stag-storenode.pl error

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stag-storenode.pl error

Mara Kim-2
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?


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Re: stag-storenode.pl error

Scott Cain
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 <[hidden email]> 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?


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: stag-storenode.pl error

Mara Kim-2
`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 <[hidden email]> 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 <[hidden email]> 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?


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="gmail_msg" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: stag-storenode.pl error

Scott Cain
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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?


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: stag-storenode.pl error

Chris Mungall

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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?


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="m_-7298875270219790245gmail_msg" target="_blank">216-392-3087
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

------------------------------------------------------------------------------
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Re: stag-storenode.pl error

Scott Cain
Probably.  I'd love to if I had a drop in replacement :-)

On Thu, Mar 23, 2017 at 7:23 PM, Chris Mungall <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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?


------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="m_-7770184498370524991m_-7298875270219790245gmail_msg" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">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_______________________________________________
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: stag-storenode.pl error

Mara Kim-3
I am unfamiliar with DBSchema.  How would I go about testing that?

On Thu, Mar 23, 2017 at 7:41 PM Scott Cain <[hidden email]> wrote:
Probably.  I'd love to if I had a drop in replacement :-)

On Thu, Mar 23, 2017 at 7:23 PM, Chris Mungall <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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?


------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="m_-6169400061178834432m_-7770184498370524991m_-7298875270219790245gmail_msg gmail_msg" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" class="gmail_msg" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Re: stag-storenode.pl error

Chris Mungall
In reply to this post by Scott Cain

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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?


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:(216)%20392-3087" value="+12163923087" target="_blank">216-392-3087
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Re: stag-storenode.pl error

Karl O. Pinc
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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: stag-storenode.pl error

Mara Kim-3
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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: stag-storenode.pl error

Naama Menda-2
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: stag-storenode.pl error

Mara Kim-3
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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: stag-storenode.pl error

Naama Menda-2
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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: stag-storenode.pl error

Mara Kim-3
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

------------------------------------------------------------------------------
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Re: stag-storenode.pl error

Naama Menda-2

Config.pm is in the GMOD git repo  (and not in Bio::GMOD that you get from CPAN) 

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
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
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Re: stag-storenode.pl error

Mara Kim-3
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 <[hidden email]> wrote:

Config.pm is in the GMOD git repo  (and not in Bio::GMOD that you get from CPAN) 

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
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
_______________________________________________
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Re: stag-storenode.pl error

Mara Kim-3
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 <[hidden email]> 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 <[hidden email]> wrote:

Config.pm is in the GMOD git repo  (and not in Bio::GMOD that you get from CPAN) 

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
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
_______________________________________________
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Re: stag-storenode.pl error

Naama Menda-2
In reply to this post by Mara Kim-3
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 <[hidden email]> 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 <[hidden email]> wrote:

Config.pm is in the GMOD git repo  (and not in Bio::GMOD that you get from CPAN) 

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: stag-storenode.pl error

Mara Kim-3
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:

Config.pm is in the GMOD git repo  (and not in Bio::GMOD that you get from CPAN) 

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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> wrote:
hi Mara, 

you could try to use the gmod_load_cvterms.pl script 
It should handle updating an existing ontology 


-Naama


--

On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <[hidden email]> 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 <[hidden email]> 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 <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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