fhir_models 1.8.2 → 1.8.3

data/.rubocop_todo.yml

@@ -0,0 +1,76 @@
+# This configuration was generated by
+# `rubocop --auto-gen-config`
+# on 2017-02-25 13:02:53 -0500 using RuboCop version 0.47.1.
+# The point is for the user to remove these configuration records
+# one by one as the offenses are removed from the code base.
+# Note that changes in the inspected code, or installation of new
+# versions of RuboCop, may require this file to be generated again.
+
+# Offense count: 37
+Metrics/AbcSize:
+  Max: 423
+
+# Offense count: 10
+# Configuration parameters: CountComments, ExcludedMethods.
+Metrics/BlockLength:
+  Max: 96
+
+# Offense count: 1
+# Configuration parameters: CountBlocks.
+Metrics/BlockNesting:
+  Max: 4
+
+# Offense count: 5
+# Configuration parameters: CountComments.
+Metrics/ClassLength:
+  Max: 499
+
+# Offense count: 26
+Metrics/CyclomaticComplexity:
+  Max: 69
+
+# Offense count: 40
+# Configuration parameters: CountComments.
+Metrics/MethodLength:
+  Max: 105
+
+# Offense count: 1
+# Configuration parameters: CountComments.
+Metrics/ModuleLength:
+  Max: 120
+
+
+# Offense count: 25
+Metrics/PerceivedComplexity:
+  Max: 72
+
+# Offense count: 16
+Style/ClassVars:
+  Exclude:
+    - 'lib/fhir_models/bootstrap/definitions.rb'
+    - 'lib/fhir_models/fluentpath/parse.rb'
+
+# Offense count: 14
+Style/Documentation:
+  Exclude:
+    - 'spec/**/*'
+    - 'test/**/*'
+    - 'lib/fhir_models/bootstrap/definitions.rb'
+    - 'lib/fhir_models/bootstrap/field.rb'
+    - 'lib/fhir_models/bootstrap/generator.rb'
+    - 'lib/fhir_models/bootstrap/hashable.rb'
+    - 'lib/fhir_models/bootstrap/json.rb'
+    - 'lib/fhir_models/bootstrap/model.rb'
+    - 'lib/fhir_models/bootstrap/preprocess.rb'
+    - 'lib/fhir_models/bootstrap/template.rb'
+    - 'lib/fhir_models/bootstrap/xml.rb'
+    - 'lib/fhir_models/fhir.rb'
+    - 'lib/fhir_models/fhir_ext/structure_definition.rb'
+    - 'lib/fhir_models/fhir_ext/structure_definition_finding.rb'
+    - 'lib/fhir_models/fluentpath/expression.rb'
+    - 'lib/fhir_models/fluentpath/parse.rb'
+
+# Offense count: 1
+Style/MethodMissing:
+  Exclude:
+    - 'lib/fhir_models/bootstrap/model.rb'

data/.travis.yml

@@ -1,10 +1,13 @@
 language: ruby
+env:
+  - TESTMEMORY=0 GCDELAY=2.0
 rvm:
   - "2.1.10"
-  - "2.2.5"
-  - "2.3.1"
+  - "2.2.6"
+  - "2.3.3"
+  - "2.4.0"
 script:
-  - bundle exec rake test
+  - bundle exec rake
   - bundle exec codeclimate-test-reporter
 notifications:
   email:
@@ -14,3 +17,6 @@ notifications:
 addons:
   code_climate:
     repo_token: 0230b3379581b30743b7b4355d7394e427648e604d19a2aba987956201eee290
+before_install:
+  - gem update --system
+  - gem update bundler

data/Gemfile

@@ -1,4 +1,4 @@
 source 'https://rubygems.org'
-
+ruby RUBY_VERSION
 # Specify your gem's dependencies in fhir_models.gemspec
 gemspec

