Menu
▾
▴
gmod-schema
|
From: Mara K. <mar...@va...> - 2017-03-23 18:43:52
|
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? |
|
From: Scott C. <sc...@sc...> - 2017-03-23 20:49:22
|
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 |
|
From: Mara K. <mar...@va...> - 2017-03-24 00:11:06
|
`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
>
|
|
From: Scott C. <sc...@sc...> - 2017-03-23 23:17:54
|
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 Ontario Institute for Cancer Research |
|
From: Chris M. <cjm...@lb...> - 2017-03-23 23:24:23
|
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 > 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 |
|
From: Scott C. <sc...@sc...> - 2017-03-23 23:41:50
|
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 |
|
From: Mara K. <mar...@gm...> - 2017-03-23 23:45:30
|
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 > |
|
From: Chris M. <cjm...@lb...> - 2017-03-23 23:53:16
|
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 |
|
From: Karl O. P. <ko...@me...> - 2017-03-24 15:53:01
|
Hi,
When we installed chado we found a number of places
where "public" was hardcoded.
The places I identify now from a quick review of our notes are:
initialize.sql
/usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm
---------------------<snip>--------------------
--- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400
+++ Pg.pm 2014-04-21 12:02:33.960290072 -0400
@@ -34,7 +34,8 @@
=cut
-sub default_db_schema { 'public'; }
+#sub default_db_schema { 'public'; }
+sub default_db_schema { 'chado'; }
sub columns {
my($proto, $dbh, $table) = @_;
---------------------<snip>--------------------
I recall getting chado to install somewhere other than the public
schema to be tedious.
Regards,
Karl <ko...@me...>
Free Software: "You don't pay back, you pay forward."
-- Robert A. Heinlein
|
|
From: Mara K. <mar...@gm...> - 2017-03-27 17:16:41
|
I temporarily renamed my `chado` schema to `public`. Now I am getting a
different error:
$ stag-storenode.pl -d 'dbi:Pg:dbname=genestation;host=localhost;port=5432'
--user rokaschado ff.xml
DBD::Pg::st execute failed: ERROR: duplicate key value violates unique
constraint "cvterm_c1"
DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already exists.
[for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES (?, ?,
?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at
/home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322.
DBD::Pg::st execute failed: ERROR: duplicate key value violates unique
constraint "cvterm_c1"
DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already exists.
[for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES (?, ?,
?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at
/home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322.
I am guessing this is because I am loading the Fantom5 ontology, which
references terms from the UBERON ontology. I have already loaded the
UBERON ontology and am using it extensively. Is stag-storenode unable to
resolve this by not recreating duplicated terms?
On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote:
> Hi,
>
> When we installed chado we found a number of places
> where "public" was hardcoded.
>
> The places I identify now from a quick review of our notes are:
>
> initialize.sql
> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm
> ---------------------<snip>--------------------
> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400
> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400
> @@ -34,7 +34,8 @@
>
> =cut
>
> -sub default_db_schema { 'public'; }
> +#sub default_db_schema { 'public'; }
> +sub default_db_schema { 'chado'; }
>
> sub columns {
> my($proto, $dbh, $table) = @_;
> ---------------------<snip>--------------------
>
> I recall getting chado to install somewhere other than the public
> schema to be tedious.
>
> Regards,
>
> Karl <ko...@me...>
> Free Software: "You don't pay back, you pay forward."
