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module OpenTox
class Application < Service
# Get representation of lazar algorithm
# @return [String] Representation
get '/lazar/?' do
algorithm = OpenTox::Algorithm::Generic.new(to('/lazar',:full))
algorithm.metadata = {
RDF::DC.title => 'lazar',
RDF::DC.creator => 'helma@in-silico.ch, andreas@maunz.de',
RDF.Type => [RDF::OT.Algorithm]
}
algorithm.parameters = [
{ RDF::DC.description => "Dataset URI", RDF::OT.paramScope => "mandatory", RDF::DC.title => "dataset_uri" },
{ RDF::DC.description => "Feature URI for dependent variable", RDF::OT.paramScope => "optional", RDF::DC.title => "prediction_feature" },
{ RDF::DC.description => "Feature generation service URI", RDF::OT.paramScope => "optional", RDF::DC.title => "feature_generation_uri" },
{ RDF::DC.description => "Feature dataset URI", RDF::OT.paramScope => "optional", RDF::DC.title => "feature_dataset_uri" },
{ RDF::DC.description => "Further parameters for the feature generation service", RDF::OT.paramScope => "optional" }
]
render algorithm
end
# Create a lazar prediction model
# @param [String] dataset_uri Training dataset URI
# @param [optional,String] prediction_feature URI of the feature to be predicted
# @param [optional,String] feature_generation_uri URI of the feature generation algorithm
# @param [optional,String] - further parameters for the feature generation service
# @return [text/uri-list] Task URI
post '/lazar/?' do
bad_request_error "Please provide a dataset_uri parameter." unless params[:dataset_uri]
#resource_not_found_error "Dataset '#{params[:dataset_uri]}' not found." unless URI.accessible? params[:dataset_uri], @subjectid # wrong URI class
bad_request_error "Please provide either a feature_generation_uri or a feature_dataset_uri parameter." unless params[:feature_generation_uri] or params[:feature_dataset_uri]
task = OpenTox::Task.run("Create lazar model", uri('/lazar')) do |task|
OpenTox::Model::Lazar.create(params)
end
response['Content-Type'] = 'text/uri-list'
halt 202,task.uri
end
# Make a lazar prediction -- not to be called directly
# @param [String] compound_uri URI of compound to be predicted
# @param [String] training_dataset_uri URI of training dataset
# @param [String] prediction_feature_uri URI of prediction feature
# @param [String] feature_dataset_uri URI of feature dataset
# @param [String] feature_calculation_algorithm Name of feature calculation algorithm
# @param [String] min_sim Numeric value for minimum similarity
# @param [String] prediction_algorithm Name of prediction algorithm
# @param [String] propositionalized Whether propositionalization should be used
# @param [optional,String] pc_type Physico-chemical descriptor type
# @param [optional,String] pc_lib Physico-chemical descriptor library
# @param [optional,String] Further parameters for the feature generation service
# @return [text/uri-list] Task URI
post '/lazar/predict/?' do
# pass parameters instead of model_uri, because model service is blocked by incoming call
task = OpenTox::Task.run("Apply lazar model",uri('/lazar/predict')) do |task|
OpenTox::Model::Lazar.new(params[:model_uri]).predict(params).uri
end
response['Content-Type'] = 'text/uri-list'
halt 202,task.uri
end
end
end
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