us_core_test_kit 0.1.1 → 0.2.0

data/lib/us_core_test_kit/generated/v4.0.0/smokingstatus/smokingstatus_reference_resolution_test.rb

@@ -0,0 +1,38 @@
+require_relative '../../../reference_resolution_test'
+require_relative '../resource_list'
+
+module USCoreTestKit
+  module USCoreV400
+    class SmokingstatusReferenceResolutionTest < Inferno::Test
+      include USCoreTestKit::ReferenceResolutionTest
+      include ResourceList
+
+      title 'MustSupport references within Observation resources can be read'
+      description %(
+        This test will attempt to read MustSupport references found in the
+        resources from the first search. This test will look through the Observation resources
+        found previously for the following must support elements:
+
+  
+      )
+
+      id :us_core_v400_smokingstatus_reference_resolution_test
+
+      def resource_type
+        'Observation'
+      end
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml')))
+      end
+
+      def scratch_resources
+        scratch[:smokingstatus_resources] ||= {}
+      end
+
+      run do
+        perform_reference_resolution_test(scratch_resources[:all])
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v4.0.0/smokingstatus/smokingstatus_validation_test.rb

@@ -0,0 +1,36 @@
+require_relative '../../../validation_test'
+
+module USCoreTestKit
+  module USCoreV400
+    class SmokingstatusValidationTest < Inferno::Test
+      include USCoreTestKit::ValidationTest
+
+      id :us_core_v400_smokingstatus_validation_test
+      title 'Observation resources returned during previous tests conform to the US Core Smoking Status Observation Profile'
+      description %(
+  This test verifies resources returned from the first search conform to
+the [US Core Smoking Status Observation Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus).
+
+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
+        'Observation'
+      end
+
+      def scratch_resources
+        scratch[:smokingstatus_resources] ||= {}
+      end
+
+      run do
+        perform_validation_test(scratch_resources[:all] || [], 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus')
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v4.0.0/smokingstatus_group.rb

@@ -0,0 +1,95 @@
+require_relative 'smokingstatus/smokingstatus_patient_code_search_test'
+require_relative 'smokingstatus/smokingstatus_patient_category_status_search_test'
+require_relative 'smokingstatus/smokingstatus_patient_code_date_search_test'
+require_relative 'smokingstatus/smokingstatus_patient_category_search_test'
+require_relative 'smokingstatus/smokingstatus_patient_category_date_search_test'
+require_relative 'smokingstatus/smokingstatus_read_test'
+require_relative 'smokingstatus/smokingstatus_provenance_revinclude_search_test'
+require_relative 'smokingstatus/smokingstatus_validation_test'
+require_relative 'smokingstatus/smokingstatus_must_support_test'
+require_relative 'smokingstatus/smokingstatus_reference_resolution_test'
+
+module USCoreTestKit
+  module USCoreV400
+    class SmokingstatusGroup < Inferno::TestGroup
+      title 'Smoking Status Observation Tests'
+      short_description 'Verify support for the server capabilities required by the US Core Smoking Status Observation Profile.'
+      description %(
+  # Background
+
+The US Core Smoking Status Observation sequence verifies that the system under test is
+able to provide correct responses for Observation queries. These queries
+must contain resources conforming to the US Core Smoking Status Observation Profile as
+specified in the US Core v4.0.0 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 + code
+* patient + category
+* patient + category + date
+
+### 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
+Observation 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 Observation 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 Smoking Status Observation Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus). 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_v400_smokingstatus
+      run_as_group
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'smokingstatus', 'metadata.yml')))
+      end
+  
+      test from: :us_core_v400_smokingstatus_patient_code_search_test
+      test from: :us_core_v400_smokingstatus_patient_category_status_search_test
+      test from: :us_core_v400_smokingstatus_patient_code_date_search_test
+      test from: :us_core_v400_smokingstatus_patient_category_search_test
+      test from: :us_core_v400_smokingstatus_patient_category_date_search_test
+      test from: :us_core_v400_smokingstatus_read_test
+      test from: :us_core_v400_smokingstatus_provenance_revinclude_search_test
+      test from: :us_core_v400_smokingstatus_validation_test
+      test from: :us_core_v400_smokingstatus_must_support_test
+      test from: :us_core_v400_smokingstatus_reference_resolution_test
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v4.0.0/us_core_test_suite.rb

