fhir_dstu2_models 1.0.7 → 1.0.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: a17b3b533c51e62bd72d84aa7281e34cb1c3d7d768397bd1856f678da4da32f5
+  metadata.gz: 440c728fbf6cc0e7764c1b7cebce1864bb0dc15757b11bb87379b39c3f740c62
+  data.tar.gz: 50cd56593e64cc04d94c463e53068acd653750e8fb32990a23f4c8829dba6d87
 SHA512:
-  metadata.gz: 7cd9c1c30d456db190949cf4a016040bb433c105481609f16b8f4aa08ae34dc96f0579a484bc92fbfeef114cbc9c8b8065f14858fa021c6c08513818f109c171
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+  metadata.gz: de740ab400448fd89ff07d835646f47adcb01708e479fb5b251c44991c3f965fa034472a8f6f08bbc70b0da39a4f04bc5c3029f5dcb34730c266b61b2eaef0bf
+  data.tar.gz: 43653566bda0db07b8a5c0275b2a85fab00d17c0172fe75ac9468e1dd702c194e3f74b09a1ee260d2be27d5b7e29ea6616e339efb456b0996cdcdf5b1179b6b1

data/.rubocop.yml

@@ -1,6 +1,6 @@
 inherit_from: .rubocop_todo.yml
 AllCops:
-  TargetRubyVersion: 2.2
+  TargetRubyVersion: 2.4
   Exclude:
     - 'test/**/*'
     - 'spec/**/*'
@@ -12,3 +12,6 @@ AllCops:
     - 'vendor/**/*'
 Metrics/LineLength:
   Enabled: false
+
+Style/FrozenStringLiteralComment:
+  Enabled: false

data/.rubocop_todo.yml

@@ -1,38 +1,35 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2017-02-25 13:02:53 -0500 using RuboCop version 0.47.1.
+# on 2019-03-28 10:35:44 -0400 using RuboCop version 0.52.1.
 # 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.
 
-Performance/Caller:
-  Enabled: false
-
-# Offense count: 37
+# Offense count: 40
 Metrics/AbcSize:
   Max: 423
 
-# Offense count: 10
+# Offense count: 9
 # Configuration parameters: CountComments, ExcludedMethods.
 Metrics/BlockLength:
-  Max: 150
+  Max: 108
 
-# Offense count: 1
+# Offense count: 15
 # Configuration parameters: CountBlocks.
 Metrics/BlockNesting:
   Max: 5
 
-# Offense count: 5
+# Offense count: 6
 # Configuration parameters: CountComments.
 Metrics/ClassLength:
-  Max: 499
+  Max: 327
 
-# Offense count: 26
+# Offense count: 27
 Metrics/CyclomaticComplexity:
   Max: 69
 
-# Offense count: 40
+# Offense count: 46
 # Configuration parameters: CountComments.
 Metrics/MethodLength:
   Max: 120
@@ -40,19 +37,39 @@ Metrics/MethodLength:
 # Offense count: 1
 # Configuration parameters: CountComments.
 Metrics/ModuleLength:
-  Max: 120
-
+  Max: 114
 
 # Offense count: 25
 Metrics/PerceivedComplexity:
   Max: 72
 
-# Offense count: 16
+# Offense count: 3
+Performance/Caller:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/model.rb'
+    - 'lib/fhir_dstu2_models/deprecate.rb'
+
+# Offense count: 3
+# Cop supports --auto-correct.
+# Configuration parameters: AutoCorrect.
+Performance/HashEachMethods:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/definitions.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/model.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/preprocess.rb'
+
+# Offense count: 15
 Style/ClassVars:
   Exclude:
     - 'lib/fhir_dstu2_models/bootstrap/definitions.rb'
     - 'lib/fhir_dstu2_models/fluentpath/parse.rb'
 
+# Offense count: 6
+Style/CommentedKeyword:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/hashable.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/model.rb'
+
 # Offense count: 14
 Style/Documentation:
   Exclude:
@@ -73,7 +90,88 @@ Style/Documentation:
     - 'lib/fhir_dstu2_models/fluentpath/expression.rb'
     - 'lib/fhir_dstu2_models/fluentpath/parse.rb'
 
