Feature/biotype sql

Created by: magaliruffier

Requirements

• Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • the PR must not fail unit testing
  • if you're adding/updating documentation of an endpoint, make sure you add/update the necessary parameters to the (template) configuration files in the ensembl-rest_private repo

Description

Raw SQL queries have been replaced with API methods. Changes to core API will need to be integrated prior to this PR.

Benefits

The REST endpoint behaviour is protected from underlying schema changes as long as the methods return consistent outputs.

Possible Drawbacks

Some of the tests are still sensitive to order of results.

Testing

Have you added/modified unit tests to test the changes?

Behaviour of the endpoints was already tested, as only the method of fetching the data has changed. However, some order-dependent tests had to be updated.

If so, do the tests pass/fail?

Yes

Have you run the entire test suite and no regression was detected?

Yes.

Changelog

The output of the various endpoints remains unchanged

lib/EnsEMBL/REST/Model/Biotype.pm

@@ -64,12 +64,12 @@ Retrieves list of biotype groups
 sub fetch_biotype_groups {
   my ($self) = @_;
 
-  my $dbc = $self->context->model('Registry')->get_adaptor( 'Homo_sapiens', 'Core', 'Biotype' )->db->dbc();
-
-  my $sql = "SELECT DISTINCT biotype_group FROM biotype WHERE biotype_group IS NOT NULL ORDER BY biotype_group";
-  my $biotypes = $dbc->sql_helper->execute_simple(-SQL => $sql);
+  my $biotype_adaptor = $self->context->model('Registry')->get_adaptor( 'Homo_sapiens', 'Core', 'Biotype' );
+  my $biotypes = $biotype_adaptor->fetch_all();
+  my %groups = grep { $_ =~ /[a-zA-Z]/ } map {$_->biotype_group, 1} @$biotypes;
+  my @keys = sort keys %groups;
 
-  return $biotypes;
+  return \@keys;
 }
 
 =head fetch_biotypes_by_group
@@ -81,26 +81,9 @@ Retrieves list of biotypes part of a provided biotype group
 sub fetch_biotypes_by_group {
   my ($self, $group, $object_type) = @_;
 
-  my $dbc = $self->context->model('Registry')->get_adaptor( 'Homo_sapiens', 'Core', 'Biotype' )->db->dbc();
-
-  my $ot_filter = '';
-  if ( $object_type ) { $ot_filter = "AND object_type = \"$object_type\"" }
-  my $sql = "SELECT name, biotype_group, object_type, so_acc FROM biotype WHERE biotype_group = \"$group\" AND db_type LIKE '%core%' $ot_filter ORDER BY object_type, name";
-
-  my @biotypes;
-
-  $dbc->sql_helper->execute_no_return(-SQL => $sql, -CALLBACK => sub {
-    my ($row) = @_;
-
-    my $biotype = {
-      'name'          => $row->[0],
-      'biotype_group' => $row->[1],
-      'object_type'   => $row->[2],
-      'so_acc'        => $row->[3]
-    };
-
-    push @biotypes, $biotype;
-  });
+  my $biotype_adaptor = $self->context->model('Registry')->get_adaptor( 'Homo_sapiens', 'Core', 'Biotype' );
+  my $biotypes = $biotype_adaptor->fetch_all_by_group_object_db_type($group, $object_type);
+  my @biotypes = map {$self->to_hash($_)} @$biotypes;
 
   return \@biotypes;
 }
@@ -114,28 +97,24 @@ Retrieves biotypes with the provided name
 sub fetch_biotypes_by_name {
   my ($self, $name, $object_type) = @_;
 
-  my $dbc = $self->context->model('Registry')->get_adaptor( 'Homo_sapiens', 'Core', 'Biotype' )->db->dbc();
-
-  my $ot_filter = '';
-  if ( $object_type ) { $ot_filter = "AND object_type = \"$object_type\"" }
-  my $sql = "SELECT name, biotype_group, object_type, so_acc FROM biotype WHERE name = \"$name\" AND db_type LIKE '%core%' $ot_filter ORDER BY object_type, name";
-
-  my @biotypes;
+  my $biotype_adaptor = $self->context->model('Registry')->get_adaptor( 'Homo_sapiens', 'Core', 'Biotype' );
+  my $biotypes = $biotype_adaptor->fetch_all_by_name($name, $object_type);
+  my @biotypes = map {$self->to_hash($_)} @$biotypes;
 
-  $dbc->sql_helper->execute_no_return(-SQL => $sql, -CALLBACK => sub {
-    my ($row) = @_;
+  return \@biotypes;
+}
 
-    my $biotype = {
-      'name'          => $row->[0],
-      'biotype_group' => $row->[1],
-      'object_type'   => $row->[2],
-      'so_acc'        => $row->[3]
-    };
+sub to_hash {
+  my ($self, $biotype) = @_;
+  my $c = $self->context();
+  my $biotype_hash;
 
-    push @biotypes, $biotype;
-  });
+  $biotype_hash->{name} = $biotype->name;
+  $biotype_hash->{biotype_group} = $biotype->biotype_group;
+  $biotype_hash->{object_type} = $biotype->object_type;
+  $biotype_hash->{so_acc} = $biotype->so_acc;
 
-  return \@biotypes;
+  return $biotype_hash;
 }
 
 1;