[Gmod-schema] stag-storenode.pl error

[Mara K. <mar...@va...>]

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?