spout 0.8.0.beta12 → 0.8.0.beta13

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,6 +1,10 @@
 ## 0.8.0
 
 ### Enhancements
+- Tests now include check for variables that reference one or more forms
+  - `include Spout::Tests::FormExistenceValidation`
+  - `include Spout::Tests::FormNameUniqueness`
+  - `include Spout::Tests::FormNameMatch`
 - Added `spout graphs` command that generates JSON charts and tables of each variable in a dataset
   - This command requires a .spout.yml file to be specified to identify the following variables:
     - `visit`: This variable is used to separate subject encounters in a histogram

data/README.md

@@ -120,6 +120,9 @@ class DictionaryTest < Test::Unit::TestCase
   include Spout::Tests::DomainExistenceValidation
   include Spout::Tests::DomainFormat
   include Spout::Tests::DomainNameUniqueness
+  include Spout::Tests::FormExistenceValidation
+  include Spout::Tests::FormNameUniqueness
+  include Spout::Tests::FormNameMatch
 end
 ```
 
@@ -233,3 +236,49 @@ This will generate a graph for ahi for the first 10 rows of each dataset CSV.
 
 
 This will generate charts and tables for each variable in the dataset plotted against the variables listed under `charts`.
+
+### Example Variable that references a Domain and a Form
+
+`variables/Demographics/gender.json`
+```json
+{
+  "id": "gender",
+  "display_name": "Gender",
+  "description": "Gender as reported by subject",
+  "type": "choices",
+  "domain": "gender12",
+  "labels": [
+    "gender"
+  ],
+  "commonly_used": true,
+  "forms": [
+    "intake_questionnaire"
+  ]
+}
+```
+
+`domains/gender12.json`
+```json
+[
+  {
+    "value": "1",
+    "display_name": "Male",
+    "description": ""
+  },
+  {
+    "value": "2",
+    "display_name": "Female",
+    "description": ""
+  }
+]
+```
+
+`forms/Baseline Visit/intake_questionnaire.json`
+```json
+{
+  "id": "intake_questionnaire",
+  "display_name": "Intake Questionnaire at Baseline Visit",
+  "code_book": "Baseline-Visit-Intake-Questionnaire.pdf"
+}
+```
+

data/lib/spout/commands/exporter.rb

@@ -1,5 +1,6 @@
 require 'csv'
 require 'json'
+require 'fileutils'
 
 module Spout
   module Commands

data/lib/spout/models/outlier_result.rb

@@ -4,7 +4,7 @@ require 'spout/helpers/json_loader'
 module Spout
   module Models
     class OutlierResult
-      attr_reader :csv_files, :method, :major_outliers, :minor_outliers, :outliers, :weight, :units, :median
+      attr_reader :csv_files, :method, :major_outliers, :minor_outliers, :outliers, :weight, :units, :display_name, :median
 
       def initialize(subjects, method, csv_files)
         @values = subjects.collect(&method.to_sym)
@@ -23,6 +23,7 @@ module Spout
         end
         variable = Spout::Helpers::JsonLoader::get_variable(method)
         @units = (variable.kind_of?(Hash) ? variable['units'] : nil)
+        @display_name = (variable.kind_of?(Hash) ? variable['display_name'] : nil)
         @median = @values.median
       end
 

data/lib/spout/tests/form_existence_validation.rb

@@ -0,0 +1,30 @@
+module Spout
+  module Tests
+    module FormExistenceValidation
+
+      def assert_form_existence(item, msg = nil)
+        form_names = Dir.glob("forms/**/*.json").collect{|file| file.split('/').last.to_s.downcase.split('.json').first}
+
+        result = begin
+          (form_names | JSON.parse(File.read(item))["forms"]).size == form_names.size
+        rescue JSON::ParserError
+          false
+        end
+
+        full_message = build_message(msg, "One or more forms referenced by ? does not exist.", item)
+        assert_block(full_message) do
