spout 0.12.1 → 0.13.0.beta1

data/lib/spout/commands/graphs.rb

@@ -1,40 +1,40 @@
 # frozen_string_literal: true
 
-require 'csv'
-require 'fileutils'
-require 'rubygems'
-require 'json'
-require 'yaml'
-require 'colorize'
-
-require 'spout/helpers/subject_loader'
-require 'spout/helpers/chart_types'
-require 'spout/models/variable'
-require 'spout/models/graphables'
-require 'spout/models/tables'
-require 'spout/helpers/config_reader'
-require 'spout/helpers/send_file'
-require 'spout/helpers/json_request'
-require 'spout/version'
+require "csv"
+require "fileutils"
+require "rubygems"
+require "json"
+require "yaml"
+require "colorize"
+
+require "spout/helpers/subject_loader"
+require "spout/helpers/chart_types"
+require "spout/models/variable"
+require "spout/models/graphables"
+require "spout/models/tables"
+require "spout/helpers/config_reader"
+require "spout/helpers/send_file"
+require "spout/helpers/json_request"
+require "spout/version"
 
 module Spout
   module Commands
     class Graphs
-      def initialize(argv, standard_version, deploy_mode = false, url = '', slug = '', token = '', webserver_name = '', subjects = nil)
+      def initialize(argv, standard_version, deploy_mode = false, url = "", slug = "", token = "", webserver_name = "", subjects = nil)
         @deploy_mode = deploy_mode
         @url = url
         @standard_version = standard_version
         @slug = slug
         @token = token
         @webserver_name = webserver_name
-        @clean = !(argv.delete('--no-resume').nil? && argv.delete('--clean').nil?)
+        @clean = !(argv.delete("--no-resume").nil? && argv.delete("--clean").nil?)
 
         @config = Spout::Helpers::ConfigReader.new
 
         @stratification_variable = Spout::Models::Variable.find_by_id @config.visit
 
         if @stratification_variable.nil?
-          if @config.visit == ''
+          if @config.visit == ""
             puts "The visit variable in .spout.yml can't be blank."
           else
             puts "Could not find the following visit variable: #{@config.visit}"
@@ -42,7 +42,7 @@ module Spout
           return self
         end
 
-        missing_variables = @config.charts.select { |c| Spout::Models::Variable.find_by_id(c['chart']).nil? }
+        missing_variables = @config.charts.select { |c| Spout::Models::Variable.find_by_id(c["chart"]).nil? }
         if missing_variables.count > 0
           puts "Could not find the following chart variable#{'s' unless missing_variables.size == 1}: #{missing_variables.join(', ')}"
           return self
@@ -50,17 +50,17 @@ module Spout
 
         rows_arg = argv.find { |arg| /^--rows=(\d*)/ =~ arg }
         argv.delete(rows_arg)
-        @number_of_rows = rows_arg.gsub(/--rows=/, '').to_i if rows_arg
+        @number_of_rows = rows_arg.gsub(/--rows=/, "").to_i if rows_arg
 
-        @valid_ids = argv.collect { |s| s.to_s.downcase }.compact.reject { |s| s == '' }
+        @valid_ids = argv.collect { |s| s.to_s.downcase }.compact.reject { |s| s == "" }
 
-        @chart_variables = @config.charts.unshift('chart' => @config.visit, 'title' => 'Histogram')
+        @chart_variables = @config.charts.unshift("chart" => @config.visit, "title" => "Histogram")
 
         @dictionary_root = Dir.pwd
-        @variable_files = Dir.glob(File.join(@dictionary_root, 'variables', '**', '*.json'))
+        @variable_files = Dir.glob(File.join(@dictionary_root, "variables", "**", "*.json"))
 
         t = Time.now
-        @graphs_folder = File.join('graphs', @standard_version)
+        @graphs_folder = File.join("graphs", @standard_version)
         FileUtils.mkpath @graphs_folder
 
