spout 0.8.0.beta1 → 0.8.0.beta2

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: spout
 version: !ruby/object:Gem::Version
-  version: 0.8.0.beta1
+  version: 0.8.0.beta2
 platform: ruby
 authors:
 - Remo Mueller
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-23 00:00:00.000000000 Z
+date: 2014-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -97,12 +97,15 @@ files:
 - lib/spout.rb
 - lib/spout/actions.rb
 - lib/spout/application.rb
+- lib/spout/commands/coverage.rb
 - lib/spout/commands/graphs.rb
-- lib/spout/commands/json_charts_and_tables.rb
+- lib/spout/commands/images.rb
 - lib/spout/helpers/array_statistics.rb
 - lib/spout/helpers/chart_types.rb
+- lib/spout/helpers/subject_loader.rb
 - lib/spout/helpers/table_formatting.rb
 - lib/spout/hidden_reporter.rb
+- lib/spout/models/coverage_result.rb
 - lib/spout/models/subject.rb
 - lib/spout/support/javascripts/data.js
 - lib/spout/support/javascripts/highcharts-convert.js

data/lib/spout/commands/json_charts_and_tables.rb

@@ -1,202 +0,0 @@
-require 'csv'
-require 'fileutils'
-require 'rubygems'
-require 'json'
-require 'yaml'
-
-
-require 'spout/models/subject'
-require 'spout/helpers/array_statistics'
-require 'spout/helpers/chart_types'
-
-
-module Spout
-  module Commands
-    class JsonChartsAndTables
-      def initialize(variables)
-        spout_config = YAML.load_file('.spout.yml')
-
-        _visit = ''
-
-        if spout_config.kind_of?(Hash)
-          _visit = spout_config['visit'].to_s.strip
-
-          chart_variables = if spout_config['charts'].kind_of?(Array)
-            spout_config['charts'].collect{|c| c.to_s.strip}.select{|c| c != ''}
-          else
-            []
-          end
-        else
-          puts "The YAML file needs to be in the following format:"
-          puts "histogram: visitnumber  # VISIT_VARIABLE\ncharts:\n  - age_s1\n  - gender\n  - race\n"
-          exit
-        end
-
-        if Spout::Helpers::ChartTypes::get_json(_visit, 'variable') == nil
-          if _visit == ''
-            puts "The visit variable in .spout.yml can't be blank."
-          else
-            puts "Could not find the following visit variable: #{_visit}"
-          end
-          exit
-        end
-        missing_variables = chart_variables.select{|c| Spout::Helpers::ChartTypes::get_json(c, 'variable') == nil}
-        if missing_variables.count > 0
-          puts "Could not find the following chart variable#{'s' unless missing_variables.size == 1}: #{missing_variables.join(', ')}"
-          exit
-        end
-
-        argv_string = variables.join(',')
-        number_of_rows = nil
-
-        if match_data = argv_string.match(/-rows=(\d*)/)
-          number_of_rows = match_data[1].to_i
-          argv_string.gsub!(match_data[0], '')
-        end
-
-        valid_ids = argv_string.split(',').compact.reject{|s| s == ''}
-
-        @visit = _visit
-
-        chart_lookup = { _visit => "Histogram" }
-
-        chart_variables.each do |chart_variable|
-          json = Spout::Helpers::ChartTypes::get_json(chart_variable, 'variable')
-          chart_lookup[chart_variable] = json['display_name']
-        end
-
-
-
-        t = Time.now
-
-
-        version = standard_version
-
-        subjects = []
-
-        FileUtils.mkpath "charts/#{version}"
-
-        csv_files = Dir.glob("csvs/#{version}/*.csv")
-
-        csv_files.each_with_index do |csv_file, index|
-          count = 0
-          puts "Parsing: #{csv_file}"
-          CSV.parse( File.open(csv_file, 'r:iso-8859-1:utf-8'){|f| f.read}, headers: true, header_converters: lambda { |h| h.to_s.downcase } ) do |line|
-
-            row = line.to_hash
-            count += 1
-            puts "Line: #{count}" if (count % 1000 == 0)
-            subjects << Spout::Models::Subject.create do |t|
-
-              t._visit = row[_visit] #.to_s.strip
-
-              row.each do |key,value|
-                unless t.respond_to?(key)
-                  t.class.send(:define_method, "#{key}") { instance_variable_get("@#{key}") }
-                  t.class.send(:define_method, "#{key}=") { |value| instance_variable_set("@#{key}", value) }
-                end
-
-                unless value == nil
-                  t.send("#{key}=", value)
-                end
-              end
-            end
-            # puts "Memory Used: " + (`ps -o rss -p #{$$}`.strip.split.last.to_i / 1024).to_s + " MB" if count % 1000 == 0
