stag-storenode.pl fails when attempting to load an ontology

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stag-storenode.pl fails when attempting to load an ontology

Mara Kim
Hi gmod-ers!

I am having issues when loading an ontology via the stag-storenode.pl perl script.  I created the chado xml using go2chado xml, but when I try to load it, I get the error below.

The PostgreSQL database is functioning, as well as ident authentication when connecting via psql.  I should also mention that I have been able to successfully load ontologies using this method just last month.


ERROR LOG (personal info redacted):

$ stag-storenode.pl -d 'dbi:Pg:dbname=mydb;host=localhost;port=5432' --user myuser --password mypass myontology.chado.xml

DBI connect('dbname=mydb;host=localhost;port=5432','myuser',...) failed: FATAL:  Ident authentication failed for user "myuser" at /opt/perl5/lib/site_perl/5.16.0/DBIx/DBStag.pm line 81.

Could not connect to database: "dbi:Pg:dbname=mydb;host=localhost;port=5432"

EITHER   The required DBD driver "Pg" is not installed
    OR   There is no such database as "dbi:Pg:dbname=mydb;host=localhost;port=5432"

Died at /opt/perl5/lib/site_perl/5.16.0/DBIx/DBStag.pm line 120.


END ERROR LOG


Thanks for the help,
Mara

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Re: stag-storenode.pl fails when attempting to load an ontology

Chris Mungall
Hi Mara

Sounds like a connection permission issue.

Can you connect like this?

psql -h localhost -p 5432 mydb

On Apr 3, 2013, at 3:20 PM, Mara Kim wrote:

Hi gmod-ers!

I am having issues when loading an ontology via the stag-storenode.pl perl script.  I created the chado xml using go2chado xml, but when I try to load it, I get the error below.

The PostgreSQL database is functioning, as well as ident authentication when connecting via psql.  I should also mention that I have been able to successfully load ontologies using this method just last month.


ERROR LOG (personal info redacted):

$ stag-storenode.pl -d 'dbi:Pg:dbname=mydb;host=localhost;port=5432' --user myuser --password mypass myontology.chado.xml

DBI connect('dbname=mydb;host=localhost;port=5432','myuser',...) failed: FATAL:  Ident authentication failed for user "myuser" at /opt/perl5/lib/site_perl/5.16.0/DBIx/DBStag.pm line 81.

Could not connect to database: "dbi:Pg:dbname=mydb;host=localhost;port=5432"

EITHER   The required DBD driver "Pg" is not installed
    OR   There is no such database as "dbi:Pg:dbname=mydb;host=localhost;port=5432"

Died at /opt/perl5/lib/site_perl/5.16.0/DBIx/DBStag.pm line 120.


END ERROR LOG


Thanks for the help,
Mara
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html_______________________________________________
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------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Gmod-schema mailing list
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