         @subjects = if subjects
@@ -79,14 +79,14 @@ module Spout
       end
 
       def load_current_progress
-        @progress_file = File.join(@graphs_folder, '.progress.json')
+        @progress_file = File.join(@graphs_folder, ".progress.json")
         @progress = JSON.parse(File.read(@progress_file)) rescue @progress = {}
-        @progress = {} if !@progress.is_a?(Hash) || @clean || @progress['SPOUT_VERSION'] != Spout::VERSION::STRING
-        @progress['SPOUT_VERSION'] = Spout::VERSION::STRING
+        @progress = {} if !@progress.is_a?(Hash) || @clean || @progress["SPOUT_VERSION"] != Spout::VERSION::STRING
+        @progress["SPOUT_VERSION"] = Spout::VERSION::STRING
       end
 
       def save_current_progress
-        File.open(@progress_file, 'w') do |f|
+        File.open(@progress_file, "w") do |f|
           f.write(JSON.pretty_generate(@progress) + "\n")
         end
       end
@@ -115,12 +115,12 @@ module Spout
           end
 
           @progress[variable.id] ||= {}
-          @progress[variable.id]['uploaded'] ||= []
-          next if (!@deploy_mode && @progress[variable.id]['generated'] == true) || (@deploy_mode && @progress[variable.id]['uploaded'].include?(@webserver_name))
+          @progress[variable.id]["uploaded"] ||= []
+          next if (!@deploy_mode && @progress[variable.id]["generated"] == true) || (@deploy_mode && @progress[variable.id]["uploaded"].include?(@webserver_name))
 
           stats = compute_stats(variable)
 
-          if @deploy_mode && !@progress[variable.id]['uploaded'].include?(@webserver_name)
+          if @deploy_mode && !@progress[variable.id]["uploaded"].include?(@webserver_name)
             values = @subjects.collect(&variable.id.to_sym).compact_empty
             variable.n = values.n
             variable.unknown = values.unknown
@@ -142,8 +142,8 @@ module Spout
         return stats unless %w(numeric integer choices).include?(variable.type)
 
         @chart_variables.each do |chart_type_hash|
-          chart_type = chart_type_hash['chart']
-          chart_title = chart_type_hash['title'].downcase.tr(' ', '-')
+          chart_type = chart_type_hash["chart"]
+          chart_title = chart_type_hash["title"].downcase.tr(" ", "-")
           chart_variable = Spout::Models::Variable.find_by_id(chart_type)
 
           filtered_subjects = @subjects.reject { |s| s.send(chart_type).nil? || s.send(variable.id).nil? }
@@ -165,8 +165,8 @@ module Spout
         end
 
         chart_json_file = File.join(@graphs_folder, "#{variable.id}.json")
-        File.open(chart_json_file, 'w') { |file| file.write(JSON.pretty_generate(stats) + "\n") }
-        @progress[variable.id]['generated'] = true
+        File.open(chart_json_file, "w") { |file| file.write(JSON.pretty_generate(stats) + "\n") }
+        @progress[variable.id]["generated"] = true
         stats
       end
 
@@ -178,7 +178,7 @@ module Spout
         params[:variable][:spout_stats] = stats.to_json
         (json, status) = Spout::Helpers::JsonRequest.post("#{@url}/api/v1/variables/create_or_update.json", params)
         if json.is_a?(Hash) && status.is_a?(Net::HTTPSuccess)
-          @progress[variable.id]['uploaded'] << @webserver_name
+          @progress[variable.id]["uploaded"] << @webserver_name
         else
           puts "\nUPLOAD FAILED: ".colorize(:red) + variable.id
           puts "- Error: #{json.inspect}"

data/lib/spout/commands/help.rb

@@ -1,6 +1,6 @@
 # frozen_string_literal: true
 
-require 'colorize'
+require "colorize"
 
