From: Scott C. <sc...@sc...> - 2017-03-23 20:49:22
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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? > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > 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 |