parent d4a9363

author 360dgries <[email protected]> 1727189567 -0400 committer 360dgries <[email protected]> 1727360442 -0400 First rebase update fhir_models Update rubocop add generated files add one readme file add excluded_files add readme files update generator add tgz add expansion file add one readme file add readme files First rebase Fix r5 Model remove redundant file Add basic unit tests for R5 Add Unit tests and version from_contents update fhir_models Update rubocop add generated files add one readme file add excluded_files add readme files update generator add tgz add expansion file Fix r5 Model remove redundant file Add basic unit tests for R5 Add Unit tests and version from_contents
fhir-crucible · Sep 26, 2024 · 64ef50f · 64ef50f
1 parent d4a9363
commit 64ef50f
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diff --git a/lib/fhir_models/fhir.rb b/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

diff --git a/lib/fhir_models/r4.rb b/lib/fhir_models/r4.rb
@@ -45,6 +45,7 @@
 
 module FHIR
  module R4
+ extend FHIR
  extend self
 
  def fhir_version_string

diff --git a/lib/fhir_models/r4b.rb b/lib/fhir_models/r4b.rb
@@ -45,6 +45,7 @@
 
 module FHIR
  module R4B
+ extend FHIR
  extend self
 
  def fhir_version_string

diff --git a/lib/fhir_models/r5.rb b/lib/fhir_models/r5.rb
@@ -18,6 +18,11 @@
  require file
 end
 
+# Require the fhir_ext code
+Dir.glob(File.join(root, 'fhir_models', 'fhir_ext', '*.rb')).sort.each do |file|
+ require file
+end
+
 Dir.glob(File.join(root, 'fhir_models', 'r5', 'bootstrap', '*.rb')).sort.each do |file|
  require file
 end
@@ -34,11 +39,21 @@
  require file
 end
 
-# Require the fhir_ext code
-Dir.glob(File.join(root, 'fhir_models', 'fhir_ext', '*.rb')).sort.each do |file|
+Dir.glob(File.join(root, 'fhir_models', 'r5', 'fhir_ext', '*.rb')).sort.each do |file|
  require file
 end
 
-Dir.glob(File.join(root, 'fhir_models', 'r5', 'fhir_ext', '*.rb')).sort.each do |file|
- require file
+module FHIR
+ module R5
+ extend FHIR
+ extend self
+
+ def fhir_version_string
+ 'R5'
+ end
+
+ def versioned_fhir_module
+ FHIR::R5
+ end
+ end
 end
diff --git a/lib/fhir_models/r5/bootstrap/definitions.rb b/lib/fhir_models/r5/bootstrap/definitions.rb
@@ -2,17 +2,10 @@ module FHIR
  module R5
  class Definitions
  include CommonDefinitions
+ extend FHIR::R5
  @ig_file_name = File.join(Dir.pwd, 'lib', 'fhir_models', 'igs', 'hl7.fhir.r5.core.tgz')
 
  load_igs(@ig_file_name)
-
- def self.fhir_version_string
- 'R5'
- end
-
- def self.versioned_fhir_module
- FHIR::R5
- end
  end
  end
 end
diff --git a/lib/fhir_models/r5/bootstrap/json.rb b/lib/fhir_models/r5/bootstrap/json.rb
@@ -0,0 +1,9 @@
+module FHIR
+ module R5
+ module Json
+ extend FHIR::R5
+ extend FHIR::ClassJson
+ include FHIR::InstanceJson
+ end
+ end
+end
diff --git a/lib/fhir_models/r5/bootstrap/model.rb b/lib/fhir_models/r5/bootstrap/model.rb
@@ -1,13 +1,7 @@
 module FHIR
  module R5
  class Model < FHIR::Model
- def fhir_version_string
- 'R5'
- end
-
- def versioned_fhir_module
- FHIR::R5
- end
+ include FHIR::R5
  end
  end
 end
diff --git a/lib/fhir_models/r5/bootstrap/xml.rb b/lib/fhir_models/r5/bootstrap/xml.rb
@@ -0,0 +1,9 @@
+module FHIR
+ module R5
+ module Xml
+ extend FHIR::R5
+ extend FHIR::ClassXml
+ include FHIR::InstanceXml
+ end
+ end
+end
diff --git a/lib/fhir_models/r5/fhir_ext/element_definition.rb b/lib/fhir_models/r5/fhir_ext/element_definition.rb
diff --git a/lib/fhir_models/r5/fhir_ext/structure_definition.rb b/lib/fhir_models/r5/fhir_ext/structure_definition.rb
diff --git a/lib/fhir_models/r5/fhir_ext/structure_definition_compare.rb b/lib/fhir_models/r5/fhir_ext/structure_definition_compare.rb
@@ -2,14 +2,6 @@ module FHIR
  module R5
  class StructureDefinitionCompare
  include CommonStructureDefinitionCompare
-
- def self.fhir_version_string
- 'R5'
- end
-
- def self.versioned_fhir_module
- FHIR::R5
- end
  end
  end
 end
diff --git a/lib/fhir_models/r5/generated/metadata.rb → lib/fhir_models/r5/generated/r5.rb b/lib/fhir_models/r5/generated/metadata.rb → lib/fhir_models/r5/generated/r5.rb
diff --git a/lib/fhir_models/r5/generated/resources/StructureDefinition.rb b/lib/fhir_models/r5/generated/resources/StructureDefinition.rb
@@ -4,6 +4,7 @@ class StructureDefinition < Model
  include FHIR::Hashable
  include FHIR::Json
  include FHIR::Xml
+ include FHIR::CommonStructureDefinition
 
