particular timeframe and hence why it might return no entries. 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 Feb 17, 2006, at 1:08 PM, Mark Wilkinson wrote: > On Fri, 2006-02-17 at 11:10 -0600, Twigger Simon wrote: >> Are these meant to >> be a list of all current services/objects or do things appear on >> there only when they are new? Mark, I see the feeds are coming from >> your group so I was wondering if you could let me know how this is >> meant to work? > > The feeds are updated daily, and contain the list of services/objects > registered in the previous 24 hours > > >> I wasnt sure if this was broken or if they are functioning correctly >> and there's just nothing there. I'd quite like it to return all the >> current services and objects, then if I subscribe I would think that >> new services/objects would pop up in my newsreader as new 'stories' >> so I would be alerted to them. > > It does work that way, except that it works only in 4 hour blocks. > > I can change that behaviour if you like. It's just a matter of > changing > ">" to ">>" when I write to the file. > > Some RSS readers will be able to figure out which "stories" are old > and > which are new, but I'm not sure if all of them can. Some people might > end up with a massive list of entities that they can't get rid of > if we > simply concatenate. > > >> If having it return everything is >> unwieldy, maybe have it return the 10 newest services or objects, > > Now that we have timestamps on our LSID's it would be possible to do > this, though it is a bit more effort (a.k.a. will take longer for > me to > code-up). The only way to determine which things were new so far has > been to do a diff against the dump of the previous day - if there were > no new services, the feed was blank. In principle, it would be > possible > now to work out which services are the most recent by examining the > LSID > timestamp, and publish those ones to the feed. > > M > > > -- > -- > ...his last words were 'Hey guys! Watch this!' > -- > 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 > > "For most of this century we have viewed communications as a conduit, > a pipe between physical locations on the planet. > What's happened now is that the conduit has become so big and > interesting > that communication has become more than a conduit, > it has become a destination in its own right..." > > Paul Saffo - Director, Institute for the Future > From edward.kawas at gmail.com Mon Feb 20 15:42:38 2006 From: edward.kawas at gmail.com (Edward Kawas) Date: Mon, 20 Feb 2006 12:42:38 -0800 Subject: [MOBY-l] Notice that the ever elusive agent will start curating in 2 weeks Message-ID: <000301c6365e$30fe3670$9d66a8c0@notebook> Hi, The RDF agent that we have heard so much about will begin 'crawling' in 2 weeks starting Monday March 6, 2006. As a service provider, your only task will be to generate one or more RDF documents describing your service(s) and to place that document somewhere reachable from the outside world. If you no longer wish to host that service, then removing its description from the document will effectively deregister the service. The place to obtain your service RDF is from the following url: http://mobycentral.icapture.ubc.ca/servlets/forms/getSignatureForm This page will update your service signature URL location. In 2 weeks, the agent will start removing services that do not have a signature url specified for it. The agent is also configured to remove any service that fails to uphold to the latest API, as specified on biomoby.org. Specifically, the agent is looking for un-named inputs or outputs (i.e. simples or collections without article names). However, if a service was modified, then the agent will use the API to re-register it and if the service was invalid for other reasons, the registry will reject that particular service. In 2 weeks, the agent will attempt to read from the signature url that you provided. If the agent cannot read from the url on 3 (maybe more or less - details will be revealed later) different consecutive occasions, then the agent will remove all services described by that url. The agent will then, depending on configuration, email the service provider and detail what happened to cause their service deregistration. If the deregistration was in error, service providers will be able to reregister their services very easily. Contained in the email message to the provider is RDF-XML that describes the last known footprint of their service. Using this RDF-XML, and a tool to be released soon, you can re-register your service in any registry. As a service provider, you are free to add any valid RDF statements to your document. At the very least, the document must contain statements with predicates found at http://biomoby.open-bio.org/index.php/for-developers/moby_extensions/moby_me tadata. All other statements are ignored by the agent. If you end up modifying the RDF-XML, and you want to verify that the XML is valid, you could always use the following tool to