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# 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
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