fhir_models 4.1.0 → 4.2.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.codeclimate.yml

@@ -9,7 +9,7 @@ engines:
     enabled: true
   rubocop:
     enabled: true
-    channel: rubocop-0-67
+    channel: rubocop-0-80
 ratings:
   paths:
   - "**.inc"

data/.github/workflows/ruby.yml

@@ -0,0 +1,26 @@
+name: Ruby
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        ruby-version: ['2.6', '2.7']
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: ${{ matrix.ruby-version }}
+        bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+    - name: Run tests
+      run: bundle exec rake
+    - name: Rubocop
+      run: bundle exec rubocop

data/.rubocop.yml

@@ -10,10 +10,16 @@ AllCops:
     - 'tmp/**/*'
     - '*.gemspec'
     - 'bin/*'
-Metrics/LineLength:
+Layout/LineLength:
   Enabled: false
 Style/FrozenStringLiteralComment:
   Enabled: false
+Style/HashEachMethods:
+  Enabled: true
+Style/HashTransformKeys:
+  Enabled: true
+Style/HashTransformValues:
+  Enabled: true
 inherit_mode:
   merge:
     - Exclude

data/.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2019-07-01 12:11:28 -0400 using RuboCop version 0.67.2.
+# on 2021-03-30 16:14:38 -0400 using RuboCop version 0.80.0.
 # 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
@@ -45,7 +45,7 @@ Metrics/AbcSize:
 Metrics/BlockLength:
   Max: 78
 
-# Offense count: 10
+# Offense count: 12
 # Configuration parameters: CountBlocks.
 Metrics/BlockNesting:
   Max: 5
@@ -53,7 +53,7 @@ Metrics/BlockNesting:
 # Offense count: 7
 # Configuration parameters: CountComments.
 Metrics/ClassLength:
-  Max: 358
+  Max: 356
 
 # Offense count: 23
 Metrics/CyclomaticComplexity:
@@ -62,7 +62,7 @@ Metrics/CyclomaticComplexity:
 # Offense count: 44
 # Configuration parameters: CountComments, ExcludedMethods.
 Metrics/MethodLength:
-  Max: 135
+  Max: 133
 
 # Offense count: 2
 # Configuration parameters: CountComments.
@@ -73,30 +73,19 @@ Metrics/ModuleLength:
 Metrics/PerceivedComplexity:
   Max: 68
 
-# Offense count: 1
-# Configuration parameters: PreferredName.
-Naming/RescuedExceptionsVariableName:
-  Exclude:
-    - 'lib/fhir_models/bootstrap/hashable.rb'
-
 # Offense count: 4
 # Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
-# AllowedNames: io, id, to, by, on, in, at, ip, db
-Naming/UncommunicativeMethodParamName:
+# AllowedNames: io, id, to, by, on, in, at, ip, db, os, pp
+Naming/MethodParameterName:
   Exclude:
     - 'lib/fhir_models/fhir_ext/structure_definition_compare.rb'
 
-# Offense count: 3
-Performance/Caller:
-  Exclude:
-    - 'lib/fhir_models/bootstrap/model.rb'
-    - 'lib/fhir_models/deprecate.rb'
-
-# Offense count: 1
+# Offense count: 2
 # Cop supports --auto-correct.
-Performance/InefficientHashSearch:
+# Configuration parameters: PreferredName.
+Naming/RescuedExceptionsVariableName:
   Exclude:
-    - 'lib/fhir_models/bootstrap/template.rb'
+    - 'lib/fhir_models/bootstrap/hashable.rb'
 
 # Offense count: 1
 # Configuration parameters: .
@@ -141,7 +130,6 @@ Style/Documentation:
 Style/IfUnlessModifier:
   Exclude:
     - 'lib/fhir_models/bootstrap/generator.rb'
-    - 'lib/fhir_models/bootstrap/hashable.rb'
     - 'lib/fhir_models/bootstrap/model.rb'
     - 'lib/fhir_models/bootstrap/template.rb'
     - 'lib/fhir_models/bootstrap/xml.rb'
@@ -175,7 +163,7 @@ Style/NumericPredicate:
     - 'spec/**/*'
     - 'lib/fhir_models/fhir_ext/structure_definition_compare.rb'
 