validate and visualize your RDF document: http://www.w3.org/RDF/Validator/. If you are new to RDF and you do make changes to the document, it's highly recommended to check your document with this tool. A common error is placing multiple tags within a single file. This is not allowed and will result in parsing errors. This error is usually achieved by downloading multiple RDF documents and then placing the contents of each document into one document. Those of you that wish to consolidate RDF documents should consolidate the contents between the tags. All questions and concerns regarding this agent should be posted to the list so that they can be discussed amongst us all. Thanks, Eddie From senger at ebi.ac.uk Mon Feb 20 19:52:34 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 21 Feb 2006 00:52:34 +0000 (GMT) Subject: [MOBY-l] [MOBY-dev] Notice that the ever elusive agent will start curating in 2 weeks In-Reply-To: <000301c6365e$30fe3670$9d66a8c0@notebook> Message-ID: Eddie, I have not seen an answer to the most pertinent question that we always had about the RDF agent: How can we ask it to come? And how often does it come if we do not ask? And please do not tell me that I cannot ask - if that would be the case, please do not start it yet. > In 2 weeks, the agent will start removing services that do not have a > signature url specified for it. > I strongy oppose this - and I said it several times. Please do not do that. It was never said that services must have the signature URL - it was always said that services without such signature are vulnerable to be remove by some malicious guys. But a mandatory existence of such signature URL has never been in the Biomoby API, and if you do what you are saying, it is breaking API without consulting us/users. It is related to the question above: if I have a way to ask an agent to come at once (by at once I mean in seconds) I am not afraid to put signature url in the service. If not, I cannot edit my service anymore and I am not willing to put there the signature. > In 2 weeks, the agent will attempt to read from the signature url that you > provided. If the agent cannot read from the url on 3 (maybe more or less - > details will be revealed later) different consecutive occasions, then the > agent will remove all services described by that url. > Again, this should not be done so rigidly. I simply need, for example, few services, that are registered to the localhost (so they will never be used by reasonably clever clients) but they are used in tutorials, and they can be used when a service is being developed (so it can be called via registry by its author, because she has the service on her local machine). There will never be many of such services, but they should stay. I also do not like your wording "details will be revealed later". This sounds like a typical dictatorship. > If the deregistration was in error, service providers will be able to > reregister their services very easily. Contained in the email message to the > provider is RDF-XML that describes the last known footprint of their > service. Using this RDF-XML, and a tool to be released soon, you can > re-register your service in any registry. > This is a home-made addition to the Biomoby API - we have never discussed it. We need a way that can be automatized - so if I need to react to the email message, I need to know first exact format of such email etc. This is doable but needs to be discussed. > All questions and concerns regarding this agent should be posted to the list > so that they can be discussed amongst us all. > Thanks, that's encouraging. 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 Sat Feb 25 11:17:36 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 25 Feb 2006 08:17:36 -0800 Subject: [MOBY-l] BioMOBY mentioned in this Infoworld article Message-ID: A brief mention, but... :-) http://www.infoworld.nl/idgns/bericht.phtml?id=002570DE00740E180025711D0082365C M From markw at illuminae.com Sat Feb 25 12:01:55 2006 From: markw at illuminae.com (Mark Wilkinson) Date: Sat, 25 Feb 2006 09:01:55 -0800 Subject: [MOBY-l] BioMOBY mentioned in this Infoworld article In-Reply-To: <4F2E6371-5899-463F-9918-F85410508B32@sonsorol.org> References: <4F2E6371-5899-463F-9918-F85410508B32@sonsorol.org> Message-ID: The reference arrived on my desktop this morning as a Google News RSS feed - I'm surprised that BioIT world isn't indexed by Google News?!? It hasn't appeared in my search... M On Sat, 25 Feb 2006 08:58:33 -0800, Chris Dagdigian wrote: > > I wouldn't trust that Dwan guy :) > > Really odd that this ended up in infoworld as well, this was a column > written for Bio-IT World, it does not make a lot of sense outside the > lifesci context and linked to previous columns we wrote. > > The real location of the column, with more useful embedded links can be > found here: > > http://www.bio-itworld.com/columns/inside-the-box/copy2_of_inside-the-box > > > -Chris > > > > On Feb 25, 2006, at 11:17 AM, Mark Wilkinson wrote: > >> A brief