[MOBY-l] Local BioMOBY Central - Ontology test fails

[Rajasekar Karthik]

Mark,
With no environment variables set, I was able to run the test suites and
most of them passed, except for Client-OntologyServer.t(13 testcases
failed).

Failed Test               Stat Wstat Total Fail  List of Failed
-------------------------------------------------------------------------------
t/Client-OntologyServer.t   13  3328    27   13  9-17 19-22
1 test skipped.
Failed 1/13 test scripts. 13/381 subtests failed.
Files=13, Tests=381, 35 wallclock secs ( 7.67 cusr +  0.78 csys =  8.45 CPU)
Failed 1/13 test programs. 13/381 subtests failed.
make: *** [test_dynamic] Error 255


When MOBY_SERVER and MOBY_URI environment variables was set to localhost.
a) MOBY_ONTOLOGYSERVER: Did not set any environment variables or did not
modify default value in OntologyServer.pm
  Client-OntologyServer.t(13 testcases failed)
b) MOBY_ONTOLOGYSERVER: Set environment variable to:
http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi
Client-OntologyServer.t(4 testcases failed).


When MOBY_SERVER and MOBY_URI environment variables was set to default (
http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl and
http://mobycentral.icapture.ubc.ca/MOBY/Central respectively),
a) MOBY_ONTOLOGYSERVER: Did not set any environment variables or did not
modify default value in OntologyServer.pm
all testcases passed
b) MOBY_ONTOLOGYSERVER: Set environment variable to:
http://mobycentral.icapture.ubc.ca/cgi-bin/OntologyServer.cgi
all testcases passed.



On 2/11/07, Mark Wilkinson <markw at illuminae.com> wrote:
>
> Can you confirm that your test suite runs when you have NO environment
> variables set?  (i.e. when you are connecting to my default mobycentral in
> all cases)?
>
>
> M
>
>
>
> On Sun, 11 Feb 2007 16:41:18 -0800, Rajasekar Karthik
> <karthik085 at gmail.com> wrote:
>
> > Also, I forgot to add:
> >> From dashboard, I am able to retrieve/register/deregister services,
> > namespaces, data types... from localhost. In data types, I can see
> > Object,
> > String, Integer, Float...so, it does exist. Testcases in
> > Client-OntologyServer.t like 11-15 tests for that.
> >
> >>
> >> I do have all the environment variables as suggested. Still, the same
> >> results. :-(
> >> I tested against the default
> >> http://mobycentral.icapture.ubc.ca/cgi-bin/On
> >>
> >> tologyServer.cgi and 4 testcases fail:
> >>
> >> ok 1 - use MOBY::Client::OntologyServer;
> >> ok 2 - MOBY::Client::OntologyServer->can(...)
> >> ok 3
> >> ok 4
> >> ok 5
> >> ok 6
> >> ok 7
> >> not ok 8 # TODO How come I cant' set proxy back to its original value?
> >> #   Failed (TODO) test at t/Client-OntologyServer.t line 101.
> >> #          got: 'bar'
> >> #     expected: undef
> >> # Couldn't return proxy to previous value
> >> not ok 9
> >> #   Failed test at t/Client-OntologyServer.t line 111.
> >> #          got: '0'
> >> #     expected: '1'
> >> # Namespace 'Rub1' reported erroneously as non-existent.
> >> not ok 10
> >> #   Failed test at t/Client-OntologyServer.t line 111.
> >> #          got: '0'
> >> #     expected: '1'
> >> # Namespace 'Rub2' reported erroneously as non-existent.
> >> ok 11
> >> ok 12
> >> ok 13
> >> ok 14
> >> ok 15
> >> not ok 16
> >> #   Failed test at t/Client-OntologyServer.t line 127.
> >> #          got: '0'
> >> #     expected: '1'
> >> # Service type 'Rub1' reported erroneously as non-existent.
> >> not ok 17
> >> #   Failed test at t/Client-OntologyServer.t line 127.
> >> #          got: '0'
> >> #     expected: '1'
> >> # Service type 'Rub2' reported erroneously as non-existent.
> >> ok 18 - MOBY::Client::OntologyServer->can('relationshipExists')
> >> ok 19
> >> ok 20
> >> ok 21
> >> ok 22
> >> ok 23
> >> ok 24
> >> ok 25
> >> ok 26
> >> ok 27
> >> 1..27
> >> # Looks like you failed 4 tests of 27.
> >>
> >>
> >> On 2/11/07, Mark Wilkinson <markw at illuminae.com > wrote:
> >> >
> >> > Hi Karthik,
> >> >
> >> > Make sure that you have all three environment variables set:
> >> >
> >> > MOBY_SERVER=http://localhost/path/to/MOBY-Central.pl
> >> > MOBY_URI=http://localhost/MOBY/Central
> >> > MOBY_ONTOLOGYSERVER= http://localhost/path/to/OntologyServer.cgi
> >> >
> >> > That should solve your problems... I hope :-)
> >> >
> >> > M
> >> >
> >> >
> >> >
> >> >
> >> > On Sun, 11 Feb 2007 14:18:25 -0800, Rajasekar Karthik
> >> > <karthik085 at gmail.com> wrote:
> >> >
> >> > > Hi,
> >> > >
> >> > > I am setting up a local biomoby central. I am following this
> >> document:
> >> > >
> >> >
> >>
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/InstallingLocalMOBYCentral.html
> >> > >
> >> > > 1. When I do, make test - all test cases passes for all the files,
> >> > except
> >> > > for Client-OntologyServer.t . I attached my test results for
> >> all('make
> >> > > test')
> >> > > and for Client-OntologyServer.t('perl t/Client-OntologyServer.t')
> >> > along
> >> > > this
> >> > > mail. Here is just the summary:
> >> > >
> >> > > Failed Test               Stat Wstat Total Fail  List of Failed
> >> > >
> >> >
> >>
> -------------------------------------------------------------------------------
> >> > > t/Client-OntologyServer.t   13  3328    27   13  9-17 19-22
> >> > > 1 test skipped.
> >> > > Failed 1/13 test scripts. 13/381 subtests failed.
> >> > > Files=13, Tests=381, 79 wallclock secs ( 7.82 cusr +  0.70 csys =
> >> > 8.52
> >> > > CPU)
> >> > > Failed 1/13 test programs. 13/381 subtests failed.
> >> > > make: *** [test_dynamic] Error 255
> >> > >
> >> > >
> >> > > 2. t/Config file is being skipped for testing. It says:
> >> > > all skipped: Required only when you have your own local MOBY
> Central
> >> > > How do I test t/Config?
> >> > >
> >> > > Any help would be appreciated.
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
> >> >
> >>
> >>
> >>
> >> --
> >> Best Regards,
> >> Rajasekar Karthik
> >> karthik085 at gmail.com
> >>
> >
> >
> >
>
>
>
> --
> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
>



-- 
Best Regards,
Rajasekar Karthik
karthik085 at gmail.com