Added rfe

1 files changed, 74 insertions, 0 deletions

diff --git a/feature_selection.rb b/feature_selection.rb
new file mode 100644
index 0000000..c69a954
--- /dev/null
+++ b/feature_selection.rb
@@ -0,0 +1,74 @@
+# Get list of feature_selection algorithms
+#
+# @return [text/uri-list] URIs of feature_selection algorithms
+get '/feature_selection/?' do
+  list = [ url_for('/feature_selection/rfe', :full) ].join("\n") + "\n"
+  case request.env['HTTP_ACCEPT']
+  when /text\/html/
+    content_type "text/html"
+    OpenTox.text_to_html list
+  else
+    content_type 'text/uri-list'
+    list
+  end
+end
+
+# Get RDF/XML representation of feature_selection rfe algorithm
+# @return [application/rdf+xml] OWL-DL representation of feature_selection rfe algorithm
+get "/feature_selection/rfe/?" do
+  algorithm = OpenTox::Algorithm::Generic.new(url_for('/feature_selection/rfe',:full))
+  algorithm.metadata = {
+    DC.title => 'recursive feature elimination',
+    DC.creator => "andreas@maunz.de, helma@in-silico.ch",
+    DC.contributor => "vorgrimmlerdavid@gmx.de",
+    BO.instanceOf => "http://opentox.org/ontology/ist-algorithms.owl#feature_selection_rfe",
+    RDF.type => [OT.Algorithm,OTA.PatternMiningSupervised],
+    OT.parameters => [
+      { DC.description => "Dataset URI", OT.paramScope => "mandatory", DC.title => "dataset_uri" },
+      { DC.description => "Feature Dataset URI", OT.paramScope => "mandatory", DC.title => "feature_dataset_uri" }
+  ]
+  }
+  case request.env['HTTP_ACCEPT']
+  when /text\/html/
+    content_type "text/html"
+    OpenTox.text_to_html algorithm.to_yaml
+  when /application\/x-yaml/
+    content_type "application/x-yaml"
+    algorithm.to_yaml
+  else
+    response['Content-Type'] = 'application/rdf+xml'  
+    algorithm.to_rdfxml
+  end
+end
+
+# Run rfe algorithm on dataset
+#
+# @param [String] dataset_uri URI of the training dataset
+# @param [String] feature_dataset_uri URI of the feature dataset
+# @return [text/uri-list] Task URI
+post '/feature_selection/rfe/?' do 
+
+  raise OpenTox::NotFoundError.new "Please submit a dataset_uri." unless params[:dataset_uri]
+  raise OpenTox::NotFoundError.new "Please submit a feature_dataset_uri." unless params[:feature_dataset_uri]
+
+  ds_csv=OpenTox::RestClientWrapper.get( params[:dataset_uri], {:accept => "text/csv"} )
+  tf_ds=Tempfile.open(['rfe_', '.csv'])
+  tf_ds.puts(ds_csv)
+  
+  fds_csv=OpenTox::RestClientWrapper.get( params[:feature_dataset_uri], {:accept => "text/csv"})
+  tf_fds=Tempfile.open(['rfe_', '.csv'])
+  tf_fds.puts(fds_csv)
+
+  task = OpenTox::Task.create("Recursive Feature Elimination", url_for('/feature_selection',:full)) do |task|
+    rfe=OpenTox::Algorithm::FeatureSelection.rfe( { :ds_csv_file => tf_ds, :fds_csv_file => tf_fds } )
+    r_result_uri=OpenTox::Dataset.create_from_csv(r_result_file).uri
+    File.unlink(r_result_file)
+    tf_ds.close!
+    tf_fds.close! 
+    r_result_uri
+  end
+  response['Content-Type'] = 'text/uri-list'
+  raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
+  halt 202,task.uri.to_s+"\n"
+end
+