diff options
Diffstat (limited to 'lazar.rb')
| -rw-r--r-- | lazar.rb | 118 |
1 files changed, 50 insertions, 68 deletions
@@ -1,72 +1,52 @@ require "haml" -helpers do - def uri_available?(urlStr) - url = URI.parse(urlStr) - unless @subjectid - Net::HTTP.start(url.host, url.port) do |http| - return http.head(url.request_uri).code == "200" - end - else - Net::HTTP.start(url.host, url.port) do |http| - return http.post(url.request_uri, "subjectid=#{@subjectid}").code == "202" - end - end - end -end - # 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/ +=begin + 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 +=end + halt 404, "Model #{params[:id]} not found." unless File.exists? @yaml_file + response['Content-Type'] = @accept + case @accept + when /application\/rdf\+xml/ s = OpenTox::Serializer::Owl.new - s.add_model(model.uri,lazar.metadata) + s.add_model(@uri,YAML.load_file(@yaml_file).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 + 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 + halt 400, "Unsupported MIME type '#{@accept}'" + end end get '/:id/metadata.?:ext?' do - metadata = YAML.load(ModelStore.get(params[:id]).yaml).metadata + metadata = YAML.load_file(@yaml_file).metadata - accept = request.env['HTTP_ACCEPT'] - accept = "application/rdf+xml" if accept == '*/*' or accept == '' or accept.nil? - if params[:ext] - case params[:ext] - when "yaml" - accept = 'application/x-yaml' - when "rdf", "rdfxml" - accept = 'application/rdf+xml' - end - end - response['Content-Type'] = accept - case accept + response['Content-Type'] = @accept + case @accept when /yaml/ metadata.to_yaml else #when /rdf/ and anything else serializer = OpenTox::Serializer::Owl.new - serializer.add_metadata url_for("/#{params[:id]}",:full), metadata + serializer.add_metadata @uri, metadata serializer.to_rdfxml end @@ -77,14 +57,17 @@ end # @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.subjectid = @subjectid - 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 + #model = ModelStore.create + #model.subjectid = @subjectid + #model.uri = url_for("/#{model.id}", :full) + @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} + response['Content-Type'] = 'text/uri-list' + @uri end # Make a lazar prediction. Predicts either a single compound or all compounds from a dataset @@ -94,15 +77,14 @@ end # @return [text/uri-list] URI of prediction task (dataset prediction) or prediction dataset (compound prediction) post '/:id/?' do - puts params.to_yaml - @lazar = YAML.load ModelStore.get(params[:id]).yaml + halt 404, "Model #{params[:id]} does not exist." unless File.exists? @yaml_file - 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] + 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 + if compound_uri cache = PredictionCache.first(:model_uri => @lazar.uri, :compound_uri => compound_uri) return cache.dataset_uri if cache and uri_available?(cache.dataset_uri) begin @@ -113,12 +95,12 @@ post '/:id/?' do 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| + 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 + end halt 503,task.uri+"\n" if task.status == "Cancelled" halt 202,task.uri - end + end end |