From: Chris M. <cjm...@lb...> - 2017-03-23 23:53:16
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I don't know what OM/ORM is favored for Chado these days. Where would the ticket go? With the OBO JSON format it should be easy to write a translation to the OM https://douroucouli.wordpress.com/2016/10/04/a-developer-friendly-json-exchange-format-for-ontologies/ https://github.com/geneontology/obographs On 23 Mar 2017, at 16:41, Scott Cain 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 > Ontario Institute for Cancer Research |