Taxonomy name endpoint created, basic tests for all taxonomy endpoints.

lib/EnsEMBL/REST/Controller/Taxonomy.pm

@@ -36,15 +36,18 @@ sub classification : Chained('taxonomy_root') PathPart('classification') Args(1)
   $self->status_ok($c, entity => $entity);
 }
 
-sub name_get {}
+sub name_GET {}
 sub name : Chained('taxonomy_root') PathPart('name') Args(1) ActionClass('REST') {
   my ($self, $c, $id) = @_;
   $id = uri_unescape($id);
+  $c->log->debug($id);
+  my $simple = $c->request->param('simple');
   my $taxons = $self->_name($c,$id);
   # remove any duplicates in the list
-  my %list = map { $_ => 1 } @$taxons;
-  @$taxons = keys %list;
-  $self->status_ok($c, entity => $self->_encode_array($taxons));  
+  my %list = map { $_->taxon_id => $_ } @$taxons;
+  @$taxons = map { $list{$_} } keys %list;
+  
+  $self->status_ok($c, entity => $self->_encode_array($taxons,$simple));  
 }
 
 sub taxon {

t/taxonomy.t

@@ -13,16 +13,70 @@ use Test::More;
 use Catalyst::Test ();
 use Bio::EnsEMBL::Test::MultiTestDB;
 
-my $dba = Bio::EnsEMBL::Test::MultiTestDB->new();
+my $dba = Bio::EnsEMBL::Test::MultiTestDB->new('multi');
 Catalyst::Test->import('EnsEMBL::REST');
 
 my $expected = qq(); 
-#is_json_GET("/lookup/id/$basic_id?expand=1;format=condensed", $expanded_response, 'Get of a known ID with expanded option will return transcripts as well');
-#is_json_GET("/taxonomy/classification/homo sapiens", $expected, 'Check taxonomy endpoint with valid data');
+$expected = {scientific_name => "Homo sapiens",
+  name => "Homo sapiens",
+  id => "9606",
+  tags => {"ensembl alias name" => ["Human"],"scientific name" => ["Homo sapiens"],"genbank common name" => ["human"],"common name" => ["man"],"name" => ["Homo sapiens"],"authority" => ["Homo sapiens Linnaeus, 1758"]},
+  leaf => 1
+};
+# Leaf => 1 is only true in test data.
 
-
-$expected = qq({"scientific_name":"Homo sapiens","name":"Homo sapiens","id":"9606","tags":{"ensembl alias name":["Human"],"scientific name":["Homo sapiens"],"genbank common name":["human"],"common name":["man"],"name":["Homo sapiens"],"authority":["Homo sapiens Linnaeus, 1758"]},"leaf":0});
 is_json_GET("/taxonomy/id/9606?content-type=application/json;simple=1", $expected, 'Check id endpoint with valid data');
-action_bad("/taxonomyid/11111111111111", 'ID should not be found. Fail');
+action_bad("/taxonomyid/-1", 'ID should not be found.');
+
+is_json_GET("/taxonomy/name/human?simple=1", [$expected], 'Test human lookup with name');
+my $result = json_GET("/taxonomy/name/canis%?simple=1",'Select wolf');
+is($result->[0]->{'id'},'9612','Wolf found by wildcarded Canis');
+is($result->[1]->{'id'},'9615','Beagle found by wildcarded Canis');
+is($result->[2]->{'id'},'9611','Canis node found by wildcarded Canis');
+$expected = [{ 
+  children => [
+    {
+      id => '33154',                        
+      leaf => 0,                            
+      name => 'Opisthokonta',               
+      scientific_name => 'Opisthokonta',    
+      tags => {                             
+        authority => ['Opisthokonta Cavalier-Smith 1987'],                                  
+        'ensembl alias name' => ['Animals and Fungi'],                                  
+        'ensembl timetree mya' => ['1500'],                                  
+        name => ['Opisthokonta'],                                  
+        'scientific name' => ['Opisthokonta'],                                  
+        synonym => ['Fungi/Metazoa group','opisthokonts']                                   
+      }                                     
+    }
+  ],
+  id => '2759',
+  leaf => 0,
+  name => 'Eukaryota',
+  parent => {
+    id => '131567' ,
+    leaf => 0 ,
+    name => 'cellular organisms' ,
+    scientific_name => 'cellular organisms' ,
+    tags => {
+      name => ['cellular organisms'],
+      'scientific name' => ['cellular organisms'],
+      synonym => ['biota'],
+    }
+  },
+  scientific_name => 'Eukaryota',
+  tags => {
+    'blast name' => ['eukaryotes'],                        
+    'common name' => ['eukaryotes'],                        
+    'genbank common name' => ['eucaryotes'],                        
+    name => ['Eukaryota'],                        
+    'scientific name' => ['Eukaryota'],                        
+    synonym => ['Eucarya','Eucaryotae','Eukarya','Eukaryotae']                         
+  },
+
+}];
+
+is_json_GET("/taxonomy/classification/2759?content-type=application/json", $expected, 'Test classification response for Eukaryotes');
+action_bad("/taxonomy/classification?A;content-type=application/json", 'Classification in bad data case');
 
 done_testing();
\ No newline at end of file