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# R integration
# workaround to initialize R non-interactively (former rinruby versions did this by default)
# avoids compiling R with X
R = nil
require "rinruby"
require "haml"
#require "lazar-helper"
# Get model representation
# @return [application/rdf+xml,application/x-yaml] Model representation
get '/:id/?' do
accept = request.env['HTTP_ACCEPT']
accept = "application/rdf+xml" if accept == '*/*' or accept == '' or accept.nil?
# workaround for browser links
case params[:id]
when /.yaml$/
params[:id].sub!(/.yaml$/,'')
accept = 'application/x-yaml'
when /.rdf$/
params[:id].sub!(/.rdf$/,'')
accept = 'application/rdf+xml'
end
halt 404, "Model #{params[:id]} not found." unless model = ModelStore.get(params[:id])
lazar = YAML.load model.yaml
case accept
when /application\/rdf\+xml/
s = OpenTox::Serializer::Owl.new
s.add_model(url_for('/lazar',:full),lazar.metadata)
response['Content-Type'] = 'application/rdf+xml'
s.to_rdfxml
when /yaml/
response['Content-Type'] = 'application/x-yaml'
model.yaml
else
halt 400, "Unsupported MIME type '#{accept}'"
end
end
=begin
get '/:id/algorithm/?' do
response['Content-Type'] = 'text/plain'
YAML.load(ModelStore.get(params[:id]).yaml).algorithm
end
get '/:id/trainingDataset/?' do
response['Content-Type'] = 'text/plain'
YAML.load(ModelStore.get(params[:id]).yaml).trainingDataset
end
get '/:id/feature_dataset/?' do
response['Content-Type'] = 'text/plain'
YAML.load(ModelStore.get(params[:id]).yaml).feature_dataset_uri
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/)
model = ModelStore.create
model.uri = url_for("/#{model.id}", :full)
lazar = YAML.load request.env["rack.input"].read
lazar.uri = model.uri
model.yaml = lazar.to_yaml
model.save
model.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,application/rdf+xml,application/x-yaml] URI of prediction task (dataset prediction) or prediction in requested representation
post '/:id/?' do
start = Time.now
@lazar = YAML.load ModelStore.get(params[:id]).yaml
halt 404, "Model #{params[:id]} does not exist." unless @lazar
halt 404, "No compound_uri or dataset_uri parameter." unless compound_uri = params[:compound_uri] or dataset_uri = params[:dataset_uri]
s = Time.now
if compound_uri
#begin
@prediction = @lazar.predict(compound_uri,true)
#rescue
#LOGGER.error "Lazar prediction failed for #{compound_uri} with #{$!} "
#halt 500, "Prediction of #{compound_uri} with #{@lazar.uri} failed."
#end
#accept = request.env['HTTP_ACCEPT']
#accept = 'application/rdf+xml' if accept == '*/*' or accept == '' or accept.nil?
LOGGER.debug "Total: #{Time.now - start} seconds"
#case accept
#when /yaml/
@prediction.uri
#else # RestClientWrapper does not send accept header
#when /application\/rdf\+xml/
#@prediction.to_rdfxml
#else
#halt 400, "MIME type \"#{request.env['HTTP_ACCEPT']}\" not supported."
#end
elsif dataset_uri
response['Content-Type'] = 'text/uri-list'
task_uri = OpenTox::Task.as_task("Predict dataset",url_for("/#{lazar.id}", :full)) do
OpenTox::Dataset.find(dataset_uri).compounds.each do |compound_uri|
#begin
predict(compound_uri,true)
#rescue
#LOGGER.error "#{prediction_type} failed for #{compound_uri} with #{$!} "
#end
end
@prediction.save
end
halt 202,task_uri
end
end
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