Commit 689ab11f authored by Ian Longden's avatar Ian Longden
Browse files

remove deprecated calls

parent b830f3fd
...@@ -529,7 +529,7 @@ sub remove_from_MiscFeature { ...@@ -529,7 +529,7 @@ sub remove_from_MiscFeature {
throw("MiscFeature is not stored in this database."); throw("MiscFeature is not stored in this database.");
} }
my $sth = $db->prepare("DELETE FROM misc_attrib " . my $sth = $db->db->prepare("DELETE FROM misc_attrib " .
"WHERE misc_feature_id = ?"); "WHERE misc_feature_id = ?");
$sth->execute($mf->dbID()); $sth->execute($mf->dbID());
......
...@@ -802,7 +802,7 @@ sub store { ...@@ -802,7 +802,7 @@ sub store {
# store the coordinate system in the database # store the coordinate system in the database
# #
my $sth = $db->prepare('INSERT INTO coord_system ' . my $sth = $db->db->prepare('INSERT INTO coord_system ' .
'SET name = ?, ' . 'SET name = ?, ' .
'version = ?, ' . 'version = ?, ' .
'attrib = ?,' . 'attrib = ?,' .
......
...@@ -191,7 +191,7 @@ sub store { ...@@ -191,7 +191,7 @@ sub store {
my $seq_region_id; my $seq_region_id;
($pexon, $seq_region_id) = $self->_pre_store($pexon); ($pexon, $seq_region_id) = $self->_pre_store($pexon);
my $sth = $db->prepare my $sth = $db->db->prepare
("INSERT into prediction_exon (prediction_transcript_id, exon_rank, " . ("INSERT into prediction_exon (prediction_transcript_id, exon_rank, " .
"seq_region_id, seq_region_start, seq_region_end, " . "seq_region_id, seq_region_start, seq_region_end, " .
"seq_region_strand, start_phase, score, p_value) " . "seq_region_strand, start_phase, score, p_value) " .
......
...@@ -1224,7 +1224,7 @@ sub store { ...@@ -1224,7 +1224,7 @@ sub store {
#store the seq_region #store the seq_region
my $sth = $db->prepare("INSERT INTO seq_region " . my $sth = $db->db->prepare("INSERT INTO seq_region " .
"SET name = ?, " . "SET name = ?, " .
" length = ?, " . " length = ?, " .
" coord_system_id = ?" ); " coord_system_id = ?" );
......
...@@ -17,7 +17,7 @@ my $dba = $ens_test->get_DBAdaptor("core"); ...@@ -17,7 +17,7 @@ my $dba = $ens_test->get_DBAdaptor("core");
ok($dba); ok($dba);
my $sth = $dba->prepare("select * from gene"); my $sth = $dba->db->prepare("select * from gene");
$sth->execute; $sth->execute;
ok(scalar($sth->rows) == 19); ok(scalar($sth->rows) == 19);
...@@ -42,10 +42,10 @@ ok(scalar($sth->rows) == 19); ...@@ -42,10 +42,10 @@ ok(scalar($sth->rows) == 19);
# delete 9 genes from the db # delete 9 genes from the db
$sth = $dba->prepare("delete from gene where gene_id >= 18266"); $sth = $dba->db->prepare("delete from gene where gene_id >= 18266");
$sth->execute; $sth->execute;
$sth = $dba->prepare("select * from gene"); $sth = $dba->db->prepare("select * from gene");
$sth->execute; $sth->execute;
ok(scalar($sth->rows) == 10); ok(scalar($sth->rows) == 10);
......
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