data/Guardfile

@@ -0,0 +1,50 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+## Uncomment and set this to only include directories you want to watch
+# directories %w(app lib config test spec features) \
+#  .select{|d| Dir.exists?(d) ? d : UI.warning("Directory #{d} does not exist")}
+
+## Note: if you are using the `directories` clause above and you are not
+## watching the project directory ('.'), then you will want to move
+## the Guardfile to a watched dir and symlink it back, e.g.
+#
+#  $ mkdir config
+#  $ mv Guardfile config/
+#  $ ln -s config/Guardfile .
+#
+# and, you'll have to watch "config/Guardfile" instead of "Guardfile"
+
+# Note: The cmd option is now required due to the increasing number of ways
+#       rspec may be run, below are examples of the most common uses.
+#  * bundler: 'bundle exec rspec'
+#  * bundler binstubs: 'bin/rspec'
+#  * spring: 'bin/rspec' (This will use spring if running and you have
+#                          installed the spring binstubs per the docs)
+#  * zeus: 'zeus rspec' (requires the server to be started separately)
+#  * 'just' rspec: 'rspec'
+
+guard :rspec, cmd: 'bundle exec rspec' do
+  require 'guard/rspec/dsl'
+  dsl = Guard::RSpec::Dsl.new(self)
+
+  # Feel free to open issues for suggestions and improvements
+
+  # RSpec files
+  rspec = dsl.rspec
+  watch(rspec.spec_helper) { rspec.spec_dir }
+  watch(rspec.spec_support) { rspec.spec_dir }
+  watch(rspec.spec_files)
+
+  # Ruby files
+  ruby = dsl.ruby
+  dsl.watch_spec_files_for(ruby.lib_files)
+end
+
+guard :test do
+  watch(%r{^test/.+_test\.rb$})
+  watch('test/test_helper.rb') { 'test' }
+
+  # Non-rails
+  watch(%r{^lib/(.+)\.rb$}) { |m| "test/#{m[1]}_test.rb" }
+end

data/Rakefile

@@ -1,5 +1,6 @@
 require 'bundler/gem_tasks'
 require 'rake/testtask'
+require 'rspec/core/rake_task'
 require 'rubocop/rake_task'
 
 Dir['lib/fhir_models/tasks/**/*.rake'].each do |file|
@@ -14,13 +15,11 @@ Rake::TestTask.new(:test) do |t|
   t.warning = false
 end
 
+RSpec::Core::RakeTask.new
+
 desc 'Run rubocop'
 task :rubocop do
   RuboCop::RakeTask.new
 end
 
-task test: [:rubocop] do
-  system('open coverage/index.html')
-end
-
-task default: [:test]
+task default: %i[rubocop spec test]

data/bin/console

@@ -7,8 +7,8 @@ require 'fhir_models'
 # with your gem easier. You can also use a different console, if you like.
 
 # (If you use this, don't forget to add pry to your Gemfile!)
-# require "pry"
-# Pry.start
+require 'pry'
+Pry.start
 
-require 'irb'
-IRB.start
+# require 'irb'
+# IRB.start

data/fhir_models.gemspec

@@ -25,12 +25,15 @@ Gem::Specification.new do |spec|
   spec.add_dependency 'bcp47', '>= 0.3'
   spec.add_dependency 'mime-types', '>= 1.16', '< 3'
 
-  spec.add_development_dependency 'bundler', '~> 1.13'
-  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'bundler'
+  spec.add_development_dependency 'rake'
   spec.add_development_dependency 'pry'
   spec.add_development_dependency 'test-unit'
+  spec.add_development_dependency 'rspec'
   spec.add_development_dependency 'simplecov'
   spec.add_development_dependency 'nokogiri-diff'
-  spec.add_development_dependency 'rubocop', '~> 0.43.0'
+  spec.add_development_dependency 'rubocop'
   spec.add_development_dependency 'codeclimate-test-reporter'
+  spec.add_development_dependency 'guard-rspec'
+  spec.add_development_dependency 'guard-test'
 end

data/lib/fhir_models.rb

@@ -1,6 +1,7 @@
 root = File.expand_path '..', File.dirname(File.absolute_path(__FILE__))
 
-require File.join(root, 'lib', 'fhir_models', 'version.rb')
+require File.join(root, 'lib', 'fhir_models', 'version')
+require File.join(root, 'lib', 'fhir_models', 'deprecate')
 
 # Need to require Hashable first
 require File.join(root, 'lib', 'fhir_models', 'bootstrap', 'hashable.rb')

data/lib/fhir_models/bootstrap/definitions.rb

@@ -1,6 +1,7 @@
 require 'tempfile'
 module FHIR
   class Definitions
+    extend FHIR::Deprecate
     @@defns = File.expand_path '../definitions', File.dirname(File.absolute_path(__FILE__))
     @@types = nil
     @@resources = nil
@@ -10,125 +11,127 @@ module FHIR
     @@valuesets = nil
     @@search_params = nil
 
