[ENSCORESW-494]. IN statement is now generically handled rather than repeating...

[ENSCORESW-494]. IN statement is now generically handled rather than repeating the same logic over and over again

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -92,7 +92,7 @@ use vars qw(@ISA @EXPORT);
 use strict;
 
 use Bio::EnsEMBL::Utils::Exception qw(throw);
-use Bio::EnsEMBL::Utils::Scalar qw(assert_ref assert_integer);
+use Bio::EnsEMBL::Utils::Scalar qw(assert_ref assert_integer wrap_array);
 use DBI qw(:sql_types);
 use Data::Dumper;
 
@@ -383,7 +383,56 @@ sub _bind_param_generic_fetch {
   return $self->{_bind_param_generic_fetch};
 }
 
+=head2 generate_in_constraint
+  
+  Arg [1]     : ArrayRef or Scalar $list
+                List or a single value of items to be pushed into an IN statement
+  Arg [2]     : Scalar $column
+                Column this IN statement is being applied to. Please fully resolve the
+                column.
+  Arg [3]     : Scalar $param_type
+                Data type which should be used when binding. Please use DBI data type symbols
+  Arg [4]     : Scalar boolean $inline_variables
+                Boolean to control if variables are inlined in the constraint. If
+                false values are bound via bind_param_generic_fetch() (the default behaviour).
+
+  Description : Used internally to generate a SQL constraint to restrict a query by an IN statement.
+                The code generates the complete IN statement.
+  Returntype  : String
+  Exceptions  : If no list is supplied, the list of values is empty or no data type was given
+  Caller      : general
+
+=cut
 
+sub generate_in_constraint {
+  my ($self, $list, $column, $param_type, $inline_variables) = @_;
+  throw("A list of values must be given") if ! defined $list;
+  $list = wrap_array($list); # homogenise into an array
+  throw "We should be given at least one value to insert" if scalar(@{$list}) == 0;
+  throw "Please supply the DBI param type" if ! defined $param_type;
+  #Figure out if we need to quote our values if we are asked to inline the variables
+  my $quote_values = 1;
+  if($param_type == SQL_INTEGER || $param_type == SQL_TINYINT || $param_type == SQL_DOUBLE ) {
+    $quote_values = 0;
+  }
+
+  my $constraint = qq{${column} IN (};
+  if($inline_variables) {
+    if($quote_values) {
+      $constraint .= join(q{,}, map { qq{"${_}"} } @{$list});  
+    }
+    else {
+      $constraint .= join(q{,}, @{$list});  
+    }
+  }
+  else {
+    my @subs = ('?') x scalar(@{$list});
+    $constraint .= join(q{,}, @subs);
+    $self->bind_param_generic_fetch($_, $param_type) for @{$list};
+  }
+  $constraint .= q{)};
+  return $constraint;
+}
 
 =head2 generic_fetch
 

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -271,7 +271,7 @@ sub fetch_all_by_biotype {
 
 =head2 biotype_constraint 
 
-  Arg [1]    : String $biotype 
+  Arg [1]    : String $biotypes 
                listref of $biotypes
                The biotype of the gene to retrieve. You can have as an argument a reference
                to a list of biotypes
@@ -284,24 +284,10 @@ sub fetch_all_by_biotype {
 =cut
 
 sub biotype_constraint {
-  my ($self, $biotype) = @_;
-  if (!defined $biotype) {
-	throw("Biotype or listref of biotypes expected");
-  }
-  my $constraint;
-  if (ref($biotype) eq 'ARRAY') {
-	$constraint = "g.biotype IN (";
-	foreach my $b (@{$biotype}) {
-	  $constraint .= "?,";
-	  $self->bind_param_generic_fetch($b, SQL_VARCHAR);
-	}
-	chop($constraint);    #remove last , from expression
-	$constraint .= ") and g.is_current = 1";
-
-  } else {
-	$constraint = "g.biotype = ? and g.is_current = 1";
-	$self->bind_param_generic_fetch($biotype, SQL_VARCHAR);
-  }
+  my ($self, $biotypes, $inline_variables) = @_;
+  my $constraint = "g.is_current = 1";
+  my $in_statement = $self->generate_in_constraint($biotypes, 'g.biotype', SQL_VARCHAR, $inline_variables);
+  $constraint .= " and $in_statement";
   return $constraint;
 }
 
@@ -571,7 +557,8 @@ sub fetch_all_by_Slice {
 	$constraint .= " and g.source = '$source'";
   }
   if (defined($biotype)) {
-	$constraint .= " and g.biotype = '$biotype'";
+    my $inline_variables = 1;
+    $constraint .= " and ".$self->generate_in_constraint($biotype, 'g.biotype', SQL_VARCHAR, $inline_variables);
   }
 
   my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint, $logic_name);