@@ -0,0 +1,116 @@
+require 'inferno/dsl/oauth_credentials'
+require_relative '../../version'
+require_relative '../../custom_groups/v4.0.0/capability_statement_group'
+require_relative '../../custom_groups/v4.0.0/clinical_notes_guidance_group'
+require_relative '../../custom_groups/data_absent_reason_group'
+require_relative 'patient_group'
+require_relative 'allergy_intolerance_group'
+require_relative 'care_plan_group'
+require_relative 'care_team_group'
+require_relative 'condition_group'
+require_relative 'device_group'
+require_relative 'diagnostic_report_lab_group'
+require_relative 'diagnostic_report_note_group'
+require_relative 'document_reference_group'
+require_relative 'goal_group'
+require_relative 'immunization_group'
+require_relative 'medication_request_group'
+require_relative 'observation_lab_group'
+require_relative 'blood_pressure_group'
+require_relative 'bmi_group'
+require_relative 'head_circumference_group'
+require_relative 'body_height_group'
+require_relative 'body_weight_group'
+require_relative 'body_temperature_group'
+require_relative 'heart_rate_group'
+require_relative 'pediatric_bmi_for_age_group'
+require_relative 'head_circumference_percentile_group'
+require_relative 'pediatric_weight_for_height_group'
+require_relative 'pulse_oximetry_group'
+require_relative 'respiratory_rate_group'
+require_relative 'smokingstatus_group'
+require_relative 'procedure_group'
+require_relative 'encounter_group'
+require_relative 'organization_group'
+require_relative 'practitioner_group'
+require_relative 'provenance_group'
+
+module USCoreTestKit
+  module USCoreV400
+    class USCoreTestSuite < Inferno::TestSuite
+      title 'US Core v4.0.0'
+      version VERSION
+
+      VALIDATION_MESSAGE_FILTERS = [
+        %r{Sub-extension url 'introspect' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris$},
+        %r{Sub-extension url 'revoke' is not defined by the Extension http://fhir-registry\.smarthealthit\.org/StructureDefinition/oauth-uris$},
+        /^Observation\.effective\.ofType\(Period\): vs-1:/, # Invalid invariant in FHIR v4.0.1
+        /^Observation\.effective\.ofType\(Period\): us-core-1:/ # Invalid invariant in US Core v3.1.1
+      ].freeze
+
+      def self.metadata
+        @metadata ||= YAML.load_file(File.join(__dir__, 'metadata.yml'))[:groups].map do |raw_metadata|
+            Generator::GroupMetadata.new(raw_metadata)
+          end
+      end
+
+      validator do
+        url ENV.fetch('V400_VALIDATOR_URL', 'http://validator_service:4567')
+        exclude_message do |message|
+          VALIDATION_MESSAGE_FILTERS.any? { |filter| filter.match? message.message }
+        end
+      end
+
+      id :us_core_v400
+
+      input :url,
+        title: 'FHIR Endpoint',
+        description: 'URL of the FHIR endpoint'
+      input :smart_credentials,
+        title: 'OAuth Credentials',
+        type: :oauth_credentials,
+        optional: true
+
+      fhir_client do
+        url :url
+        oauth_credentials :smart_credentials
+      end
+
+      group from: :us_core_v400_capability_statement
+  
+      group from: :us_core_v400_patient
+      group from: :us_core_v400_allergy_intolerance
+      group from: :us_core_v400_care_plan
+      group from: :us_core_v400_care_team
+      group from: :us_core_v400_condition
+      group from: :us_core_v400_device
+      group from: :us_core_v400_diagnostic_report_lab
+      group from: :us_core_v400_diagnostic_report_note
+      group from: :us_core_v400_document_reference
+      group from: :us_core_v400_goal
+      group from: :us_core_v400_immunization
+      group from: :us_core_v400_medication_request
+      group from: :us_core_v400_observation_lab
+      group from: :us_core_v400_blood_pressure
+      group from: :us_core_v400_bmi
+      group from: :us_core_v400_head_circumference
+      group from: :us_core_v400_body_height
+      group from: :us_core_v400_body_weight
+      group from: :us_core_v400_body_temperature
+      group from: :us_core_v400_heart_rate
+      group from: :us_core_v400_pediatric_bmi_for_age
+      group from: :us_core_v400_head_circumference_percentile
+      group from: :us_core_v400_pediatric_weight_for_height
+      group from: :us_core_v400_pulse_oximetry
+      group from: :us_core_v400_respiratory_rate
+      group from: :us_core_v400_smokingstatus
+      group from: :us_core_v400_procedure
+      group from: :us_core_v400_encounter
+      group from: :us_core_v400_organization
+      group from: :us_core_v400_practitioner
+      group from: :us_core_v400_provenance
+      group from: :us_core_v400_clinical_notes_guidance
+      group from: :us_core_311_data_absent_reason
+    end
+  end
+end

data/lib/us_core_test_kit/generator/group_generator.rb

@@ -5,17 +5,18 @@ module USCoreTestKit
   class Generator
     class GroupGenerator
       class << self
-        def generate(ig_metadata)
+        def generate(ig_metadata, base_output_dir)
           ig_metadata.ordered_groups
-            .reject { |group| SpecialCases.exclude_resource? group.resource }
-            .each { |group| new(group).generate }
+            .reject { |group| SpecialCases.exclude_group? group }
+            .each { |group| new(group, base_output_dir).generate }
         end
       end
 