  MULTIPLE_TYPES = {
  'versionAlgorithm' => ['string', 'Coding']

diff --git a/lib/fhir_models/r5/generated/types/ElementDefinition.rb b/lib/fhir_models/r5/generated/types/ElementDefinition.rb
@@ -4,6 +4,7 @@ class ElementDefinition < Model
  include FHIR::Hashable
  include FHIR::Json
  include FHIR::Xml
+ include FHIR::CommonElementDefinition
 
  MULTIPLE_TYPES = {
  'defaultValue' => ['base64Binary', 'boolean', 'canonical', 'code', 'date', 'dateTime', 'decimal', 'id', 'instant', 'integer', 'integer64', 'markdown', 'oid', 'positiveInt', 'string', 'time', 'unsignedInt', 'uri', 'url', 'uuid', 'Address', 'Age', 'Annotation', 'Attachment', 'CodeableConcept', 'CodeableReference', 'Coding', 'ContactPoint', 'Count', 'Distance', 'Duration', 'HumanName', 'Identifier', 'Money', 'Period', 'Quantity', 'Range', 'Ratio', 'RatioRange', 'Reference', 'SampledData', 'Signature', 'Timing', 'ContactDetail', 'DataRequirement', 'Expression', 'ParameterDefinition', 'RelatedArtifact', 'TriggerDefinition', 'UsageContext', 'Availability', 'ExtendedContactDetail', 'Dosage', 'Meta'],

diff --git a/spec/lib/fhir_models/r5/definition_spec.rb b/spec/lib/fhir_models/r5/definition_spec.rb
@@ -0,0 +1,11 @@
+require_relative '../../../../lib/fhir_models/r5/bootstrap/definitions'
+
+RSpec.describe FHIR::R5::Definitions do
+ describe '#resource_definition' do
+ it 'returns R5 resource definition' do
+ result = FHIR::R5::Definitions.resource_definition('Patient')
+ expect(result.id).to eq('Patient')
+ expect(result.version).to eq('5.0.0')
+ end
+ end
+end
diff --git a/test/unit/contents_test.rb b/test/unit/contents_test.rb
@@ -54,4 +54,41 @@ def test_negative_xml_contents
  nothing = FHIR.from_contents('<?xml version="1.0" encoding="UTF-8"?><Nothing/>')
  assert nothing.nil?, 'From contents should have returned nil.'
  end
+
+ def test_versioned_from_contents
+ xml = File.read(EXAMPLE_XML)
+ json = File.read(EXAMPLE_JSON)
+
+ # infer XML
+ patient_xml= FHIR.from_contents(xml)
+ assert !patient_xml.nil?, 'From contents did not succeed with XML.'
+ assert patient_xml.id == 'example', 'Patient did not deserialize correctly.'
+ assert patient_xml.versioned_fhir_module == FHIR::R4
+
+ patient_xml_r4b = FHIR::R4B.from_contents(xml)
+ assert !patient_xml_r4b.nil?, 'From contents did not succeed with XML.'
+ assert patient_xml_r4b.id == 'example', 'Patient did not deserialize correctly.'
+ assert patient_xml_r4b.versioned_fhir_module == FHIR::R4B
+
+ patient_xml_r5 = FHIR::R5.from_contents(xml)
+ assert !patient_xml_r5.nil?, 'From contents did not succeed with XML.'
+ assert patient_xml_r5.id == 'example', 'Patient did not deserialize correctly.'
+ assert patient_xml_r5.versioned_fhir_module == FHIR::R5
+
+ # infer json
+ patient_json= FHIR.from_contents(json)
+ assert !patient_json.nil?, 'From contents did not succeed with JSON.'
+ assert patient_json.id == 'example', 'Patient did not deserialize correctly.'
+ assert patient_json.versioned_fhir_module == FHIR::R4
+
+ patient_json_r4b = FHIR::R4B.from_contents(json)
+ assert !patient_json_r4b.nil?, 'From contents did not succeed with JSON.'
+ assert patient_json_r4b.id == 'example', 'Patient did not deserialize correctly.'
+ assert patient_json_r4b.versioned_fhir_module == FHIR::R4B
+
+ patient_json_r5 = FHIR::R5.from_contents(json)
+ assert !patient_json_r5.nil?, 'From contents did not succeed with JSON.'
+ assert patient_json_r5.id == 'example', 'Patient did not deserialize correctly.'
+ assert patient_json_r5.versioned_fhir_module == FHIR::R5
+ end
 end