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Diffstat (limited to 'fs.rb')
| -rw-r--r-- | fs.rb | 106 |
1 files changed, 106 insertions, 0 deletions
@@ -0,0 +1,106 @@ +# fs.rb +# Feature Selection +# Author: Andreas Maunz + + +# Get list of feature selection algorithms +# @return [text/uri-list] URIs of feature selection algorithms +get '/fs/?' 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 representation of recursive feature elimination algorithm +# @return [application/rdf+xml] OWL-DL representation of recursive feature elimination algorithm +get "/fs/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 => "Prediction Feature URI", OT.paramScope => "mandatory", DC.title => "prediction_feature" }, + { DC.description => "Feature Dataset URI", OT.paramScope => "mandatory", DC.title => "feature_dataset_uri" }, + { DC.description => "Delete Instances with missing values", OT.paramScope => "optional", DC.title => "del_missing" } + ] + } + case request.env['HTTP_ACCEPT'] + when /text\/html/ + content_type "text/html" + OpenTox.text_to_html algorithm.to_yaml + when /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] prediction_feature URI +# @param [String] feature_dataset_uri URI +# @return [text/uri-list] Task URI +post '/fs/rfe/?' do + + raise OpenTox::NotFoundError.new "Please submit a dataset_uri." unless params[:dataset_uri] + raise OpenTox::NotFoundError.new "Please submit a prediction_feature." unless params[:prediction_feature] + 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"} ) + ds=Tempfile.open(['rfe_', '.csv']) + ds.puts(ds_csv) + ds.flush() + + prediction_feature = params[:prediction_feature].split('/').last # get col name + + fds_features = OpenTox::Dataset.new(params[:feature_dataset_uri]).load_features + fds_csv=OpenTox::RestClientWrapper.get( params[:feature_dataset_uri], {:accept => "text/csv"}) + fds=Tempfile.open(['rfe_', '.csv']) + fds.puts(fds_csv) + fds.flush() + + del_missing = params[:del_missing] == "true" ? true : false + + task = OpenTox::Task.create("Recursive Feature Elimination", url_for('/feature_selection',:full)) do |task| + r_result_file = OpenTox::Algorithm::FeatureSelection.rfe( { :ds_csv_file => ds.path, :prediction_feature => prediction_feature, :fds_csv_file => fds.path, :del_missing => del_missing } ) + + + # # # Upload dataset + ds = OpenTox::Dataset.find ( + OpenTox::RestClientWrapper.post( + File.join(CONFIG[:services]["opentox-dataset"]), File.open(r_result_file).read, {:content_type => "text/csv"} + ) + ) + ds.features.each { |id,info| # rewrite features + fds_features.each { |fid,finfo| + if ( (fid.split('/').last == id.split('/').last) && (finfo[DC.title] == info[DC.title]) ) + ds.features[id] = finfo + break + end + } + } + r_result_uri = ds.save + begin + ds.close!; fds.close! + File.unlink(r_result_file) + rescue + end + 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 + |