us_core_test_kit 0.1.0

data/lib/us_core_test_kit/custom_groups/data_absent_reason_group.rb

@@ -0,0 +1,59 @@
+module USCoreTestKit
+  class DataAbsentReasonGroup < Inferno::TestGroup
+    id :us_core_311_data_absent_reason
+    title 'Missing Data Tests'
+    short_description 'Verify that the server is capable of representing missing data.'
+
+    description %(
+      The [US Core Missing Data
+      Guidance](http://hl7.org/fhir/us/core/STU3.1.1/general-guidance.html#missing-data)
+      gives instructions on how to represent various types of missing data.
+
+      In the previous resource tests, each resource returned from the server was
+      checked for the presence of missing data. These tests will pass if the
+      specified method of representing missing data was observed in the earlier
+      tests.
+    )
+    run_as_group
+
+    test do
+      title 'Server represents missing data with the DataAbsentReason Extension'
+      id :us_core_311_data_absent_reason_extension
+      description %(
+        For non-coded data elements, servers SHALL use the DataAbsentReason
+        Extension to represent missing data in a required field
+      )
+      input :dar_extension_found,
+            title: 'Data Absent Reason Extension Found',
+            locked: true,
+            optional: true,
+            default: 'false'
+
+      run do
+        assert dar_extension_found == 'true',
+               'No resources using the DataAbsentReason Extension have been found'
+      end
+    end
+
+    test do
+      title 'Server represents missing data with the DataAbsentReason CodeSystem'
+      id :us_core_311_data_absent_reason_code_system
+      description %(
+        For coded data elements with example, preferred, or extensible binding
+        strengths to ValueSets which do not include an appropriate "unknown"
+        code, servers SHALL use the "unknown" code from the DataAbsentReason
+        CodeSystem.
+      )
+      input :dar_code_found,
+            title: 'Data Absent Reason Extension Found',
+            locked: true,
+            optional: true,
+            default: 'false'
+
+      run do
+        assert dar_code_found == 'true',
+               'No resources using the DataAbsentReason CodeSystem have been found'
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/date_search_validation.rb