-# Offense count: 2
+# Offense count: 1
 # Cop supports --auto-correct.
 Style/OrAssignment:
   Exclude:
@@ -200,8 +188,8 @@ Style/RescueStandardError:
 
 # Offense count: 4
 # Cop supports --auto-correct.
-# Configuration parameters: ConvertCodeThatCanStartToReturnNil, Whitelist.
-# Whitelist: present?, blank?, presence, try, try!
+# Configuration parameters: ConvertCodeThatCanStartToReturnNil, AllowedMethods.
+# AllowedMethods: present?, blank?, presence, try, try!
 Style/SafeNavigation:
   Exclude:
     - 'lib/fhir_models/bootstrap/definitions.rb'

data/Gemfile.lock

@@ -1,28 +1,28 @@
 PATH
   remote: .
   specs:
-    fhir_models (4.1.0)
+    fhir_models (4.2.1)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.10.4)
+      nokogiri (>= 1.11.4)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    ast (2.4.0)
+    ast (2.4.2)
     bcp47 (0.3.3)
       i18n
-    coderay (1.1.2)
-    concurrent-ruby (1.1.6)
+    coderay (1.1.3)
+    concurrent-ruby (1.1.9)
     coolline (0.5.0)
       unicode_utils (~> 1.4)
     date_time_precision (0.8.1)
-    diff-lcs (1.3)
+    diff-lcs (1.4.4)
     docile (1.3.2)
-    ffi (1.11.1)
+    ffi (1.13.1)
     formatador (0.2.5)
-    guard (2.15.0)
+    guard (2.16.2)
       formatador (>= 0.2.4)
       listen (>= 2.7, < 4.0)
       lumberjack (>= 1.0.12, < 2.0)
@@ -39,78 +39,78 @@ GEM
     guard-test (2.0.8)
       guard-compat (~> 1.2)
       test-unit (~> 3.0)
-    i18n (1.8.2)
+    i18n (1.8.10)
       concurrent-ruby (~> 1.0)
-    jaro_winkler (1.5.3)
-    json (2.2.0)
-    listen (3.1.5)
-      rb-fsevent (~> 0.9, >= 0.9.4)
-      rb-inotify (~> 0.9, >= 0.9.7)
-      ruby_dep (~> 1.2)
-    lumberjack (1.0.13)
-    method_source (0.9.2)
+    jaro_winkler (1.5.4)
+    json (2.3.1)
+    listen (3.3.1)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    lumberjack (1.2.8)
+    method_source (1.0.0)
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2019.1009)
-    mini_portile2 (2.4.0)
+    mime-types-data (3.2021.0901)
+    mini_portile2 (2.5.3)
     nenv (0.3.0)
-    nokogiri (1.10.8)
-      mini_portile2 (~> 2.4.0)
+    nokogiri (1.11.7)
+      mini_portile2 (~> 2.5.0)
+      racc (~> 1.4)
     nokogiri-diff (0.2.0)
       nokogiri (~> 1.5)
       tdiff (~> 0.3, >= 0.3.2)
     notiffany (0.1.3)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.17.0)
-    parser (2.6.3.0)
-      ast (~> 2.4.0)
-    power_assert (1.1.5)
-    pry (0.12.2)
-      coderay (~> 1.1.0)
-      method_source (~> 0.9.0)
+    parallel (1.20.1)
+    parser (3.0.0.0)
+      ast (~> 2.4.1)
+    power_assert (1.2.0)
+    pry (0.13.1)
+      coderay (~> 1.1)
+      method_source (~> 1.0)
     pry-coolline (0.2.5)
       coolline (~> 0.5)
-    psych (3.1.0)
+    racc (1.5.2)
     rainbow (3.0.0)
-    rake (12.3.3)
-    rb-fsevent (0.10.3)
-    rb-inotify (0.10.0)
+    rake (13.0.1)
+    rb-fsevent (0.10.4)
+    rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rspec (3.8.0)
-      rspec-core (~> 3.8.0)
-      rspec-expectations (~> 3.8.0)
-      rspec-mocks (~> 3.8.0)
-    rspec-core (3.8.2)
-      rspec-support (~> 3.8.0)
-    rspec-expectations (3.8.4)
+    rexml (3.2.5)
+    rspec (3.10.0)
+      rspec-core (~> 3.10.0)
+      rspec-expectations (~> 3.10.0)
+      rspec-mocks (~> 3.10.0)
+    rspec-core (3.10.0)
+      rspec-support (~> 3.10.0)
+    rspec-expectations (3.10.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-mocks (3.8.1)
+      rspec-support (~> 3.10.0)
+    rspec-mocks (3.10.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.8.0)
-    rspec-support (3.8.2)
-    rubocop (0.67.0)
+      rspec-support (~> 3.10.0)
+    rspec-support (3.10.0)
+    rubocop (0.80.0)
       jaro_winkler (~> 1.5.1)
       parallel (~> 1.10)
-      parser (>= 2.5, != 2.5.1.1)
-      psych (>= 3.1.0)
+      parser (>= 2.7.0.1)
       rainbow (>= 2.2.2, < 4.0)
+      rexml
       ruby-progressbar (~> 1.7)
-      unicode-display_width (>= 1.4.0, < 1.6)
-    ruby-progressbar (1.10.1)
-    ruby_dep (1.5.0)
+      unicode-display_width (>= 1.4.0, < 1.7)
+    ruby-progressbar (1.11.0)
     shellany (0.0.1)
-    simplecov (0.17.0)
+    simplecov (0.17.1)
       docile (~> 1.1)
       json (>= 1.8, < 3)
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.2)
     tdiff (0.3.4)
-    test-unit (3.3.3)
+    test-unit (3.3.6)
       power_assert
-    thor (0.20.3)
-    unicode-display_width (1.5.0)
+    thor (1.0.1)
+    unicode-display_width (1.6.1)
     unicode_utils (1.4.0)
 