 module Spout
   module Commands

data/lib/spout/commands/importer.rb

@@ -1,16 +1,17 @@
 # frozen_string_literal: true
 
-require 'csv'
-require 'json'
-require 'fileutils'
-require 'colorize'
+require "csv"
+require "json"
+require "fileutils"
+require "colorize"
 
 module Spout
   module Commands
     class Importer
       def initialize(argv)
-        use_domains = !argv.delete('--domains').nil?
-        use_forms = !argv.delete('--forms').nil?
+        use_domains = !argv.delete("--domains").nil?
+        use_forms = !argv.delete("--forms").nil?
+        @preserve_case = !argv.delete("--preserve-case").nil?
         @csv_file = argv[1].to_s
         unless File.exist?(@csv_file)
           puts csv_usage
@@ -37,36 +38,36 @@ EOT
       end
 
       def import_variables
-        CSV.parse(File.open(@csv_file, 'r:iso-8859-1:utf-8', &:read), headers: true) do |line|
+        CSV.parse(File.open(@csv_file, "r:iso-8859-1:utf-8", &:read), headers: true) do |line|
           row = line.to_hash
-          if not row.keys.include?('id')
+          if not row.keys.include?("id")
             puts "\nMissing column header `".colorize( :red ) + "id".colorize( :light_cyan ) + "` in data dictionary.".colorize( :red ) + additional_csv_info
             exit(1)
           end
-          next if row['id'] == ''
-          folder = File.join('variables', row.delete('folder').to_s)
+          next if row["id"] == ""
+          folder = File.join("variables", row.delete("folder").to_s)
           FileUtils.mkpath folder
           hash = {}
-          id = row.delete('id').to_s.downcase
-          hash['id'] = id
-          hash['display_name'] = tenderize(row.delete('display_name').to_s)
-          hash['description'] = row.delete('description').to_s
-          hash['type'] = row.delete('type')
-          domain = row.delete('domain').to_s.downcase
-          hash['domain'] = domain if domain != ''
-          units = row.delete('units').to_s
-          hash['units'] = units if units != ''
-          calculation = row.delete('calculation').to_s
-          hash['calculation'] = calculation if calculation != ''
-          labels = row.delete('labels').to_s.split(';')
-          hash['labels'] = labels unless labels.empty?
-          hash['commonly_used'] = true if row.delete('commonly_used').to_s.casecmp('true').zero?
-          forms = row.delete('forms').to_s.split(';')
-          hash['forms'] = forms unless forms.empty?
-          hash['other'] = row unless row.empty?
+          id = row.delete("id").to_s.downcase
+          hash["id"] = id
+          hash["display_name"] = tenderize(row.delete("display_name").to_s)
+          hash["description"] = row.delete("description").to_s
+          hash["type"] = row.delete("type")
+          domain = row.delete("domain").to_s.downcase
+          hash["domain"] = domain if domain != ""
+          units = row.delete("units").to_s
+          hash["units"] = units if units != ""
+          calculation = row.delete("calculation").to_s
+          hash["calculation"] = calculation if calculation != ""
+          labels = row.delete("labels").to_s.split(";")
+          hash["labels"] = labels unless labels.empty?
+          hash["commonly_used"] = true if row.delete("commonly_used").to_s.casecmp("true").zero?
+          forms = row.delete("forms").to_s.split(";")
+          hash["forms"] = forms unless forms.empty?
+          hash["other"] = row unless row.empty?
 
           file_name = File.join(folder, "#{id}.json")
-          File.open(file_name, 'w') do |file|
+          File.open(file_name, "w") do |file|
             file.write(JSON.pretty_generate(hash) + "\n")
           end
           puts "      create".colorize( :green ) + "  #{file_name}"
@@ -76,33 +77,33 @@ EOT
       def import_domains
         domains = {}
 
