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# 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 => "Prediction Feature URI", OT.paramScope => "mandatory", DC.title => "prediction_feature_uri" },
{ 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 /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 prediction_feature_uri." unless params[:prediction_feature_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)
tf_ds.flush()
prediction_feature = URI.escape(params[:prediction_feature_uri].split('/').last) # get col name
fds_csv=OpenTox::RestClientWrapper.get( params[:feature_dataset_uri], {:accept => "text/csv"})
tf_fds=Tempfile.open(['rfe_', '.csv'])
tf_fds.puts(fds_csv)
tf_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 => tf_ds.path, :prediction_feature => prediction_feature, :fds_csv_file => tf_fds.path, :del_missing => del_missing } )
r_result_uri = OpenTox::Dataset.create_from_csv_file(r_result_file).uri
begin
tf_ds.close!; tf_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
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