 PLATFORMS
@@ -126,12 +126,12 @@ DEPENDENCIES
   pry-coolline
   rake
   rspec
-  rubocop (= 0.67)
+  rubocop (= 0.80)
   simplecov (~> 0.17.0)
   test-unit
 
 RUBY VERSION
-   ruby 2.5.1p57
+   ruby 2.5.6p201
 
 BUNDLED WITH
-   2.0.1
+   2.2.21

data/LICENSE

@@ -0,0 +1,201 @@
+Apache License
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data/README.md

@@ -54,6 +54,16 @@ $ bundle exec rake fhir:console
     'system' => 'http://unitsofmeasure.org'
   )
   ```
+  
+  Iterating over all elements in a resource, including nested elements...
+  ```ruby
+  patient.each_element do |value, metadata, path|
+    puts "Info for #{path}:"
+    puts "- value: #{value}"
+    puts "- type: #{metadata['type']}"
+    puts "- cardinality: #{metadata['min']}..#{metadata['max']}"
+  end
+  ```
 
   ### Validation
 
@@ -73,7 +83,7 @@ $ bundle exec rake fhir:console
   ```
 # License
 
-Copyright 2014-2019 The MITRE Corporation
+Copyright 2014-2021 The MITRE Corporation
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

data/fhir_models.gemspec

@@ -8,6 +8,7 @@ Gem::Specification.new do |spec|
   spec.version       = FHIR::Models::VERSION
   spec.authors       = ['Jason Walonoski', 'Andre Quina', "Michael O'Keefe", 'Robert Scanlon', 'Reece Adamson']
   spec.email         = ['jwalonoski@mitre.org']
+  spec.licenses      = ['Apache-2.0']
 
   spec.summary       = %q{A Gem for handling FHIR models in ruby}
   spec.description   = %q{A Gem for handling FHIR models in ruby}
@@ -20,7 +21,7 @@ Gem::Specification.new do |spec|
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ['lib']
 
-  spec.add_dependency 'nokogiri', '>= 1.10.4'
+  spec.add_dependency 'nokogiri', '>= 1.11.4'
   spec.add_dependency 'date_time_precision', '>= 0.8'
   spec.add_dependency 'bcp47', '>= 0.3'
   spec.add_dependency 'mime-types', '>= 3.0'
@@ -33,7 +34,7 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'rspec'
   spec.add_development_dependency 'simplecov', '~> 0.17.0'
   spec.add_development_dependency 'nokogiri-diff'
-  spec.add_development_dependency 'rubocop', '0.67'
+  spec.add_development_dependency 'rubocop', '0.80'
   spec.add_development_dependency 'guard-rspec'
   spec.add_development_dependency 'guard-test'
 end

data/lib/fhir_models/bootstrap/json.rb

@@ -6,8 +6,8 @@ module FHIR
     #  This module includes methods to serialize or deserialize FHIR resources to and from JSON.
     #
 
