Merge pull request #209 from teharrison/develop

new api resource m5nr, currently returns static data structures
MG-RAST · Dec 19, 2012 · 12df0ea · 12df0ea
2 parents c2b5652 + e194215
commit 12df0ea
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diff --git a/src/MGRAST/lib/resources2/m5nr.pm b/src/MGRAST/lib/resources2/m5nr.pm
@@ -0,0 +1,121 @@
+package resources2::m5nr;
+
+use strict;
+use warnings;
+no warnings('once');
+
+use MGRAST::Analysis;
+use Conf;
+use parent qw(resources2::resource);
+
+# Override parent constructor
+sub new {
+    my ($class, @args) = @_;
+
+    # Call the constructor of the parent class
+    my $self = $class->SUPER::new(@args);
+
+    # Add name / attributes
+    $self->{name} = "m5nr";
+    $self->{attributes} = { 'hierarchy' => { 'NCBI'       => [ 'hash', '7 level NCBI taxonomy' ],
+                                             'COG'        => [ 'hash', '3 level COG ontology' ],
+                                             'NOG'        => [ 'hash', '3 level NOG ontology' ],
+                                             'KO'         => [ 'hash', '4 level KEGG-KO ontology' ],
+                                             'Subsystems' => [ 'hash', '4 level SEED-Subsystems ontology' ] },
+                            'sources'   => [ 'hash', [['key',   ['string', 'source name']],
+                                                      ['value', ['object', [ { 'name'        => ['string', 'source name'],
+                                                                               'description' => ['string', 'description of source'],
+                                                                               'type'        => ['string', 'type of source'],
+                                                                               'link'        => ['string', 'link for source id'] },
+                                                                             'information about source' ]]]
+                                           ]]
+                          };
+    return $self;
+}
+
+
+# resource is called without any parameters
+# this method must return a description of the resource
+sub info {
+    my ($self) = @_;
+    my $content = { 'name'          => $self->name,
+                    'url'           => $self->cgi->url."/".$self->name,
+                    'description'   => "M5NR provides data through a comprehensive non-redundant protein / rRNA database",
+                    'type'          => 'object',
+                    'documentation' => '',
+                    'requests'      => [ { 'name'        => "info",
+            				               'request'     => $self->cgi->url."/".$self->name,
+            				               'description' => "Returns description of parameters and attributes.",
+            				               'method'      => "GET",
+            				               'type'        => "synchronous",  
+            				               'attributes'  => "self",
+            				               'parameters'  => { 'options'  => {},
+            							                      'required' => {},
+            							                      'body'     => {} }
+            							 },
+                                         { 'name'        => "hierarchy",
+                                           'request'     => $self->cgi->url."/".$self->name."/hierarchy",
+                                           'description' => "",
+                                           'method'      => "GET",
+                                           'type'        => "synchronous",  
+                                           'attributes'  => $self->attributes->{hierarchy},
+                                           'parameters'  => { 'options'  => { 'source' => ['cv', ['NCBI',       'returns 7 level NCBI taxonomy'],
+                                                                                                 ['COG',        'returns 3 level COG ontology'],
+                                                                                                 ['NOG',        'returns 3 level NOG ontology'],
+                                                                                                 ['KO',         'returns 4 level KEGG-KO ontology' ],
+                                                                                                 ['Subsystems', 'returns 4 level SEED-Subsystems ontology' ]]
+                                                                             },
+                                                              'required' => {},
+                                                              'body'     => {} }
+                                         },
+                                         { 'name'        => "sources",
+                                           'request'     => $self->cgi->url."/".$self->name."/sources",
+                                           'description' => "",
+                                           'method'      => "GET",
+                                           'type'        => "synchronous",  
+                                           'attributes'  => $self->attributes->{sources},
+                                           'parameters'  => { 'options'  => {},
+                                                              'required' => {},
+                                                              'body'     => {} }
+                                         } ]
+                };
+    $self->return_data($content);
+}
+
+# Override parent request function
+sub request {
+    my ($self) = @_;
+    # determine sub-module to use
+    if (scalar(@{$self->rest}) == 0) {
+        $self->info();
+    } elsif (($self->rest->[0] eq 'hierarchy') || ($self->rest->[0] eq 'sources')) {
+        $self->static($self->rest->[0]);
+    } else {
+        $self->info();
+    }
+}
+
+# return static data: hierarchy or source
+sub static {
+    my ($self, $type) = @_;
+
+    # get database
+    my $master = $self->connect_to_datasource();
+    my $mgdb   = MGRAST::Analysis->new( $master->db_handle );
+    unless (ref($mgdb)) {
+        $self->return_data({"ERROR" => "could not connect to analysis database"}, 500);
+    }
+
+    my $data = {};
+    if ($type eq 'hierarchy') {
+        my $source = $self->cgi->param('source') || 'NCBI';
+        $data = ($source eq 'NCBI') ? $mgdb->get_hierarchy('organism') : $mgdb->get_hierarchy('ontology', $source);
+    } elsif ($type eq 'sources') {
+        $data = $mgdb->_sources();
+        delete $data->{GO};
+    }
+    $self->return_data($data);
+}
+
+1;
+
diff --git a/src/MGRAST/lib/resources2/metagenome_statistics.pm b/src/MGRAST/lib/resources2/metagenome_statistics.pm
@@ -86,9 +86,9 @@ sub info {
 				      'type'        => "synchronous" ,  
 				      'attributes'  => $self->attributes,
 				      'parameters'  => { 'options' => { 'verbosity' => ['cv',
-                                                               [['minimal','returns only sequence statistics'],
+                                                               [['minimal','returns only sequence_stats attribute'],
-                                                                ['verbose','returns all but qc statistics'],
+                                                                ['verbose','returns all but qc attribute'],
-                                                                ['full','returns all statistics']] ] },
+                                                                ['full','returns all attributes']] ] },
 							             'required' => { "id" => [ "string", "metagenome id" ] },
 							             'body'     => {} } }
 				  ]