diff --git a/misc-scripts/xref_mapping/BaseParser.pm b/misc-scripts/xref_mapping/BaseParser.pm index 64fc69f79a7c40611032c78930e48ae7b1769f11..941286c8d9c3148561d41d7a349211393f83fe4c 100644 --- a/misc-scripts/xref_mapping/BaseParser.pm +++ b/misc-scripts/xref_mapping/BaseParser.pm @@ -119,8 +119,8 @@ sub get_source_id_for_filename { my ($self, $file) = @_; my $sql = "SELECT source_id FROM source WHERE url LIKE '%/" . $file . "'"; - print $sql . "\n"; - my $sth = $dbi->prepare($sql); + #print $sql . "\n"; + my $sth = dbi()->prepare($sql); $sth->execute(); my @row = $sth->fetchrow_array(); my $source_id; @@ -151,7 +151,7 @@ sub upload_xrefs { $del_sth->execute(); # upload new ones - my $xref_sth = $dbi->prepare("INSERT INTO xref (accession,label,source_id,species_id) VALUES(?,?,?,?)"); + my $xref_sth = $dbi->prepare("INSERT INTO xref (accession,label,description,source_id,species_id) VALUES(?,?,?,?,?)"); my $pri_sth = $dbi->prepare("INSERT INTO primary_xref VALUES(?,?,?,?,?)"); my $syn_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?,?)"); my $dep_sth = $dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)"); @@ -161,6 +161,7 @@ sub upload_xrefs { # Create entry in xref table and note ID $xref_sth->execute($xref->{ACCESSION}, $xref->{LABEL}, + $xref->{DESCRIPTION}, $xref->{SOURCE_ID}, $xref->{SPECIES_ID}) || die $dbi->errstr;