fhir_models 4.0.1 → 4.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 63863939853fa9990d3971159c4e7ed4e0db0ecec65c1c8f24fd36fbb875b720
+  metadata.gz: a2b2f1ce045f2f9bd1c15b6768091ca4c754997f6af10485428d23a85bf7a433
+  data.tar.gz: 17f3457b9d076f56ee03de4494736ac2df7081b876ec7dc2a5e753259a186751
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+  data.tar.gz: 054f76a7de1a789353ff47a3c8feab7cf34a8c8bc9a5693468eee2e3a7c94318e4bc8397dd0b4dd5250670abcb2d34e839760459270078840d1970efb555e299

data/.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2019-04-22 22:20:52 -0400 using RuboCop version 0.67.0.
+# on 2019-07-01 12:11:28 -0400 using RuboCop version 0.67.2.
 # 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
@@ -43,9 +43,9 @@ Metrics/AbcSize:
 # Configuration parameters: CountComments, ExcludedMethods.
 # ExcludedMethods: refine
 Metrics/BlockLength:
-  Max: 74
+  Max: 78
 
-# Offense count: 8
+# Offense count: 10
 # Configuration parameters: CountBlocks.
 Metrics/BlockNesting:
   Max: 5
@@ -53,7 +53,7 @@ Metrics/BlockNesting:
 # Offense count: 7
 # Configuration parameters: CountComments.
 Metrics/ClassLength:
-  Max: 354
+  Max: 358
 
 # Offense count: 23
 Metrics/CyclomaticComplexity:
@@ -62,7 +62,7 @@ Metrics/CyclomaticComplexity:
 # Offense count: 44
 # Configuration parameters: CountComments, ExcludedMethods.
 Metrics/MethodLength:
-  Max: 131
+  Max: 135
 
 # Offense count: 2
 # Configuration parameters: CountComments.
@@ -73,15 +73,11 @@ Metrics/ModuleLength:
 Metrics/PerceivedComplexity:
   Max: 68
 
-# Offense count: 5
+# Offense count: 1
 # Configuration parameters: PreferredName.
 Naming/RescuedExceptionsVariableName:
   Exclude:
     - 'lib/fhir_models/bootstrap/hashable.rb'
-    - 'lib/fhir_models/bootstrap/json.rb'
-    - 'lib/fhir_models/bootstrap/xml.rb'
-    - 'lib/fhir_models/fhir_ext/structure_definition.rb'
-    - 'lib/fhir_models/fhir_ext/structure_definition_finding.rb'
 
 # Offense count: 4
 # Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
@@ -140,7 +136,7 @@ Style/Documentation:
     - 'lib/fhir_models/fluentpath/expression.rb'
     - 'lib/fhir_models/fluentpath/parse.rb'
 
-# Offense count: 29
+# Offense count: 28
 # Cop supports --auto-correct.
 Style/IfUnlessModifier:
   Exclude:
@@ -202,7 +198,7 @@ Style/RescueStandardError:
     - 'lib/fhir_models/fluentpath/expression.rb'
     - 'lib/fhir_models/fluentpath/parse.rb'
 
-# Offense count: 6
+# Offense count: 4
 # Cop supports --auto-correct.
 # Configuration parameters: ConvertCodeThatCanStartToReturnNil, Whitelist.
 # Whitelist: present?, blank?, presence, try, try!

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    fhir_models (4.0.1)
+    fhir_models (4.0.2)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)

data/lib/fhir_models/bootstrap/hashable.rb

@@ -68,13 +68,7 @@ module FHIR
         if !klass.nil? && !value.nil?
           # handle array of objects
           if value.is_a?(Array)
-            value = value.map do |child|
-              obj = child
-              unless [FHIR::RESOURCES, FHIR::TYPES].flatten.include? child.class.name.gsub('FHIR::', '')
-                obj = make_child(child, klass)
-              end
-              obj
-            end
+            value = value.map { |child| make_child(child, klass) }
           else # handle single object
             value = make_child(value, klass)
             # if there is only one of these, but cardinality allows more, we need to wrap it in an array.
@@ -99,6 +93,8 @@ module FHIR
     end
 
     def make_child(child, klass)
+      return child if child.is_a?(FHIR::Model)
+
       if child['resourceType'] && !klass::METADATA['resourceType']
         klass = begin
           FHIR.const_get(child['resourceType'])
@@ -112,7 +108,6 @@ module FHIR
       begin
         obj = klass.new(child)
       rescue => exception
-        # TODO: this appears to be a dead code branch
         # TODO: should this re-raise the exception if encountered instead of silently swallowing it?
         FHIR.logger.error("Unable to inflate embedded class #{klass}\n#{exception.backtrace}")
       end

data/lib/fhir_models/bootstrap/json.rb

@@ -1,3 +1,5 @@
+require 'json'
+
 module FHIR
   module Json
     #
@@ -15,8 +17,8 @@ module FHIR
         resource_type = hash['resourceType']
         klass = Module.const_get("FHIR::#{resource_type}")
         resource = klass.new(hash)
-      rescue => e
-        FHIR.logger.error("Failed to deserialize JSON:\n#{e.backtrace}")
+      rescue => ex
+        FHIR.logger.error("Failed to deserialize JSON:\n#{ex.backtrace}")
         FHIR.logger.debug("JSON:\n#{json}")
         resource = nil
       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 => e
-        FHIR.logger.error("Failed to deserialize XML:\n#{e.backtrace}")
+      rescue => ex
+        FHIR.logger.error("Failed to deserialize XML:\n#{ex.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 => e
-          @errors << "Failed to parse JSON: #{e.message} %n #{h} %n #{e.backtrace.join("\n")}"
+        rescue => ex
+          @errors << "Failed to parse JSON: #{ex.message} %n #{h} %n #{ex.backtrace.join("\n")}"
           return false
         end
       end
@@ -198,38 +198,49 @@ 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
-                end
+            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 && element.binding.valueSet
-              if valueset_uri.include?('|')
+              valueset_uri = element&.binding&.valueSet
+              if valueset_uri&.include?('|')
                 x = valueset_uri.index('|')
                 valueset_uri = valueset_uri[0..x - 1]
               end
-              vcc = FHIR::CodeableConcept.new(value)
-              if valueset_uri && self.class.vs_validators[valueset_uri]
+              check_code = lambda do |coding|
+                # Can't validate if both code and system are not given
+                if coding['code'].nil? || coding['system'].nil?
+                  @warnings << "#{describe_element(element)} code: #{coding.to_json} missing code" if coding['code'].nil?
+                  @warnings << "#{describe_element(element)} code: #{coding.to_json} missing system" if coding['system'].nil?
+                  return
+                end
+
+                # 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.call(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.call(value) unless element.path == 'CodeableConcept.coding'
               end
 
             elsif data_type_found == 'String' && !element.maxLength.nil? && (value.size > element.maxLength)

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 => e
-          FHIR.logger.error "Failed to parse JSON: #{e.message}"
+        rescue => ex
+          FHIR.logger.error "Failed to parse JSON: #{ex.message}"
           return nil
         end
       end

data/lib/fhir_models/version.rb

@@ -1,5 +1,5 @@
 module FHIR
   module Models
-    VERSION = '4.0.1'.freeze
+    VERSION = '4.0.2'.freeze
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: fhir_models
 version: !ruby/object:Gem::Version
-  version: 4.0.1
+  version: 4.0.2
 platform: ruby
 authors:
 - Jason Walonoski
@@ -12,7 +12,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-08-26 00:00:00.000000000 Z
+date: 2019-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri