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