mention, but... :-) >> >> http://www.infoworld.nl/idgns/bericht.phtml? >> id=002570DE00740E180025711D0082365C >> >> M From dag at sonsorol.org Sat Feb 25 11:58:33 2006 From: dag at sonsorol.org (Chris Dagdigian) Date: Sat, 25 Feb 2006 11:58:33 -0500 Subject: [MOBY-l] BioMOBY mentioned in this Infoworld article In-Reply-To: References: Message-ID: <4F2E6371-5899-463F-9918-F85410508B32@sonsorol.org> I wouldn't trust that Dwan guy :) Really odd that this ended up in infoworld as well, this was a column written for Bio-IT World, it does not make a lot of sense outside the lifesci context and linked to previous columns we wrote. The real location of the column, with more useful embedded links can be found here: http://www.bio-itworld.com/columns/inside-the-box/copy2_of_inside-the- box -Chris On Feb 25, 2006, at 11:17 AM, Mark Wilkinson wrote: > A brief mention, but... :-) > > http://www.infoworld.nl/idgns/bericht.phtml? > id=002570DE00740E180025711D0082365C > > M From nsutanto at purdue.edu Sun Feb 26 21:42:32 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Sun, 26 Feb 2006 21:42:32 -0500 Subject: [MOBY-l] ./build.sh correction Message-ID: <44026718.90306@purdue.edu> Hi, I'm trying to do ./build.sh from moby/moby-live/Java folder. But it seems that I have to hack around a little bit in the build.sh file to set the JAVA_HOME. So I have to put this JAVA_HOME=/usr/java from my build.sh If I just do it with setenv or put it in the .cshrc file.. somehow it doesn't work well for some reason.., I don't know why. Best Regards, Nicholas Sutanto. From senger at ebi.ac.uk Sun Feb 26 21:53:59 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 27 Feb 2006 02:53:59 +0000 (GMT) Subject: [MOBY-l] ./build.sh correction In-Reply-To: <44026718.90306@purdue.edu> Message-ID: > But it seems that I have to hack around a little bit in the build.sh > file to set the JAVA_HOME. > Why? What was the problem? > So I have to put this JAVA_HOME=/usr/java from my build.sh > We need to find a solution for your problem but not by changing your local copy of the build.sh - because it could be overwritten the next time you do cvs update. > If I just do it with setenv or put it in the .cshrc file.. somehow it > doesn't work well for some reason.., I don't know why. > Could you see it (just before you start ./build.sh) by typing?: echo $JAVA_HOME What does it show? 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 nsutanto at purdue.edu Sun Feb 26 21:31:13 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Sun, 26 Feb 2006 21:31:13 -0500 Subject: [MOBY-l] mysql version Message-ID: <44026471.8020309@purdue.edu> Hi, I'm trying to set up MOBY daemon. Do I have to insatall mySQL? If so, what version of mySQL do I have to install? Thanks Nicholas. From nsutanto at purdue.edu Sun Feb 26 21:33:03 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Sun, 26 Feb 2006 21:33:03 -0500 Subject: [MOBY-l] java error Message-ID: <440264DF.2020306@purdue.edu> Hi, I'm trying to do ./build.sh from the moby/moby-live/Java folder But it give me this error.. Any idea what's happening? Thanks, Nicholas Sutanto. BUILD SUCCESSFUL Total time: 5 seconds Buildfile: build.xml init: config: compile-normal: [javac] Compiling 227 source files to /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/build/classes [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:34: cannot find symbol [javac] symbol : class Registration [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] private Registration registration; [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:363: cannot find symbol [javac] symbol : class Registration [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] public Registration getRegistration() { [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:59: cannot find symbol [javac] symbol : class Registration [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] registration = new Registration("MyObject", proto); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:99: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] LinkedList linkedlist = MobyUtilities.GetRelations(whatIam); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:147: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] LinkedList ll = MobyUtilities.GetRelations(whatIhave); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:160: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] Pair p = MobyUtilities.ParseRelation(s); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:180: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] Pair p = MobyUtilities.ParseRelation(s); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:216: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] myParent = (MobyUtilities.ParseRelation(myParent)).getAttribute(); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:218: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] LinkedList temp = MobyUtilities.GetRelations(myParent); [javac] ^ [javac] Note: * uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 9 errors BUILD FAILED /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/build.xml:252: Compile failed; see the compiler error output for details. From senger at ebi.ac.uk Sun Feb 26 22:33:22 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 27 Feb 2006 03:33:22 +0000 (GMT) Subject: [MOBY-l] mysql version In-Reply-To: <44026471.8020309@purdue.edu> Message-ID: > I'm trying to set up MOBY daemon. > What is a MOBY daemon - a Moby registry, or a Moby service? 