-    def to_json
-      JSON.pretty_unparse(to_hash)
+    def to_json(opts = nil)
+      JSON.pretty_generate(to_hash, opts)
     end
 
     def self.from_json(json)
@@ -17,8 +17,8 @@ module FHIR
         resource_type = hash['resourceType']
         klass = Module.const_get("FHIR::#{resource_type}")
         resource = klass.new(hash)
-      rescue => ex
-        FHIR.logger.error("Failed to deserialize JSON:\n#{ex.backtrace}")
+      rescue => e
+        FHIR.logger.error("Failed to deserialize JSON:\n#{e.backtrace}")
         FHIR.logger.debug("JSON:\n#{json}")
         resource = nil
       end

data/lib/fhir_models/bootstrap/model.rb

@@ -55,7 +55,7 @@ module FHIR
           return ext.first.value.nil? ? ext.first : ext.first.value
         end
       end
-      raise NoMethodError.new("undefined method `#{method}' for #{inspect}", method)
+      raise NoMethodError.new("undefined method `#{method}' for #{self.class.name}", method)
     end
 
     def to_reference
@@ -300,6 +300,27 @@ module FHIR
       valid
     end
 
+    def each_element(path = nil, &block)
+      self.class::METADATA.each do |element_name, metadata|
+        local_name = metadata.fetch :local_name, element_name
+        values = [instance_variable_get("@#{local_name}")].flatten.compact
+        next if values.empty?
+
+        values.each_with_index do |value, i|
+          child_path =
+            if path.nil?
+              element_name
+            else
+              "#{path}.#{element_name}"
+            end
+          child_path += "[#{i}]" if metadata['max'] > 1
+          yield value, metadata, child_path
+          value.each_element child_path, &block unless FHIR::PRIMITIVES.include? metadata['type']
+        end
+      end
+      self
+    end
+
     private :validate_reference_type, :check_binding_uri, :validate_field
   end
 end

data/lib/fhir_models/bootstrap/xml.rb

@@ -78,8 +78,8 @@ module FHIR
         resource_type = doc.root.name
         klass = Module.const_get("FHIR::#{resource_type}")
         resource = klass.new(hash)
-      rescue => ex
-        FHIR.logger.error("Failed to deserialize XML:\n#{ex.backtrace}")
+      rescue => e
+        FHIR.logger.error("Failed to deserialize XML:\n#{e.backtrace}")
         FHIR.logger.debug("XML:\n#{xml}")
         resource = nil
       end

data/lib/fhir_models/fhir_ext/structure_definition.rb

@@ -59,8 +59,8 @@ module FHIR
       if json.is_a? String
         begin
           json = JSON.parse(json)
-        rescue => ex
-          @errors << "Failed to parse JSON: #{ex.message} %n #{h} %n #{ex.backtrace.join("\n")}"
+        rescue => e
+          @errors << "Failed to parse JSON: #{e.message} %n #{h} %n #{e.backtrace.join("\n")}"
           return false
         end
       end
@@ -161,7 +161,6 @@ module FHIR
       if !element.type.empty? && element.path != id
         # element.type not being empty implies data_type_found != nil, for valid profiles
         codeable_concept_pattern = element.pattern && element.pattern.is_a?(FHIR::CodeableConcept)
-        codeable_concept_binding = element.binding
         matching_pattern = false
         nodes.each do |value|
           matching_type = 0

data/lib/fhir_models/fhir_ext/structure_definition_finding.rb

@@ -30,8 +30,8 @@ module FHIR
           hash.each do |key, value|
             obj.send("#{key}=".to_sym, value) if value
           end
-        rescue => ex
-          FHIR.logger.error "Failed to parse JSON: #{ex.message}"
+        rescue => e
+          FHIR.logger.error "Failed to parse JSON: #{e.message}"
           return nil
         end
       end

