[Bioperl-l] [ANNOUNCEMENT] Alpha 1.6 releases of BioPerl-db

Johann PELLET johann.pellet at inserm.fr
Mon Feb 2 12:09:42 EST 2009



Le 2 févr. 09 à 17:40, Chris Fields a écrit :

> So, for this particular test, should it pass with either an empty  
> string or undef?  It apparently works for all other tests.
>
>
> chris
Here, my t/DBHarness.biosql.conf :
{
	'port' => '',
	'schema_sql' => ['../biosql-schema/sql/biosqldb-mysql.sql'],
	'dbname' => 'biosql',
	'host' => 'localhost',
	'database' => 'biosql',
	'password' => '****',
	'user' => '****',
	'driver' => 'Pg',
}

I have as I said this error:
>>> t/01dbadaptor.....1/23
>>> #   Failed test in t/01dbadaptor.t at line 44.
>>> #          got: undef
>>> #     expected: ''
>>> # Looks like you failed 1 test of 23.
>>> t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100)
>>> Failed 1/23 subtests

If I change  the postgresql port in the t/DBHarness.biosql.conf
'port' => '5432',

./Build test

t/01dbadaptor.....ok

t/02species.......80/67 # Looks like you planned 67 tests but ran 54  
extra.
t/02species....... Dubious, test returned 255 (wstat 65280, 0xff00)
All 67 subtests passed

t/09fuzzy2........7/23
#   Failed (TODO) test in t/09fuzzy2.t at line 64.
#          got: undef
#     expected: 'Q9QYG8'
t/09fuzzy2........ok

Tt/02species   (Wstat: 65280 Tests: 121 Failed: 54)
   Failed tests:  68-121
   Non-zero exit status: 255
   Parse errors: Bad plan.  You planned 67 tests but ran 121.
Files=16, Tests=1533, 120 wallclock secs ( 0.29 usr  0.10 sys + 11.51  
cusr  1.14 csys = 13.04 CPU)
Result: FAIL
Failed 1/16 test programs. 54/1533 subtests failed.

So for the first test, if the port is not empty, it's ok now. But I  
still have other errors t02 and t09.

Johann


>
>
> On Jan 30, 2009, at 11:13 AM, Hilmar Lapp wrote:
>
>> I think this has something to do with the database connection  
>> configuration file (t/DBHarness.conf). I suspect in your version it  
>> sets 'port' to an empty string, rather than not setting it at all,  
>> or setting it explicitly to undef.
>>
>> The test that's failing is one of a series of tests that verify  
>> that the connection attributes can be round-tripped through a DSN  
>> string. Specifying 'port' in the DSN string as an empty value is  
>> illegal though, so it gets left out whether it's undef or an empty  
>> string. When parsed back, the port isn't found in the string and  
>> hence left undef (meaning, use whatever your DBD driver thinks is  
>> the right default).
>>
>> 	-hilmar
>>
>> On Jan 29, 2009, at 7:28 AM, Johann PELLET wrote:
>>
>>> Dear Chris,
>>>
>>> I have the following error on my Mac machine: (BioPerl 1.6,  
>>> BioPerl-run
>>> 1.6) when I try to install Bioperl-db ( biosql-1.0.1):
>>>
>>> t/01dbadaptor.....1/23
>>> #   Failed test in t/01dbadaptor.t at line 44.
>>> #          got: undef
>>> #     expected: ''
>>> # Looks like you failed 1 test of 23.
>>> t/01dbadaptor..... Dubious, test returned 1 (wstat 256, 0x100)
>>> Failed 1/23 subtests
>>> t/02species.......ok
>>> t/03simpleseq.....ok
>>> t/04swiss.........ok
>>> t/05seqfeature....ok
>>> t/06comment.......ok
>>> t/07dblink........ok
>>> t/08genbank.......ok
>>> t/09fuzzy2........5/23
>>> #   Failed (TODO) test in t/09fuzzy2.t at line 64.
>>> #          got: undef
>>> #     expected: 'Q9QYG8'
>>> t/09fuzzy2........ok
>>> t/10ensembl.......ok
>>> t/11locuslink.....ok
>>> t/12ontology......ok
>>> t/13remove........ok
>>> t/14query.........ok
>>> t/15cluster.......ok
>>> t/16obda..........ok
>>>
>>> Test Summary Report
>>> -------------------
>>> t/01dbadaptor (Wstat: 256 Tests: 23 Failed: 1)
>>> Failed test:  16
>>> Non-zero exit status: 1
>>> Files=16, Tests=1479, 15 wallclock secs ( 0.27 usr  0.10 sys +  
>>> 11.15 cusr  1.11 csys = 12.63 CPU)
>>> Result: FAIL
>>> Failed 1/16 test programs. 1/1479 subtests failed.
>>>
>>> -- --
>>>
>>> Johann Pellet
>>> IE Bioinformatique
>>> INSERM U851, I-MAP CERVI
>>> 21, Avenue Tony Garnier
>>> 69365 Lyon cedex 07 France
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
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>




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