diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index 8cec47afb5ab279fc0ee6904f67653d060c7b922..dc11a4b34851b5c34be33561539f9dd9d4147157 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -494,12 +494,16 @@ sub _seq_region_name_to_id {
$sth->bind_param(2,$cs_id,SQL_INTEGER);
$sth->execute();
- if(!$sth->rows() == 1) {
- throw("Ambiguous or non-existant seq_region [$sr_name] " .
- "in coord system $cs_id");
+ my @row = $sth->fetchrow_array();
+ unless ( @row ) {
+ throw("No-existent seq_region [$sr_name] in coord system $cs_id");
+ }
+ my @more = $sth->fetchrow_array();
+ if ( @more ) {
+ throw("Ambiguous seq_region [$sr_name] in coord system $cs_id");
}
- my ($sr_id, $sr_length) = $sth->fetchrow_array();
+ my ($sr_id, $sr_length) = @row;
$sth->finish();
$arr = [ $sr_id, $sr_name, $cs_id, $sr_length ];
@@ -532,11 +536,12 @@ sub _seq_region_id_to_name {
$sth->bind_param(1,$sr_id,SQL_INTEGER);
$sth->execute();
+ my @row = $sth->fetchrow_array();
if(!$sth->rows() == 1) {
throw("non-existant seq_region [$sr_id]");
}
- my ($sr_name, $sr_length, $cs_id) = $sth->fetchrow_array();
+ my ($sr_name, $sr_length, $cs_id) = @row;
$sth->finish();
$arr = [ $sr_id, $sr_name, $cs_id, $sr_length ];
@@ -615,6 +620,8 @@ sub register_component {
$sth->bind_param(2,$asm_cs_id,SQL_INTEGER);
$sth->execute();
+ my @rows = $sth->fetchrow_array();
+
if($sth->rows() == 0) {
#this component is not used in the assembled part i.e. gap
$asm_mapper->register_component($cmp_seq_region);
@@ -627,6 +634,7 @@ sub register_component {
# chromosome:EquCab2#contig ( use'#' for multiple mappings )
# chromosome:EquCab2|contig ( use '|' delimiter for 1-1 mappings )
#
+ my @more = $sth->fetchrow_array();
if($sth->rows() != 1) {
$sth->finish();
throw("Multiple assembled regions for single " .
@@ -636,7 +644,7 @@ sub register_component {
}
my ($asm_start, $asm_end, $asm_seq_region_id,
- $asm_seq_region, $asm_seq_region_length) = $sth->fetchrow_array();
+ $asm_seq_region, $asm_seq_region_length) = @rows;
my $arr = [ $asm_seq_region_id, $asm_seq_region,
$asm_cs_id, $asm_seq_region_length ];
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
index d615f2d7de073c54f07d108a06b72df818de1400..dfc0b0e041d70e95ca6d165d9f5bec196bc3ae87 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscSetAdaptor.pm
@@ -260,12 +260,12 @@ sub store {
$sth2->bind_param(1,$ms->code,SQL_VARCHAR);
$sth2->execute();
+ ($dbID) = $sth2->fetchrow_array();
+
if($sth2->rows() != 1) {
throw("Could not retrieve or store MiscSet, code=[".$ms->code."]\n".
"Wrong database user/permissions?");
}
-
- ($dbID) = $sth2->fetchrow_array();
} else {
$dbID = $sth->{'mysql_insertid'};
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
index 158c1b25a15fbffc27011e240540a7765fd2d25d..5e9269b1a3f699c2c3aff413b10368592131c7c9 100755
--- a/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ProteinFeatureAdaptor.pm
@@ -150,14 +150,15 @@ sub fetch_by_dbID {
$sth->bind_param(1, $protfeat_id, SQL_INTEGER);
my $res = $sth->execute();
+
+ my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart,
+ $hend, $hseqname, $idesc, $interpro_ac) = $sth->fetchrow_array();
- if ($sth->rows == 0) {
- $sth->finish();
- return undef;
+ if($sth->rows == 0) {
+ $sth->finish();
+ return undef;
}
- my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart, $hend, $hseqname, $idesc, $interpro_ac) = $sth->fetchrow_array();
-
$sth->finish();
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 327b0eb922f3b54c5b9adff7b0fcd98fe8d8ca23..ca4c883c1a24dabea20a975540d2c448250fe68e 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -299,10 +299,10 @@ sub fetch_by_region {
}
$sth->execute();
+ my @row = $sth->fetchrow_array();
+ $sth->finish();
- if ( $sth->rows() == 0 ) {
- $sth->finish();
-
+ unless ( @row ) {
# try synonyms
my $syn_sql_sth = $self->prepare("select s.name, cs.name, cs.version from seq_region s join seq_region_synonym ss using (seq_region_id) join coord_system cs using (coord_system_id) where ss.synonym = ? and cs.species_id =?");
@@ -407,9 +407,7 @@ sub fetch_by_region {
} else {
my ( $id, $cs_id );
- ( $seq_region_name, $id, $length, $cs_id ) =
- $sth->fetchrow_array();
- $sth->finish();
+ ( $seq_region_name, $id, $length, $cs_id ) = @row;
# cache to speed up for future queries
my $arr = [ $id, $seq_region_name, $cs_id, $length ];
@@ -832,7 +830,8 @@ sub fetch_by_seq_region_id {
$sth->bind_param( 1, $seq_region_id, SQL_INTEGER );
$sth->execute();
- if ( $sth->rows() == 0 ) {
+ my @row = $sth->fetchrow_array();
+ unless ( @row ) {
# This could have been an old seq region id so see if we can
# translate it into a more recent version.
if($check_prior_ids) {
@@ -845,7 +844,7 @@ sub fetch_by_seq_region_id {
return undef;
}
- ( $name, $cs_id, $length ) = $sth->fetchrow_array();
+ ( $name, $cs_id, $length ) = @row;
$sth->finish();
$cs = $self->db->get_CoordSystemAdaptor->fetch_by_dbID($cs_id);
@@ -914,14 +913,16 @@ sub get_seq_region_id {
$sth->bind_param(2,$cs_id,SQL_INTEGER);
$sth->execute();
- if($sth->rows() != 1) {
- throw("Non existant or ambigous seq_region:\n" .
- " coord_system=[$cs_id],\n" .
- " name=[$seq_region_name],\n");
-
+ my @row = $sth->fetchrow_array();
+ unless ( @row ) {
+ throw("No-existent seq_region [$seq_region_name] in coord system [$cs_id]");
+ }
+ my @more = $sth->fetchrow_array();
+ if ( @more ) {
+ throw("Ambiguous seq_region [$seq_region_name] in coord system [$cs_id]");
}
- my($seq_region_id, $length) = $sth->fetchrow_array();
+ my($seq_region_id, $length) = @row;
$sth->finish();
#cache information for future requests
@@ -2618,13 +2619,13 @@ sub fetch_by_clone_accession{
$sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
$sth->execute();
+ ($name) = $sth->fetchrow_array();
+
if(!$sth->rows()) {
$sth->finish();
throw("Clone $name not found in database");
}
- ($name) = $sth->fetchrow_array();
-
$sth->finish();
}