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 senger at ebi.ac.uk Sun Feb 26 22:41:51 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 27 Feb 2006 03:41:51 +0000 (GMT) Subject: [MOBY-l] java error In-Reply-To: <440264DF.2020306@purdue.edu> Message-ID: > But it give me this error.. Any idea what's happening? > I have just checked, bth with Java 1.4 and .1.5, both using the native compiler and jikes, both with the property java.version.latest=false, and without - and in all cases it compiled fine. Try again the latest: cvs update -dP first, then tell me what version of java you are using: java -version. 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 senger at ebi.ac.uk Sun Feb 26 23:11:32 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Mon, 27 Feb 2006 04:11:32 +0000 (GMT) Subject: [MOBY-l] ./build.sh correction In-Reply-To: <1141013082.44027a5a5c5fb@webmail.purdue.edu> Message-ID: > I think the problem was I don't set up the JAVA_HOME correctly.. I suppose to > set the JAVA_HOME to the exact path of where the Java is located. > Actually, I do not think so. JAVA_HOME should point to the directory where the whole Java is installed, not just 'bin' subdirectiry. This is what I have on my machine: /usr/local/j2sdk1.4.2_10 bin java (executable) ... demo include ... And my JAVA_HOME should be: export JAVA_HOME=/usr/local/j2sdk1.4.2_10. But, as a matter of fact, I do not have JAVA_HOME set at all. The build.sh script will find it itself, assuming that java executable is on your PATH. 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 nsutanto at purdue.edu Sun Feb 26 23:04:42 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Sun, 26 Feb 2006 23:04:42 -0500 Subject: [MOBY-l] ./build.sh correction In-Reply-To: References: Message-ID: <1141013082.44027a5a5c5fb@webmail.purdue.edu> Ups.. sorry.. my bad.. I think the problem was I don't set up the JAVA_HOME correctly.. I suppose to set the JAVA_HOME to the exact path of where the Java is located.. before I set it up to JAVA_HOME=/usr/bin/java... where this is actually point to usr/java.. Thanks anyway, Nicholas. Quoting Martin Senger : > > But it seems that I have to hack around a little bit in the build.sh > > file to set the JAVA_HOME. > > > Why? What was the problem? > > > So I have to put this JAVA_HOME=/usr/java from my build.sh > > > We need to find a solution for your problem but not by changing your > local copy of the build.sh - because it could be overwritten the next time > you do cvs update. > > > If I just do it with setenv or put it in the .cshrc file.. somehow it > > doesn't work well for some reason.., I don't know why. > > > Could you see it (just before you start ./build.sh) by typing?: > echo $JAVA_HOME > What does it show? > > 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 nsutanto at purdue.edu Mon Feb 27 18:17:39 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Mon, 27 Feb 2006 18:17:39 -0500 Subject: [MOBY-l] java error In-Reply-To: References: Message-ID: <44038893.6030804@purdue.edu> Hi, I already tried to update the file using cvs update -dP. But I still found the problem. This is the Java version running on my machine. java version "1.5.0_04" Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_04-b05) Java HotSpot(TM) Server VM (build 1.5.0_04-b05, mixed mode) Thanks, Nicholas. Martin Senger wrote: >> But it give me this error.. Any idea what's happening? >> >> > I have just checked, bth with Java 1.4 and .1.5, both using the native > compiler and jikes, both with the property java.version.latest=false, and > without - and in all cases it compiled fine. > Try again the latest: cvs update -dP first, then tell me what version > of java you are using: java -version. > > Martin > > From senger at ebi.ac.uk Tue Feb 28 07:55:50 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 28 Feb 2006 12:55:50 +0000 (GMT) Subject: [MOBY-l] java error In-Reply-To: <44038893.6030804@purdue.edu> Message-ID: > But I still found the problem. >... > java version "1.5.0_04" > Well, the next thing I can think of is to give me a list of the contents of your 'lib' directory (made by 'ls -l' so it contains also file sizes). I will look at it and compare with my version. Could you give me again the error messages please (I have removed your previous email with them)? 