@@ -0,0 +1,101 @@
+# frozen_string_literal: true
+
+module USCoreTestKit
+  module DateSearchValidation
+    def get_fhir_datetime_range(datetime)
+      range = { start: DateTime.xmlschema(datetime), end: nil }
+      range[:end] =
+        if /^\d{4}$/.match?(datetime) # YYYY
+          range[:start].next_year - 1.seconds
+        elsif /^\d{4}-\d{2}$/.match?(datetime) # YYYY-MM
+          range[:start].next_month - 1.seconds
+        elsif /^\d{4}-\d{2}-\d{2}$/.match?(datetime) # YYYY-MM-DD
+          range[:start].next_day - 1.seconds
+        else # YYYY-MM-DDThh:mm:ss+zz:zz
+          range[:start]
+        end
+      range
+    end
+
+    def get_fhir_period_range(period)
+      range = { start: nil, end: nil }
+      range[:start] = DateTime.xmlschema(period.start) unless period.start.nil?
+      return range if period.end.nil?
+
+      period_end_beginning = DateTime.xmlschema(period.end)
+      range[:end] =
+        if /^\d{4}$/.match?(period.end) # YYYY
+          period_end_beginning.next_year - 1.seconds
+        elsif /^\d{4}-\d{2}$/.match?(period.end) # YYYY-MM
+          period_end_beginning.next_month - 1.seconds
+        elsif /^\d{4}-\d{2}-\d{2}$/.match?(period.end) # YYYY-MM-DD
+          period_end_beginning.next_day - 1.seconds
+        else # YYYY-MM-DDThh:mm:ss+zz:zz
+          period_end_beginning
+        end
+      range
+    end
+
+    def fhir_date_comparer(search_range, target_range, comparator)
+      # Implicitly, a missing lower boundary is "less than" any actual date. A missing upper boundary is "greater than" any actual date.
+      case comparator
+      when 'eq' # the range of the search value fully contains the range of the target value
+        !target_range[:start].nil? && !target_range[:end].nil? && search_range[:start] <= target_range[:start] && search_range[:end] >= target_range[:end]
+      when 'ne' # the range of the search value does not fully contain the range of the target value
+        target_range[:start].nil? || target_range[:end].nil? || search_range[:start] > target_range[:start] || search_range[:end] < target_range[:end]
+      when 'gt' #  the range above the search value intersects (i.e. overlaps) with the range of the target value
+        target_range[:end].nil? || search_range[:end] < target_range[:end]
+      when 'lt' # the range below the search value intersects (i.e. overlaps) with the range of the target value
+        target_range[:start].nil? || search_range[:start] > target_range[:start]
+      when 'ge'
+        fhir_date_comparer(search_range, target_range, 'gt') || fhir_date_comparer(search_range, target_range, 'eq')
+      when 'le'
+        fhir_date_comparer(search_range, target_range, 'lt') || fhir_date_comparer(search_range, target_range, 'eq')
+      when 'sa' # the range above the search value contains the range of the target value
+        !target_range[:start].nil? && search_range[:end] < target_range[:start]
+      when 'eb' # the range below the search value contains the range of the target value
+        !target_range[:end].nil? && search_range[:start] > target_range[:end]
+      when 'ap' # the range of the search value overlaps with the range of the target value
+        if target_range[:start].nil? || target_range[:end].nil?
+          (target_range[:start].nil? && search_range[:start] < target_range[:end]) ||
+            (target_range[:end].nil? && search_range[:end] > target_range[:start])
+        else
+          (search_range[:start] >= target_range[:start] && search_range[:start] <= target_range[:end]) ||
+            (search_range[:end] >= target_range[:start] && search_range[:end] <= target_range[:end])
+        end
+      end
+    end
+
+    def validate_date_search(search_value, target_value)
+      if target_value.instance_of? FHIR::Period
+        validate_period_search(search_value, target_value)
+      else
+        validate_datetime_search(search_value, target_value)
+      end
+    end
+
+    def validate_datetime_search(search_value, target_value)
+      comparator = search_value[0..1]
+      if ['eq', 'ge', 'gt', 'le', 'lt', 'ne', 'sa', 'eb', 'ap'].include? comparator
+        search_value = search_value[2..-1]
+      else
+        comparator = 'eq'
+      end
+      search_range = get_fhir_datetime_range(search_value)
+      target_range = get_fhir_datetime_range(target_value)
+      fhir_date_comparer(search_range, target_range, comparator)
+    end
+
+    def validate_period_search(search_value, target_value)
+      comparator = search_value[0..1]
+      if ['eq', 'ge', 'gt', 'le', 'lt', 'ne', 'sa', 'eb', 'ap'].include? comparator
+        search_value = search_value[2..-1]
+      else
+        comparator = 'eq'
+      end
+      search_range = get_fhir_datetime_range(search_value)
+      target_range = get_fhir_period_range(target_value)
+      fhir_date_comparer(search_range, target_range, comparator)
+    end
+  end
+end

data/lib/us_core_test_kit/ext/fhir_models.rb

@@ -0,0 +1,59 @@
+require 'json'
+
+# Extension to FHIR::Model. Prepending this into FHIR::Model (done below)
+# allows us to call super() on initialize when we overriding it,
+# while also defining new methods and attributes
+module InfernoFHIRModelExtensions
+  attr_accessor :source_hash, :source_text
+
+  def initialize(hash = {})
+    super(hash)
+    @source_hash = hash
+  end
+
+  def source_contents
+    @source_text || JSON.generate(@source_hash)
+  end
+end
+
+module FHIR
+  class Model
+    prepend ::InfernoFHIRModelExtensions
+  end
+end
+
+# Extension to FHIR::Json. Prepending this into FHIR::Json (done below)
+# allows us to call super() on from_json
+module InfernoJson
+  def from_json(json)
+    resource = super(json)
+    resource.source_text = json
+    resource
+  end
+end
+
+# Extension to FHIR::Xml. Prepending this into FHIR::Xml (done below)
+# allows us to call super() on from_xml
+module InfernoXml
+  def from_xml(xml)
+    resource = super(xml)
+    resource.source_text = xml
+    resource
+  end
+end
+
+module FHIR
+  module Json
+    class << self
+      prepend InfernoJson
+    end
+  end
+end
+
+module FHIR
+  module Xml
+    class << self
+      prepend InfernoXml
+    end
+  end
+end

