From 741701df8ff0861b3607a30e9aaf8b8a0c303cdf Mon Sep 17 00:00:00 2001 From: gebele Date: Thu, 13 Jun 2019 15:28:59 +0000 Subject: update with API --- lib/api.rb | 28 ++++++-- lib/compound.rb | 6 +- lib/dataset.rb | 133 ++++--------------------------------- lib/endpoint.rb | 10 +-- lib/feature.rb | 4 +- lib/model.rb | 16 ++--- lib/report.rb | 193 ++---------------------------------------------------- lib/substance.rb | 18 ++--- lib/swagger.rb | 6 +- lib/validation.rb | 24 +++---- 10 files changed, 80 insertions(+), 358 deletions(-) (limited to 'lib') diff --git a/lib/api.rb b/lib/api.rb index 28e33df..c3b27ce 100644 --- a/lib/api.rb +++ b/lib/api.rb @@ -1,9 +1,23 @@ -# route to swagger API file -get "/api/api.json" do - response['Content-Type'] = "application/json" +get "/api" do api_file = File.join("api", "api.json") - bad_request_error "API Documentation in Swagger JSON is not implemented." 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 + halt 400, "API Documentation in Swagger JSON is not implemented." unless File.exists?(api_file) + case @accept + when "text/html" + response['Content-Type'] = "text/html" + index_file = File.join(ENV['HOME'],"swagger-ui/dist/index.html") + File.read(index_file) + when "application/json" + response['Content-Type'] = "application/json" + api_hash = JSON.parse(File.read(api_file)) + api_hash["host"] = request.env['HTTP_HOST'] + return api_hash.to_json + else + halt 400, "unknown MIME type '#{@accept}'" + end +end + +get "/api/api.json" do + response['Content-Type'] = "text/html" + index_file = File.join(ENV['HOME'],"swagger-ui/dist/index.html") + File.read(index_file) end diff --git a/lib/compound.rb b/lib/compound.rb index 77948ab..4606aa4 100644 --- a/lib/compound.rb +++ b/lib/compound.rb @@ -2,7 +2,7 @@ # @param [Header] Accept one of text/plain, application/json # @param [Path] Descriptor name or descriptor ID (e.G.: Openbabel.HBA1, 5755f8eb3cf99a00d8fedf2f) # @return [text/plain, application/json] list of all prediction models -get "/compound/descriptor/?:descriptor?" do +get "/api/compound/descriptor/?:descriptor?" do case @accept when "application/json" return "#{JSON.pretty_generate PhysChem::DESCRIPTORS} " unless params[:descriptor] @@ -15,7 +15,7 @@ get "/compound/descriptor/?:descriptor?" do end end -post "/compound/descriptor/?" do +post "/api/compound/descriptor/?" do bad_request_error "Missing Parameter " unless params[:identifier] && params[:descriptor] descriptors = params['descriptor'].split(',') compound = Compound.from_smiles params[:identifier] @@ -38,7 +38,7 @@ post "/compound/descriptor/?" do end end -get %r{/compound/(InChI.+)} do |input| +get %r{/api/compound/(InChI.+)} do |input| compound = Compound.from_inchi URI.unescape(input) if compound response['Content-Type'] = @accept diff --git a/lib/dataset.rb b/lib/dataset.rb index 749167b..00685b8 100644 --- a/lib/dataset.rb +++ b/lib/dataset.rb @@ -1,136 +1,29 @@ # Get all datasets -get "/dataset/?" do - datasets = Dataset.all +get "/api/dataset/?" do + datasets = Dataset.all #.limit(100) case @accept - when "text/uri-list" - uri_list = datasets.collect{|dataset| uri("/dataset/#{dataset.id}")} - return uri_list.join("\n") + "\n" when "application/json" - datasets = JSON.parse datasets.to_json - list = [] - datasets.each{|d| list << uri("/dataset/#{d["_id"]["$oid"]}")} - return list.to_json + list = datasets.collect{|dataset| uri("/api/dataset/#{dataset.id}")}.to_json + return list else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end # Get a dataset -get "/dataset/:id/?" do - if Task.where(id: params[:id]).exists? - task = Task.find params[:id] - halt 404, "Dataset with id: #{params[:id]} not found." unless task.percent == 100 - $logger.debug task.inspect - response['Content-Type'] = "text/csv" - m = Model::Validation.find task.model_id - dataset = Batch.find task.dataset_id - @ids = dataset.ids - warnings = dataset.warnings.blank? ? nil : dataset.warnings.join("\n") - unless warnings.nil? - @parse = [] - warnings.split("\n").each do |warning| - if warning =~ /^Cannot/ - smi = warning.split("SMILES compound").last.split("at").first - line = warning.split("SMILES compound").last.split("at line").last.split("of").first.strip.to_i - @parse << "Cannot parse SMILES compound#{smi}at line #{line} of #{dataset.source.split("/").last}\n" - end - end - keys_array = [] - warnings.split("\n").each do |warning| - if warning =~ /^Duplicate/ - text = warning.split("ID").first - numbers = warning.split("ID").last.split("and") - keys_array << numbers.collect{|n| n.strip.to_i} - end - end - @dups = {} - keys_array.each do |keys| - keys.each do |key| - @dups[key] = "Duplicate compound at ID #{keys.join(" and ")}\n" - end - end - end - $logger.debug "dups: #{@dups}" - endpoint = "#{m.endpoint}_(#{m.species})" - tempfile = Tempfile.new - header = task.csv - lines = [] - $logger.debug task.predictions - task.predictions[m.id.to_s].each_with_index do |hash,idx| - identifier = hash.keys[0] - prediction_id = hash.values[0] - # add duplicate warning at the end of a line if ID matches - if @dups[idx+1] - if prediction_id.is_a? BSON::ObjectId - if @ids.blank? - lines << "#{idx+1},#{identifier},#{Prediction.find(prediction_id).csv.tr("\n","")},#{@dups[idx+1]}" - else - lines << "#{idx+1},#{@ids[idx]},#{identifier},#{Prediction.find(prediction_id).csv.tr("\n","")},#{@dups[idx+1]}" - end - else - if @ids.blank? - lines << "#{idx+1},#{identifier},\n" - else - lines << "#{idx+1},#{@ids[idx]}#{identifier},\n" - end - end - else - if prediction_id.is_a? BSON::ObjectId - if @ids.blank? - lines << "#{idx+1},#{identifier},#{Prediction.find(prediction_id).csv}" - else - lines << "#{idx+1},#{@ids[idx]},#{identifier},#{Prediction.find(prediction_id).csv}" - end - else - if @ids.blank? - lines << "#{idx+1},#{identifier},\n" - else - lines << "#{idx+1},#{@ids[idx]}#{identifier},\n" - end - end - end - end - (@parse && !@parse.blank?) ? tempfile.write(header+lines.join("")+"\n"+@parse.join("\n")) : tempfile.write(header+lines.join("")) - #tempfile.write(header+lines.join("")) - tempfile.rewind - ######################## -=begin - header = task.csv - lines = [] - task.predictions.each_with_index do |result,idx| - identifier = result[0] - prediction_id = result[1] - prediction = Prediction.find prediction_id - lines << "#{idx+1},#{identifier},#{prediction.csv.tr("\n","")}" - end - return header+lines.join("\n") -=end - return tempfile.read +get "/api/dataset/:id/?" do + dataset = Dataset.find :id => params[:id] + halt 400, "Dataset with id: #{params[:id]} not found." unless dataset + case @accept + when "text/csv", "application/csv" + return dataset.to_csv else - dataset = Dataset.find :id => params[:id] - halt 400, "Dataset with id: #{params[:id]} not found." unless dataset - case @accept - when "application/json" - dataset.data_entries.each do |k, v| - dataset.data_entries[k][:URI] = uri("/substance/#{k}") - end - dataset[:URI] = uri("/dataset/#{dataset.id}") - dataset[:substances] = uri("/dataset/#{dataset.id}/substances") - dataset[:features] = uri("/dataset/#{dataset.id}/features") - return dataset.to_json - when "text/csv", "application/csv" - return dataset.to_csv - else - bad_request_error "Mime type #{@accept} is not supported." - end + bad_request_error "Mime type #{@accept} is not supported." end end # Get a dataset attribute. One of compounds, nanoparticles, substances, features -get "/dataset/:id/:attribute/?" do - if Task.where(id: params[:id]).exists? - halt 400, "No attributes selection available for dataset with id: #{params[:id]}.".to_json - end +get "/api/dataset/:id/:attribute/?" do dataset = Dataset.find :id => params[:id] halt 400, "Dataset with id: #{params[:id]} not found." unless dataset attribs = ["compounds", "nanoparticles", "substances", "features"] diff --git a/lib/endpoint.rb b/lib/endpoint.rb index ef39787..66b7ab2 100644 --- a/lib/endpoint.rb +++ b/lib/endpoint.rb @@ -1,7 +1,7 @@ # Get a list of all endpoints # @param [Header] Accept one of text/uri-list, # @return [text/uri-list] list of all prediction models -get "/endpoint/?" do +get "/api/endpoint/?" do models = Model::Validation.all endpoints = models.collect{|m| m.endpoint}.uniq case @accept @@ -10,14 +10,14 @@ get "/endpoint/?" do when "application/json" return endpoints.to_json else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end -get "/endpoint/:endpoint/?" do +get "/api/endpoint/:endpoint/?" do models = Model::Validation.where(endpoint: params[:endpoint]) list = [] - models.each{|m| list << {m.species => uri("/model/#{m.id}")} } - not_found_error "Endpoint: #{params[:endpoint]} not found." if models.blank? + models.each{|m| list << {m.species => uri("/api/model/#{m.id}")} } + halt 404, "Endpoint: #{params[:endpoint]} not found." if models.blank? return list.to_json end diff --git a/lib/feature.rb b/lib/feature.rb index 06a5b37..3123997 100644 --- a/lib/feature.rb +++ b/lib/feature.rb @@ -1,5 +1,5 @@ # Get all Features -get "/feature/?" do +get "/api/feature/?" do features = Feature.all case @accept when "text/uri-list" @@ -16,7 +16,7 @@ get "/feature/?" do end # Get a feature -get "/feature/:id/?" do +get "/api/feature/:id/?" do case @accept when "application/json" feature = Feature.find :id => params[:id] diff --git a/lib/model.rb b/lib/model.rb index 42f3a95..9bf4f53 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -1,29 +1,29 @@ # 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 +get "/api/model/?" do models = Model::Validation.all case @accept when "text/uri-list" - uri_list = models.collect{|model| uri("/model/#{model.id}")} + uri_list = models.collect{|model| uri("/api/model/#{model.id}")} return uri_list.join("\n") + "\n" when "application/json" models = JSON.parse models.to_json list = [] - models.each{|m| list << uri("/model/#{m["_id"]["$oid"]}")} + models.each{|m| list << uri("/api/model/#{m["_id"]["$oid"]}")} return list.to_json else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end -get "/model/:id/?" do +get "/api/model/:id/?" do model = Model::Validation.find params[:id] - not_found_error "Model with id: #{params[:id]} not found." unless model + halt 400, "Model with id: #{params[:id]} not found." unless model return model.to_json end -post "/model/:id/?" do +post "/api/model/:id/?" do if request.content_type == "application/x-www-form-urlencoded" identifier = params[:identifier].strip.gsub(/\A"|"\Z/,'') compound = Compound.from_smiles identifier @@ -146,6 +146,6 @@ post "/model/:id/?" do tid = @task.id.to_s return 202, to("/task/#{tid}").to_json else - bad_request_error "No accepted content type" + halt 400, "No accepted content type" end end diff --git a/lib/report.rb b/lib/report.rb index f576106..7c06d60 100644 --- a/lib/report.rb +++ b/lib/report.rb @@ -1,208 +1,29 @@ # Get a list of all possible reports to prediction models # @param [Header] Accept one of text/uri-list, # @return [text/uri-list] list of all prediction models -get "/report/?" do +get "/api/report/?" do models = Model::Validation.all case @accept when "text/uri-list" - uri_list = models.collect{|model| uri("/report/#{model.model_id}")} + uri_list = models.collect{|model| uri("/api/report/#{model.model_id}")} return uri_list.join("\n") + "\n" when "application/json" models = JSON.parse models.to_json list = [] - models.each{|m| list << uri("/report/#{m["model_id"]["$oid"]}")} + models.each{|m| list << uri("/api/report/#{m["_id"]["$oid"]}")} return list.to_json else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end -get "/report/:id/?" do +get "/api/report/:id/?" do case @accept when "application/xml" - model = Model::Lazar.find params[:id] - not_found_error "Model with id: #{params[:id]} not found." unless model - prediction_model = Model::Validation.find_by :model_id => params[:id] - validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") - - if File.directory?("#{File.dirname(__FILE__)}/../../lazar") - lazar_commit = `cd #{File.dirname(__FILE__)}/../../lazar; git rev-parse HEAD`.strip - lazar_commit = "https://github.com/opentox/lazar/tree/#{lazar_commit}" - else - lazar_commit = "https://github.com/opentox/lazar/releases/tag/v#{Gem.loaded_specs["lazar"].version}" - end - - report = OpenTox::QMRFReport.new - - # QSAR Identifier Title 1.1 - report.value "QSAR_title", "Lazar model for #{prediction_model.species} #{prediction_model.endpoint}" - - # Software coding the model 1.3 - report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :description => "lazar Lazy Structure- Activity Relationships", :number => "1", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} - report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware - - # Date of QMRF 2.1 - report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}" - - # QMRF author(s) and contact details 2.1 - report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} - report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor - - # Model developer(s) and contact details 2.5 - report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Rastatterstr. 