diff options
Diffstat (limited to 'application.rb')
| -rw-r--r-- | application.rb | 218 |
1 files changed, 0 insertions, 218 deletions
diff --git a/application.rb b/application.rb deleted file mode 100644 index 0d0cb63..0000000 --- a/application.rb +++ /dev/null @@ -1,218 +0,0 @@ -include OpenTox - -require 'rack/cors' - -set :show_exceptions => false - -# add CORS support for swagger -use Rack::Cors do |config| - config.allow do |allow| - allow.origins '*' - allow.resource "/#{SERVICE}/*", - :methods => [:head, :get, :post, :put, :delete, :options], - :headers => :any, - :max_age => 0 - end -end -before do - @accept = request.env['HTTP_ACCEPT'] - response['Content-Type'] = @accept -end - -# route to swagger API file -get "/api/api.json" do - response['Content-Type'] = "application/json" - api_file = File.join("api", "api.json") - bad_request_error "API Documentation in Swagger JSON is not implemented.", uri("/#{SERVICE}/api") unless File.exists?(api_file) - api_hash = JSON.parse(File.read(api_file)) - api_hash["host"] = request.env['HTTP_HOST'] - return api_hash.to_json -end - - -# Get a list of all prediction models -# @param [Header] Accept one of text/uri-list, -# @return [text/uri-list] list of all prediction models -get "/model/?" do - models = OpenTox::Model::Prediction.all - case @accept - when "text/uri-list" - uri_list = models.collect{|model| uri("/model/#{model.model_id}")} - return uri_list.join("\n") + "\n" - when "application/json" - models = JSON.parse models.to_json - models.each_index do |idx| - models[idx][:URI] = uri("/model/#{models[idx]["model_id"]["$oid"]}") - models[idx][:crossvalidation_uri] = uri("/crossvalidation/#{models[idx]["crossvalidation_id"]["$oid"]}") if models[idx]["crossvalidation_id"] - end - return models.to_json - else - bad_request_error "Mime type #{@accept} is not supported." - end -end - -get "/model/:id/?" do - model = OpenTox::Model::Lazar.find params[:id] - resource_not_found_error "Model with id: #{params[:id]} not found." unless model - model[:URI] = uri("/model/#{model.id}") - model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id] - model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id - model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id - return model.to_json -end - - - -post "/model/:id/?" do - identifier = params[:identifier].split(",") - begin - # get compound from SMILES - compounds = identifier.collect{ |i| Compound.from_smiles i.strip } - rescue - @error_report = "Attention, '#{params[:identifier]}' is not a valid SMILES string." - return @error_report - end - model = OpenTox::Model::Lazar.find params[:id] - batch = {} - compounds.each do |compound| - prediction = model.predict(compound) - batch[compound] = {:id => compound.id, :inchi => compound.inchi, :smiles => compound.smiles, :model => model, :prediction => prediction} - end - return batch.to_json -end - -VALIDATION_TYPES = ["repeatedcrossvalidation", "leaveoneout", "crossvalidation", "regressioncrossvalidation"] - - -# Get a list of ayll possible validation types -# @param [Header] Accept one of text/uri-list, application/json -# @return [text/uri-list] URI list of all validation types -get "/validation/?" do - case @accept - when "text/uri-list" - uri_list = VALIDATION_TYPES.collect{|validationtype| uri("/validation/#{validationtype}")} - return uri_list.join("\n") + "\n" - when "application/json" - return VALIDATION_TYPES.to_json - else - bad_request_error "Mime type #{@accept} is not supported." - end -end - - -# Get a list of all validations -# @param [Header] Accept one of text/uri-list, application/json -# @param [Path] Validationtype One of "repeatedcrossvalidation", "leaveoneout", "crossvalidation", "regressioncrossvalidation" -# @return [text/uri-list] list of all validations of a validation type -get "/validation/:validationtype/?" do - bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] - case params[:validationtype] - when "repeatedcrossvalidation" - validations = OpenTox::Validation::RepeatedCrossValidation.all - when "leaveoneout" - validations = OpenTox::Validation::LeaveOneOut.all - when "crossvalidation" - validations = OpenTox::Validation::CrossValidation.all - when "regressioncrossvalidation" - validations = OpenTox::Validation::RegressionCrossValidation.all - end - - case @accept - when "text/uri-list" - uri_list = validations.collect{|validation| uri("/validation/#{params[:validationtype]}/#{validation.id}")} - return uri_list.join("\n") + "\n" - when "application/json" - validations = JSON.parse validations.to_json - validations.each_index do |idx| - validations[idx][:URI] = uri("/validation/#{params[:validationtype]}/#{validations[idx]["$oid"]}") - #models[idx][:crossvalidation_uri] = uri("/crossvalidation/#{models[idx]["crossvalidation_id"]["$oid"]}") if models[idx]["crossvalidation_id"] - end - return validations.to_json - else - bad_request_error "Mime type #{@accept} is not supported." - end -end - -get "/validation/:validationtype/:id/?" do - bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] - case params[:validationtype] - when "repeatedcrossvalidation" - validation = OpenTox::Validation::RepeatedCrossValidation.find params[:id] - when "leaveoneout" - validation = OpenTox::Validation::LeaveOneOut.find params[:id] - when "crossvalidation" - validation = OpenTox::Validation::CrossValidation.find params[:id] - when "regressioncrossvalidation" - validation = OpenTox::Validation::RegressionCrossValidation.find params[:id] - end - - resource_not_found_error "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation - #model[:URI] = uri("/model/#{model.id}") - #model[:neighbor_algorithm_parameters][:feature_dataset_uri] = uri("/dataset/#{model[:neighbor_algorithm_parameters][:feature_dataset_id]}") if model[:neighbor_algorithm_parameters][:feature_dataset_id] - #model[:training_dataset_uri] = uri("/dataset/#{model.training_dataset_id}") if model.training_dataset_id - #model[:prediction_feature_uri] = uri("/dataset/#{model.prediction_feature_id}") if model.prediction_feature_id - return validation.to_json -end - -# Get a list of a single or all descriptors -# @param [Header] Accept one of text/plain, application/json -# @param [Path] Descriptor name (e.G.: Openbabel.HBA1) -# @return [text/plain, application/json] list of all prediction models -get "/compound/descriptor/?:descriptor?" do - case @accept - when "application/json" - return "#{JSON.pretty_generate OpenTox::PhysChem::DESCRIPTORS} " unless params[:descriptor] - return {params[:descriptor] => OpenTox::PhysChem::DESCRIPTORS[params[:descriptor]]}.to_json - else - return OpenTox::PhysChem::DESCRIPTORS.collect{|k, v| "#{k}: #{v}\n"} unless params[:descriptor] - return OpenTox::PhysChem::DESCRIPTORS[params[:descriptor]] - end -end - -post "/compound/descriptor/?" do - bad_request_error "Missing Parameter " unless (params[:identifier] or params[:file]) and params[:descriptor] - descriptor = params['descriptor'].split(',') - if params[:file] - data = OpenTox::Dataset.from_csv_file params[:file][:tempfile] - else - data = OpenTox::Compound.from_smiles params[:identifier] - end - d = Algorithm::Descriptor.physchem data, descriptor - csv = d.to_csv - csv = "SMILES,#{params[:descriptor]}\n#{params[:identifier]},#{csv}" if params[:identifier] - case @accept - when "application/csv" - return csv - when "application/json" - lines = CSV.parse(csv) - keys = lines.delete lines.first - data = lines.collect{|values|Hash[keys.zip(values)]} - return JSON.pretty_generate(data) - end -end - -get %r{/compound/(.+)} do |inchi| - bad_request_error "Input parameter #{inchi} is not an InChI" unless inchi.match(/^InChI=/) - compound = OpenTox::Compound.from_inchi URI.unescape(inchi) - response['Content-Type'] = @accept - case @accept - when "application/json" - return JSON.pretty_generate JSON.parse(compound.to_json) - when "chemical/x-daylight-smiles" - return compound.smiles - when "chemical/x-inchi" - return compound.inchi - when "chemical/x-mdl-sdfile" - return compound.sdf - when "chemical/x-mdl-molfile" - when "image/png" - return compound.png - when "image/svg+xml" - return compound.svg - when "text/plain" - return "#{compound.names}\n" - else - return compound.inspect - end -end - |