add valueset and code system validation with tests

lib/fhir_models/fhir_ext/structure_definition.rb

@@ -15,6 +15,20 @@ class StructureDefinition
  # Profile Validation
  # -------------------------------------------------------------------------
 
+ class << self; attr_accessor :vs_validators end
+ @vs_validators = {}
+ def self.validates_vs(valueset_uri, &validator_fn)
+ @vs_validators[valueset_uri] = validator_fn
+ end
+
+ def self.clear_validates_vs(valueset_uri)
+ @vs_validators.delete valueset_uri
+ end
+
+ def self.clear_all_validates_vs
+ @vs_validators = {}
+ end
+
  def validates_resource?(resource)
  validate_resource(resource).empty?
  end
@@ -147,6 +161,7 @@ def verify_element(element, json)
  if !element.type.empty? && element.path != id
  # element.type not being empty implies data_type_found != nil, for valid profiles
  codeable_concept_pattern = element.pattern && element.pattern.is_a?(FHIR::CodeableConcept)
+ codeable_concept_binding = element.binding
  matching_pattern = false
  nodes.each do |value|
  matching_type = 0
@@ -169,26 +184,60 @@ def verify_element(element, json)
  temp_messages += @errors
  @errors = temp
  end
- if verified_extension || verified_data_type
- matching_type += 1
- if data_type_found == 'code' # then check the binding
- unless element.binding.nil?
- matching_type += check_binding_element(element, value)
+ if data_type_found && (verified_extension || verified_data_type)
+ matching_type += 1
+ if data_type_found == 'code' # then check the binding
+ unless element.binding.nil?
+ matching_type += check_binding_element(element, value)
+ end
+ elsif data_type_found == 'CodeableConcept' && codeable_concept_pattern
+ vcc = FHIR::CodeableConcept.new(value)
+ pattern = element.pattern.coding
+ pattern.each do |pcoding|
+ vcc.coding.each do |vcoding|
+ 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 data_type_found == 'CodeableConcept' && codeable_concept_pattern
- vcc = FHIR::CodeableConcept.new(value)
- pattern = element.pattern.coding
- pattern.each do |pcoding|
- vcc.coding.each do |vcoding|
- matching_pattern = true if vcoding.system == pcoding.system && vcoding.code == pcoding.code
+
+ valueset_uri = element.binding && element.binding.valueSetReference && element.binding.valueSetReference.reference
+ vcc = FHIR::CodeableConcept.new(value)
+ if valueset_uri && self.class.vs_validators[valueset_uri]
+ check_fn = self.class.vs_validators[valueset_uri]
+ has_valid_code = vcc.coding && vcc.coding.any? { |c| check_fn.call(c) }
+ unless has_valid_code
+ binding_issues << "#{describe_element(element)} has no codings from #{valueset_uri}. Codings evaluated: #{vcc.to_json}"
+ 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
  end
- elsif data_type_found == 'String' && !element.maxLength.nil? && (value.size > element.maxLength)
- @errors << "#{describe_element(element)} exceed maximum length of #{element.maxLength}: #{value}"
  end
- else
- temp_messages << "#{describe_element(element)} is not a valid #{data_type_found}: '#{value}'"
+
+ elsif data_type_found == 'String' && !element.maxLength.nil? && (value.size > element.maxLength)
+ @errors << "#{describe_element(element)} exceed maximum length of #{element.maxLength}: #{value}"
  end
+ elsif data_type_found
+ temp_messages << "#{describe_element(element)} is not a valid #{data_type_found}: '#{value}'"
+ else
+ # we don't know the data type... so we say "OK"
+ matching_type += 1
+ @warnings >> "Unable to guess data type for #{describe_element(element)}"
+ end
 
  if matching_type <= 0
  @errors += temp_messages

test/unit/profile_validation_test.rb

@@ -55,6 +55,66 @@ def test_profile_validation
  assert_memory(before, after)
  end
 
+ def validate_vital_sign_resource
+ example_name = 'sample-us-core-record.json'
+ patient_record = File.join(FIXTURES_DIR, example_name)
+ input_json = File.read(patient_record)
+ bundle = FHIR::Json.from_json(input_json)
+
+ vitalsign = bundle.entry.find do |entry|
+ entry.resource.meta and (entry.resource.meta.profile.first == 'http://hl7.org/fhir/StructureDefinition/vitalsigns')
+ end
+ assert vitalsign, 'Unable to find vital sign Observation resource'
+ profile = PROFILES['http://hl7.org/fhir/StructureDefinition/vitalsigns']
+ assert profile, 'Failed to find http://hl7.org/fhir/StructureDefinition/vitalsigns profile'
+ profile.validate_resource(vitalsign.resource)
+ profile
+ end
+
+ def test_profile_code_system_check
+ # Clear any registered validators
+ FHIR::StructureDefinition.clear_all_validates_vs
+ FHIR::StructureDefinition.validates_vs "http://hl7.org/fhir/ValueSet/observation-vitalsignresult" do |coding|
+ false # fails so that the code system validation happens
+ end
+ FHIR::StructureDefinition.validates_vs "http://loinc.org" do |coding|
+ false # errors related to code system validation should be present
+ end
+ profile = validate_vital_sign_resource
+ assert profile.errors.empty?, 'Expected no errors.'
+ assert profile.warnings.detect{|x| x.start_with?('Observation.code has no codings from http://hl7.org/fhir/ValueSet/observation-vitalsignresult')}
+ assert profile.warnings.detect{|x| x.start_with?("Observation.code has no codings from it's specified system: http://loinc.org")}
+ # check memory
+ before = check_memory
+ resource = nil
+ profile = nil
+ wait_for_gc
+ after = check_memory
+ assert_memory(before, after)
+ end
+
+ def test_profile_valueset_check
+ # Clear any registered validators
+ FHIR::StructureDefinition.clear_all_validates_vs
+ FHIR::StructureDefinition.validates_vs "http://hl7.org/fhir/ValueSet/observation-vitalsignresult" do |coding|
+ true # fails so that the code system validation never happens
+ end
+ FHIR::StructureDefinition.validates_vs "http://loinc.org" do |coding|
+ false # no errors related to code system should be present
+ end
+ profile = validate_vital_sign_resource
+ assert profile.errors.empty?, 'Expected no errors.'
+ assert !profile.warnings.detect{|x| x.start_with?('Observation.code has no codings from http://hl7.org/fhir/ValueSet/observation-vitalsignresult')}
+ assert !profile.warnings.detect{|x| x.start_with?("Observation.code has no codings from it's specified system: http://loinc.org")}
+ # check memory
+ before = check_memory
+ resource = nil
+ profile = nil
+ wait_for_gc
+ after = check_memory
+ assert_memory(before, after)
+ end
+
  def test_invalid_profile_validation
  example_name = 'invalid-us-core-record.json'
  patient_record = File.join(FIXTURES_DIR, example_name)