Merge pull request #114 from fhir-crucible/FI-2833-r5

FI-2833 Add R5 Support

.gitignore

@@ -9,4 +9,4 @@ tmp/
 .idea
 
 # ig-extraction
-lib/fhir_models/igs/packages
+lib/fhir_models/igs/package

.rubocop.yml

@@ -6,8 +6,7 @@ AllCops:
     - 'spec/**/*'
     - 'lib/fhir_models/fhir/**/*'
     - 'lib/fhir_models/fhirpath/evaluate.rb'
-    - 'lib/fhir_models/r4/generated/**/*'
-    - 'lib/fhir_models/r4b/generated/**/*'
+    - 'lib/fhir_models/*/generated/**/*'
     - 'lib/**/*.rake'
     - 'tmp/**/*'
     - '*.gemspec'

.rubocop_todo.yml

@@ -1,50 +1,21 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2024-08-29 16:52:13 UTC using RuboCop version 1.23.0.
+# on 2024-09-30 12:52:20 UTC using RuboCop version 1.23.0.
 # 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
 # versions of RuboCop, may require this file to be generated again.
 
-# Offense count: 1
-# Cop supports --auto-correct.
-# Configuration parameters: EmptyLineBetweenMethodDefs, EmptyLineBetweenClassDefs, EmptyLineBetweenModuleDefs, AllowAdjacentOneLineDefs, NumberOfEmptyLines.
-Layout/EmptyLineBetweenDefs:
-  Exclude:
-    - 'lib/fhir_models/fhir_ext/common_structure_definition.rb'
-
-# Offense count: 3
-# Cop supports --auto-correct.
-# Configuration parameters: EnforcedStyle.
-# SupportedStyles: empty_lines, empty_lines_except_namespace, empty_lines_special, no_empty_lines
-Layout/EmptyLinesAroundModuleBody:
-  Exclude:
-    - 'lib/fhir_models/fhir_ext/common_element_definition.rb'
-    - 'lib/fhir_models/fhir_ext/common_structure_definition.rb'
-    - 'lib/fhir_models/fhir_ext/common_structure_definition_finding.rb'
-
 # Offense count: 7
 # Cop supports --auto-correct.
 # Configuration parameters: EnforcedStyle.
 # SupportedStyles: final_newline, final_blank_line
 Layout/TrailingEmptyLines:
   Exclude:
     - 'lib/fhir_models/bootstrap/json.rb'
-    - 'lib/fhir_models/r4/fhir_ext/structure_definition.rb'
     - 'lib/fhir_models/r4/fhir_ext/structure_definition_compare.rb'
-    - 'lib/fhir_models/r4/fhir_ext/structure_definition_finding.rb'
-    - 'lib/fhir_models/r4b/fhir_ext/structure_definition.rb'
     - 'lib/fhir_models/r4b/fhir_ext/structure_definition_compare.rb'
-    - 'lib/fhir_models/r4b/fhir_ext/structure_definition_finding.rb'
-
-# Offense count: 3
-# Cop supports --auto-correct.
-# Configuration parameters: AllowInHeredoc.
-Layout/TrailingWhitespace:
-  Exclude:
-    - 'lib/fhir_models/fhir_ext/common_structure_definition.rb'
-    - 'lib/fhir_models/fhir_ext/common_structure_definition_compare.rb'
-    - 'lib/fhir_models/fhir_ext/common_structure_definition_finding.rb'
+    - 'lib/fhir_models/r5/fhir_ext/structure_definition_compare.rb'
 
 # Offense count: 43
 # Configuration parameters: IgnoredMethods, CountRepeatedAttributes.
@@ -80,20 +51,13 @@ Metrics/MethodLength:
 # Offense count: 4
 # Configuration parameters: CountComments, CountAsOne.
 Metrics/ModuleLength:
-  Max: 354
+  Max: 347
 
 # Offense count: 30
 # Configuration parameters: IgnoredMethods.
 Metrics/PerceivedComplexity:
   Max: 76
 
-# Offense count: 5
-# Configuration parameters: EnforcedStyle, IgnoredPatterns.
-# SupportedStyles: snake_case, camelCase
-Naming/MethodName:
-  Exclude:
-    - 'lib/fhir_models/fhir_ext/common_structure_definition_finding.rb'
-
 # Offense count: 4
 # Configuration parameters: MinNameLength, AllowNamesEndingInNumbers, AllowedNames, ForbiddenNames.
 # AllowedNames: at, by, db, id, in, io, ip, of, on, os, pp, to

lib/fhir_models.rb

@@ -1,3 +1,2 @@
 # require versions
 require_relative 'fhir_models/r4'
-require_relative 'fhir_models/r4b'

lib/fhir_models/fhir.rb

@@ -3,6 +3,19 @@
 require 'uri'
 
 module FHIR
+  module ClassMethods
+    def from_contents(contents)
+      doc = Nokogiri::XML(contents)
+      if doc.errors.empty?
+        versioned_fhir_module::Xml.from_xml(contents)
+      else
+        versioned_fhir_module::Json.from_json(contents)
+      end
+    end
+  end
+  include ClassMethods
+  extend ClassMethods
+
   def self.logger
     @logger || default_logger
   end
@@ -15,15 +28,6 @@ def self.default_logger
     @default_logger ||= Logger.new(ENV['FHIR_LOGGER'] || $stdout)
   end
 
-  def self.from_contents(contents)
-    doc = Nokogiri::XML(contents)
-    if doc.errors.empty?
-      FHIR::Xml.from_xml(contents)
-    else
-      FHIR::Json.from_json(contents)
-    end
-  end
-
   # TODO: pull regexes from metadata
   def self.primitive?(datatype:, value:)
     # Remaining data types: handle special cases before checking type StructureDefinitions

lib/fhir_models/generator/generator.rb

@@ -5,7 +5,8 @@
 
 VERSION_MAP = {
   '4.0.1' => 'r4',
-  '4.3.0' => 'r4b'
+  '4.3.0' => 'r4b',
+  '5.0.0' => 'r5'
 }.freeze
 
 module FHIR

lib/fhir_models/generator/ig_resources.rb

@@ -63,7 +63,7 @@ def get_search_parameters(type_name = nil)
           resources_by_type['SearchParameter']
         else
           resources_by_type['SearchParameter'].select do |p|
-            p['base']&.include?(type_name) && p['xpath'] && !p['xpath'].include?('extension')
+            p['base']&.include?(type_name) && p['expression'] && !p['expression'].include?('extension')
           end
         end
       end

lib/fhir_models/igs/hl7.fhir.r5.core/package_exclude/README.md

@@ -0,0 +1,10 @@
+# FHIR NPM Package Supplement Files
+
+The files in this directory will excluded from the hl7.fhir.<version>.core.tgz package.
+FHIR NPM Package may contains some files which are not to be processed, such as examples.
+Add files to the excluded list to prevent code generator from processing them.
+These files will not supersede the files in the IG.
+
+## excluded_files.json
+
+This file contains list of file names to be excluded from processing.

lib/fhir_models/igs/hl7.fhir.r5.core/package_exclude/excluded_files.json

@@ -0,0 +1,2 @@
+[
+]

lib/fhir_models/igs/hl7.fhir.r5.core/package_supplement/README.md

@@ -0,0 +1,9 @@
+# FHIR NPM Package Supplement Files
+
+The files in this directory will supplement files in the hl7.fhir.<version>.core.tgz package.
+Add files to this directory if you need to add information that may be missing from the package.
+These files will not supersede the files in the IG.
+
+## expansions.json
+
+This file contains ValueSet expansions which are used by code generator