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 > |