data/lib/us_core_test_kit/fhir_resource_navigation.rb

@@ -0,0 +1,63 @@
+module USCoreTestKit
+  module FHIRResourceNavigation
+    def resolve_path(elements, path)
+      elements = Array.wrap(elements)
+      return elements if path.blank?
+
+      paths = path.split('.')
+      segment = paths.first
+      remaining_path = paths.drop(1).join('.')
+
+      elements.flat_map do |element|
+        child = get_next_value(element, segment)
+        resolve_path(child, remaining_path)
+      end.compact
+    end
+
+    def find_a_value_at(element, path)
+      return nil if element.nil?
+
+      elements = Array.wrap(element)
+
+      if path.empty?
+        return elements.find { |el| yield(el) } if block_given?
+
+        return elements.first
+      end
+
+      path_segments = path.split('.')
+      segment = path_segments.shift.delete_suffix('[x]').to_sym
+
+      no_elements_present =
+        elements.none? do |element|
+        child = get_next_value(element, segment)
+
+        child.present? || child == false
+      end
+
+      return nil if no_elements_present
+
+      remaining_path = path_segments.join('.')
+
+      elements.each do |element|
+        child = get_next_value(element, segment)
+        element_found =
+          if block_given?
+            find_a_value_at(child, remaining_path) { |value_found| yield(value_found) }
+          else
+            find_a_value_at(child, remaining_path)
+          end
+
+        return element_found if element_found.present? || element_found == false
+      end
+
+      nil
+    end
+
+    def get_next_value(element, property)
+      element.send(property)
+    rescue NoMethodError
+      nil
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_must_support_test.rb

@@ -0,0 +1,40 @@
+require_relative '../../must_support_test'
+
+module USCoreTestKit
+  class AllergyIntoleranceMustSupportTest < Inferno::Test
+    include USCoreTestKit::MustSupportTest
+
+    title 'All must support elements are provided in the AllergyIntolerance resources returned'
+    description %(
+      US Core Responders SHALL be capable of populating all data elements as
+      part of the query results as specified by the US Core Server Capability
+      Statement. This test will look through the AllergyIntolerance resources
+      found previously for the following must support elements:
+
+      * AllergyIntolerance.clinicalStatus
+      * AllergyIntolerance.code
+      * AllergyIntolerance.patient
+      * AllergyIntolerance.reaction
+      * AllergyIntolerance.reaction.manifestation
+      * AllergyIntolerance.verificationStatus
+    )
+
+    id :us_core_311_allergy_intolerance_must_support_test
+
+    def resource_type
+      'AllergyIntolerance'
+    end
+
+    def self.metadata
+      @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml')))
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    run do
+      perform_must_support_test(all_scratch_resources)
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_patient_clinical_status_search_test.rb

@@ -0,0 +1,46 @@
+require_relative '../../search_test'
+require_relative '../../generator/group_metadata'
+
+module USCoreTestKit
+  class AllergyIntolerancePatientClinicalStatusSearchTest < Inferno::Test
+    include USCoreTestKit::SearchTest
+
+    title 'Server returns valid results for AllergyIntolerance search by patient + clinical-status'
+    description %(
+A server SHOULD support searching by
+patient + clinical-status on the AllergyIntolerance resource. This test
+will pass if resources are returned and match the search criteria. If
+none are returned, the test is skipped.
+
+[US Core Server CapabilityStatement](http://hl7.org/fhir/us/core/STU3.1.1/CapabilityStatement-us-core-server.html)
+
+    )
+
+    id :us_core_311_allergy_intolerance_patient_clinical_status_search_test
+    optional
+
+    input :patient_ids,
+      title: 'Patient IDs',
+      description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
+
+    def self.properties
+      @properties ||= SearchTestProperties.new(
+        resource_type: 'AllergyIntolerance',
+        search_param_names: ['patient', 'clinical-status'],
+        token_search_params: ['clinical-status']
+      )
+    end
+
+    def self.metadata
+      @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml')))
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    run do
+      run_search_test
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_patient_search_test.rb

