[Gmod-schema-cmts] schema/chado/lib/Bio/GMOD/DB Adapter.pm, 1.44, 1.45

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/lib/Bio/GMOD/DB
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv30487/lib/Bio/GMOD/DB

Modified Files:
	Adapter.pm 
Log Message:
making gff3 bulk loader accept dbxref as a valid tag (should be Dbxref, but the other is in common usage);
also updating schema


Index: Adapter.pm
===================================================================
RCS file: /cvsroot/gmod/schema/chado/lib/Bio/GMOD/DB/Adapter.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** Adapter.pm	18 Mar 2007 17:14:08 -0000	1.44
--- Adapter.pm	23 Mar 2007 15:18:00 -0000	1.45
***************
*** 2278,2282 ****
        unless ($self->cache('type','synonym')) {
          my $sth
!           = $self->dbh->prepare("SELECT cvterm_id FROM cvterm WHERE name='synonym'");
          $sth->execute;
          my ($syn_type) = $sth->fetchrow_array;
--- 2278,2287 ----
        unless ($self->cache('type','synonym')) {
          my $sth
!           = $self->dbh->prepare("SELECT cvterm_id FROM cvterm WHERE 
!               (name='synonym' and cv_id in 
!                  (SELECT cv_id FROM cv WHERE name='null' OR name='local')) OR
!               (name='exact' and cv_id in 
!                  (SELECT cv_id FROM cv WHERE name='synonym_type') )
!               ORDER BY name");
          $sth->execute;
          my ($syn_type) = $sth->fetchrow_array;
***************
*** 2618,2621 ****
--- 2623,2627 ----
  
      my @dbxrefs = $feature->annotation->get_Annotations('Dbxref');
+     push @dbxrefs, $feature->annotation->get_Annotations('dbxref');
      my ($dbxref_id,$primary_dbxref_id,$primary_pattern);
      if (defined $self->dbxref and $self->dbxref ne '1') {
***************
*** 2860,2864 ****
                              AND cv_id in
                                (SELECT cv_id FROM cv WHERE name='null' OR
!                                                           name='local')");
            $sth->execute();
            my ($note_type) = $sth->fetchrow_array;
--- 2866,2871 ----
                              AND cv_id in
                                (SELECT cv_id FROM cv WHERE name='null' OR
!                                                     name='local' OR
!                                                     name='feature_property')");
            $sth->execute();
            my ($note_type) = $sth->fetchrow_array;
***************
*** 2891,2895 ****
                              AND cv_id in
                                (SELECT cv_id FROM cv WHERE name='null' OR
!                                                           name='local')");
            $sth->execute();
            my ($gap_type) = $sth->fetchrow_array; 
--- 2898,2903 ----
                              AND cv_id in
                                (SELECT cv_id FROM cv WHERE name='null' OR
!                                                     name='local' OR
!                                                     name='feature_property')");
            $sth->execute();
            my ($gap_type) = $sth->fetchrow_array; 
***************
*** 2990,2994 ****
      }
  
!     return;
  }
  
--- 2998,3002 ----
      }
  
!     return 1;
  }