> -- Robert A. Heinlein
>
>
> ------------------------------------------------------------------------------
> 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
>
|
|
From: Naama M. <naa...@gm...> - 2017-03-27 17:21:40
|
hi Mara, you could try to use the gmod_load_cvterms.pl <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> script It should handle updating an existing ontology -Naama -- On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > 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 > > > ------------------------------------------------------------------------------ > 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 > |
|
From: Mara K. <mar...@gm...> - 2017-04-12 17:30:56
|
Hi Naama, I am trying to use the gmod_load_cvterms.pl script, but I get the following error: $ perl gmod_load_cvterms.pl -H localhost -D genestation /raid/chado/ontology/ff-phase2-140729.obo Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi /home/kimmm/perl5/lib/perl5/5.10.1 /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at gmod_load_cvterms.pl line 155. BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. I have Bio::GMOD installed. Are there other dependencies that I am missing? On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> wrote: > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > 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 > > > ------------------------------------------------------------------------------ > 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 > > |
|
From: Naama M. <naa...@gm...> - 2017-04-12 17:46:20
|
hi Mara, where did you install Bio::GMOD ? If that directory is not in @INC then you need to add it to your $PERL5LIB -Naama On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > 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 > > > ------------------------------------------------------------------------------ > 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 > > |
|
From: Mara K. <mar...@gm...> - 2017-04-12 18:23:27
|
Ok, so I checked the location of my Bio::GMOD and I noticed that there is no subfolder `Config` which the script seems to be looking for: $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm *Util* Am I missing something? I have version 0.028 installed using cpanm. On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> wrote: > hi Mara, > > where did you install Bio::GMOD ? > If that directory is not in @INC then you need to add it to your $PERL5LIB > > -Naama > > > > On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > 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 > > > ------------------------------------------------------------------------------ > 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 > > |
|
From: Naama M. <naa...@gm...> - 2017-04-13 02:01:18
|
Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get from CPAN) https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD you should have the chado scripts in a chado/bin directory, and the Bio::GMOD modules in chado/lib/GMOD... then add the path for chado/lib to your $PERL5LIB -Naama On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: > Ok, so I checked the location of my Bio::GMOD and I noticed that there is > no subfolder `Config` which the script seems to be looking for: > > $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD > > *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm *Util* > > > Am I missing something? I have version 0.028 installed using cpanm. > > On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > where did you install Bio::GMOD ? > If that directory is not in @INC then you need to add it to your $PERL5LIB > > -Naama > > > > On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > 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 > > > ------------------------------------------------------------------------------ > 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 > > |
|
From: Mara K. <mar...@gm...> - 2017-04-17 20:45:15
|
Ok, so I think I have fixed the previous errors. Now I am getting this message: $ perl gmod_load_cvterms.pl -H localhost -D genestation /raid/chado/ontology/ff-phase2-140729.obo Need -s db.name argument! (e.g. GO , PO, etc. at gmod_load_cvterms.pl line 180. Is this asking for a command line argument? I'm not sure what the proper value should be because this ontology spans / includes terms from many existing ontologies. On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > > Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get from > CPAN) > https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD > > you should have the chado scripts in a chado/bin directory, and the > Bio::GMOD modules in chado/lib/GMOD... > then add the path for chado/lib to your $PERL5LIB > > > -Naama > > > > > > On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: > >> Ok, so I checked the location of my Bio::GMOD and I noticed that there is >> no subfolder `Config` which the script seems to be looking for: >> >> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >> >> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >> *Util* >> >> >> Am I missing something? I have version 0.028 installed using cpanm. >> >> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >> wrote: >> >> hi Mara, >> >> where did you install Bio::GMOD ? >> If that directory is not in @INC then you need to add it to your >> $PERL5LIB >> >> -Naama >> >> >> >> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >> >> Hi Naama, >> >> I am trying to use the gmod_load_cvterms.pl script, but I get the >> following error: >> >> $ perl gmod_load_cvterms.pl -H localhost -D genestation >> /raid/chado/ontology/ff-phase2-140729.obo >> >> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >> /home/kimmm/perl5/lib/perl5/5.10.1 >> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >> gmod_load_cvterms.pl line 155. >> >> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >> >> >> I have Bio::GMOD installed. Are there other dependencies that I am >> missing? >> >> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >> wrote: >> >> hi Mara, >> >> you could try to use the gmod_load_cvterms.pl >> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >> script >> It should handle updating an existing ontology >> >> >> -Naama >> >> >> -- >> >> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >> >> I temporarily renamed my `chado` schema to `public`. Now I am getting a >> different error: >> >> $ stag-storenode.pl -d >> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >> ff.xml >> >> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >> constraint "cvterm_c1" >> >> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >> >> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >> constraint "cvterm_c1" >> >> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >> >> >> I am guessing this is because I am loading the Fantom5 ontology, which >> references terms from the UBERON ontology. I have already loaded the >> UBERON ontology and am using it extensively. Is stag-storenode unable to >> resolve this by not recreating duplicated terms? >> >> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >> >> Hi, >> >> When we installed chado we found a number of places >> where "public" was hardcoded. >> >> The places I identify now from a quick review of our notes are: >> >> initialize.sql >> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >> ---------------------<snip>-------------------- >> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >> @@ -34,7 +34,8 @@ >> >> =cut >> >> -sub default_db_schema { 'public'; } >> +#sub default_db_schema { 'public'; } >> +sub default_db_schema { 'chado'; } >> >> sub columns { >> my($proto, $dbh, $table) = @_; >> ---------------------<snip>-------------------- >> >> I recall getting chado to install somewhere other than the public >> schema to be tedious. >> >> Regards, >> >> Karl <ko...@me...> >> Free Software: "You don't pay back, you pay forward." >> -- Robert A. Heinlein >> >> >> ------------------------------------------------------------------------------ >> 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 >> >> >> ------------------------------------------------------------------------------ >> 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 >> >> |
|
From: Mara K. <mar...@gm...> - 2017-04-17 21:01:08
|
This is further complicated by the fact that the ids use multiple db.names On Mon, Apr 17, 2017 at 3:44 PM Mara Kim <mar...@gm...> wrote: > Ok, so I think I have fixed the previous errors. Now I am getting this > message: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Need -s db.name argument! (e.g. GO , PO, etc. > > at gmod_load_cvterms.pl line 180. > > > Is this asking for a command line argument? I'm not sure what the proper > value should be because this ontology spans / includes terms from many > existing ontologies. > > On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > >> >> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >> from CPAN) >> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >> >> you should have the chado scripts in a chado/bin directory, and the >> Bio::GMOD modules in chado/lib/GMOD... >> then add the path for chado/lib to your $PERL5LIB >> >> >> -Naama >> >> >> >> >> >> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >> >>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>> is no subfolder `Config` which the script seems to be looking for: >>> >>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>> >>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>> *Util* >>> >>> >>> Am I missing something? I have version 0.028 installed using cpanm. >>> >>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> where did you install Bio::GMOD ? >>> If that directory is not in @INC then you need to add it to your >>> $PERL5LIB >>> >>> -Naama >>> >>> >>> >>> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >>> >>> Hi Naama, >>> >>> I am trying to use the gmod_load_cvterms.pl script, but I get the >>> following error: >>> >>> $ perl gmod_load_cvterms.pl -H localhost -D genestation >>> /raid/chado/ontology/ff-phase2-140729.obo >>> >>> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >>> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.1 >>> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >>> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >>> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >>> gmod_load_cvterms.pl line 155. >>> >>> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >>> >>> >>> I have Bio::GMOD installed. Are there other dependencies that I am >>> missing? >>> >>> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> you could try to use the gmod_load_cvterms.pl >>> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >>> script >>> It should handle updating an existing ontology >>> >>> >>> -Naama >>> >>> >>> -- >>> >>> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >>> >>> I temporarily renamed my `chado` schema to `public`. Now I am getting a >>> different error: >>> >>> $ stag-storenode.pl -d >>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >>> ff.xml >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> >>> I am guessing this is because I am loading the Fantom5 ontology, which >>> references terms from the UBERON ontology. I have already loaded the >>> UBERON ontology and am using it extensively. Is stag-storenode unable to >>> resolve this by not recreating duplicated terms? >>> >>> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >>> >>> Hi, >>> >>> When we installed chado we found a number of places >>> where "public" was hardcoded. >>> >>> The places I identify now from a quick review of our notes are: >>> >>> initialize.sql >>> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >>> ---------------------<snip>-------------------- >>> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >>> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >>> @@ -34,7 +34,8 @@ >>> >>> =cut >>> >>> -sub default_db_schema { 'public'; } >>> +#sub default_db_schema { 'public'; } >>> +sub default_db_schema { 'chado'; } >>> >>> sub columns { >>> my($proto, $dbh, $table) = @_; >>> ---------------------<snip>-------------------- >>> >>> I recall getting chado to install somewhere other than the public >>> schema to be tedious. >>> >>> Regards, >>> >>> Karl <ko...