+          result
+        end
+      end
+
+      Dir.glob("variables/**/*.json").each do |file|
+        if (not [nil, ''].include?(JSON.parse(File.read(file))["forms"]) rescue false)
+          define_method("test_form_exists: "+file) do
+            assert_form_existence file
+          end
+        end
+      end
+
+    end
+  end
+end

data/lib/spout/tests/form_name_match.rb

@@ -0,0 +1,11 @@
+module Spout
+  module Tests
+    module FormNameMatch
+      Dir.glob("forms/**/*.json").each do |file|
+        define_method("test_form_name_match: "+file) do
+          assert_equal file.gsub(/^.*\//, '').gsub('.json', '').downcase, (begin JSON.parse(File.read(file))["id"] rescue nil end)
+        end
+      end
+    end
+  end
+end

data/lib/spout/tests/form_name_uniqueness.rb

@@ -0,0 +1,10 @@
+module Spout
+  module Tests
+    module FormNameUniqueness
+      def test_form_name_uniqueness
+        files = Dir.glob("forms/**/*.json").collect{|file| file.split('/').last.downcase }
+        assert_equal [], files.select{ |f| files.count(f) > 1 }.uniq
+      end
+    end
+  end
+end

data/lib/spout/tests/json_validation.rb

@@ -27,6 +27,12 @@ module Spout
         end
       end
 
+      Dir.glob("forms/**/*.json").each do |file|
+        define_method("test_json: "+file) do
+          assert_valid_json file
+        end
+      end
+
     end
   end
 end

data/lib/spout/tests.rb

@@ -11,6 +11,9 @@ require 'spout/tests/domain_existence_validation'
 require 'spout/tests/domain_format'
 require 'spout/tests/domain_name_uniqueness'
 require 'spout/tests/domain_specified'
+require 'spout/tests/form_existence_validation'
+require 'spout/tests/form_name_uniqueness'
+require 'spout/tests/form_name_match'
 
 module Spout
   module Tests
@@ -22,6 +25,9 @@ module Spout
     include Spout::Tests::DomainFormat
     include Spout::Tests::DomainNameUniqueness
     include Spout::Tests::DomainSpecified
+    include Spout::Tests::FormExistenceValidation
+    include Spout::Tests::FormNameUniqueness
+    include Spout::Tests::FormNameMatch
 
     Turn.config.trace = 1
   end

data/lib/spout/version.rb

@@ -3,7 +3,7 @@ module Spout
     MAJOR = 0
     MINOR = 8
     TINY = 0
-    BUILD = "beta12" # nil, "pre", "rc", "rc2"
+    BUILD = "beta13" # nil, "pre", "rc", "rc2"
 
     STRING = [MAJOR, MINOR, TINY, BUILD].compact.join('.')
   end

data/lib/spout/views/outliers.html.erb

@@ -115,6 +115,7 @@ tfoot td {
             <tr>
               <th>CSV</th>
               <th>Column</th>
+              <th>Display Name</th>
               <th>Median</th>
               <th>Major Outliers</th>
               <th>Minor Outliers</th>
@@ -130,6 +131,7 @@ tfoot td {
                     <code class="<%= css_class %>"><%= csv_file %></code><br />
                   <% end %></td>
                 <td><%= outlier_result.method %></td>
+                <td><%= outlier_result.display_name.to_s[0..20] %></td>
                 <td>
                   <% if outlier_result.median.kind_of?(Numeric) %>
                     <code class="default"><%= number_with_delimiter(outlier_result.median.round(2)) %></code>

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: spout
 version: !ruby/object:Gem::Version
-  version: 0.8.0.beta12
+  version: 0.8.0.beta13
 platform: ruby
 authors:
 - Remo Mueller
@@ -95,7 +95,6 @@ files:
 - Rakefile
 - bin/spout
 - lib/spout.rb
-- lib/spout/actions.rb
 - lib/spout/application.rb
 - lib/spout/commands/coverage.rb
 - lib/spout/commands/exporter.rb
@@ -135,6 +134,9 @@ files:
 - lib/spout/tests/domain_format.rb
 - lib/spout/tests/domain_name_uniqueness.rb
