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require "haml"
# Get model representation
# @return [application/rdf+xml,application/x-yaml] Model representation
get '/:id/?' do
raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @yaml_file
case @accept
when /application\/rdf\+xml/
response['Content-Type'] = 'application/rdf+xml'
s = OpenTox::Serializer::Owl.new
metadata = YAML.load_file(@yaml_file).metadata
s.add_model(@uri,metadata)
s.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
File.read @yaml_file
when /html/
response['Content-Type'] = 'text/html'
OpenTox.text_to_html File.read(@yaml_file)
else
raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
end
end
get '/:id/metadata.?:ext?' do
raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @yaml_file
@accept = "application/x-yaml" if params[:ext] and params[:ext].match(/yaml/)
metadata = YAML.load_file(@yaml_file).metadata
case @accept
when /yaml/
metadata.to_yaml
else #when /rdf/ and anything else
serializer = OpenTox::Serializer::Owl.new
serializer.add_metadata @uri, metadata
serializer.to_rdfxml
end
end
get '/:id/dependent.?:ext?' do
raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @yaml_file
@accept = "application/x-yaml" if params[:ext] and params[:ext].match(/yaml/)
feature_uri = YAML.load_file(@yaml_file).metadata[OT.dependentVariables]
case @accept
when /yaml/
OpenTox::Feature.find(feature_uri, @subjectid).to_yaml
when "text/uri-list"
feature_uri
when /rdf/
OpenTox::Feature.find(feature_uri, @subjectid).to_rdfxml
when /html/
OpenTox.text_to_html OpenTox::Feature.find(feature_uri, @subjectid).to_yaml
else
raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
end
end
get '/:id/predicted/:prop' do
raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @yaml_file
if params[:prop] == "value" or params[:prop] == "confidence"
feature = eval "YAML.load_file(@yaml_file).prediction_#{params[:prop]}_feature"
case @accept
when /yaml/
content_type "application/x-yaml"
feature.metadata.to_yaml
when /rdf/
content_type "application/rdf+xml"
feature.to_rdfxml
when /html/
content_type "text/html"
OpenTox.text_to_html feature.metadata.to_yaml
else
raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
end
else
raise OpenTox::BadRequestError.new "Unknown URI #{@uri}"
end
end
get '/:id/predicted.?:ext?' do
raise OpenTox::NotFoundError.new "Model #{params[:id]} not found." unless File.exists? @yaml_file
@accept = "application/x-yaml" if params[:ext] and params[:ext].match(/yaml/)
features = YAML.load_file(@yaml_file).prediction_features
case @accept
when "text/uri-list"
"#{features.collect{|f| f.uri}.join("\n")}\n"
when /yaml/
features.to_yaml
when /rdf/
serializer = OpenTox::Serializer::Owl.new
features.each{|f| serializer.add_feature(f.uri,f.metadata)}
serializer.to_rdfxml
#feature.to_rdfxml
when /html/
OpenTox.text_to_html features.to_yaml
else
raise OpenTox::BadRequestError.new "Unsupported MIME type '#{@accept}'"
end
end
# Store a lazar model. This method should not be called directly, use OpenTox::Algorithm::Lazr to create a lazar model
# @param [Body] lazar Model representation in YAML format
# @return [String] Model URI
post '/?' do # create model
raise OpenTox::BadRequestError.new "MIME type \"#{request.content_type}\" not supported." unless request.content_type.match(/yaml/)
@id = next_id
@uri = uri @id
@yaml_file = "public/#{@id}.yaml"
lazar = YAML.load request.env["rack.input"].read
lazar.uri = @uri
value_feature_uri = File.join( @uri, "predicted", "value")
confidence_feature_uri = File.join( @uri, "predicted", "confidence")
lazar.metadata[OT.predictedVariables] = [value_feature_uri, confidence_feature_uri]
File.open(@yaml_file,"w+"){|f| f.puts lazar.to_yaml}
OpenTox::Authorization.check_policy(@uri, @subjectid) if File.exists? @yaml_file
response['Content-Type'] = 'text/uri-list'
@uri
end
# Make a lazar prediction. Predicts either a single compound or all compounds from a dataset
# @param [optional,String] dataset_uri URI of the dataset to be predicted
# @param [optional,String] compound_uri URI of the compound to be predicted
# @param [optional,Header] Accept Content-type of prediction, can be either `application/rdf+xml or application/x-yaml`
# @return [text/uri-list] URI of prediction task (dataset prediction) or prediction dataset (compound prediction)
post '/:id/?' do
raise OpenTox::NotFoundError.new "Model #{params[:id]} does not exist." unless File.exists? @yaml_file
raise OpenTox::NotFoundError.new "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
@lazar = YAML.load_file @yaml_file
response['Content-Type'] = 'text/uri-list'
if compound_uri
cache = PredictionCache.find(:model_uri => @lazar.uri, :compound_uri => compound_uri).first
if cache and uri_available?(cache.dataset_uri)
return cache.dataset_uri
else
begin
prediction_uri = @lazar.predict(compound_uri,true,@subjectid).uri
PredictionCache.create(:model_uri => @lazar.uri, :compound_uri => compound_uri, :dataset_uri => prediction_uri)
prediction_uri
rescue
LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} "
raise "Prediction of #{compound_uri} with #{@lazar.uri} failed."
end
end
elsif dataset_uri
task = OpenTox::Task.create("Predict dataset",url_for("/#{@lazar.id}", :full)) do |task|
@lazar.predict_dataset(dataset_uri, @subjectid, task).uri
end
raise OpenTox::ServiceUnavailableError.newtask.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri
end
end
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