@me...> >>> Free Software: "You don't pay back, you pay forward." >>> -- Robert A. Heinlein >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >>> |
|
From: Naama M. <naa...@gm...> - 2017-04-18 00:15:51
|
hi Mara, yes, this is a command line arg. It requires a number of arguments, it's listed in the perldoc. This script loads one ontology at a time, so it expects all terms to have one prefix If you have more than one and also references to other ontologies, you might hit some more roadblocks Can you send me the obo for the ontology you are trying to load? I could see if I could make some changes to make this script compatible with it best, -Naama On Mon, Apr 17, 2017 at 4:45 PM Mara Kim <mar...@gm...> wrote: > Ok, so I think I have fixed the previous errors. Now I am getting this > message: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Need -s db.name argument! (e.g. GO , PO, etc. > > at gmod_load_cvterms.pl line 180. > > > Is this asking for a command line argument? I'm not sure what the proper > value should be because this ontology spans / includes terms from many > existing ontologies. > > On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > >> >> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >> from CPAN) >> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >> >> you should have the chado scripts in a chado/bin directory, and the >> Bio::GMOD modules in chado/lib/GMOD... >> then add the path for chado/lib to your $PERL5LIB >> >> >> -Naama >> >> >> >> >> >> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >> >>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>> is no subfolder `Config` which the script seems to be looking for: >>> >>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>> >>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>> *Util* >>> >>> >>> Am I missing something? I have version 0.028 installed using cpanm. >>> >>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> where did you install Bio::GMOD ? >>> If that directory is not in @INC then you need to add it to your >>> $PERL5LIB >>> >>> -Naama >>> >>> >>> >>> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >>> >>> Hi Naama, >>> >>> I am trying to use the gmod_load_cvterms.pl script, but I get the >>> following error: >>> >>> $ perl gmod_load_cvterms.pl -H localhost -D genestation >>> /raid/chado/ontology/ff-phase2-140729.obo >>> >>> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >>> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.1 >>> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >>> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >>> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >>> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >>> gmod_load_cvterms.pl line 155. >>> >>> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >>> >>> >>> I have Bio::GMOD installed. Are there other dependencies that I am >>> missing? >>> >>> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> hi Mara, >>> >>> you could try to use the gmod_load_cvterms.pl >>> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >>> script >>> It should handle updating an existing ontology >>> >>> >>> -Naama >>> >>> >>> -- >>> >>> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >>> >>> I temporarily renamed my `chado` schema to `public`. Now I am getting a >>> different error: >>> >>> $ stag-storenode.pl -d >>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >>> ff.xml >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> DBD::Pg::st execute failed: ERROR: duplicate key value violates unique >>> constraint "cvterm_c1" >>> >>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>> >>> >>> I am guessing this is because I am loading the Fantom5 ontology, which >>> references terms from the UBERON ontology. I have already loaded the >>> UBERON ontology and am using it extensively. Is stag-storenode unable to >>> resolve this by not recreating duplicated terms? >>> >>> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >>> >>> Hi, >>> >>> When we installed chado we found a number of places >>> where "public" was hardcoded. >>> >>> The places I identify now from a quick review of our notes are: >>> >>> initialize.sql >>> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >>> ---------------------<snip>-------------------- >>> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >>> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >>> @@ -34,7 +34,8 @@ >>> >>> =cut >>> >>> -sub default_db_schema { 'public'; } >>> +#sub default_db_schema { 'public'; } >>> +sub default_db_schema { 'chado'; } >>> >>> sub columns { >>> my($proto, $dbh, $table) = @_; >>> ---------------------<snip>-------------------- >>> >>> I recall getting chado to install somewhere other than the public >>> schema to be tedious. >>> >>> Regards, >>> >>> Karl <ko...@me...> >>> Free Software: "You don't pay back, you pay forward." >>> -- Robert A. Heinlein >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >>> >>> |
|
From: Mara K. <mar...@gm...> - 2017-04-19 00:17:40
|