-        CSV.parse(File.open(@csv_file, 'r:iso-8859-1:utf-8', &:read), headers: true) do |line|
+        CSV.parse(File.open(@csv_file, "r:iso-8859-1:utf-8", &:read), headers: true) do |line|
           row = line.to_hash
-          if not row.keys.include?('domain_id')
+          if not row.keys.include?("domain_id")
             puts "\nMissing column header `".colorize( :red ) + "domain_id".colorize( :light_cyan ) + "` in data dictionary.".colorize( :red ) + additional_csv_info
             exit(1)
           end
-          if not row.keys.include?('value')
+          if not row.keys.include?("value")
             puts "\nMissing column header `".colorize( :red ) + "value".colorize( :light_cyan ) + "` in data dictionary.".colorize( :red ) + additional_csv_info
             exit(1)
           end
-          if not row.keys.include?('display_name')
+          if not row.keys.include?("display_name")
             puts "\nMissing column header `".colorize( :red ) + "display_name".colorize( :light_cyan ) + "` in data dictionary.".colorize( :red ) + additional_csv_info
             exit(1)
           end
 
-          next if row['domain_id'].to_s == '' or row['value'].to_s == '' or row['display_name'].to_s == ''
-          folder = File.join('domains', row['folder'].to_s).gsub(/[^a-zA-Z0-9_\/\.-]/, '_')
-          domain_name = row['domain_id'].to_s.gsub(/[^a-zA-Z0-9_\/\.-]/, '_').downcase
+          next if row["domain_id"].to_s == "" or row["value"].to_s == "" or row["display_name"].to_s == ""
+          folder = File.join("domains", row["folder"].to_s).gsub(/[^a-zA-Z0-9_\/\.-]/, "_")
+          domain_name = row["domain_id"].to_s.gsub(/[^a-zA-Z0-9_\/\.-]/, "_").downcase
           domains[domain_name] ||= {}
           domains[domain_name]["folder"] = folder
           domains[domain_name]["options"] ||= []
 
           hash = {}
-          hash['value'] = row.delete('value').to_s
-          hash['display_name'] = tenderize(row.delete('display_name').to_s)
-          hash['description'] = row.delete('description').to_s
-          hash['missing'] = true if hash['value'].match(/^[\.-]/)
+          hash["value"] = row.delete("value").to_s
+          hash["display_name"] = tenderize(row.delete("display_name").to_s)
+          hash["description"] = row.delete("description").to_s
+          hash["missing"] = true if hash["value"].match(/^[\.-]/)
 
           domains[domain_name]["options"] << hash
         end
@@ -111,9 +112,9 @@ EOT
           folder = domain_hash["folder"]
           FileUtils.mkpath folder
 
-          file_name = File.join(folder, domain_name + '.json')
+          file_name = File.join(folder, "#{domain_name}.json")
 
-          File.open(file_name, 'w') do |file|
+          File.open(file_name, "w") do |file|
             file.write(JSON.pretty_generate(domain_hash["options"]) + "\n")
           end
           puts "      create".colorize( :green ) + "  #{file_name}"
@@ -121,36 +122,36 @@ EOT
       end
 
