Re: [Gmod-schema] stag-storenode.pl error

[Scott C. <sc...@sc...>]

It seems like DBIx::DBSchema is failing from the first error message, and
if that's failing, nothing else is going to work.  It's trying to call the
DBSchema table method.  I just looked at the test suite for DBSchema and it
is surprisingly useless.  It might be worthwhile to create a simple test
script that talks to your Chado database via DBSchema and calls the table
method for the cv table to see if it works.

One thing I wonder about is the version of Postgres: 9.6.2 is newer than
any I've seen used, but I would hope that it would still work.


On Thu, Mar 23, 2017 at 5:36 PM, Mara Kim <mar...@va...> wrote:

> `search_path` seems to be set correctly:
>
> $ psql -U rokaschado genestation
>
> psql (9.6.2)
>
> Type "help" for help.
>
>
> genestation=# SHOW search_path;
>
>   search_path
>
> ---------------
>
>  chado, public
>
> (1 row)
>
>
> genestation=# SELECT * FROM cv LIMIT 1;
>
>  cv_id |     name     | definition
>
> -------+--------------+------------
>
>      1 | relationship |
>
> (1 row)
>
> On Thu, Mar 23, 2017 at 4:26 PM Scott Cain <sc...@sc...> wrote:
>
>> Hi Mara,
>>
>> Is your chado database in a schema other than public?  If so, you'll have
>> to modify your search path for the user that is running stag-storenode.
>> See http://tripal.info/documentation/search_path for more info.
>>
>> Scott
>>
>>
>> On Thu, Mar 23, 2017 at 2:43 PM, Mara Kim <mar...@va...>
>> wrote:
>>
>> Hello,
>>
>> I am trying to use stag-storenode.pl to load the Fantom5 FF ontology.
>>
>> I took the following steps:
>>
>> wget http://fantom.gsc.riken.jp/5/datafiles/latest/extra/
>> Ontology/ff-phase2-140729.obo.txt #Download ontology
>>
>> ex ff-phase2-140729.obo.txt -c '%s/{.*} ' -c 'wq' #Remove comments
>>
>> go2chadoxml ff-phase2-140729.obo.txt > ff.xml #Convert to XML
>>
>> stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432'
>> --user rokaschado ff.xml  #Load into DB
>>
>>
>>
>> When invoking stag-storenode.pl I get the following error:
>>
>> $ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432'
>> --user rokaschado ff.xml
>>
>> Can't get table cv from db.
>>
>> Maybe DBIx::DBSchema does not work with your database? at
>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 427
>>
>>         DBIx::DBStag::get_pk_col('DBIx::DBStag=HASH(0x1950fb8)', 'cv')
>> called at /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1265
>>
>>         DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x1950fb8)',
>> 'Data::Stag::StagImpl=ARRAY(0x2749fe8)') called at
>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 1180
>>
>>         DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x1950fb8)',
>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/
>> stag-storenode.pl line 85
>>
>>         eval {...} called at /home/kimmm/perl5/bin/stag-storenode.pl
>> line 84
>>
>>         main::store('Data::Stag::BaseHandler=HASH(0x2542658)',
>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at /home/kimmm/perl5/bin/
>> stag-storenode.pl line 134
>>
>>         main::__ANON__('Data::Stag::BaseHandler=HASH(0x2542658)',
>> 'Data::Stag::StagImpl=ARRAY(0x26c0128)') called at
>> /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm line 594
>>
>>         Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x2542658)',
>> 'cv') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseHandler.pm
>> line 742
>>
>>         Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x2542658)',
>> 'HASH(0x1a02da0)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm
>> line 239
>>
>>         XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x26543e8)',
>> 'XML::Parser::Expat=HASH(0x25898a8)', 'cv') called at
>> /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm line 79
>>
>>         XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x25898a8)',
>> 'cv') called at /usr/lib64/perl5/XML/Parser/Expat.pm line 469
>>
>>         XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x25898a8)',
>> 'FileHandle=GLOB(0x2688330)') called at /usr/lib64/perl5/XML/Parser.pm line
>> 187
>>
>>         eval {...} called at /usr/lib64/perl5/XML/Parser.pm line 186
>>
>>         XML::Parser::parse('XML::Parser=HASH(0x24a4200)',
>> 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/XML/Parser/PerlSAX.pm
>> line 146
>>
>>         XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x26543e8)',
>> 'Handler', 'Data::Stag::BaseHandler=HASH(0x2542658)', 'Source',
>> 'HASH(0x26547f0)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm
>> line 69
>>
>>         Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x2542400)',
>> 'FileHandle=GLOB(0x2688330)') called at /home/kimmm/perl5/lib/perl5/Data/Stag/BaseGenerator.pm
>> line 476
>>
>>         Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x2542400)',
>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at
>> /home/kimmm/perl5/lib/perl5/Data/Stag/XMLParser.pm line 58
>>
>>         Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x2542400)',
>> '-file', 'ff.xml', '-str', undef, '-fh', undef) called at
>> /home/kimmm/perl5/lib/perl5/Data/Stag/StagImpl.pm line 275
>>
>>         Data::Stag::StagImpl::parse('Data::Stag', '-format', undef,
>> '-file', 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)')
>> called at /home/kimmm/perl5/lib/perl5/Data/Stag.pm line 181
>>
>>         Data::Stag::AUTOLOAD('Data::Stag', '-format', undef, '-file',
>> 'ff.xml', '-handler', 'Data::Stag::BaseHandler=HASH(0x2542658)') called
>> at /home/kimmm/perl5/bin/stag-storenode.pl line 140
>>
>>
>> Any ideas what might be the problem?
>>
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>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> <(216)%20392-3087>
>> Ontario Institute for Cancer Research
>>
>


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