rows() doesn't work on SQLite for SELECT unless all rows actually fetched!

[Adaptors]

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 ];

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'};
     }

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);

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();
   }