@@ -0,0 +1,60 @@
+require_relative '../../search_test'
+require_relative '../../generator/group_metadata'
+
+module USCoreTestKit
+  class AllergyIntolerancePatientSearchTest < Inferno::Test
+    include USCoreTestKit::SearchTest
+
+    title 'Server returns valid results for AllergyIntolerance search by patient'
+    description %(
+A server SHALL support searching by
+patient on the AllergyIntolerance resource. This test
+will pass if resources are returned and match the search criteria. If
+none are returned, the test is skipped.
+
+This test verifies that the server supports searching by reference using
+the form `patient=[id]` as well as `patient=Patient/[id]`. The two
+different forms are expected to return the same number of results. US
+Core requires that both forms are supported by US Core responders.
+
+Because this is the first search of the sequence, resources in the
+response will be used for subsequent tests.
+
+Additionally, this test will check that GET and POST search methods
+return the same number of results. Search by POST is required by the
+FHIR R4 specification, and these tests interpret search by GET as a
+requirement of US Core v3.1.1.
+
+[US Core Server CapabilityStatement](http://hl7.org/fhir/us/core/STU3.1.1/CapabilityStatement-us-core-server.html)
+
+    )
+
+    id :us_core_311_allergy_intolerance_patient_search_test
+    input :patient_ids,
+      title: 'Patient IDs',
+      description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
+
+    def self.properties
+      @properties ||= SearchTestProperties.new(
+        first_search: true,
+        resource_type: 'AllergyIntolerance',
+        search_param_names: ['patient'],
+        possible_status_search: true,
+        test_reference_variants: true,
+        test_post_search: true
+      )
+    end
+
+    def self.metadata
+      @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml')))
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    run do
+      run_search_test
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_provenance_revinclude_search_test.rb

@@ -0,0 +1,49 @@
+require_relative '../../search_test'
+require_relative '../../generator/group_metadata'
+
+module USCoreTestKit
+  class AllergyIntoleranceProvenanceRevincludeSearchTest < Inferno::Test
+    include USCoreTestKit::SearchTest
+
+    title 'Server returns Provenance resources from AllergyIntolerance search by patient + revInclude:Provenance:target'
+    description %(
+      A server SHALL be capable of supporting _revIncludes:Provenance:target.
+
+      This test will perform a search by patient + revInclude:Provenance:target and
+      will pass if a Provenance resource is found in the response.
+    %)
+
+    id :us_core_311_allergy_intolerance_provenance_revinclude_search_test
+
+    input :patient_ids,
+      title: 'Patient IDs',
+      description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
+
+    def properties
+      @properties ||= SearchTestProperties.new(
+        resource_type: 'AllergyIntolerance',
+        search_param_names: ['patient']
+      )
+    end
+
+    def self.metadata
+      @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml')))
+    end
+
+    def self.provenance_metadata
+      @provenance_metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, '..', 'provenance', 'metadata.yml')))
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    def scratch_provenance_resources
+      scratch[:provenance_resources] ||= {}
+    end
+
+    run do
+      run_provenance_revinclude_search_test
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_read_test.rb

@@ -0,0 +1,24 @@
+require_relative '../../read_test'
+
+module USCoreTestKit
+  class AllergyIntoleranceReadTest < Inferno::Test
+    include USCoreTestKit::ReadTest
+
+    title 'Server returns correct AllergyIntolerance resource from AllergyIntolerance read interaction'
+    description 'A server SHALL support the AllergyIntolerance read interaction.'
+
+    id :us_core_311_allergy_intolerance_read_test
+
+    def resource_type
+      'AllergyIntolerance'
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    run do
+      perform_read_test(all_scratch_resources)
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_reference_resolution_test.rb

@@ -0,0 +1,28 @@
+require_relative '../../reference_resolution_test'
+
+module USCoreTestKit
+  class AllergyIntoleranceReferenceResolutionTest < Inferno::Test
+    include USCoreTestKit::ReferenceResolutionTest
+
+    title 'Every reference within AllergyIntolerance resources can be read'
+    description %(
+      This test will attempt to read the first 50 references found in the
+      resources from the first search. The test will fail if Inferno fails to
+      read any of those references.
+    )
+
+    id :us_core_311_allergy_intolerance_reference_resolution_test
+
+    def resource_type
+      'AllergyIntolerance'
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    run do
+      perform_reference_resolution_test(scratch_resources[:all])
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance/allergy_intolerance_validation_test.rb