       def import_forms
-        CSV.parse(File.open(@csv_file, 'r:iso-8859-1:utf-8', &:read), headers: true) do |line|
+        CSV.parse(File.open(@csv_file, "r:iso-8859-1:utf-8", &:read), headers: true) do |line|
           row = line.to_hash
-          unless row.keys.include?('id')
+          unless row.keys.include?("id")
             puts "\nMissing column header `".colorize(:red) +
-                 'id'.colorize(:light_cyan) +
-                 '` in data dictionary.'.colorize(:red) +
+                 "id".colorize(:light_cyan) +
+                 "` in data dictionary.".colorize(:red) +
                  additional_csv_info
             exit(1)
           end
-          unless row.keys.include?('display_name')
+          unless row.keys.include?("display_name")
             puts "\nMissing column header `".colorize(:red) +
-                 'display_name'.colorize(:light_cyan) +
-                 '` in data dictionary.'.colorize(:red) +
+                 "display_name".colorize(:light_cyan) +
+                 "` in data dictionary.".colorize(:red) +
                  additional_csv_info
             exit(1)
           end
-          next if row['id'] == ''
-          folder = File.join('forms', row.delete('folder').to_s)
+          next if row["id"] == ""
+          folder = File.join("forms", row.delete("folder").to_s)
           FileUtils.mkpath folder
           hash = {}
-          id = row.delete('id').to_s.downcase
-          hash['id'] = id
-          hash['display_name'] = tenderize(row.delete('display_name').to_s)
-          hash['code_book'] = row.delete('code_book').to_s
-          hash['other'] = row unless row.empty?
+          id = row.delete("id").to_s.downcase
+          hash["id"] = id
+          hash["display_name"] = tenderize(row.delete("display_name").to_s)
+          hash["code_book"] = row.delete("code_book").to_s
+          hash["other"] = row unless row.empty?
           file_name = File.join(folder, "#{id}.json")
-          File.open(file_name, 'w') do |file|
+          File.open(file_name, "w") do |file|
             file.write(JSON.pretty_generate(hash) + "\n")
           end
-          puts '      create'.colorize(:green) + "  #{file_name}"
+          puts "      create".colorize(:green) + "  #{file_name}"
         end
       end
 
@@ -158,6 +159,7 @@ EOT
       # Ex: BODY MASS INDEX changes to Body Mass Index
       # Ex: Patient ID stays the same as Patient ID
       def tenderize(text)
+        return text if @preserve_case
         if /[a-z]/ =~ text
           text
         else

data/lib/spout/commands/outliers.rb

@@ -1,13 +1,13 @@
 # frozen_string_literal: true
 
-require 'yaml'
-require 'erb'
-require 'fileutils'
+require "yaml"
+require "erb"
+require "fileutils"
 
-require 'spout/helpers/subject_loader'
-require 'spout/models/outlier_result'
-require 'spout/helpers/number_helper'
-require 'spout/helpers/config_reader'
+require "spout/helpers/subject_loader"
+require "spout/models/outlier_result"
+require "spout/helpers/number_helper"
+require "spout/helpers/config_reader"
 
 module Spout
   module Commands
@@ -16,9 +16,9 @@ module Spout
 
       def initialize(standard_version, argv)
         @standard_version = standard_version
-        @console = (argv.delete('--console') != nil)
+        @console = (argv.delete("--console") != nil)
 
-        @variable_files = Dir.glob('variables/**/*.json')
+        @variable_files = Dir.glob("variables/**/*.json")
         @valid_ids = []
         @number_of_rows = nil
 
@@ -37,7 +37,7 @@ module Spout
           Spout::Models::OutlierResult.new(@subjects, method, csv_files)
         end
 
-        @outlier_results.select!{|outlier_result| ['numeric', 'integer'].include?(outlier_result.variable_type) }
+        @outlier_results.select!{|outlier_result| ["numeric", "integer"].include?(outlier_result.variable_type) }
         @outlier_results.sort!{|a,b| [a.weight, a.method] <=> [b.weight, b.method]}
 
         @overall_results = @subject_loader.csv_files.collect do |csv_file|
@@ -47,20 +47,20 @@ module Spout
           [ csv_file, major_outliers, minor_outliers, total_outliers ]
         end
 
-        coverage_folder = File.join(Dir.pwd, 'coverage')
+        coverage_folder = File.join(Dir.pwd, "coverage")
         FileUtils.mkpath coverage_folder
-        html_file = File.join(coverage_folder, 'outliers.html')
+        html_file = File.join(coverage_folder, "outliers.html")
 
-        File.open(html_file, 'w+') do |file|
-          erb_location = File.join( File.dirname(__FILE__), '../views/outliers.html.erb' )
+        File.open(html_file, "w+") do |file|
+          erb_location = File.join( File.dirname(__FILE__), "../views/outliers.html.erb" )
           file.puts ERB.new(File.read(erb_location)).result(binding)
         end
 
         unless @console
-          open_command = 'open'  if RUBY_PLATFORM.match(/darwin/) != nil
-          open_command = 'start' if RUBY_PLATFORM.match(/mingw/) != nil
+          open_command = "open"  if RUBY_PLATFORM.match(/darwin/) != nil
+          open_command = "start" if RUBY_PLATFORM.match(/mingw/) != nil
 
