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class Example
@@file=File.new("data/hamster_carcinogenicity.owl","r")
@@model=File.join @@config[:services]["opentox-model"],"1"
@@feature="http://www.epa.gov/NCCT/dsstox/CentralFieldDef.html#ActivityOutcome_CPDBAS_Hamster"
@@alg = File.join @@config[:services]["opentox-algorithm"],"lazar"
@@alg_params = "feature_generation_uri="+File.join(@@config[:services]["opentox-algorithm"],"fminer")
@@data=File.join @@config[:services]["opentox-dataset"],"1"
@@train_data=File.join @@config[:services]["opentox-dataset"],"2"
@@test_data=File.join @@config[:services]["opentox-dataset"],"3"
def self.transform_example
file = File.new("EXAMPLES", "r")
res = ""
while (line = file.gets)
res += line
end
file.close
sub = { "validation_service" => @@config[:services]["opentox-validation"],
"validation_id" => "1",
"model_uri" => @@model,
"dataset_uri" => @@data,
"training_dataset_uri" => @@train_data,
"test_dataset_uri" => @@test_data,
"prediction_feature" => @@feature,
"algorithm_uri" => @@alg,
"algorithm_params" => @@alg_params,
"crossvalidation_id" => "1",}
sub.each do |k,v|
res.gsub!(/<#{k}>/,v)
end
res
end
def self.delete_all(uri_list_service)
uri_list = RestClient.get(uri_list_service)
uri_list.split("\n").each do |uri|
RestClient.delete(uri)
end
end
def self.prepare_example_resources
delete_all(@@config[:services]["opentox-dataset"])
data = File.read(@@file.path)
data_uri = RestClient.post @@config[:services]["opentox-dataset"], data, :content_type => "application/rdf+xml"
puts "uploaded dataset "+data_uri
raise "failed to prepare demo" unless data_uri==@@data
Lib::Validation.auto_migrate!
delete_all(@@config[:services]["opentox-model"])
vali_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/validation/training_test_split'), { :dataset_uri => data_uri,
:algorithm_uri => @@alg,
:prediction_feature => @@feature,
:algorithm_params => @@alg_params }
puts "created validation via training test split "+vali_uri
raise "failed to prepare demo" unless vali_uri==File.join(@@config[:services]["opentox-validation"],'/validation/1')
Lib::Crossvalidation.auto_migrate!
cv_uri = RestClient.post File.join(@@config[:services]["opentox-validation"],'/crossvalidation'), { :dataset_uri => data_uri,
:algorithm_uri => @@alg,
:prediction_feature => @@feature,
:algorithm_params => @@alg_params,
:num_folds => 5, :stratified => false }
puts "created crossvalidation "+cv_uri
raise "failed to prepare demo" unless cv_uri==File.join(@@config[:services]["opentox-validation"],'/crossvalidation/1')
end
end
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