us_core_test_kit 0.6.2 → 0.6.4

data/lib/us_core_test_kit/generated/v7.0.0-ballot/treatment_intervention_preference/treatment_intervention_preference_provenance_revinclude_search_test.rb

@@ -0,0 +1,53 @@
+require_relative '../../../search_test'
+require_relative '../../../generator/group_metadata'
+
+module USCoreTestKit
+  module USCoreV700_BALLOT
+    class TreatmentInterventionPreferenceProvenanceRevincludeSearchTest < Inferno::Test
+      include USCoreTestKit::SearchTest
+
+      title 'Server returns Provenance resources from Observation search by patient + code + revInclude:Provenance:target'
+      description %(
+        A server SHALL be capable of supporting _revIncludes:Provenance:target.
+
+        This test will perform a search by patient + code + revInclude:Provenance:target and
+        will pass if a Provenance resource is found in the response.
+      %)
+
+      id :us_core_v700_ballot_treatment_intervention_preference_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(
+          fixed_value_search: true,
+        resource_type: 'Observation',
+        search_param_names: ['patient', 'code'],
+        possible_status_search: true
+        )
+      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'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:treatment_intervention_preference_resources] ||= {}
+      end
+
+      def scratch_provenance_resources
+        scratch[:provenance_resources] ||= {}
+      end
+
+      run do
+        run_provenance_revinclude_search_test
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v7.0.0-ballot/treatment_intervention_preference/treatment_intervention_preference_read_test.rb

@@ -0,0 +1,26 @@
+require_relative '../../../read_test'
+
+module USCoreTestKit
+  module USCoreV700_BALLOT
+    class TreatmentInterventionPreferenceReadTest < Inferno::Test
+      include USCoreTestKit::ReadTest
+
+      title 'Server returns correct Observation resource from Observation read interaction'
+      description 'A server SHALL support the Observation read interaction.'
+
+      id :us_core_v700_ballot_treatment_intervention_preference_read_test
+
+      def resource_type
+        'Observation'
+      end
+
+      def scratch_resources
+        scratch[:treatment_intervention_preference_resources] ||= {}
+      end
+
+      run do
+        perform_read_test(all_scratch_resources)
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v7.0.0-ballot/treatment_intervention_preference/treatment_intervention_preference_reference_resolution_test.rb

@@ -0,0 +1,40 @@
+require_relative '../../../reference_resolution_test'
+
+module USCoreTestKit
+  module USCoreV700_BALLOT
+    class TreatmentInterventionPreferenceReferenceResolutionTest < Inferno::Test
+      include USCoreTestKit::ReferenceResolutionTest
+
+      title 'MustSupport references within Observation resources are valid'
+      description %(
+        This test will attempt to read external references provided within elements
+        marked as 'MustSupport', if any are available.
+
+        It verifies that at least one external reference for each MustSupport Reference element
+        can be accessed by the test client, and conforms to corresponding US Core profile.
+
+        Elements which may provide external references include:
+
+        * Observation.subject
+      )
+
+      id :us_core_v700_ballot_treatment_intervention_preference_reference_resolution_test
+
+      def resource_type
+        'Observation'
+      end
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:treatment_intervention_preference_resources] ||= {}
+      end
+
+      run do
+        perform_reference_resolution_test(scratch_resources[:all])
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v7.0.0-ballot/treatment_intervention_preference/treatment_intervention_preference_validation_test.rb

@@ -0,0 +1,40 @@
+require_relative '../../../validation_test'
+
+module USCoreTestKit
+  module USCoreV700_BALLOT
+    class TreatmentInterventionPreferenceValidationTest < Inferno::Test
+      include USCoreTestKit::ValidationTest
+
+      id :us_core_v700_ballot_treatment_intervention_preference_validation_test
+      title 'Observation resources returned during previous tests conform to the US Core Treatment Intervention Preference Profile'
+      description %(
+This test verifies resources returned from the first search conform to
+the [US Core Treatment Intervention Preference Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-treatment-intervention-preference).
+Systems must demonstrate at least one valid example in order to pass this test.
+
+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[:treatment_intervention_preference_resources] ||= {}
+      end
+
+      run do
+        perform_validation_test(scratch_resources[:all] || [],
+                                'http://hl7.org/fhir/us/core/StructureDefinition/us-core-treatment-intervention-preference',
+                                '7.0.0-ballot',
+                                skip_if_empty: true)
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v7.0.0-ballot/treatment_intervention_preference_group.rb