+# Offense count: 29
+# Cop supports --auto-correct.
+Style/IfUnlessModifier:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/generator.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/hashable.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/model.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/template.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/xml.rb'
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition.rb'
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition_compare.rb'
+
+# Offense count: 1
+# Cop supports --auto-correct.
+# Configuration parameters: EnforcedStyle.
+# SupportedStyles: line_count_dependent, lambda, literal
+Style/Lambda:
+  Exclude:
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition.rb'
+
+# Offense count: 2
+# Cop supports --auto-correct.
+# Configuration parameters: EnforcedStyle.
+# SupportedStyles: call, braces
+Style/LambdaCall:
+  Exclude:
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition.rb'
+
 # Offense count: 1
 Style/MethodMissing:
   Exclude:
     - 'lib/fhir_dstu2_models/bootstrap/model.rb'
+
+# Offense count: 2
+# Cop supports --auto-correct.
+# Configuration parameters: AutoCorrect, EnforcedStyle.
+# SupportedStyles: predicate, comparison
+Style/NumericPredicate:
+  Exclude:
+    - 'spec/**/*'
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition_compare.rb'
+
+# Offense count: 1
+# Cop supports --auto-correct.
+Style/OrAssignment:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/generator.rb'
+
+# Offense count: 17
+# Cop supports --auto-correct.
+# Configuration parameters: EnforcedStyle.
+# SupportedStyles: implicit, explicit
+Style/RescueStandardError:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/definitions.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/hashable.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/json.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/model.rb'
+    - 'lib/fhir_dstu2_models/bootstrap/xml.rb'
+    - 'lib/fhir_dstu2_models/fhir.rb'
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition.rb'
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition_finding.rb'
+    - 'lib/fhir_dstu2_models/fluentpath/expression.rb'
+    - 'lib/fhir_dstu2_models/fluentpath/parse.rb'
+
+# Offense count: 2
+# Cop supports --auto-correct.
+# Configuration parameters: ConvertCodeThatCanStartToReturnNil.
+Style/SafeNavigation:
+  Exclude:
+    - 'lib/fhir_dstu2_models/bootstrap/definitions.rb'
+
+# Offense count: 1
+# Cop supports --auto-correct.
+# Configuration parameters: EnforcedStyle.
+# SupportedStyles: require_parentheses, require_no_parentheses
+Style/StabbyLambdaParentheses:
+  Exclude:
+    - 'lib/fhir_dstu2_models/fhir_ext/structure_definition.rb'
+
+# Offense count: 309
+# Configuration parameters: AllowHeredoc, AllowURI, URISchemes, IgnoreCopDirectives, IgnoredPatterns.
+# URISchemes: http, https
+Metrics/LineLength:
+  Max: 292

data/.travis.yml

@@ -2,7 +2,6 @@ language: ruby
 env:
   - TESTMEMORY=0 GCDELAY=2.0
 rvm:
-  - 2.3
   - 2.4
   - 2.5
   - 2.6
@@ -18,4 +17,5 @@ addons:
   code_climate:
     repo_token: 0230b3379581b30743b7b4355d7394e427648e604d19a2aba987956201eee290
 before_install:
+  - gem update --system
   - gem install bundler

