[Gmod-schema] [Gmod-help] Alternatives to DBIx::DBStag for loading ontologies
Scott Cain
scott at scottcain.net
Mon Jan 25 11:29:55 EST 2010
Hi Chris,
Here is end of the stag-storenode.pl STDERR output. Note that I am
pretty sure the error messages are coming from the database server,
not stag-storenode, but it would be nice if we could keep that from
happening; people don't like it even if it is harmless.
Thanks,
Scott
On Fri, Jan 22, 2010 at 2:58 PM, Chris Mungall <cjm at berkeleybop.org> wrote:
>
> 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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>>>> attendees to learn about information security's most important issues
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>>>> companies.
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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
>> _______________________________________________
>> Gmod-schema mailing list
>> Gmod-schema at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>
--
------------------------------------------------------------------------
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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