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

[Chris Mungall]

if you run this with DBSTAG_TRACE=1 pipe stderr to a file and send me  
the results of

grep -B1000 ERROR

cheers

On Jan 21, 2010, at 3:59 PM, Scott Cain wrote:

> 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
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts  
> the
> world's best and brightest in the field, creating opportunities for  
> Conference
> attendees to learn about information security's most important  
> issues through
> interactions with peers, luminaries and emerging and established  
> companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
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> Gmod-schema at lists.sourceforge.net
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