41, CH-4057 Basel", :email => "info@in-silico.ch", :number => "1", :url => "www.in-silico.ch"} - report.ref_catalog :model_authors, :authors_catalog, :modelauthor - - # Date of model development and/or publication 2.6 - report.value "model_date", "#{Time.parse(model.created_at.to_s).strftime('%Y')}" - - # Reference(s) to main scientific papers and/or software package 2.7 - report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "Maunz, Guetlein, Rautenberg, Vorgrimmler, Gebele and Helma (2013), lazar: a modular predictive toxicology framework ", :url => "http://dx.doi.org/10.3389/fphar.2013.00038"} - report.ref_catalog :references, :publications_catalog, :publications_catalog_1 - - # Reference(s) to main scientific papers and/or software package 2.7 - report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "Maunz A and Helma C (2008) Prediction of chemical toxicity with local support vector regression and activity-specific kernels. SAR & QSAR in Environmental Research 19 (5-6), 413-431", :url => "http://dx.doi.org/10.1080/10629360802358430"} - report.ref_catalog :references, :publications_catalog, :publications_catalog_2 - - # Species 3.1 - report.value "model_species", prediction_model.species - - # Endpoint 3.2 - report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""} - report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1 - - # Endpoint Units 3.4 - report.value "endpoint_units", "#{prediction_model.unit}" - - model_type = model.class.to_s.gsub('OpenTox::Model::Lazar','') - - # Type of model 4.1 - report.value "algorithm_type", "#{model_type}" - - # Explicit algorithm 4.2 - report.change_catalog :algorithms_catalog, :algorithms_catalog_1, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Neighbor algorithm: #{model.algorithms["similarity"]["method"].gsub('_',' ').titleize}#{(model.algorithms["similarity"][:min] ? ' with similarity > ' + model.algorithms["similarity"][:min].to_s : '')}"} - report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_1 - report.change_catalog :algorithms_catalog, :algorithms_catalog_3, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "modified k-nearest neighbor #{model_type}"} - report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_3 - if model.algorithms["prediction"] - pred_algorithm_params = (model.algorithms["prediction"][:method] == "rf" ? "random forest" : model.algorithms["prediction"][:method]) - end - report.change_catalog :algorithms_catalog, :algorithms_catalog_2, {:definition => "see Helma 2016 and lazar.in-silico.ch, submitted version: #{lazar_commit}", :description => "Prediction algorithm: #{model.algorithms["prediction"].to_s.gsub('OpenTox::Algorithm::','').gsub('_',' ').gsub('.', ' with ')} #{(pred_algorithm_params ? pred_algorithm_params : '')}"} - report.ref_catalog :algorithm_explicit, :algorithms_catalog, :algorithms_catalog_2 - - # Descriptors in the model 4.3 - if model.algorithms["descriptors"][:type] - report.change_catalog :descriptors_catalog, :descriptors_catalog_1, {:description => "", :name => "#{model.algorithms["descriptors"][:type]}", :publication_ref => "", :units => ""} - report.ref_catalog :algorithms_descriptors, :descriptors_catalog, :descriptors_catalog_1 - end - - # Descriptor selection 4.4 - report.value "descriptors_selection", "#{model.algorithms["feature_selection"].gsub('_',' ')} #{model.algorithms["feature_selection"].collect{|k,v| k.to_s + ': ' + v.to_s}.join(', ')}" if model.algorithms["feature_selection"] - - # Algorithm and descriptor generation 4.5 - report.value "descriptors_generation", "exhaustive breadth first search for paths in chemical graphs (simplified MolFea algorithm)" - - # Software name and version for descriptor generation 4.6 - report.change_catalog :software_catalog, :software_catalog_2, {:name => "lazar, submitted version: #{lazar_commit}", :description => "simplified MolFea algorithm", :number => "2", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} - report.ref_catalog :descriptors_generation_software, :software_catalog, :software_catalog_2 - - # Chemicals/Descriptors ratio 4.7 - report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)" - - # Description of the applicability domain of the model 5.1 - report.value "app_domain_description", " -

