From: Scott C. <sc...@sc...> - 2017-03-23 23:41:50
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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 Ontario Institute for Cancer Research |