data/Gemfile.lock

@@ -41,6 +41,7 @@ GEM
       test-unit (~> 3.0)
     i18n (1.5.3)
       concurrent-ruby (~> 1.0)
+    jaro_winkler (1.5.2)
     json (2.1.0)
     listen (3.1.5)
       rb-fsevent (~> 0.9, >= 0.9.4)
@@ -59,16 +60,15 @@ GEM
     notiffany (0.1.1)
       nenv (~> 0.1)
       shellany (~> 0.0)
-    parallel (1.12.1)
-    parser (2.5.1.0)
+    parallel (1.14.0)
+    parser (2.6.2.0)
       ast (~> 2.4.0)
     power_assert (1.1.1)
-    powerpack (0.1.1)
+    powerpack (0.1.2)
     pry (0.11.3)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
-    rainbow (2.2.2)
-      rake
+    rainbow (3.0.0)
     rake (12.3.1)
     rb-fsevent (0.10.3)
     rb-inotify (0.9.10)
@@ -86,14 +86,14 @@ GEM
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.7.0)
     rspec-support (3.7.1)
-    rubocop (0.49.0)
+    rubocop (0.52.1)
       parallel (~> 1.10)
-      parser (>= 2.3.3.1, < 3.0)
+      parser (>= 2.4.0.2, < 3.0)
       powerpack (~> 0.1)
-      rainbow (>= 1.99.1, < 3.0)
+      rainbow (>= 2.2.2, < 4.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (~> 1.0, >= 1.0.1)
-    ruby-progressbar (1.9.0)
+    ruby-progressbar (1.10.0)
     ruby_dep (1.5.0)
     shellany (0.0.1)
     simplecov (0.13.0)
@@ -105,7 +105,7 @@ GEM
     test-unit (3.2.7)
       power_assert
     thor (0.20.0)
-    unicode-display_width (1.3.2)
+    unicode-display_width (1.5.0)
 
 PLATFORMS
   ruby
@@ -120,7 +120,7 @@ DEPENDENCIES
   pry
   rake
   rspec
-  rubocop (= 0.49)
+  rubocop (= 0.52.1)
   simplecov
   test-unit
 
@@ -128,4 +128,4 @@ RUBY VERSION
    ruby 2.5.1p57
 
 BUNDLED WITH
-   1.16.2
+   2.0.1

data/fhir_dstu2_models.gemspec

@@ -32,7 +32,7 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency 'rspec'
   spec.add_development_dependency 'simplecov'
   spec.add_development_dependency 'nokogiri-diff'
-  spec.add_development_dependency 'rubocop', '0.49'
+  spec.add_development_dependency 'rubocop', '0.52.1'
   spec.add_development_dependency 'codeclimate-test-reporter'
   spec.add_development_dependency 'guard-rspec'
   spec.add_development_dependency 'guard-test'

data/lib/fhir_dstu2_models/fhir_ext/structure_definition.rb

@@ -168,7 +168,6 @@ module FHIR
         # Check the datatype for each node, only if the element has one declared, and it isn't the root element
         if !element.type.empty? && element.path != id
           codeable_concept_pattern = element.pattern && element.pattern.is_a?(FHIR::DSTU2::CodeableConcept)
-          codeable_concept_binding = element.binding
           matching_pattern = false
           nodes.each do |value|
             matching_type = 0
@@ -205,35 +204,45 @@ module FHIR
                     matching_pattern = true if vcoding.system == pcoding.system && vcoding.code == pcoding.code
                   end
                 end
-              elsif data_type_found == 'CodeableConcept' && codeable_concept_binding
-                binding_issues =
-                  if element.binding.strength == 'extensible'
-                    @warnings
-                  elsif element.binding.strength == 'required'
-                    @errors
-                  else # e.g., example-strength or unspecified
-                    [] # Drop issues errors on the floor, in throwaway array
+              elsif %w[CodeableConcept Coding Quantity].include? data_type_found
+                required_strength = element&.binding&.strength == 'required'
+                binding_issues = required_strength ? @errors : @warnings
+
+                valueset_uri = element&.binding&.valueSetReference&.reference
+                check_code = ->coding do
+                  # Can't validate if both code and system are not given
+                  if coding['code'].nil? || coding['system'].nil?
+                    binding_issues << "#{describe_element(element)} code: #{coding.to_json} missing code" if coding['code'].nil?
+                    binding_issues << "#{describe_element(element)} code: #{coding.to_json} missing system" if coding['system'].nil?
+                    return
                   end
 
-                valueset_uri = element.binding && element.binding.valueSetReference && element.binding.valueSetReference.reference
-                vcc = FHIR::DSTU2::CodeableConcept.new(value)
-                if valueset_uri && self.class.vs_validators[valueset_uri]
+                  # ValueSet Validation
                   check_fn = self.class.vs_validators[valueset_uri]
-                  has_valid_code = vcc.coding && vcc.coding.any? { |c| check_fn.call(c) }
+                  has_valid_code = false
+                  if check_fn
+                    has_valid_code = check_fn.call(coding)
+                    binding_issues << "#{describe_element(element)} has no codings from #{valueset_uri}. Codings evaluated: #{coding.to_json}" unless has_valid_code
+                  end
 