- The applicability domain (AD) of the training set is characterized by - the confidence index of a prediction (high confidence index: close to - the applicability domain of the training set/reliable prediction, low - confidence: far from the applicability domain of the - trainingset/unreliable prediction). The confidence index considers (i) - the similarity and number of neighbors and (ii) contradictory examples - within the neighbors. A formal definition can be found in Helma 2006. -

-

- The reliability of predictions decreases gradually with increasing - distance from the applicability domain (i.e. decreasing confidence index) -

- - " - - # Method used to assess the applicability domain 5.2 - report.value "app_domain_method", "see Helma 2006 and Maunz 2008" - - # Software name and version for applicability domain assessment 5.3 - report.change_catalog :software_catalog, :software_catalog_3, {:name => "lazar, submitted version: #{lazar_commit}", :description => "integrated into main lazar algorithm", :number => "3", :url => "https://lazar.in-silico.ch", :contact => "info@in-silico.ch"} - report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3 - - # Limits of applicability 5.4 - report.value "applicability_limits", "Predictions with low confidence index, unknown substructures and neighbors that might act by different mechanisms" - - # Availability of the training set 6.1 - report.change_attributes "training_set_availability", {:answer => "Yes"} - - # Available information for the training set 6.2 - report.change_attributes "training_set_data", {:cas => "Yes", :chemname => "Yes", :formula => "Yes", :inchi => "Yes", :mol => "Yes", :smiles => "Yes"} - - # Data for each descriptor variable for the training set 6.3 - report.change_attributes "training_set_descriptors", {:answer => "No"} - - # Data for the dependent variable for the training set 6.4 - report.change_attributes "dependent_var_availability", {:answer => "All"} - - # Other information about the training set 6.5 - report.value "other_info", "#{prediction_model.source}" - - # Pre-processing of data before modelling 6.6 - report.value "preprocessing", (model.class == OpenTox::Model::LazarRegression ? "-log10 transformation" : "none") - - # Robustness - Statistics obtained by leave-many-out cross-validation 6.9 - if prediction_model.repeated_crossvalidation - crossvalidations = prediction_model.crossvalidations - out = haml File.read(validation_template), :layout=> false, :locals => {:model => prediction_model} - report.value "lmo", out - end - - # Mechanistic basis of the model 8.1 - report.value "mechanistic_basis"," -

- Compounds with similar structures (neighbors) are assumed to have - similar activities as the query compound. For the determination of - activity specific similarities only statistically relevant subtructures - (paths) are used. For this reason there is a priori no bias towards - specific mechanistic hypothesis. -

- - " - - # A priori or a posteriori mechanistic interpretation 8.2 - report.value "mechanistic_basis_comments","a posteriori for individual predictions" - - # Other information about the mechanistic interpretation 8.3 - report.value "mechanistic_basis_info","

Hypothesis about biochemical mechanisms can be derived from individual - predictions by inspecting neighbors and relevant fragments.

-

Neighbors are compounds that are similar in respect to a certain - endpoint and it is likely that compounds with high similarity act by - similar mechanisms as the query compound. Links at the webinterface - prove an easy access to additional experimental data and literature - citations for the neighbors and the query structure.