+    @@cache = {}
+
     # ----------------------------------------------------------------
     #  Types
     # ----------------------------------------------------------------
 
-    def self.load_types
-      if @@types.nil?
+    def self.types
+      @@types ||= begin
         # load the types
         filename = File.join(@@defns, 'structures', 'profiles-types.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@types = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
     end
+    deprecate :load_types, :types
+    private_class_method :types
 
-    def self.get_primitive_types
-      load_types
+    def self.primitive_types
       # primitive data types start with a lowercase letter
-      @@types.select { |t| t['id'][0] == t['id'][0].downcase }
+      @primitive_types ||= types.select { |t| t['id'].start_with?(*('a'..'z').to_a) }
     end
+    deprecate :get_primitive_types, :primitive_types
 
-    def self.get_complex_types
-      load_types
+    def self.complex_types
       # complex data types start with an uppercase letter
       # and we'll filter out profiles on types (for example, Age is a profile on Quantity)
-      @@types.select { |t| (t['id'][0] == t['id'][0].upcase) && (t['id'] == t['snapshot']['element'].first['path']) }
+      @complex_types ||= types.select { |t| t['id'].start_with?(*('A'..'Z').to_a) && (t['id'] == t['snapshot']['element'].first['path']) }
     end
+    deprecate :get_complex_types, :complex_types
 
-    def self.get_type_definition(type_name)
+    def self.type_definition(type_name)
       return nil if type_name.nil?
-      load_types
-      d = @@types.find { |x| x['xmlId'] == type_name || x['name'] == type_name || x['url'] == type_name }
-      d = FHIR::StructureDefinition.new(d) unless d.nil?
-      d
+      return @@cache[type_name] if @@cache[type_name]
+      definition = types.find { |x| x['xmlId'] == type_name || x['name'] == type_name || x['url'] == type_name }
+      @@cache[type_name] = FHIR::StructureDefinition.new(definition) if definition
+      @@cache[type_name]
     end
+    deprecate :get_type_definition, :type_definition
 
     # ----------------------------------------------------------------
     #  Resources, Profiles, Extensions
     # ----------------------------------------------------------------
 
-    def self.load_resources
-      if @@resources.nil?
+    def self.resources
+      @@resources ||= begin
         # load the resources
         filename = File.join(@@defns, 'structures', 'profiles-resources.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@resources = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
     end
+    deprecate :load_resources, :resources
+    private_class_method :resources
 
-    def self.get_resource_definitions
-      load_resources
-      @@resources
+    def self.resource_definitions
+      resources.select { |r| r['kind'] == 'resource' }
     end
+    deprecate :get_resource_definitions, :resource_definitions
 
-    def self.get_resource_definition(resource_name)
+    def self.resource_definition(resource_name)
       return nil if resource_name.nil?
-      load_resources
-      d = @@resources.find { |x| x['xmlId'] == resource_name || x['name'] == resource_name || x['url'] == resource_name }
-      d = FHIR::StructureDefinition.new(d) unless d.nil?
-      d
+      return @@cache[resource_name] if @@cache[resource_name]
+      definition = resources.find { |x| x['xmlId'] == resource_name || x['name'] == resource_name || x['url'] == resource_name }
+      @@cache[resource_name] = FHIR::StructureDefinition.new(definition) if definition
+      @@cache[resource_name]
     end
+    deprecate :get_resource_definition, :resource_definition
 
-    def self.load_profiles
-      if @@profiles.nil?
+    def self.profiles
+      @@profiles ||= begin
         # load the built-in profiles
         filename = File.join(@@defns, 'structures', 'profiles-others.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@profiles = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
     end
+    deprecate :load_profiles, :profiles
+    private_class_method :profiles
 
-    def self.load_extensions
-      if @@extensions.nil?
+    def self.extensions
+      @@extensions ||= begin
         # load the built-in extensions
         filename = File.join(@@defns, 'structures', 'extension-definitions.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@extensions = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
     end
+    deprecate :load_extensions, :extensions
+    private_class_method :extensions
 
