[Gmod-schema] [Gmod-help] Alternatives to DBIx::DBStag for loading ontologies
Chris Mungall
cjm at berkeleybop.org
Mon Jan 25 17:22:55 EST 2010
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>
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