-          system "#{open_command} #{html_file}" if ['start', 'open'].include?(open_command)
+          system "#{open_command} #{html_file}" if ["start", "open"].include?(open_command)
         end
         puts "#{html_file}\n\n"
         return self

data/lib/spout/commands/project_generator.rb

@@ -1,9 +1,9 @@
 # frozen_string_literal: true
 
-require 'colorize'
-require 'fileutils'
+require "colorize"
+require "fileutils"
 
-require 'spout/helpers/framework'
+require "spout/helpers/framework"
 
 module Spout
   module Commands
@@ -16,7 +16,7 @@ module Spout
       end
 
       def generate_folder_structure!(argv)
-        skip_gemfile = !argv.delete('--skip-gemfile').nil?
+        skip_gemfile = !argv.delete("--skip-gemfile").nil?
         @project_name = argv[1].to_s.strip
         @full_path = File.join(@project_name)
         usage = <<-EOT
@@ -26,33 +26,33 @@ Usage: spout new FOLDER
 The FOLDER must be empty or new.
 
 EOT
-        if @full_path == '' || (Dir.exist?(@full_path) && (Dir.entries(@full_path) & ['.gitignore', '.ruby-version', '.travis.yml', 'Gemfile', 'Rakefile', 'domains', 'variables', 'test']).size > 0)
+        if @full_path == "" || (Dir.exist?(@full_path) && (Dir.entries(@full_path) & [".gitignore", ".ruby-version", ".travis.yml", "Gemfile", "Rakefile", "domains", "variables", "test"]).size > 0)
           puts usage
           exit(0)
         end
         FileUtils.mkpath(@full_path)
-        copy_file 'gitignore', '.gitignore'
-        copy_file 'ruby-version', '.ruby-version'
-        copy_file 'travis.yml', '.travis.yml'
-        evaluate_file 'spout.yml.erb', '.spout.yml'
-        evaluate_file 'CHANGELOG.md.erb', 'CHANGELOG.md'
-        copy_file 'Gemfile'
-        copy_file 'Rakefile'
-        evaluate_file 'README.md.erb', 'README.md'
-        copy_file 'VERSION'
-        directory 'domains'
-        copy_file 'keep', 'domains/.keep'
-        directory 'variables'
-        copy_file 'keep', 'variables/.keep'
-        directory 'forms'
-        copy_file 'keep', 'forms/.keep'
-        directory 'test'
-        copy_file 'test/dictionary_test.rb'
-        copy_file 'test/test_helper.rb'
+        copy_file "gitignore", ".gitignore"
+        copy_file "ruby-version", ".ruby-version"
+        copy_file "travis.yml", ".travis.yml"
+        evaluate_file "spout.yml.erb", ".spout.yml"
+        evaluate_file "CHANGELOG.md.erb", "CHANGELOG.md"
+        copy_file "Gemfile"
+        copy_file "Rakefile"
+        evaluate_file "README.md.erb", "README.md"
+        copy_file "VERSION"
+        directory "domains"
+        copy_file "keep", "domains/.keep"
+        directory "variables"
+        copy_file "keep", "variables/.keep"
+        directory "forms"
+        copy_file "keep", "forms/.keep"
+        directory "test"
+        copy_file "test/dictionary_test.rb"
+        copy_file "test/test_helper.rb"
         return if skip_gemfile
-        puts '         run'.colorize(:green) + '  bundle install'.colorize(:light_cyan)
+        puts "         run".colorize(:green) + "  bundle install".colorize(:light_cyan)
         Dir.chdir(@full_path)
-        system 'bundle install'
+        system "bundle install"
       end
     end
   end