-            # break if count >= 1000
-            break if number_of_rows != nil and count >= number_of_rows
-          end
-        end
-
-        variable_files = Dir.glob('variables/**/*.json')
-        variable_files_count = variable_files.count
-
-        variable_files.each do |variable_file|
-          json = JSON.parse(File.read(variable_file)) rescue json = nil
-          next unless json
-          next unless valid_ids.include?(json["id"].to_s.downcase) or valid_ids.size == 0
-          next unless ["numeric", "integer"].include?(json["type"])
-          method  = json['id'].to_s.downcase
-          next unless Spout::Models::Subject.method_defined?(method)
-
-          subjects.each{ |s| s.send(method) != nil ? s.send("#{method}=", s.send("#{method}").to_f) : nil }
-        end
-
-        variable_files.each_with_index do |variable_file, file_index|
-          json = JSON.parse(File.read(variable_file)) rescue json = nil
-          next unless json
-          next unless valid_ids.include?(json["id"].to_s.downcase) or valid_ids.size == 0
-          next unless ["numeric", "integer", "choices"].include?(json["type"])
-          variable_name  = json['id'].to_s.downcase
-          next unless Spout::Models::Subject.method_defined?(variable_name)
-
-          puts "#{file_index+1} of #{variable_files_count}: #{variable_file.gsub(/(^variables\/|\.json$)/, '').gsub('/', ' / ')}"
-
-
-          stats = {
-            charts: {},
-            tables: {}
-          }
-
-          chart_types = case json['type'] when 'integer', 'numeric', 'choices'
-            chart_lookup.keys
-          else
-            []
-          end
-
-          chart_types.each do |chart_type|
-            if chart_type == _visit
-              filtered_subjects = subjects.select{ |s| s.send(chart_type) != nil }  # and s.send(variable_name) != nil
-              if filtered_subjects.count > 0
-                stats[:charts][chart_lookup[chart_type].downcase] = Spout::Helpers::ChartTypes::chart_histogram(chart_type, filtered_subjects, json, variable_name)
-                stats[:tables][chart_lookup[chart_type].downcase] = Spout::Helpers::ChartTypes::table_arbitrary(chart_type, filtered_subjects, json, variable_name)
-              end
-            else
-              filtered_subjects = subjects.select{ |s| s.send(chart_type) != nil } # and s.send(variable_name) != nil
-              if filtered_subjects.count > 0
-                stats[:charts][chart_lookup[chart_type].downcase] = Spout::Helpers::ChartTypes::chart_arbitrary(chart_type, filtered_subjects, json, variable_name, visits)
-                stats[:tables][chart_lookup[chart_type].downcase] = visits.collect do |visit_display_name, visit_value|
-                  visit_subjects = filtered_subjects.select{ |s| s._visit == visit_value }
-                  unknown_subjects = visit_subjects.select{ |s| s.send(variable_name) == nil }
-                  (visit_subjects.count > 0 && visit_subjects.count != unknown_subjects.count) ? Spout::Helpers::ChartTypes::table_arbitrary(chart_type, visit_subjects, json, variable_name, visit_display_name) : nil
-                end.compact
-              end
-            end
-          end
-
-          chart_json_file = File.join('charts', version, "#{json['id']}.json")
-          File.open(chart_json_file, 'w') { |file| file.write( JSON.pretty_generate(stats) + "\n" ) }
-
-        end
-
-        puts "Took #{Time.now - t} seconds."
-
-
-      end
-
-      # [["Visit 1", "1"], ["Visit 2", "2"], ["CVD Outcomes", "3"]]
-      def visits
-        @visits ||= begin
-          Spout::Commands::JsonChartsAndTables::domain_array(@visit)
-        end
-      end
-
-      # This is directly from Spout
-      def self.standard_version
-        version = File.open('VERSION', &:readline).strip rescue ''
-        version == '' ? '1.0.0' : version
-      end
-
-      def self.domain_array(variable_name)
-        variable_file = Dir.glob("variables/**/#{variable_name}.json").first
-        json = JSON.parse(File.read(variable_file)) rescue json = nil
-        if json
-          domain_json = Spout::Helpers::ChartTypes::get_domain(json)
-          domain_json ? domain_json.collect{|option_hash| [option_hash['display_name'], option_hash['value']]} : []
-        else
-          []
-        end
-      end
-
-    end
-  end
-end