[Bioperl-l] bioperl-db tests

[Hilmar Lapp]

Hi Shawn, this maybe doesn't interfere a lot with what I'm 
re-organizing but maybe it does. It will take at least another week 
until I will be to ready to commit, otherwise I lose too many rounds 
of beer ... If that makes you uncomfortable then go ahead and 
commit, I'll have to somehow figure out then how to merge in your 
changes. Actually, if your changes aren't in the adaptors, then go 
commit.

	-hilmar

On Wednesday, August 21, 2002, at 03:35  AM, Shawn wrote:

> Hi Hilmar,
> thanks for the reply.
> What I want to do is to have an option of caching sequences when
> fetching. The default behavior is still lazy. This is because for
> certain pipelines, we fetch quite a number of sequences at one 
> time, and
> this is done before sending the inputs to the analysis.  So what we 
> want
> to do is really to fetch  the actual sequences when we do the fetch and
> not til we call ->seq thereby allowing us to release the db connection
> and avoiding those too many dbconnection errors.
>
> so it just involves adding an option. Maybe I should wait til your
> changes are done then integrate them ?
>
> shawn
>
>
>
>
>
> On Wed, 2002-08-21 at 02:44, Hilmar Lapp wrote:
>> You need to get and install the bioperl main trunk latest revision 
>> in order to work with the live bioperl-db code. The errors you're 
>> seeing are all related to the map database except remove.t. I 
>> changed the config files and some other things; look into 
>> t/DBHarness.conf.example for a documented example, then copy that 
>> file to both t/DBHarness.conf and t/DBHarness.markerdb.conf and 
>> edit accordingly. You can also ignore the markerdb-related errors 
>> if you don't care about that.
>>
>> Getting the config files right should make the get_MapAdaptor() 
>> error go away.
>>
>> As for the exception in remove.t, the new location parser doesn't 
>> recognize the replace(...) operator, as it violates the official 
>> Genbank FT definition. The replace(...) operator was an early 
>> version of what is meanwhile a 'variation' feature tag with a 
>> standard location. Unless replace() operators still occur in 
>> current genbank downloads, I'd prefer to remove this test. Having 
>> to deal with replace() in location strings would be /really/ ugly 
>> because that operator folds location and annotation into one 
>> string.
>>
>> Iùb=
>>
>> Can you give me an idea what you'll be changing? I'm currently 
>> orking on a reorganization and partial rewrite of the entire 
>> Bio::DB::* code layout, but I didn't want to commit before all 
>> tests pass.
>>
>> 	-hilmar
>>
>>> -----Original Message-----
>>> From: Shawn [mailto:shawnh@fugu-sg.org]
>>> Sent: Tuesday, August 20, 2002 7:01 PM
>>> To: bioperl
>>> Subject: [Bioperl-l] bioperl-db tests
>>>
>>>
>>>
>>> Hi,
>>> 	I'm trying to find out which version of bioperl works
>>> best with the
>>> live version of bioperl-db. I'm trying to get make test to
>>> work. So far
>>> I've tried bioperl-live, bioperl-1.0.2 and bioperl-0-7-2. So far the
>>> main trunk seems to give me the least errors.
>>>
>>> Failed Test Status Wstat Total Fail  Failed  List of Failed
>>> --------------------------------------------------------------
>>> ------------------
>>> t/ePCRdb.t       255 65280     3    1  33.33%  3
>>> t/map.t          255 65280     6    4  66.67%  3-6
>>> t/marker.t       255 65280    19   15  78.95%  5-19
>>> t/remove.t                    20    1   5.00%  9
>>>
>>> Two main errors
>>> one involves get_MapAdaptor not found in Bio::DB::BioSQL::DBAdaptor
>>> while the other is a little less obvious to me :
>>>
>>> ------------- EXCEPTION  -------------
>>> MSG: operator "replace" unrecognized by parser
>>> STACK Bio::Factory::FTLocationFactory::from_string
>>> /usr/users/shawnh//src/bioperl-live//Bio/Factory/FTLocationFac
>>> tory.pm:159
>>> STACK (eval)
>>> /usr/users/shawnh//src/bioperl-live//Bio/SeqIO/FTHelper.pm:124
>>> STACK Bio::SeqIO::FTHelper::_generic_seqfeature
>>> /usr/users/shawnh//src/bioperl-live//Bio/SeqIO/FTHelper.pm:123
>>> STACK Bio::SeqIO::genbank::next_seq
>>> /usr/users/shawnh//src/bioperl-live//Bio/SeqIO/genbank.pm:298
>>> STACK BioSQLBase::store_seq t/BioSQLBase.pm:62
>>> STACK (eval) t/remove.t:31
>>> STACK toplevel t/remove.t:30
>>>
>>> basically I want to make sure the tests pass before I make
>>> any commits.
>>>
>>> thanks,
>>>
>>> shawn
>>>
>>>
>>>
>>>
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>>> Bioperl-l@bioperl.org
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>>>
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>
>
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------