 - lib/spout/tests/domain_specified.rb
+- lib/spout/tests/form_existence_validation.rb
+- lib/spout/tests/form_name_match.rb
+- lib/spout/tests/form_name_uniqueness.rb
 - lib/spout/tests/json_helper.rb
 - lib/spout/tests/json_validation.rb
 - lib/spout/tests/variable_name_match.rb

data/lib/spout/actions.rb

@@ -1,92 +0,0 @@
-# module Spout
-#   class Actions
-
-#     def interpret(argv)
-#       # case argv.first.to_s.scan(/\w/).first
-#       case argv.first
-#       when 'new', 'n', 'ne', '-new', '-n', '-ne'
-#         new_template_dictionary(argv)
-#       when '--version', '-v', '-ve', '-ver', 'version', 'v', 've', 'ver'
-#         puts "Spout #{Spout::VERSION::STRING}"
-#       when 'test', 't', 'te', 'tes', '--test', '-t', '-te', '-tes'
-#         system "bundle exec rake HIDE_PASSING_TESTS=true"
-#       # when 'tv'
-#       #   system "bundle exec rake"
-#       when 'import', 'i', 'im', 'imp', '--import', '-i', '-im', '-imp'
-#         import_from_csv(argv)
-#       when 'import_domain', '--import_domain', 'import_domains', '--import_domains'
-#         import_from_csv(argv, 'domains')
-#       when 'export', 'e', 'ex', 'exp', '--export', '-e', '-ex', '-exp'
-#         new_data_dictionary_export(argv)
-#       when 'coverage', '-coverage', '--coverage', 'c', '-c'
-#         coverage_report(argv)
-#       when 'pngs', '-pngs', '--pngs', 'p', '-p'
-#         generate_images(argv.last(argv.size - 1))
-#       when 'graphs', '-graphs', '--graphs', 'g', '-g'
-#         generate_charts_and_tables(argv.last(argv.size - 1))
-#       when 'outliers', '-outliers', '--outliers', 'o', '-o'
-#         outliers_report(argv)
-#       # else
-#       #   help
-#       end
-#     end
-
-#     protected
-
-#       def csv_usage
-#         usage = <<-EOT
-
-# Usage: spout import CSVFILE
-
-# The CSVFILE must be the location of a valid CSV file.
-
-# EOT
-#         usage
-#       end
-
-#       def import_from_csv(argv, type = "")
-#         csv_file = File.join(argv[1].to_s.strip)
-#         if File.exists?(csv_file)
-#           system "bundle exec rake spout:import CSV=#{csv_file} #{'TYPE='+type if type.to_s != ''}"
-#         else
-#           puts csv_usage
-#         end
-#       end
-
-#       def new_data_dictionary_export(argv)
-#         version = argv[1].to_s.gsub(/[^a-zA-Z0-9\.-]/, '_').strip
-#         version_string = (version == '' ? "" : "VERSION=#{version}")
-#         system "bundle exec rake spout:create #{version_string}"
-#       end
-
-#       def coverage_report(argv)
-#         require 'spout/commands/coverage'
-#         Spout::Commands::Coverage.new(standard_version, argv)
-#         # system "bundle exec rake spout:coverage"
-#       end
-
-#       def outliers_report(argv)
-#         system "bundle exec rake spout:outliers"
-#       end
-
-#       def flag_values(flags, param)
-#         flags.select{|f| f[0..((param.size + 3) - 1)] == "--#{param}-" and f.length > param.size + 3}.collect{|f| f[(param.size + 3)..-1]}
-#       end
-
-#       def generate_images(flags)
-#         params = {}
-#         params['types']        = flag_values(flags, 'type')
-#         params['variable_ids'] = flag_values(flags, 'id')
-#         params['sizes']        = flag_values(flags, 'size')
-
-#         params_string = params.collect{|key, values| "#{key}=#{values.join(',')}"}.join(' ')
-
-#         system "bundle exec rake spout:images #{params_string}"
-#       end
-
-#       def generate_charts_and_tables(variables)
-#         system "bundle exec rake spout:json variables=#{variables.join(',')}"
-#       end
-
-#   end
-# end