Hi Naama, I am trying to load the FF ontology used to describe samples from the FANTOM5 project: http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology/ff-phase2-140729.obo.txt Thank you so much for all the help, Mara On Mon, Apr 17, 2017 at 7:15 PM Naama Menda <naa...@gm...> wrote: > hi Mara, > yes, this is a command line arg. It requires a number of arguments, it's > listed in the perldoc. > This script loads one ontology at a time, so it expects all terms to have > one prefix > If you have more than one and also references to other ontologies, you > might hit some more roadblocks > Can you send me the obo for the ontology you are trying to load? I could > see if I could make some changes to make this script compatible with it > > best, > -Naama > > > On Mon, Apr 17, 2017 at 4:45 PM Mara Kim <mar...@gm...> wrote: > >> Ok, so I think I have fixed the previous errors. Now I am getting this >> message: >> >> $ perl gmod_load_cvterms.pl -H localhost -D genestation >> /raid/chado/ontology/ff-phase2-140729.obo >> >> Need -s db.name argument! (e.g. GO , PO, etc. >> >> at gmod_load_cvterms.pl line 180. >> >> >> Is this asking for a command line argument? I'm not sure what the proper >> value should be because this ontology spans / includes terms from many >> existing ontologies. >> >> On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> >> wrote: >> >>> >>> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >>> from CPAN) >>> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >>> >>> you should have the chado scripts in a chado/bin directory, and the >>> Bio::GMOD modules in chado/lib/GMOD... >>> then add the path for chado/lib to your $PERL5LIB >>> >>> >>> -Naama >>> >>> >>> >>> >>> >>> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >>> >>>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>>> is no subfolder `Config` which the script seems to be looking for: >>>> >>>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>>> >>>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>>> *Util* >>>> >>>> >>>> Am I missing something? I have version 0.028 installed using cpanm. >>>> >>>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>>> wrote: >>>> >>>> hi Mara, >>>> >>>> where did you install Bio::GMOD ? >>>> If that directory is not in @INC then you need to add it to your >>>> $PERL5LIB >>>> >>>> -Naama >>>> >>>> >>>> >>>> On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: >>>> >>>> Hi Naama, >>>> >>>> I am trying to use the gmod_load_cvterms.pl script, but I get the >>>> following error: >>>> >>>> $ perl gmod_load_cvterms.pl -H localhost -D genestation >>>> /raid/chado/ontology/ff-phase2-140729.obo >>>> >>>> Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: >>>> /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi >>>> /home/kimmm/perl5/lib/perl5/5.10.1 >>>> /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi >>>> /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 >>>> /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl >>>> /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at >>>> gmod_load_cvterms.pl line 155. >>>> >>>> BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. >>>> >>>> >>>> I have Bio::GMOD installed. Are there other dependencies that I am >>>> missing? >>>> >>>> On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> >>>> wrote: >>>> >>>> hi Mara, >>>> >>>> you could try to use the gmod_load_cvterms.pl >>>> <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> >>>> script >>>> It should handle updating an existing ontology >>>> >>>> >>>> -Naama >>>> >>>> >>>> -- >>>> >>>> On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: >>>> >>>> I temporarily renamed my `chado` schema to `public`. Now I am getting >>>> a different error: >>>> >>>> $ stag-storenode.pl -d >>>> 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado >>>> ff.xml >>>> >>>> DBD::Pg::st execute failed: ERROR: duplicate key value violates >>>> unique constraint "cvterm_c1" >>>> >>>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>>> >>>> DBD::Pg::st execute failed: ERROR: duplicate key value violates >>>> unique constraint "cvterm_c1" >>>> >>>> DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already >>>> exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES >>>> (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at >>>> /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. >>>> >>>> >>>> I am guessing this is because I am loading the Fantom5 ontology, which >>>> references terms from the UBERON ontology. I have already loaded the >>>> UBERON ontology and am using it extensively. Is stag-storenode unable to >>>> resolve this by not recreating duplicated terms? >>>> >>>> On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: >>>> >>>> Hi, >>>> >>>> When we installed chado we found a number of places >>>> where "public" was hardcoded. >>>> >>>> The places I identify now from a quick review of our notes are: >>>> >>>> initialize.sql >>>> /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm >>>> ---------------------<snip>-------------------- >>>> --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 >>>> +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 >>>> @@ -34,7 +34,8 @@ >>>> >>>> =cut >>>> >>>> -sub default_db_schema { 'public'; } >>>> +#sub default_db_schema { 'public'; } >>>> +sub default_db_schema { 'chado'; } >>>> >>>> sub columns { >>>> my($proto, $dbh, $table) = @_; >>>> ---------------------<snip>-------------------- >>>> >>>> I recall getting chado to install somewhere other than the public >>>> schema to be tedious. >>>> >>>> Regards, >>>> >>>> Karl <ko...@me...> >>>> Free Software: "You don't pay back, you pay forward." >>>> -- Robert A. Heinlein >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> 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 >>>> >>>> |
Thanks for helping keep SourceForge clean.
X