+                  # CodeSystem Validation
                   unless has_valid_code
-                    binding_issues << "#{describe_element(element)} has no codings from #{valueset_uri}. Codings evaluated: #{vcc.to_json}"
+                    check_fn = self.class.vs_validators[coding['system']]
+                    if check_fn && !check_fn.call(coding)
+                      binding_issues << "#{describe_element(element)} has no codings from it's specified system: #{coding['system']}.  "\
+                                      "Codings evaluated: #{coding.to_json}"
+                    end
                   end
                 end
 
-                unless has_valid_code
-                  vcc.coding.each do |c|
-                    check_fn = self.class.vs_validators[c.system]
-                    if check_fn && !check_fn.call(c)
-                      binding_issues << "#{describe_element(element)} has no codings from it's specified system: #{c.system}.  "\
-                                        "Codings evaluated: #{vcc.to_json}"
-                    end
+                if data_type_found == 'CodeableConcept'
+                  value['coding']&.each do |coding|
+                    check_code.(coding)
                   end
+                else
+                  # avoid checking Codings twice if they are already checked as part of a CodeableConcept
+                  # The CodeableConcept should contain the binding for the children Codings
+                  check_code.(value) unless element.path == 'CodeableConcept.coding'
                 end
 
               elsif data_type_found == 'String' && !element.maxLength.nil? && (value.size > element.maxLength)
@@ -284,13 +293,9 @@ module FHIR
           unless definition.nil?
             ret_val = false
             begin
-              # klass = Module.const_get("FHIR::DSTU2::#{data_type_code}")
-              # ret_val = definition.validates_resource?(klass.new(deep_copy(value)))
               ret_val = definition.validates_hash?(value)
-              unless ret_val
-                @errors += definition.errors
-                @warnings += definition.warnings
-              end
+              @errors += definition.errors
+              @warnings += definition.warnings
             rescue
               @errors << "Unable to verify #{data_type_code} as a FHIR::DSTU2 Resource."
             end
@@ -308,13 +313,9 @@ module FHIR
           if !definition.nil?
             ret_val = false
             begin
-              # klass = Module.const_get("FHIR::DSTU2::#{resource_type}")
-              # ret_val = definition.validates_resource?(klass.new(deep_copy(value)))
               ret_val = definition.validates_hash?(value)
-              unless ret_val
-                @errors += definition.errors
-                @warnings += definition.warnings
-              end
+              @errors += definition.errors
+              @warnings += definition.warnings
             rescue
               @errors << "Unable to verify #{resource_type} as a FHIR::DSTU2 Resource."
             end
@@ -334,13 +335,9 @@ module FHIR
           if !definition.nil?
             ret_val = false
             begin
-              # klass = Module.const_get("FHIR::DSTU2::#{data_type_code}")
-              # ret_val = definition.validates_resource?(klass.new(deep_copy(value)))
               ret_val = definition.validates_hash?(value)
-              unless ret_val
-                @errors += definition.errors
-                @warnings += definition.warnings
-              end
+              @errors += definition.errors
+              @warnings += definition.warnings
             rescue
               @errors << "Unable to verify #{data_type_code} as a FHIR::DSTU2 type."
             end

data/lib/fhir_dstu2_models/version.rb

@@ -1,7 +1,7 @@
 module FHIR
   module DSTU2
     module Models
-      VERSION = '1.0.7'.freeze
+      VERSION = '1.0.8'.freeze
     end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_dstu2_models
 version: !ruby/object:Gem::Version
-  version: 1.0.7
+  version: 1.0.8
 platform: ruby
 authors:
 - Jason Walonoski
@@ -11,7 +11,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-02-26 00:00:00.000000000 Z
+date: 2019-03-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -179,14 +179,14 @@ dependencies:
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '0.49'
+        version: 0.52.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - '='
       - !ruby/object:Gem::Version
-        version: '0.49'
+        version: 0.52.1
 - !ruby/object:Gem::Dependency
   name: codeclimate-test-reporter
   requirement: !ruby/object:Gem::Requirement