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require "haml"
# Get model representation
# @return [application/rdf+xml,application/x-yaml] Model representation
get '/:id/?' do
halt 404, "Model #{params[:id]} not found." unless File.exists? @yaml_file
case @accept
when /application\/rdf\+xml/
s = OpenTox::Serializer::Owl.new
s.add_model(@uri,YAML.load_file(@yaml_file).metadata)
s.to_rdfxml
when /yaml/
File.read @yaml_file
when /html/
OpenTox.text_to_html File.read(@yaml_file)
else
halt 400, "Unsupported MIME type '#{@accept}'"
end
end
get '/:id/metadata.?:ext?' do
halt 404, "Model #{params[:id]} not found." unless File.exists? @yaml_file
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' do
halt 404, "Model #{params[:id]} not found." unless File.exists? @yaml_file
feature_uri = YAML.load_file(@yaml_file).metadata[OT.dependentVariables]
case @accept
when /yaml/
OpenTox::Feature.find(feature_uri).to_yaml
when "text/uri-list"
feature_uri
when /rdf/
OpenTox::Feature.find(feature_uri).to_rdfxml
when /html/
OpenTox.text_to_html OpenTox::Feature.find(feature_uri).to_yaml
else
halt 400, "Unsupported MIME type '#{@accept}'"
end
end
get '/:id/predicted' do
halt 404, "Model #{params[:id]} not found." unless File.exists? @yaml_file
return feature_uri if @accept == "text/uri-list"
predicted = OpenTox::Feature.new(File.join @uri,"predicted")
dependent = OpenTox::Feature.find(YAML.load_file(@yaml_file).metadata[OT.dependentVariables])
predicted.metadata[RDF.type] = dependent.metadata[RDF.type]
#predicted.metadata[OT.hasSource] = @uri
#predicted.metadata[DC.creator] = @uri
predicted.metadata[DC.title] = dependent.metadata[DC.title]
case @accept
when /yaml/
predicted.to_yaml
when /rdf/
predicted.to_rdfxml
when /html/
OpenTox.text_to_html predicted.to_yaml
else
halt 400, "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
halt 400, "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
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
halt 404, "Model #{params[:id]} does not exist." unless File.exists? @yaml_file
halt 404, "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
return cache.dataset_uri if cache and uri_available?(cache.dataset_uri)
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 #{$!} "
halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed."
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
halt 503,task.uri+"\n" if task.status == "Cancelled"
halt 202,task.uri
end
end
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