[ENSCORESW-720] and [ENSCORESW-721]. Allowing default HashRef in execute() and...

[ENSCORESW-720] and [ENSCORESW-721]. Allowing default HashRef in execute() and sleep for less than a second.

First issue raised by Lee from EG. He wanted to be able to work with hash refs
in the same way you can do with ArrayRefs. Done and dusted.

Second issue raised by me. Want to sleep for periods less than 1 second for the test
suite sanity.

modules/Bio/EnsEMBL/Utils/SqlHelper.pm

@@ -84,6 +84,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw);
 use Bio::EnsEMBL::Utils::Iterator;
 use English qw( -no_match_vars ); #Used for $PROCESS_ID
 use Scalar::Util qw(weaken); #Used to not hold a strong ref to DBConnection
+use Time::HiRes;
 
 =pod
 
@@ -264,8 +265,12 @@ sub execute {
 	
 	#If no callback then we execute using a default one which returns a 2D array
 	if(!defined $callback) {
-    throw('Cannot use fetchrow_hashref() with default mappers. Turn off this option') if $use_hashrefs;
-    $callback = $self->_mappers()->{array_ref};
+    if($use_hashrefs) {
+      $callback = $self->_mappers()->{hash_ref};
+    }
+    else {
+      $callback = $self->_mappers()->{array_ref};
+    }    
 	}
 	
 	return $self->_execute( $sql, $callback, $has_return, $use_hashrefs, $params, $prepare_params, $iterator );
@@ -523,7 +528,8 @@ sub execute_single_result {
   Arg [RETRY]         : integer the number of retries to attempt with this 
                         transactional block. Defaults to 0. 
   Arg [PAUSE]         : integer the time in seconds to pause in-between retries.
-                        Defaults to 1.
+                        Defaults to 1. Fractions are allowed as use delegate to
+                        Time::HiRes' sleep function
   Arg [CONDITION]     : CodeRef allows you to inspect the exception raised
                         and should your callback return true then the 
                         retry will be attempted. If not given then all 
@@ -658,7 +664,7 @@ sub transaction {
       if($iteration != $retry) {
         if($condition->($error)) {
           warn("Encountered error on attempt ${iteration} of ${retry} and have issued a rollback. Will retry after sleeping for $pause second(s): $error");
-          sleep $pause;
+          Time::HiRes::sleep $pause;
         }
         else {
           last; #break early if condition of error was not matched
@@ -888,7 +894,11 @@ my $default_mappers = {
   },
   array_ref => sub {
     my $row = shift @_;
-   return [@{$row}];
+    return [@{$row}]; #copy of array done because DBI's array is read only
+  },
+  hash_ref => sub {
+    my $row = shift @_;
+    return {%{$row}}; #applying same logic as above
   }
 }; 
 

modules/t/sqlHelper.t

@@ -226,7 +226,7 @@ my $get_value = sub {
   # First try retries until the very last attempt
   {
     my $counter = 0;
-    $helper->transaction( -RETRY => 3, -SLEEP => 1, -CALLBACK => sub {
+    $helper->transaction( -RETRY => 3, -PAUSE => 0.1, -CALLBACK => sub {
       #Die for the first 3 times (so we will succeed on the final attempt)
       $counter++;
       if($counter != 4) {
@@ -243,7 +243,7 @@ my $get_value = sub {
   {
     my $counter = 0;
     throws_ok {
-      $helper->transaction( -RETRY => 2, -CALLBACK => sub {
+      $helper->transaction( -RETRY => 2, -PAUSE => 0.1, -CALLBACK => sub {
         $counter++;
         die 'Throwing an error 2';
       })
@@ -257,7 +257,7 @@ my $get_value = sub {
   {
     my $counter = 0;
     throws_ok {
-      $helper->transaction( -RETRY => 1, -CALLBACK => sub {
+      $helper->transaction( -RETRY => 1, -PAUSE => 0.1, -CALLBACK => sub {
         $helper->transaction( -RETRY => 10, -CALLBACK => sub {
           $counter++;
           die 'Throwing an error 3';
@@ -273,7 +273,8 @@ my $get_value = sub {
     my $counter = 0;
     throws_ok {
       $helper->transaction( 
-        -RETRY => 4, 
+        -RETRY => 4,
+        -PAUSE => 0.1,
         -CALLBACK => sub {
           $counter++;
           die 'fake deadlock' if $counter <= 2;
@@ -313,7 +314,7 @@ my $get_value = sub {
   #Sixth says you cannot repeat the transaction if it worked
   {
     my $counter = 0;
-    $helper->transaction( -RETRY => 5, -CALLBACK => sub {
+    $helper->transaction( -RETRY => 5, -PAUSE => 0.1, -CALLBACK => sub {
       $helper->execute_single_result('select 1');
       $counter++;
     });
@@ -330,17 +331,27 @@ my $get_value = sub {
 #Doing hashref checks
 {
   my $sql = 'select meta_key, meta_value from meta where meta_key =?';
-  my $callback = sub {
-    my ($row) = @_;
-    return { name => $row->{meta_value} };
-  };
-  my $array_of_hashes = $helper->execute(
-    -SQL => $sql,
-    -CALLBACK => $callback,
-    -USE_HASHREFS => 1,
-    -PARAMS => ['species.common_name']
-  );
-  is_deeply($array_of_hashes, [ { name => 'Human' } ], 'HashRefs in a callback works');
+  my $params = ['species.common_name'];
+  {
+    my $array_of_hashes = $helper->execute(
+      -SQL => $sql,
+      -CALLBACK => sub {
+        my ($row) = @_;
+        return { name => $row->{meta_value} };
+      },
+      -USE_HASHREFS => 1,
+      -PARAMS => $params
+    );
+    is_deeply($array_of_hashes, [ { name => 'Human' } ], 'HashRefs in a callback works');
+  }
+  {
+    my $array_of_hashes = $helper->execute(
+      -SQL => $sql,
+      -USE_HASHREFS => 1,
+      -PARAMS => $params
+    );
+    is_deeply($array_of_hashes, [ { meta_key => $params->[0], meta_value => 'Human' } ], 'HashRefs using a default callback works'); 
+  }
 }
 
 $dba->dbc()->do('alter table meta engine=MyISAM');