[MOBY-dev] [moby] setting up a MOBY central registry

[Mark Wilkinson]

I would say, based on the messages you are getting, that your MOBY
configuration file doesn't exist :-)

You may need to restart your server to get that environment variable
into the Apache process...

M


On Fri, 2005-12-09 at 01:20 +0800, Anacleto, Mylah Rystie (IRRI) wrote:
> Dear Mark,
> 
> Thank you for your fast reply.
> 
> I got errors in make test, am pasting it below. I will also look at the database...
> 
> There is nothing to edit in OntologyServer.cgi? please confirm...
> 
> Mylah
> 
> 
> # make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/Central...................................ok
> t/Client-Central............................ok 1/0
> 
> 
>     This is the MOBY Client Central test suite.
> 
>     by default this connects to the server at mobycentral.icapture.ubc.ca
>     (or whatever the default server is set to in the code)
> 
>     If you want to test a different server you must set the following
>     ENVIRONEMNT VARABLES:
> 
>     MOBY_SERVER='http://your.server.name/path/to/mobycentral.pl'
>     MOBY_URI='http://your.server.name/MOBY/Central'
> 
> 
> t/Client-Central............................ok 2/0
> 
>     For the following tests I will be using the server at:
>         http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl
> 
> 
> t/Client-Central............................ok 6/0MOBY Configuration file  doesn't exist No such file or directory
> 
>  ERROR ERROR ERROR
> # Looks like your test died just after 6.
> t/Client-Central............................dubious
>         Test returned status 255 (wstat 65280, 0xff00)
>         after all the subtests completed successfully
> t/Client-CollectionArticle..................ok
> t/Client-OntologyServer.....................ok 1/0MOBY Configuration file  doesn't exist No such file or directory
> 
>  ERROR ERROR ERROR
> BEGIN failed--compilation aborted at t/Client-OntologyServer.t line 48.
> # Looks like your test died just after 1.
> t/Client-OntologyServer.....................dubious
>         Test returned status 255 (wstat 65280, 0xff00)
>         after all the subtests completed successfully
> t/Client-Registration.......................ok
> t/Client-SecondaryArticle...................ok
> t/Client-Service............................ok 2/0MOBY Configuration file  doesn't exist No such file or directory
> 
>  ERROR ERROR ERROR
> MOBY Configuration file  doesn't exist No such file or directory
> 
>  ERROR ERROR ERROR
> END failed--call queue aborted.
> # Looks like your test died just after 2.
> t/Client-Service............................dubious
>         Test returned status 255 (wstat 65280, 0xff00)
>         after all the subtests completed successfully
> t/Client-ServiceInstance....................ok
> t/Client-SimpleArticle......................ok
> t/CommonSubs................................ok 2/0MOBY Configuration file  doesn't exist No such file or directory
> 
>  ERROR ERROR ERROR
> BEGIN failed--compilation aborted at t/CommonSubs.t line 41.
> # Looks like your test died just after 2.
> t/CommonSubs................................dubious
>         Test returned status 255 (wstat 65280, 0xff00)
>         after all the subtests completed successfully
> t/Config....................................skipped
>         all skipped: Required only for local MOBY Central
> t/CrossReference............................ok
> t/dbConnect.................................ok
> t/lsid-authority-ClassResolver..............ok
> t/lsid-authority-dbConnect..................ok
> t/lsid-authority-Error......................ok
> t/lsid-authority-NamespaceResolver..........ok
> t/lsid-authority-PredicateResolver..........ok
> t/lsid-authority-RDFConfigure...............ok
> t/lsid-authority-RelationshipResolver.......ok
> t/lsid-authority-ServiceInstanceResolver....skipped
>         all skipped: Skip until apparent namespace pollution fixed in ServiceInstanceResolver
> t/lsid-authority-ServiceResolver............ok
> t/Template..................................skipped
>         all skipped: This is just a template
> Failed Test               Stat Wstat Total Fail  Failed  List of Failed
> -------------------------------------------------------------------------------
> t/Client-Central.t         255 65280     6    0   0.00%  ??
> t/Client-OntologyServer.t  255 65280     1    0   0.00%  ??
> t/Client-Service.t         255 65280     2    0   0.00%  ??
> t/CommonSubs.t             255 65280     2    0   0.00%  ??
> 3 tests skipped.
> Failed 4/23 test scripts, 82.61% okay. 0/118 subtests failed, 100.00% okay.
> make: *** [test_dynamic] Error 255
> 
> 
> -----Original Message-----
> From: moby-dev-bounces at biomoby.org on behalf of Mark Wilkinson
> Sent: Fri 12/9/2005 12:50 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] [moby]  setting up a MOBY central registry
>  
> Hi Mylah, 
> 
> I need to deprecate that test script because it is out of date.  Please
> use the "make test" command as part of your regular make/make install
> process to test your installation (note that you will have to do a "make
> install" prior to "make test" in order to ensure that the test is using
> the most updated libraries)
> 
> M
> 
> 
> 
-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274