data/lib/fhir_models/fhirpath/evaluate.rb

@@ -287,7 +287,7 @@ module FHIRPath
             tree[index] = (previous_node == :null || previous_node.empty? rescue previous_node.nil?)
             clean_index(tree, previous_index)
           when :exists
-            tree[index] = !previous_node.nil? && previous_node != :null
+            tree[index] = !previous_node.nil? && previous_node != :null && previous_node != []
             clean_index(tree, previous_index)
           when :distinct
             tree[index] = (previous_node.uniq rescue previous_node)

data/lib/fhir_models/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   module Models
-    VERSION = '4.1.0'.freeze
+    VERSION = '4.2.1'.freeze
   end
 end

data/lib/fhir_models.rb

@@ -7,29 +7,29 @@ require File.join(root, 'lib', 'fhir_models', 'deprecate')
 require File.join(root, 'lib', 'fhir_models', 'bootstrap', 'hashable.rb')
 require File.join(root, 'lib', 'fhir_models', 'bootstrap', 'json.rb')
 
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'bootstrap', '*.rb')).each do |file|
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'bootstrap', '*.rb')).sort.each do |file|
   require file
 end
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'bootstrap', '**', '*.rb')).each do |file|
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'bootstrap', '**', '*.rb')).sort.each do |file|
   require file
 end
 
 require File.join(root, 'lib', 'fhir_models', 'fhir.rb')
 
 # Require the generated code
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir', '*.rb')).each do |file|
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir', '*.rb')).sort.each do |file|
   require file
 end
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir', '**', '*.rb')).each do |file|
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir', '**', '*.rb')).sort.each do |file|
   require file
 end
 
 # Require the FHIRPath code
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhirpath', '*.rb')).each do |file|
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhirpath', '*.rb')).sort.each do |file|
   require file
 end
 
 # Require the fhir_ext code
-Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir_ext', '*.rb')).each do |file|
+Dir.glob(File.join(root, 'lib', 'fhir_models', 'fhir_ext', '*.rb')).sort.each do |file|
   require file
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_models
 version: !ruby/object:Gem::Version
-  version: 4.1.0
+  version: 4.2.1
 platform: ruby
 authors:
 - Jason Walonoski
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-04-08 00:00:00.000000000 Z
+date: 2021-09-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -20,14 +20,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.10.4
+        version: 1.11.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.10.4
+        version: 1.11.4
 - !ruby/object:Gem::Dependency
   name: date_time_precision
   requirement: !ruby/object:Gem::Requirement
@@ -188,14 +188,14 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '0.67'
+        version: '0.80'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '0.67'
+        version: '0.80'
 - !ruby/object:Gem::Dependency
   name: guard-rspec
   requirement: !ruby/object:Gem::Requirement
@@ -233,15 +233,16 @@ extra_rdoc_files: []
 files:
 - ".codeclimate.yml"
 - ".gitattributes"
+- ".github/workflows/ruby.yml"
 - ".gitignore"
 - ".rspec"
 - ".rubocop.yml"
 - ".rubocop_todo.yml"
 - ".simplecov"
-- ".travis.yml"
 - Gemfile
 - Gemfile.lock
 - Guardfile
+- LICENSE
 - README.md
 - Rakefile
 - bin/console
@@ -3955,7 +3956,8 @@ files:
 - lib/fhir_models/tasks/tasks.rake
 - lib/fhir_models/version.rb
 homepage: https://github.com/fhir-crucible/fhir_models
-licenses: []
+licenses:
+- Apache-2.0
 metadata: {}
 post_install_message: 
 rdoc_options: []
@@ -3972,7 +3974,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.2
+rubygems_version: 3.1.6
 signing_key: 
 specification_version: 4
 summary: A Gem for handling FHIR models in ruby

data/.travis.yml

@@ -1,23 +0,0 @@
-language: ruby
-env:
-  - TESTMEMORY=0 GCDELAY=2.0
-rvm:
-  - 2.4
-  - 2.5
-  - 2.6
-before_script:
-  - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
-  - chmod +x ./cc-test-reporter
-  - ./cc-test-reporter before-build
-script:
-  - travis_wait bundle exec rake
-after_script:
-  - ./cc-test-reporter after-build -t simplecov --exit-code $TRAVIS_TEST_RESULT
-notifications:
-  email:
-    recipients:
-      - fhir-testing-list@lists.mitre.org
-    on_failure: change
-before_install:
-  - gem update --system
-  - gem update bundler