-      attr_accessor :group_metadata
+      attr_accessor :group_metadata, :base_output_dir
 
-      def initialize(group_metadata)
+      def initialize(group_metadata, base_output_dir)
         self.group_metadata = group_metadata
+        self.base_output_dir = base_output_dir
       end
 
       def template
@@ -38,6 +39,10 @@ module USCoreTestKit
         "#{Naming.upper_camel_case_for_profile(group_metadata)}Group"
       end
 
+      def module_name
+        "USCore#{group_metadata.reformatted_version.upcase}"
+      end
+
       def title
         group_metadata.title
       end
@@ -47,11 +52,11 @@ module USCoreTestKit
       end
 
       def output_file_name
-        File.join(__dir__, '..', 'generated', base_output_file_name)
+        File.join(base_output_dir, base_output_file_name)
       end
 
       def metadata_file_name
-        File.join(__dir__, '..', 'generated', profile_identifier, base_metadata_file_name)
+        File.join(base_output_dir, profile_identifier, base_metadata_file_name)
       end
 
       def profile_identifier
@@ -59,7 +64,7 @@ module USCoreTestKit
       end
 
       def group_id
-        "us_core_311_#{profile_identifier}"
+        "us_core_#{group_metadata.reformatted_version}_#{profile_identifier}"
       end
 
       def resource_type
@@ -75,12 +80,30 @@ module USCoreTestKit
       end
 
       def generate
+        add_special_tests
         File.open(output_file_name, 'w') { |f| f.write(output) }
         group_metadata.id = group_id
         group_metadata.file_name = base_output_file_name
         File.open(metadata_file_name, 'w') { |f| f.write(YAML.dump(group_metadata.to_hash)) }
       end
 
+      def add_special_tests
+        return unless group_metadata.reformatted_version == 'v400'
+
+        case group_metadata.resource
+        when 'Device'
+          group_metadata.add_test(
+            id: 'us_core_v400_device_udi_pi_test',
+            file_name: '../../custom_groups/v4.0.0/device_udi_pi_test.rb'
+          )
+        when 'DocumentReference'
+          group_metadata.add_test(
+            id: 'us_core_v400_document_reference_custodian_test',
+            file_name: '../../custom_groups/v4.0.0/document_reference_custodian_test.rb'
+          )
+        end
+      end
+
       def test_id_list
         @test_id_list ||=
           group_metadata.tests.map { |test| test[:id] }
@@ -88,7 +111,10 @@ module USCoreTestKit
 
       def test_file_list
         @test_file_list ||=
-          group_metadata.tests.map { |test| test[:file_name].delete_suffix('.rb') }
+          group_metadata.tests.map do |test|
+            name_without_suffix = test[:file_name].delete_suffix('.rb')
+            name_without_suffix.start_with?('..') ? name_without_suffix : "#{profile_identifier}/#{name_without_suffix}"
+          end
       end
 
       def required_searches
@@ -139,7 +165,7 @@ module USCoreTestKit
         The US Core #{title} sequence verifies that the system under test is
         able to provide correct responses for #{resource_type} queries. These queries
         must contain resources conforming to the #{profile_name} as
-        specified in the US Core v3.1.1 Implementation Guide.
+        specified in the US Core #{group_metadata.version} Implementation Guide.
 
         # Testing Methodology
         #{search_description}

data/lib/us_core_test_kit/generator/group_metadata.rb

@@ -77,7 +77,7 @@ module USCoreTestKit
       end
 
       def to_hash
-        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) }
+        ATTRIBUTES.each_with_object({}) { |key, hash| hash[key] = send(key) unless send(key).nil? }
       end
 
       def add_delayed_references(delayed_profiles, ig_resources)

data/lib/us_core_test_kit/generator/group_metadata_extractor.rb

@@ -57,26 +57,28 @@ module USCoreTestKit
       def mark_mandatory_and_must_support_searches
         searches.each do |search|
           search[:names_not_must_support_or_mandatory] = search[:names].reject do |name|
-            path = search_definitions[name.to_sym][:full_path]
+            full_paths = search_definitions[name.to_sym][:full_paths]
             any_must_support_elements = (must_supports[:elements]).any? do |element|
-              full_must_support_path = "#{resource}.#{element[:path]}"
+              full_must_support_paths = ["#{resource}.#{element[:original_path]}", "#{resource}.#{element[:path]}"]
 