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 senger at ebi.ac.uk Tue Feb 28 09:14:43 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 28 Feb 2006 14:14:43 +0000 (GMT) Subject: [MOBY-l] java error In-Reply-To: <440456D5.60104@purdue.edu> Message-ID: > Here is the contents of the lib folder: > Okay, theee list is the same as I have. No problem come from here. So I had a look at the first error: ...src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:34: > cannot find symbol > [javac] symbol : class Registration > [javac] location: class > org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML > [javac] private Registration registration; > [javac] ^ > Interestingly it points to the line 34 - but in my MobyXML.java file the culprit line (private Registration registration;) is the line number 31. So let's make sure that we have the same version. Could you please look into src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/ and check that this subdirectory contains also file Registration.java (it should have size 4362)? Also how big is your MobyXML.java (mine is 10585). 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 nsutanto at purdue.edu Tue Feb 28 08:57:41 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Tue, 28 Feb 2006 08:57:41 -0500 Subject: [MOBY-l] java error In-Reply-To: References: Message-ID: <440456D5.60104@purdue.edu> Here you go: Here is the contents of the lib folder: alhagib 16 % ls -al total 33716 drwxr-x--- 3 nsutanto nsutanto 1536 Feb 21 17:38 . drwxr-x--- 9 nsutanto nsutanto 512 Feb 21 17:38 .. -rw-r----- 1 nsutanto nsutanto 38 Sep 24 2003 .cvsignore.template -rw-r----- 1 nsutanto nsutanto 1319 Jul 19 2005 README -rw-r----- 1 nsutanto nsutanto 54665 Sep 4 08:15 activation.jar -rw-r----- 1 nsutanto nsutanto 806310 Jun 10 2005 adenine.jar -rw-r----- 1 nsutanto nsutanto 78933 Feb 12 11:40 alltools2.jar drwxr-x--- 3 nsutanto nsutanto 512 Dec 31 1969 ant_home -rw-r----- 1 nsutanto nsutanto 33506 Sep 4 08:15 axis-ant.jar -rw-r----- 1 nsutanto nsutanto 1604162 Sep 4 08:15 axis.jar -rw-r----- 1 nsutanto nsutanto 71442 Sep 4 08:15 commons-discovery-0.2.jar -rw-r----- 1 nsutanto nsutanto 277722 Sep 4 08:15 commons-httpclient-3.0-rc2.jar -rw-r----- 1 nsutanto nsutanto 45550 Nov 17 08:04 commons-io-1.0.jar -rw-r----- 1 nsutanto nsutanto 207723 Feb 2 04:35 commons-lang-2.1.jar -rw-r----- 1 nsutanto nsutanto 38015 Sep 4 08:15 commons-logging-1.0.4.jar -rw-r----- 1 nsutanto nsutanto 140837 Jun 10 2005 concurrent.jar -rw-r----- 1 nsutanto nsutanto 80090 Nov 7 19:01 fetaEngine.jar -rw-r----- 1 nsutanto nsutanto 2497198 Jun 10 2005 icu4j.jar -rw-r----- 1 nsutanto nsutanto 84366 Jun 10 2005 jakarta-oro-2.0.5.jar -rw-r----- 1 nsutanto nsutanto 172053 Jun 10 2005 jaxen-core.jar -rw-r----- 1 nsutanto nsutanto 7459 Jun 10 2005 jaxen-jdom.jar -rw-r----- 1 nsutanto nsutanto 32071 Sep 4 08:15 jaxrpc.jar -rw-r----- 1 nsutanto nsutanto 112356 Feb 5 06:25 jcalendar.jar -rw-r----- 1 nsutanto nsutanto 153253 Aug 24 2005 jdom.jar -rw-r----- 1 nsutanto nsutanto 2625127 Jun 10 2005 jena.jar -rw-r----- 1 nsutanto nsutanto 128823 Jun 10 2005 junit.jar -rw-r----- 1 nsutanto nsutanto 358085 Oct 12 06:09 log4j-1.2.12.jar -rw-r----- 1 nsutanto nsutanto 311284 Jun 10 2005 lsid-client-1.1.2.jar -rw-r----- 1 nsutanto nsutanto 98629 Jun 10 2005 lsid-server-1.1.2.jar -rw-r----- 1 nsutanto nsutanto 280984 Jun 10 2005 mail.jar -rw-r----- 1 nsutanto nsutanto 174777 Sep 4 08:15 mailapi_1_3_1.jar -rw-r----- 1 nsutanto nsutanto 397032 Jun 10 2005 mysql-connector-java-3.1.7-bin.jar -rw-r----- 1 nsutanto nsutanto 224823 Jun 10 2005 rdf-api-2001-01-19.jar -rw-r----- 1 nsutanto nsutanto 19427 Sep 4 08:15 saaj.jar -rw-r----- 1 nsutanto nsutanto 25828 Jun 10 2005 saxpath.jar -rw-r----- 1 nsutanto nsutanto 79265 Sep 4 08:15 servlet.jar -rw-r----- 1 nsutanto nsutanto 1276781 Jun 10 2005 taverna.jar -rw-r----- 1 nsutanto nsutanto 126771 Sep 4 08:15 wsdl4j-1.5.1.jar -rw-r----- 1 nsutanto nsutanto 2952605 Jun 10 2005 xalan.jar -rw-r----- 1 nsutanto nsutanto 1010806 Sep 4 08:15 xercesImpl.jar -rw-r----- 1 nsutanto nsutanto 115666 Jun 10 2005 xercesSamples.jar -rw-r----- 1 nsutanto nsutanto 108484 Jun 10 2005 xml-apis.jar -rw-r----- 1 nsutanto nsutanto 124724 Sep 4 08:15 xmlParserAPIs.jar Below are the error message that I got: BUILD SUCCESSFUL Total time: 5 seconds Buildfile: build.xml init: config: compile-normal: [javac] Compiling 227 source files to /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/build/classes [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:34: cannot find symbol [javac] symbol : class Registration [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] private Registration registration; [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:363: cannot find symbol [javac] symbol : class Registration [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] public Registration getRegistration() { [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:59: cannot find symbol [javac] symbol : class Registration [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] registration = new Registration("MyObject", proto); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:99: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] LinkedList linkedlist = MobyUtilities.GetRelations(whatIam); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:147: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] LinkedList ll = MobyUtilities.GetRelations(whatIhave); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:160: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] Pair p = MobyUtilities.ParseRelation(s); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:180: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] Pair p = MobyUtilities.ParseRelation(s); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:216: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] myParent = (MobyUtilities.ParseRelation(myParent)).getAttribute(); [javac] ^ [javac] /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:218: cannot find symbol [javac] symbol : variable MobyUtilities [javac] location: class org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML [javac] LinkedList temp = MobyUtilities.GetRelations(myParent); [javac] ^ [javac] Note: * uses or overrides a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 9 errors BUILD FAILED /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Java/build.xml:252: Compile failed; see the compiler error output for details. Total time: 14 seconds Martin Senger wrote: >> But I still found the problem. >> ... >> java version "1.5.0_04" >> >> > Well, the next thing I can think of is to give me a list of the > contents of your 'lib' directory (made by 'ls -l' so it contains also file > sizes). I will look at it and compare with my version. Could you give me > again the error messages please (I have removed your previous email with > them)? > > Martin > > From senger at ebi.ac.uk Tue Feb 28 10:31:40 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 28 Feb 2006 15:31:40 +0000 (GMT) Subject: [MOBY-l] java error In-Reply-To: <44046B5C.9070603@purdue.edu> Message-ID: > It seems that I have the same file with you... > Mystery... Never mind, let's continue: 1) Try from the scratch by cleaning first: ./build-dev.sh clean compile Have you got a beter result? Probably not. So continue: 2) Show me what CLASSPATH is really used. Edit script ./build-dev.sh by inserting echo (close to the end): # --- call Ant to do the building echo $CLASSPATH JAVA=$JAVA_HOME/bin/java $JAVA -classpath $CLASSPATH -Dant.home=$ANT_HOME org.apache.tools.ant.Main "$@" -buildfile build.xml What is the output? 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 nsutanto at purdue.edu Tue Feb 28 10:57:05 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Tue, 28 Feb 2006 10:57:05 -0500 Subject: [MOBY-l] java error In-Reply-To: References: Message-ID: <440472D1.5080708@purdue.edu> Hi Martin, 1. Yes, I don't get better result. 2. I tried to put echo "CLASSPATH = $CLASSPATH" in the build-dev.sh file. But I don't see the output anywhere when running the ./build.sh. Did I miss something? Nicholas. Martin Senger wrote: >> It seems that I have the same file with you... >> >> > Mystery... Never mind, let's continue: > > 1) Try from the scratch by cleaning first: > ./build-dev.sh clean compile > Have you got a beter result? Probably not. So continue: > > 2) Show me what CLASSPATH is really used. Edit script ./build-dev.sh by > inserting echo (close to the end): > > # --- call Ant to do the building > echo $CLASSPATH > JAVA=$JAVA_HOME/bin/java > $JAVA -classpath $CLASSPATH -Dant.home=$ANT_HOME org.apache.tools.ant.Main > "$@" -buildfile build.xml > > What is the output? > Martin > > From nsutanto at purdue.edu Tue Feb 28 10:59:11 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Tue, 28 Feb 2006 10:59:11 -0500 Subject: [MOBY-l] java error In-Reply-To: References: Message-ID: <4404734F.8020506@purdue.edu> Ups.. sorry.. Here is the output for #2. USING CLASSPATH: ./lib/ant_home/lib/ant-antlr.jar:./lib/ant_home/lib/ant-apache-bcel.jar:./lib/ant_home/lib/ant-apache-bsf.jar:./lib/ant_home/lib/ant-apache-log4j.jar:./lib/ant_home/lib/ant-apache-oro.jar:./lib/ant_home/lib/ant-apache-regexp.jar:./lib/ant_home/lib/ant-apache-resolver.jar:./lib/ant_home/lib/ant-commons-logging.jar:./lib/ant_home/lib/ant-commons-net.jar:./lib/ant_home/lib/ant-contrib.jar:./lib/ant_home/lib/ant-icontract.jar:./lib/ant_home/lib/ant-jai.jar:./lib/ant_home/lib/ant-javamail.jar:./lib/ant_home/lib/ant-jdepend.jar:./lib/ant_home/lib/ant-jmf.jar:./lib/ant_home/lib/ant-jsch.jar:./lib/ant_home/lib/ant-junit.jar:./lib/ant_home/lib/ant-launcher.jar:./lib/ant_home/lib/ant-netrexx.jar:./lib/ant_home/lib/ant-nodeps.jar:./lib/ant_home/lib/ant-starteam.jar:./lib/ant_home/lib/ant-stylebook.jar:./lib/ant_home/lib/ant-swing.jar:./lib/ant_home/lib/ant-trax.jar:./lib/ant_home/lib/ant-vaj.jar:./lib/ant_home/lib/ant-weblogic.jar:./lib/ant_home/lib/ant-xalan1.jar:./lib/ant_home/lib/ant-xslp.jar:./lib/ant_home/lib/ant.jar:./lib/ant_home/lib/xercesImpl.jar:./lib/ant_home/lib/xml-apis.jar:/usr/java/lib/tools.jar. -Nicholas. Martin Senger wrote: >> It seems that I have the same file with you... >> >> > Mystery... Never mind, let's continue: > > 1) Try from the scratch by cleaning first: > ./build-dev.sh