From: Mara K. <mar...@gm...> - 2017-03-23 23:45:30
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I am unfamiliar with DBSchema. How would I go about testing that? On Thu, Mar 23, 2017 at 7:41 PM Scott Cain <sc...@sc...> wrote: > Probably. I'd love to if I had a drop in replacement :-) > > On Thu, Mar 23, 2017 at 7:23 PM, Chris Mungall <cjm...@lb...> wrote: > > Is there a ticket already open somewhere about replacing stag-storenode? > > On 23 Mar 2017, at 16:17, Scott Cain wrote: > > 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? > > > ------------------------------------------------------------------------------ > 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 > <(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 > <(216)%20392-3087> > Ontario Institute for Cancer Research > > > ------------------------------------------------------------------------------ > 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 > <(216)%20392-3087> > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > 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 > |