-              # allow for non-choice, choice types, and _id
-              name == '_id' || full_must_support_path == path || full_must_support_path == "#{path}[x]"
+              full_paths.any? do |path|
+                # allow for non-choice, choice types, and _id
+                name == '_id' || full_must_support_paths.include?(path) || full_must_support_paths.include?("#{path}[x]")
+              end
             end
 
             any_must_support_slices = must_supports[:slices].any? do |slice|
               # only handle type slices because that is all we need for now
               if slice[:discriminator] && slice[:discriminator][:type] == 'type'
                 full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
-                full_must_support_path == path
+                full_paths.include?(full_must_support_path)
               else
                 false
               end
             end
 
             any_mandatory_elements = mandatory_elements.any? do |element|
-              element == path
+              full_paths.include?(element)
             end
 
             any_must_support_elements || any_must_support_slices || any_mandatory_elements
@@ -114,17 +116,6 @@ module USCoreTestKit
 
       def handle_special_cases
         set_first_search
-
-        case profile_url
-        when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-implantable-device'
-          must_supports[:elements].delete_if do |element|
-            ['udiCarrier.carrierAIDC', 'udiCarrier.carrierHRF'].include? element[:path]
-          end
-        when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference'
-          must_supports[:elements].delete_if do |element|
-            ['content.attachment.data', 'content.attachment.url'].include? element[:path]
-          end
-        end
       end
 
       def set_first_search
@@ -230,7 +221,7 @@ module USCoreTestKit
       def required_concepts
         # The base FHIR vital signs profile has a required binding that isn't
         # relevant for any of its child profiles
-        return if resource == 'Observation'
+        return [] if resource == 'Observation'
 
         profile_elements
           .select { |element| element.type&.any? { |type| type.code == 'CodeableConcept' } }
@@ -263,6 +254,7 @@ module USCoreTestKit
           profile_elements
             .select { |element| element.min.positive? }
             .map { |element| element.path }
+            .uniq
       end
 
       def references

data/lib/us_core_test_kit/generator/ig_loader.rb

@@ -7,6 +7,12 @@ require_relative 'ig_resources'
 module USCoreTestKit
   class Generator
     class IGLoader
+      attr_accessor :base_ig_directory
+
+      def initialize(base_ig_directory)
+        self.base_ig_directory = base_ig_directory
+      end
+
       def ig_resources
         @ig_resources ||= IGResources.new
       end
@@ -17,7 +23,7 @@ module USCoreTestKit
       end
 
       def load_ig
-        tar = Gem::Package::TarReader.new(Zlib::GzipReader.open(File.join(__dir__, '..', 'igs', 'package.tgz')))
+        tar = Gem::Package::TarReader.new(Zlib::GzipReader.open(File.join(base_ig_directory, 'package.tgz')))
 
         tar.each do |entry|
           next if entry.directory?
@@ -43,7 +49,7 @@ module USCoreTestKit
       end
 
       def load_standalone_resources
-        Dir.glob(File.join(__dir__, '..', 'igs', '*.json')).each do |file_path|
+        Dir.glob(File.join(base_ig_directory, '*.json')).each do |file_path|
           begin
             resource = FHIR.from_contents(File.read(file_path))
             next if resource.nil?

data/lib/us_core_test_kit/generator/ig_metadata_extractor.rb

@@ -29,16 +29,18 @@ module USCoreTestKit
       # The US Core Server Capability Statement does not list support for the
       # required vital signs profiles, so they need to be added
       def add_vital_signs_profiles
-        ig_resources.capability_statement.rest.first.resource
-          .find { |resource| resource.type == 'Observation' }
-          .supportedProfile.concat [
-            'http://hl7.org/fhir/StructureDefinition/bodyheight',
-            'http://hl7.org/fhir/StructureDefinition/bodytemp',
-            'http://hl7.org/fhir/StructureDefinition/bp',
-            'http://hl7.org/fhir/StructureDefinition/bodyweight',
-            'http://hl7.org/fhir/StructureDefinition/heartrate',
-            'http://hl7.org/fhir/StructureDefinition/resprate'
-          ]
+        if ig_resources.ig.version == "3.1.1"
+          ig_resources.capability_statement.rest.first.resource
+            .find { |resource| resource.type == 'Observation' }
+            .supportedProfile.concat [
+              'http://hl7.org/fhir/StructureDefinition/bodyheight',
+              'http://hl7.org/fhir/StructureDefinition/bodytemp',
+              'http://hl7.org/fhir/StructureDefinition/bp',
+              'http://hl7.org/fhir/StructureDefinition/bodyweight',
+              'http://hl7.org/fhir/StructureDefinition/heartrate',
+              'http://hl7.org/fhir/StructureDefinition/resprate'
+            ]
+        end
       end
 
       def add_metadata_from_resources