[MOBY-dev] Re: Failing tests in the Perl API.

Fri Sep 16 15:01:12 UTC 2005

Hi Frank,

On 16-Sep-2005, at 4:26 PM, Gibbons, Francis wrote:

> Pieter,
>
> I wrote many of the tests for the  Perl API. When I run them, I see  
> a 99% pass rate, or better. I'm very interested to know which ones  
> are failing for you, and what your local installation looks like (I  
> guess you have a local registry? what's your OS? Perl version? etc.)

I'm running SuSE Linux Enterprise Server 9 (SLES9) with all the  
latest and greatest updates / patches. My Perl version is 5.8.3  
(default that comes with SLES9) I do have a local biomobycentral, but  
that shouldn't make any difference for the tests. I haven't set  
MOBY_xxx ENV vars, so for the tests  everything should default to the  
central mobycentral.

I see 3/361 subtests failed, 99.17% okay and 8 subtests UNEXPECTEDLY  
SUCCEEDED. The 99.17% might seem not too shabby, but for a user like  
me it's pretty difficult to figure out how essential the failing  
stuff is :(.... I'll just give it try anyway. If it doesn't work I'll  
downgrade again. Keeping my fingers crossed...

Below is what I got from the tests.

Cheers,

Pieter

pieter at bioinfw05:~/moby-live/Perl> 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............................NOK 3#     Failed test (t/ 
Client-Central.t at line 73)
#     MOBY::Client::Central->can('retrieveObjectSchema') failed
# Registry failed to supply mandatory methods
t/Client-Central............................ok 134/0# Looks like you  
failed 1 tests of 134.
t/Client-Central............................dubious
         Test returned status 1 (wstat 256, 0x100)
Scalar found where operator expected at (eval 153) line 1, near  
"'int'  $__val"
         (Missing operator before   $__val?)
DIED. FAILED test 3
         Failed 1/134 tests, 99.25% okay
t/Client-CollectionArticle..................ok
t/Client-OntologyServer.....................NOK 2#     Failed test (t/ 
Client-OntologyServer.t at line 36)
#     MOBY::Client::OntologyServer->can('relationshipExists') failed
# OntologyServer doesn't implement full API
t/Client-OntologyServer.....................ok 24/0Use of  
uninitialized value in pattern match (m//) at /mnt/geninf01/home/ 
geninf/pieter/moby-live/Perl/blib/lib/MOBY/Client/OntologyServer.pm  
line 98.
Use of uninitialized value in pattern match (m//) at /mnt/geninf01/ 
home/geninf/pieter/moby-live/Perl/blib/lib/MOBY/Client/ 
OntologyServer.pm line 98.
t/Client-OntologyServer.....................ok 25/0No such method:  
MOBY::Client::OntologyServer::relationshipExists at t/Client- 
OntologyServer.t line 76
# Looks like you failed 1 tests of 25.
# Looks like your test died just after 25.
t/Client-OntologyServer.....................dubious
         Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED test 2
         Failed 1/25 tests, 96.00% okay
t/Client-Registration.......................ok
t/Client-SecondaryArticle...................ok
t/Client-Service............................NOK 3#     Failed test (t/ 
Client-Service.t at line 36)
#     MOBY::Client::Service->can('serviceName') failed
# MOBY::Client::Service doesn't implement full API.
t/Client-Service............................ok 6/0# Looks like you  
failed 1 tests of 6.
t/Client-Service............................dubious
         Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 3
         Failed 1/6 tests, 83.33% okay
t/Client-ServiceInstance....................ok
t/Client-SimpleArticle......................ok
t/CommonSubs................................ok 18/0MOBY::CommonSubs  
WARNING ** the namespace 'bogus NS' does not exist in the MOBY  
ontology, and does not have a valid LSID
t/CommonSubs................................ok
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           1   256   134    1   0.75%  3
t/Client-OntologyServer.t  255 65280    25    1   4.00%  2
t/Client-Service.t           1   256     6    1  16.67%  3
  (8 subtests UNEXPECTEDLY SUCCEEDED), 3 tests skipped.
Failed 3/23 test scripts, 86.96% okay. 3/361 subtests failed, 99.17%  
okay.
make: *** [test_dynamic] Error 255

> Clearly, we should have a test suite that passes for most  
> developers most of the time, so that they can be alerted quickly if  
> they break something. So it's really important for me to know which  
> tests are failing and why: the tests may need to be rewritten.
>
> Thanks for your feedback.
>
> -Frank
> -----Original Message-----
> From: moby-dev-bounces at portal.open-bio.org on behalf of Edward Kawas
> Sent: Fri 9/16/2005 9:54 AM
> To: 'Core developer announcements'
> Cc: 'Pieter Neerincx'
> Subject: RE: [MOBY-dev] Moby objects in Taverna. Where do they come  
> from?
>
> >I assume I need to update my BioMOBY API stuff as
> >well. So I tried an cvs up -d of moby-live. When I try make
> >test for the Perl stuff I see a lot of tests failing....
> >Can I safely ignore them for now?
>
> I am not sure about this question. I know that Mark has a
> new test suite but I am not sure if this is the suite that
> you are running.
>
> One more thing, if the servlets work, you would be able to
> do the following:
> http://yourURL:port/types/Objects
> http://yourURL:port/RESOURCES/MOBY-S/Objects
> http://yourURL:port/authority
>
> These 3 links should show you something meaningful (html, a
> file, more html).
>
> Eddie
>
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> MOBY-dev at biomoby.org
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>

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