-

Activating and deactivating parts of the query compound are highlighted - in red and green on the webinterface. Fragments that are unknown (or too - infrequent for statistical evaluation are marked in yellow and - additional statistical information about the individual fragments can be - retrieved. Please note that lazar predictions are based on neighbors and - not on fragments. Fragments and their statistical significance are used - for the calculation of activity specific similarities.

" - - # Bibliography 9.2 - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2 - report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "Helma (2006), Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity.", :url => "http://dx.doi.org/10.1007/s11030-005-9001-5"} - report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3 - - # output - response['Content-Type'] = "application/xml" + report = qmrf_report params[:id] return report.to_xml else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end diff --git a/lib/substance.rb b/lib/substance.rb index f493714..5d57505 100644 --- a/lib/substance.rb +++ b/lib/substance.rb @@ -1,5 +1,5 @@ # Get all substances -get "/substance/?" do +get "/api/substance/?" do substances = Substance.all case @accept when "text/uri-list" @@ -10,25 +10,25 @@ get "/substance/?" do substances = JSON.parse list.to_json return JSON.pretty_generate substances else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end # Get a substance by ID -get "/substance/:id/?" do +get "/api/substance/:id/?" do case @accept when "application/json" - mongoid = /^[a-f\d]{24}$/i - halt 400, "Input #{params[:id]} is no valid ID.".to_json unless params[:id].match(mongoid) substance = Substance.find params[:id] if substance - out = {"compound": {"id": substance.id, "inchi": substance.inchi, "smiles": substance.smiles, "warnings": substance.warnings}} - response['Content-Type'] = @accept + out = {"compound": {"id": substance.id, + "inchi": substance.inchi, + "smiles": substance.smiles + }} return JSON.pretty_generate JSON.parse(out.to_json) else - halt 400, "Substance with ID #{input} not found." + halt 400, "Substance with ID #{params[:id]} not found." end else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end diff --git a/lib/swagger.rb b/lib/swagger.rb index acb2ad0..2c3ea87 100644 --- a/lib/swagger.rb +++ b/lib/swagger.rb @@ -1,5 +1,3 @@ -get "/" do - response['Content-Type'] = "text/html" - index_file = File.join(ENV['HOME'],"swagger-ui/dist/index.html") - File.read(index_file) +get "/swagger" do + redirect("/api") end diff --git a/lib/validation.rb b/lib/validation.rb index fad8a44..031b9e1 100644 --- a/lib/validation.rb +++ b/lib/validation.rb @@ -4,7 +4,7 @@ VALIDATION_TYPES = ["repeatedcrossvalidation", "leaveoneout", "crossvalidation", # 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 +get "/api/validation/?" do uri_list = VALIDATION_TYPES.collect{|validationtype| uri("/validation/#{validationtype}")} case @accept when "text/uri-list" @@ -12,7 +12,7 @@ get "/validation/?" do when "application/json" return uri_list.to_json else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end @@ -20,8 +20,8 @@ end # @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] +get "/api/validation/:validationtype/?" do + halt 400, "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] case params[:validationtype] when "repeatedcrossvalidation" validations = Validation::RepeatedCrossValidation.all @@ -35,22 +35,22 @@ get "/validation/:validationtype/?" do case @accept when "text/uri-list" - uri_list = validations.collect{|validation| uri("/validation/#{params[:validationtype]}/#{validation.id}")} + uri_list = validations.collect{|validation| uri("/api/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]["_id"]["$oid"]}") + validations[idx][:URI] = uri("/api/validation/#{params[:validationtype]}/#{validations[idx]["_id"]["$oid"]}") end return validations.to_json else - bad_request_error "Mime type #{@accept} is not supported." + halt 400, "Mime type #{@accept} is not supported." end end # Get validation representation -get "/validation/:validationtype/:id/?" do - bad_request_error "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] +get "/api/validation/:validationtype/:id/?" do + halt 400, "There is no such validation type as: #{params[:validationtype]}" unless VALIDATION_TYPES.include? params[:validationtype] case params[:validationtype] when "repeatedcrossvalidation" validation = Validation::RepeatedCrossValidation.find params[:id] @@ -62,10 +62,6 @@ get "/validation/:validationtype/:id/?" do validation = Validation::RegressionCrossValidation.find params[:id] end - 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 + halt 404, "#{params[:validationtype]} with id: #{params[:id]} not found." unless validation return validation.to_json end -- cgit v1.2.3