[Gmod-schema] [Gmod-help] Alternatives to DBIx::DBStag for loading ontologies

[Chris Mungall]

It appears DBIx::DBSchema 0.38 treats defaults differently, creating a  
reference for them. It also appears to DBI-quote defaults of '',  
meaning that

  version varchar(255) not null default '',

Is stored internally as "\'\'"

which ends up getting DBI-quoted again..

Anyway, I have fixed DBStag on github such that it works around this  
and should work with both earlier and current versions of DBSchema. I  
will propagate this to CPAN later if it looks fine.

http://github.com/cmungall/DBIx-DBStag

On Jan 21, 2010, at 12:50 PM, Scott Cain wrote:

> Hi James,
>
> There was a report of this just a few days ago on the schema mailing
> list.  It appears that a new release of DBIx::DBSchema breaks
> DBIx::DBStag.  Try going to cpan and getting an older version to see
> if it fixes it.
>
> Scott
>
> On Thursday, January 21, 2010, James Estill  
> <jestill at plantbio.uga.edu> wrote:
>> I am to the point where I am attempting to load ontologies into my  
>> CHADO installation.
>>
>> Using 'make ontologies' gives
>>
>> Died at lib/Bio/Chado/Builder.pm line 315, <STDIN> line 1.
>> make: *** [ontologies] Error 2
>>
>> I can download the ontologies and convert to xml manually, but it  
>> looks like DBIx::DBStag is broken in some way, when I do
>>
>> stag-storenode.pl -d  
>> 'dbi:Pg:dbname=chado_test;host=localhost;port=5432' --user myname -- 
>> password mypassword ro.oboxml
>>
>> I get the error message
>>
>> Cannot quote a reference at /Library/Perl/5.8.8/DBIx/DBStag.pm line  
>> 3736.
>>
>> Is there an alternative way to load ontologies into the database  
>> that do not rely on DBIx::DBStag? I installed DBIx::DBStag the  
>> "manual" way and it is apparently not doing its job.
>>
>> -- Jamie Estill
>> -- jestill at uga.edu
>> -- http://jestill.myweb.uga.edu
>> -- http://www.epernicus.com/people/jestill
>>
>>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
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