@@ -0,0 +1,34 @@
+require_relative '../../validation_test'
+
+module USCoreTestKit
+  class AllergyIntoleranceValidationTest < Inferno::Test
+    include USCoreTestKit::ValidationTest
+
+    id :us_core_311_allergy_intolerance_validation_test
+    title 'AllergyIntolerance resources returned during previous tests conform to the US Core AllergyIntolerance Profile'
+    description %(
+This test verifies resources returned from the first search conform to
+the [US Core AllergyIntolerance Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance).
+
+It verifies the presence of mandatory elements and that elements with
+required bindings contain appropriate values. CodeableConcept element
+bindings will fail if none of their codings have a code/system belonging
+to the bound ValueSet. Quantity, Coding, and code element bindings will
+fail if their code/system are not found in the valueset.
+
+    )
+    output :dar_code_found, :dar_extension_found
+
+    def resource_type
+      'AllergyIntolerance'
+    end
+
+    def scratch_resources
+      scratch[:allergy_intolerance_resources] ||= {}
+    end
+
+    run do
+      perform_validation_test(scratch_resources[:all] || [], 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance')
+    end
+  end
+end

data/lib/us_core_test_kit/generated/allergy_intolerance_group.rb

@@ -0,0 +1,85 @@
+require_relative 'allergy_intolerance/allergy_intolerance_patient_search_test'
+require_relative 'allergy_intolerance/allergy_intolerance_patient_clinical_status_search_test'
+require_relative 'allergy_intolerance/allergy_intolerance_read_test'
+require_relative 'allergy_intolerance/allergy_intolerance_provenance_revinclude_search_test'
+require_relative 'allergy_intolerance/allergy_intolerance_validation_test'
+require_relative 'allergy_intolerance/allergy_intolerance_must_support_test'
+require_relative 'allergy_intolerance/allergy_intolerance_reference_resolution_test'
+
+module USCoreTestKit
+  class AllergyIntoleranceGroup < Inferno::TestGroup
+    title 'AllergyIntolerance Tests'
+    short_description 'Verify support for the server capabilities required by the US Core AllergyIntolerance Profile.'
+    description %(
+# Background
+
+The US Core AllergyIntolerance sequence verifies that the system under test is
+able to provide correct responses for AllergyIntolerance queries. These queries
+must contain resources conforming to the US Core AllergyIntolerance Profile as
+specified in the US Core v3.1.1 Implementation Guide.
+
+# Testing Methodology
+## Searching
+This test sequence will first perform each required search associated
+with this resource. This sequence will perform searches with the
+following parameters:
+
+* patient
+
+### Search Parameters
+The first search uses the selected patient(s) from the prior launch
+sequence. Any subsequent searches will look for its parameter values
+from the results of the first search. For example, the `identifier`
+search in the patient sequence is performed by looking for an existing
+`Patient.identifier` from any of the resources returned in the `_id`
+search. If a value cannot be found this way, the search is skipped.
+
+### Search Validation
+Inferno will retrieve up to the first 20 bundle pages of the reply for
+AllergyIntolerance resources and save them for subsequent tests. Each of
+these resources is then checked to see if it matches the searched
+parameters in accordance with [FHIR search
+guidelines](https://www.hl7.org/fhir/search.html). The test will fail,
+for example, if a Patient search for `gender=male` returns a `female`
+patient.
+
+
+## Must Support
+Each profile contains elements marked as "must support". This test
+sequence expects to see each of these elements at least once. If at
+least one cannot be found, the test will fail. The test will look
+through the AllergyIntolerance resources found in the first test for these
+elements.
+
+## Profile Validation
+Each resource returned from the first search is expected to conform to
+the [US Core AllergyIntolerance Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-allergyintolerance). Each element is checked against
+teminology binding and cardinality requirements.
+
+Elements with a required binding are validated against their bound
+ValueSet. If the code/system in the element is not part of the ValueSet,
+then the test will fail.
+
+## Reference Validation
+Each reference within the resources found from the previous tests must
+resolve. The test will attempt to read each reference found and will
+fail if any attempted read fails.
+
+    )
+
+    id :us_core_311_allergy_intolerance
+    run_as_group
+
+    def self.metadata
+      @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'allergy_intolerance', 'metadata.yml')))
+    end
+
+    test from: :us_core_311_allergy_intolerance_patient_search_test
+    test from: :us_core_311_allergy_intolerance_patient_clinical_status_search_test
+    test from: :us_core_311_allergy_intolerance_read_test
+    test from: :us_core_311_allergy_intolerance_provenance_revinclude_search_test
+    test from: :us_core_311_allergy_intolerance_validation_test
+    test from: :us_core_311_allergy_intolerance_must_support_test
+    test from: :us_core_311_allergy_intolerance_reference_resolution_test
+  end
+end