diff options
Diffstat (limited to 'lib/dataset.rb')
| -rw-r--r-- | lib/dataset.rb | 133 |
1 files changed, 13 insertions, 120 deletions
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"] |