-    def self.get_extension_definition(extension_name)
+    def self.extension_definition(extension_name)
       return nil if extension_name.nil?
-      load_extensions
-      d = @@extensions.find { |x| x['xmlId'] == extension_name || x['name'] == extension_name || x['url'] == extension_name }
-      d = FHIR::StructureDefinition.new(d) unless d.nil?
-      d
+      extension = extensions.find { |x| x['xmlId'] == extension_name || x['name'] == extension_name || x['url'] == extension_name }
+      return nil if extension.nil?
+      FHIR::StructureDefinition.new(extension)
     end
+    deprecate :get_extension_definition, :extension_definition
 
     # Get the basetype (String) for a given profile or extension.
-    def self.get_basetype(uri)
+    def self.basetype(uri)
       return nil if uri.nil?
-      load_profiles
-      load_extensions
-
-      defn = @@profiles.select { |x| x['url'] == uri }.first
-      defn = @@extensions.select { |x| x['url'] == uri }.first if defn.nil?
-
-      basetype = nil
-      basetype = defn['baseType'] unless defn.nil?
-      basetype
+      defn = profiles.detect { |x| x['url'] == uri } || extensions.detect { |x| x['url'] == uri }
+      return nil if defn.nil?
+      defn['baseType']
     end
+    deprecate :get_basetype, :basetype
 
     # Get the StructureDefinition for a given profile.
-    def self.get_profile(uri)
+    def self.profile(uri)
       return nil if uri.nil?
-      load_profiles
-      load_extensions
-
-      defn = @@profiles.select { |x| x['url'] == uri }.first
-      defn = @@extensions.select { |x| x['url'] == uri }.first if defn.nil?
-
-      profile = nil
-      profile = FHIR::StructureDefinition.new(defn) unless defn.nil?
-      profile
+      defn = profiles.detect { |x| x['url'] == uri } || extensions.detect { |x| x['url'] == uri }
+      return nil if defn.nil?
+      FHIR::StructureDefinition.new(defn)
     end
+    deprecate :get_profile, :profile
 
-    def self.get_profiles_for_resource(resource_name)
+    def self.profiles_for_resource(resource_name)
       return nil if resource_name.nil?
-      load_profiles
-      @@profiles.select { |x| x['baseType'] == resource_name }.map { |x| FHIR::StructureDefinition.new(x) }
+      profiles.select { |x| x['baseType'] == resource_name }.map { |x| FHIR::StructureDefinition.new(x) }
     end
+    deprecate :get_profiles_for_resource, :profile_for_resource
 
     # Get a dynamically generated class for a given profile.
     def self.get_profile_class(uri)
@@ -171,66 +174,69 @@ module FHIR
     #  ValueSet Code Expansions
     # ----------------------------------------------------------------
 
-    def self.load_expansions
-      if @@expansions.nil?
+    def self.expansions
+      @@expansions ||= begin
         # load the expansions
         filename = File.join(@@defns, 'valuesets', 'expansions.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@expansions = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
-      if @@valuesets.nil?
+    end
+    deprecate :load_expansions, :expansions
+
+    def self.valuesets
+      @@valuesets ||= begin
         # load the valuesets
         filename = File.join(@@defns, 'valuesets', 'valuesets.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@valuesets = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
     end
 
     # Get codes (Array of Strings) for a given expansion.
     def self.get_codes(uri)
       return nil if uri.nil?
-      load_expansions
-      codes = nil
-      valueset = @@expansions.select { |x| x['url'] == uri }.first
+      return @@cache[uri] if @@cache[uri]
+      valueset = expansions.select { |x| x['url'] == uri }.first
       unless valueset.nil?
-        codes = {}
+        @@cache[uri] = {}
         if !valueset['expansion'].nil? && !valueset['expansion']['contains'].nil?
           keys = valueset['expansion']['contains'].map { |x| x['system'] }.uniq
-          keys.each { |x| codes[x] = [] }
-          valueset['expansion']['contains'].each { |x| codes[x['system']] << x['code'] }
+          keys.each { |x| @@cache[uri][x] = [] }
+          valueset['expansion']['contains'].each { |x| @@cache[uri][x['system']] << x['code'] }
         end
         if !valueset['compose'].nil? && !valueset['compose']['include'].nil?
           included_systems = valueset['compose']['include'].map { |x| x['system'] }.uniq
-          included_systems.each { |x| codes[x] = [] unless codes.keys.include?(x) }
-          systems = @@valuesets.select { |x| x['resourceType'] == 'CodeSystem' && included_systems.include?(x['url']) }
+          included_systems.each { |x| @@cache[uri][x] = [] unless @@cache[uri].keys.include?(x) }
+          systems = valuesets.select { |x| x['resourceType'] == 'CodeSystem' && included_systems.include?(x['url']) }
           systems.each do |x|
-            x['concept'].each { |y| codes[x['url']] << y['code'] } if x['concept']
+            x['concept'].each { |y| @@cache[uri][x['url']] << y['code'] } if x['concept']
           end
         end
       end
-      codes
+      @@cache[uri]
     end
 
