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Commit bda133ff authored by Glenn Proctor's avatar Glenn Proctor
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Update gene description in update() method

parent b12572af
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......@@ -749,7 +749,7 @@ sub store {
if(!ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
throw("Must store a gene object, not a $gene");
}
print "in gene store\n";
my $db = $self->db();
if($gene->is_stored($db)) {
......@@ -876,16 +876,20 @@ sub store {
}
# update gene to point to display xref if it is set
print $gene->display_xref . "\n";
if(my $display_xref = $gene->display_xref) {
my $dxref_id;
print "here 1\n";
if($display_xref->is_stored($db)) {
$dxref_id = $display_xref->dbID();
print "stored\n";
} else {
$dxref_id = $dbEntryAdaptor->exists($display_xref);
print "exists\n";
}
print "dxref_id $dxref_id\n";
if(defined($dxref_id)) {
print "here\n";
$sth = $self->prepare
("UPDATE gene SET display_xref_id = ? WHERE gene_id = ?");
$sth->execute($dxref_id, $gene_dbID);
......@@ -1064,7 +1068,8 @@ sub update {
SET biotype = ?,
analysis_id = ?,
display_xref_id = ?,
status = ?
status = ?,
description = ?
WHERE gene_id = ?";
my $display_xref = $gene->display_xref();
......@@ -1081,10 +1086,11 @@ sub update {
$gene->analysis->dbID(),
$display_xref_id,
$gene->status(),
$gene->description(),
$gene->dbID()
);
# maybe should update stable id or gene description ???
# maybe should update stable id ???
}
......
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