[Gmod-schema] [Gmod-help] Alternatives to DBIx::DBStag for loading ontologies
Scott Cain
scott at scottcain.net
Tue Jan 26 08:14:44 EST 2010
Hi Chris,
Ah, of course that is the (most immediate) problem. I forgot that I
did that; as I recall, stag-storenode was following GO's orders and
replacing is_a and part_of in REL with the ones in GO, and thus
breaking other things. I need to rewrite the queries in this fix to
use a little less sledgehammer and a little more finesse.
Thanks,
Scott
On Mon, Jan 25, 2010 at 5:22 PM, Chris Mungall <cjm at berkeleybop.org> wrote:
>
> Aha, this is coming from Bio::Chado::Builder, I'm not too familiar with this
> code:
>
> #fix up DBIx::DBStag stomping on part_of and derives_from
> $m->log->debug("fix up DBIx::DBStag stomping on part_of and derives_from");
> my $dbh =
> DBI->connect("dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port",
> $db_user, $db_pass);
> $dbh->do("UPDATE cvterm SET
> cv_id = (SELECT cv_id FROM cv WHERE name='relationship')
> WHERE name='derives_from'");
> $dbh->do("UPDATE cvterm SET
> cv_id = (SELECT cv_id FROM cv WHERE name='relationship')
> WHERE name='part_of'");
> $dbh->disconnect;
>
> Ok, so it looks like the original source of the prob may be dbstag / the
> chadoxml. I guess you could apply a band-aid to the band-aid just now, but
> the source problem is a bit trickier.
>
> cheers
> c
>
> On Jan 25, 2010, at 11:29 AM, Scott Cain wrote:
>
>> Hi Chris,
>>
>> Here is end of the stag-storenode.pl STDERR output. Note that I am
>> pretty sure the error messages are coming from the database server,
>> not stag-storenode, but it would be nice if we could keep that from
>> happening; people don't like it even if it is harmless.
>>
>> Thanks,
>> Scott
>>
>>
>> On Fri, Jan 22, 2010 at 2:58 PM, Chris Mungall <cjm at berkeleybop.org>
>> wrote:
>>>
>>> if you run this with DBSTAG_TRACE=1 pipe stderr to a file and send me the
>>> results of
>>>
>>> grep -B1000 ERROR
>>>
>>> cheers
>>>
>>> On Jan 21, 2010, at 3:59 PM, Scott Cain wrote:
>>>
>>>> Hi Chris,
>>>>
>>>> Thanks so much for looking into this. When I got your email, I had
>>>> started doing some debugging to give you more info on what was wrong.
>>>> I got your latest from github, and it appears to work fine.
>>>>
>>>> While I have your attention, though: what would also really be great
>>>> would be if we could get rid of the error/warning messages after
>>>> loading ontologies into a database that already has some ontologies
>>>> loaded. They look like this:
>>>>
>>>> scott-cains-macbook-pro:chado cain$ 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> 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
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>> <stag_error.out>
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
More information about the Gmod-help
mailing list