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

[Scott Cain]

Hi Chris,

Thanks so much for looking into this.  When I got your email, I had
started doing some debugging to give you more info on what was wrong.
I got your latest from github, and it appears to work fine.

While I have your attention, though: what would also really be great
would be if we could get rid of the error/warning messages after
loading ontologies into a database that already has some ontologies
loaded.  They look like this:

 scott-cains-macbook-pro:chado cain$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Cell Ontology
[6] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  2,4
fetching files for Sequence Ontology
  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
    updated
    loading...done!
fetching files for Chado Feature Properties
  +load/etc/feature_property.obo
    loading...done!
DBD::Pg::db do failed: ERROR:  duplicate key value violates unique
constraint "cvterm_c1" at lib/Bio/Chado/Builder.pm line 366, <STDIN>
line 1.
DBD::Pg::db do failed: ERROR:  duplicate key value violates unique
constraint "cvterm_c1" at lib/Bio/Chado/Builder.pm line 369, <STDIN>
line 1.

Thanks,
Scott


On Thu, Jan 21, 2010 at 6:17 PM, Chris Mungall <cjm at berkeleybop.org> wrote:
> 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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>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research