     # Get the "display" (human-readable title) for a given code in a code system (uri)
     # If one can't be found, return nil
     def self.get_display(uri, code)
       return nil if uri.nil? || code.nil?
-      load_expansions
-      valuesets = @@expansions.select { |x| x['compose']['include'].detect {|i| i['system'] == uri } }
-      valuesets += @@valuesets.select { |x| x['url'] == uri }
+      valuesets_and_expansions = expansions.select { |ex| ex['compose']['include'].detect { |i| i['system'] == uri } }
+      valuesets_and_expansions += valuesets.select { |vs| vs['url'] == uri }
       code_hash = nil
-      valuesets.each do |valueset|
-        if !valueset['expansion'].nil? && !valueset['expansion']['contains'].nil?
-          code_hash = valueset['expansion']['contains'].select { |x| x['system'] == uri && x['code'] == code}.first
-        elsif !valueset['compose'].nil? && !valueset['compose']['include'].nil?
-          included_systems = valueset['compose']['include'].map { |x| x['system'] }.uniq
-          systems = @@valuesets.select { |x| x['resourceType'] == 'CodeSystem' && included_systems.include?(x['url']) }
-          systems.each do |x|
-            code_hash = x['concept'].select { |con| con['url'] == uri && con['code'] == code }.first if x['concept']
+      valuesets_and_expansions.each do |valueset|
+        if valueset['expansion'] && valueset['expansion']['contains']
+          # This currently only matches 'expansions', not 'valuesets'
+          code_hash = valueset['expansion']['contains'].detect { |contained| contained['system'] == uri && contained['code'] == code }
+        elsif valueset['compose'] && valueset['compose']['include']
+          # This seems to only match 'valuesets'
+          valueset['compose']['include'].each do |code_system|
+            code_hash = code_system['concept'].detect { |con| con['code'] == code } if code_system['concept']
             break if code_hash
           end
         elsif valueset['concept']
-          code_hash = valueset['concept'].select { |v| v['code'] == code }.first
+          # This currently only matches 'valuesets', not 'expansions'
+          code_hash = valueset['concept'].detect { |vs| vs['code'] == code }
         end
         break if code_hash
       end
@@ -241,21 +247,21 @@ module FHIR
     #  Search Params
     # ----------------------------------------------------------------
 
-    def self.load_search_params
-      if @@search_params.nil?
+    def self.search_params
+      @@search_params ||= begin
         # load the search parameters
         filename = File.join(@@defns, 'structures', 'search-parameters.json')
         raw = File.open(filename, 'r:UTF-8', &:read)
-        @@search_params = JSON.parse(raw)['entry'].map { |e| e['resource'] }
+        JSON.parse(raw)['entry'].map { |e| e['resource'] }
       end
     end
+    deprecate :load_search_params, :search_params
+    private_class_method :search_params
 
-    def self.get_search_parameters(type_name)
+    def self.search_parameters(type_name)
       return nil if type_name.nil?
-      load_search_params
-      @@search_params.select { |p| p['base'].include?(type_name) && p['xpath'] && !p['xpath'].include?('extension') }.map { |p| p['code'] }
+      search_params.select { |p| p['base'].include?(type_name) && p['xpath'] && !p['xpath'].include?('extension') }.map { |p| p['code'] }
     end
-
-    private_class_method :load_types, :load_extensions, :load_expansions, :load_profiles, :load_resources, :load_search_params
+    deprecate :get_search_parameters, :search_parameters
   end
 end