Preservation commit for taxonomy name endpoint

ensembl_rest.conf

@@ -111,6 +111,7 @@ msgpack=0 # control usage of Data::MessagePack as a serialisation option
     
     taxon=9606
     taxon_name=Homo sapiens
+    taxon_nameish=Homo%
     target_taxon=10090
     target_species=cow
     

lib/EnsEMBL/REST/Controller/Taxonomy.pm

@@ -5,6 +5,7 @@ use namespace::autoclean;
 use Try::Tiny;
 use Bio::EnsEMBL::Utils::Scalar qw/check_ref/;
 use Scalar::Util qw/looks_like_number/;
+use URI::Escape;
 require EnsEMBL::REST;
 EnsEMBL::REST->turn_on_config_serialisers(__PACKAGE__);
 
@@ -35,6 +36,17 @@ sub classification : Chained('taxonomy_root') PathPart('classification') Args(1)
   $self->status_ok($c, entity => $entity);
 }
 
+sub name_get {}
+sub name : Chained('taxonomy_root') PathPart('name') Args(1) ActionClass('REST') {
+  my ($self, $c, $id) = @_;
+  $id = uri_unescape($id);
+  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));  
+}
+
 sub taxon {
   my ($self, $c, $id) = @_;
   my $taxon;
@@ -48,6 +60,14 @@ sub taxon {
   return $taxon;
 }
 
+sub _name {
+  my ($self, $c, $name) = @_;
+  my @taxons;
+  @taxons = @{ $c->stash->{taxon_adaptor}->fetch_all_nodes_by_name($name) };
+  $c->go('ReturnError', 'custom', ["No taxons found with given name '$name'"]) if scalar(@taxons) == 0;
+  return \@taxons;
+}
+
 sub _encode_array {
   my ($self, $taxons, $ignore_relations) = @_;
   return [ map {$self->_encode($_, $ignore_relations)} @{$taxons}];

root/documentation/taxonomy.conf

@@ -66,5 +66,33 @@
       </two>
     </examples>
   </taxonomy_classification>
-
+  <taxonomy_name>
+    description=Search for a taxonomic id by a non-scientific name
+    endpoint="taxonomy/name/:name"
+    method=GET
+    group=Ontologies and Taxonomy
+    output=json
+    output=xml
+    output=yaml
+    <params>
+      <name>
+        type=String
+        description=The non-scientific name to search for. Can include SQL wildcards
+        example=__VAR(taxon_nameish)__
+        required=1
+      </name>
+    </params>
+    <examples>
+      <one>
+        path=/taxonomy/name/
+        capture=__VAR(taxon_nameish)__
+        content=application/json
+      </one>
+      <two>
+        path=/taxonomy/name/
+        capture=__VAR(species_common)__
+        content=application/json
+      </two>
+    </examples>
+  </taxonomy_name>
 </endpoints>
\ No newline at end of file

t/taxonomy.t

+use strict;
+use warnings;
+
+BEGIN {
+  use FindBin qw/$Bin/;
+  use lib "$Bin/lib";
+  use RestHelper;
+  $ENV{CATALYST_CONFIG} = "$Bin/../ensembl_rest_testing.conf";
+  $ENV{ENS_REST_LOG4PERL} = "$Bin/../log4perl_testing.conf";
+}
+
+use Test::More;
+use Catalyst::Test ();
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+my $dba = Bio::EnsEMBL::Test::MultiTestDB->new();
+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 = 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');
+
+done_testing();
\ No newline at end of file