clean compile > Have you got a beter result? Probably not. So continue: > > 2) Show me what CLASSPATH is really used. Edit script ./build-dev.sh by > inserting echo (close to the end): > > # --- call Ant to do the building > echo $CLASSPATH > JAVA=$JAVA_HOME/bin/java > $JAVA -classpath $CLASSPATH -Dant.home=$ANT_HOME org.apache.tools.ant.Main > "$@" -buildfile build.xml > > What is the output? > Martin > > From senger at ebi.ac.uk Tue Feb 28 11:00:25 2006 From: senger at ebi.ac.uk (Martin Senger) Date: Tue, 28 Feb 2006 16:00:25 +0000 (GMT) Subject: [MOBY-l] java error In-Reply-To: <440472D1.5080708@purdue.edu> Message-ID: > 2. I tried to put echo "CLASSPATH = $CLASSPATH" in the build-dev.sh > file. But I don't see the output anywhere when running the ./build.sh. > Did I miss something? > You do not need to run ./build.sh - this is good only for checking that you have the latest contents of the 'lib' (which you have) - normally use ./build-dev.sh. That's why I suggested to edit ./build-dev.sh (and then to run ./build-dev.sh - but I have not sais ir, sorry) 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 nsutanto at purdue.edu Tue Feb 28 10:25:16 2006 From: nsutanto at purdue.edu (Nicholas Sutanto) Date: Tue, 28 Feb 2006 10:25:16 -0500 Subject: [MOBY-l] java error In-Reply-To: References: Message-ID: <44046B5C.9070603@purdue.edu> It seems that I have the same file with you... alhagib 55 % ls -al total 218 drwxr-x--- 2 nsutanto nsutanto 512 Feb 28 10:08 . drwxr-x--- 8 nsutanto nsutanto 512 Feb 28 10:08 .. -rw-r----- 1 nsutanto nsutanto 4501 Jun 2 2005 MobyPlainText.java -rw-r----- 1 nsutanto nsutanto 5374 Aug 29 2005 MobyUtilities.java -rw-r----- 1 nsutanto nsutanto 10585 Feb 20 00:51 MobyXML.java -rw-r----- 1 nsutanto nsutanto 53411 Aug 29 2005 ObjectCreationTool.java -rw-r----- 1 nsutanto nsutanto 1218 Jun 2 2005 Pair.java -rw-r----- 1 nsutanto nsutanto 3300 Apr 7 2005 PopUpWindow.java -rw-r----- 1 nsutanto nsutanto 4362 Jul 19 2005 Registration.java -rw-r----- 1 nsutanto nsutanto 4526 Apr 7 2005 SubmissionWindow.java -rw-r----- 1 nsutanto nsutanto 3698 Apr 7 2005 TreeMouseListener.java -rw-r----- 1 nsutanto nsutanto 10777 Jul 19 2005 TreeWindow.java -rw-r----- 1 nsutanto nsutanto 783 Sep 30 09:45 retrieveObjectXML.cgi -Nicholas. Martin Senger wrote: >> Here is the contents of the lib folder: >> >> > Okay, theee list is the same as I have. No problem come from here. > > So I had a look at the first error: > > ...src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/MobyXML.java:34: > >> cannot find symbol >> [javac] symbol : class Registration >> [javac] location: class >> org.biomoby.client.ui.graphical.applets.objectCreationTool.MobyXML >> [javac] private Registration registration; >> [javac] ^ >> >> > Interestingly it points to the line 34 - but in my MobyXML.java file > the culprit line (private Registration registration;) is the line number > 31. So let's make sure that we have the same version. Could you please > look into > src/main/org/biomoby/client/ui/graphical/applets/objectCreationTool/ and > check that this subdirectory contains also file Registration.java (it > should have size 4362)? Also how big is your MobyXML.java (mine is 10585). > > Martin > > From letondal at pasteur.fr Mon Feb 27 03:39:33 2006 From: letondal at pasteur.fr (Catherine Letondal) Date: Mon, 27 Feb 2006 09:39:33 +0100 Subject: [MOBY-l] Swoogle: Google for Semantic web Message-ID: <7338237488d6d6193ca5caf66777f218@pasteur.fr> Hi, Answers to requests for e.g: 'gene ontology' were not empty, so ... : swoogle.umbc.edu Best, Catherine Letondal Begin forwarded message: > From: Nathalie Aussenac-Gilles > Date: February 5, 2006 11:00:21 PM CET > To: info-ic > Subject: [info-ic] Swoogle 2006 released > > > > We've released a major new version of Swoogle [1], a search > engine for Semantic Web ontologies, terms and data. This > replaces 'Swoogle 2005', which is still available at [2]. > > The new version enjoys a simpler model and cleaner > foundation and includes data on over 850K semantic web > documents collected from the web. Some old features (e.g., > the triple shop) are currently absent, but we'll be adding > features over the next few months. > > See our blog's Swoogle section [3] for more information; > send comments and suggestions to [4]; and consider joining > Swooglers [5], a Google Group for Swoogle users. > > [1] http://swoogle.umbc.edu/ > [2] http://swoogle.umbc.edu/2005/ > [3] http://ebiquity.umbc.edu/blogger/index.php?cat=24 > [4] mailto:swoogle-developers at cs.umbc.edu > [5] http://groups.google.com/group/swooglers/ > > > -- > Tim Finin, Computer Science & Electrical Engineering, Univ of Maryland > Baltimore County, 1000 Hilltop Cir, Baltimore MD 21250. finin at umbc.edu > http://umbc.edu/~finin 410-455-3522 fax:-3969 http://ebiquity.umbc.edu > > > From Phillip.Lord at newcastle.ac.uk Tue Feb 28 15:33:13 2006 From: Phillip.Lord at newcastle.ac.uk (Phillip Lord) Date: Tue, 28 Feb 2006 20:33:13 -0000 Subject: [MOBY-l] CFP: The Joint BioLink and Bio-Ontologies Meeting, August 4-5, 2006 Message-ID: <6942EE35B530F84EAD432959F5E4DAB501C4B4C8@largo.campus.ncl.ac.uk> The Joint BioLINK and Bio-Ontologies SIG Meeting, August 4-5, 2006 In association with ISMB 2006, Fortaleza, Brazil, 2006 NEW THIS YEAR: The two long-standing ISMB SIGS, Bio-ontologies and BioLINK, will hold a single joint two-day workshop this year. The meeting will consist of sessions that focus on the intersection of bio-ontologies and text mining, as well as individual sessions on ontologies in the life sciences (organized by the BioOntologies committee (http://www.jbb06.org/ont-organisers.html), and on biomedical text mining, linking text data to biology, (organized by the BioLINK committee: http://www.jbb06.org/link-organisers.html) Registration and participation will be for a single two-day workshop. Key Information Program chairs: Bio-Ontologies Section: Robert Stevens (1), Phillip Lord (2), Robin McEntire (3), James.A.Butler(3) 1. School of Computer Science, University of Manchester, United Kingdom 2. School of Computing Science, University of Newcastle, United Kingdom 3. GlaxoSmithKline, USA BioLINK Section: Hagit Shatkay (1), Lynette Hirschman (2), Christian Blaschke (3), Alfonso Valencia (4) 1. School of Computing, Queen's University, Canada 2. MITRE, USA 3. Bioalma, Spain 4. Centro Nacional de Biotecnologia, Universidad Autonoma, Spain Website: http://www.jbb06.org Main Conference: http://www.iscb.org/ismb2006 About the Workshop Our goals in organizing the workshop are: 1. To allow researchers in the two communities to participate in the activities of both SIGs; 2. To encourage exchange of ideas and presentation cross-cutting research. The joint sessions will encourage discussion on topics such as ontology-based curation from the biomedical literature, (semi-)automated creation of ontologies, use of ontologies to improve text mining, and evaluation of ontologies, especially in terms of ability to consistently capture biologically significant concepts from the literature. The ontology session will continue the important topics from previous workshops. Ontologies provide a mechanism for organising, sharing and reconciling data. Within recent years, there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information. With the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressiveness and best practices for modeling are becoming more important. On the ontologies side, we are therefore particularly interested in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems. The BioLink session will explore resources and tools for biomedical text-mining. As biomedical literature and text in biology continue their exponential growth, text-mining, information retrieval, and natural language processing (NLP) are all becoming main-stream practices in bioinformatics. This field is interdisciplinary in nature and brings researchers applying NLP, text mining, information extraction and retrieval in the biomedical domain, together with scientists from bioinformatics and biology. We solicit submissions from researchers working on all aspects of text mining as they apply to bioinformatics and bio-medicine. The workshop will offer an informal environment for presentation and discussion of current research in biomedical ontologies and text-mining. The program will include presentations of short papers, invited talks and posters. Papers and poster-abstracts will be reviewed by the program committee. All accepted submissions will be included in the SIG notes. Submissions We are inviting two types of submissions: 1. Short papers (up to 4 pages) 2. Poster abstracts (up to 1/2 page). Authors should clearly indicate whether they would like their work to be considered as related to Bio-Ontologies, Biomedical Text Mining (BioLINK) or to the joint session. Submissions details to be released soon. Listed below are suggested topics for each section. However, we particularly encourage submissions that integrate aspects of both text-mining and ontologies, for instance discussing the role of ontologies and knowledge bases in text mining, use of ontologies to improve biomedical text analysis, automated text categorization based on ontology structure etc. Suggested topics for Bio-Ontologies include but are not restricted to: - Biological Applications of Ontologies. - Reports on Newly Developed or Existing Bio-Ontologies. - Tools for Developing Ontologies. - Use of Semantic Web technologies in Bioinformatics - The implications of Bio-Ontologies or the Semantic Web for the drug discovery process - Current Research In Ontology Languages and its implication for Bio-Ontologies Suggested topics for BioLINK include but are not restricted to: - Knowledge Representation - Testing and Evaluation - Corpus Construction Efforts - Entity Identification and Normalization - Information Extraction - Information Retrieval - Text categorization. May 1: Papers (up to 4 pages) and poster-abstracts (up to 1 page) due. June 10: Notification to authors June 20: Final version due