@@ -0,0 +1,96 @@
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_patient_code_search_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_patient_category_search_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_patient_category_date_search_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_patient_category_status_search_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_patient_code_date_search_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_read_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_provenance_revinclude_search_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_validation_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_must_support_test'
+require_relative 'treatment_intervention_preference/treatment_intervention_preference_reference_resolution_test'
+
+module USCoreTestKit
+  module USCoreV700_BALLOT
+    class TreatmentInterventionPreferenceGroup < Inferno::TestGroup
+      title 'Observation Treatment Intervention Preference Tests'
+      short_description 'Verify support for the server capabilities required by the US Core Treatment Intervention Preference Profile.'
+      description %(
+  # Background
+
+The US Core Observation Treatment Intervention Preference 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 Treatment Intervention Preference Profile as
+specified in the US Core v7.0.0-ballot 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 Treatment Intervention Preference Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-treatment-intervention-preference). 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
+At least one instance of each external reference in elements marked as
+"must support" within the resources provided by the system must resolve.
+The test will attempt to read each reference found and will fail if no
+read succeeds.
+
+      )
+
+      id :us_core_v700_ballot_treatment_intervention_preference
+      run_as_group
+
+      def self.metadata
+        @metadata ||= Generator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'treatment_intervention_preference', 'metadata.yml'), aliases: true))
+      end
+  
+      test from: :us_core_v700_ballot_treatment_intervention_preference_patient_code_search_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_patient_category_search_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_patient_category_date_search_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_patient_category_status_search_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_patient_code_date_search_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_read_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_provenance_revinclude_search_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_validation_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_must_support_test
+      test from: :us_core_v700_ballot_treatment_intervention_preference_reference_resolution_test
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v7.0.0-ballot/us_core_test_suite.rb

@@ -0,0 +1,216 @@
+require 'inferno/dsl/oauth_credentials'
+require_relative '../../version'
+require_relative '../../custom_groups/v7.0.0-ballot/capability_statement_group'
+require_relative '../../custom_groups/v4.0.0/clinical_notes_guidance_group'
+require_relative '../../custom_groups/data_absent_reason_group'
+require_relative '../../custom_groups/smart_app_launch_group'
+require_relative '../../custom_groups/v7.0.0-ballot/smart_granular_scopes_group'
+require_relative '../../provenance_validator'
+require_relative '../../us_core_options'
+
+require_relative 'patient_group'
+require_relative 'allergy_intolerance_group'
+require_relative 'care_plan_group'
+require_relative 'care_team_group'
+require_relative 'condition_encounter_diagnosis_group'
+require_relative 'condition_problems_health_concerns_group'
+require_relative 'coverage_group'
+require_relative 'device_group'
+require_relative 'diagnostic_report_note_group'
+require_relative 'diagnostic_report_lab_group'
+require_relative 'document_reference_group'
+require_relative 'encounter_group'
+require_relative 'goal_group'
+require_relative 'immunization_group'
+require_relative 'medication_dispense_group'
+require_relative 'medication_request_group'
+require_relative 'observation_lab_group'
+require_relative 'observation_pregnancystatus_group'
+require_relative 'observation_pregnancyintent_group'
+require_relative 'observation_occupation_group'
+require_relative 'respiratory_rate_group'
+require_relative 'simple_observation_group'
+require_relative 'treatment_intervention_preference_group'
+require_relative 'care_experience_preference_group'
+require_relative 'heart_rate_group'
+require_relative 'body_temperature_group'
+require_relative 'pediatric_weight_for_height_group'
+require_relative 'pulse_oximetry_group'
+require_relative 'smokingstatus_group'
+require_relative 'observation_sexual_orientation_group'
+require_relative 'head_circumference_group'
+require_relative 'body_height_group'
+require_relative 'bmi_group'
+require_relative 'observation_screening_assessment_group'
+require_relative 'average_blood_pressure_group'
+require_relative 'blood_pressure_group'
+require_relative 'observation_clinical_result_group'
+require_relative 'pediatric_bmi_for_age_group'
+require_relative 'head_circumference_percentile_group'
+require_relative 'body_weight_group'
+require_relative 'procedure_group'
+require_relative 'questionnaire_response_group'
+require_relative 'service_request_group'
+require_relative 'location_group'
+require_relative 'organization_group'
+require_relative 'practitioner_group'
+require_relative 'practitioner_role_group'
+require_relative 'provenance_group'
+require_relative 'related_person_group'
+require_relative 'specimen_group'
+
+module USCoreTestKit
+  module USCoreV700_BALLOT
+    class USCoreTestSuite < Inferno::TestSuite
+      title 'US Core v7.0.0-ballot'
+      description %(
+        The US Core Test Kit tests systems for their conformance to the [US Core
+        Implementation Guide]().
+
+        HL7® FHIR® resources are validated with the Java validator using
+        `tx.fhir.org` as the terminology server. Users should note that the
+        although the ONC Certification (g)(10) Standardized API Test Suite
+        includes tests from this suite, [it uses a different method to perform
+        terminology
+        validation](https://github.com/onc-healthit/onc-certification-g10-test-kit/wiki/FAQ#q-why-do-some-resources-fail-in-us-core-test-kit-with-terminology-validation-errors).
+        As a result, resource validation results may not be consistent between
+        the US Core Test Suite and the ONC Certification (g)(10) Standardized
+        API Test Suite.
+      )
+      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
+        /Provenance.agent\[\d*\]: Rule provenance-1/, #Invalid invariant in US Core v5.0.1
+        %r{Unknown Code System 'http://hl7.org/fhir/us/core/CodeSystem/us-core-tags'}, # Validator has an issue with this US Core 5 code system in US Core 6 resource
+        %r{URL value 'http://hl7.org/fhir/us/core/CodeSystem/us-core-tags' does not resolve} # Validator has an issue with this US Core 5 code system in US Core 6 resource
+      ].freeze
+
+      VERSION_SPECIFIC_MESSAGE_FILTERS = [].freeze
+
+      def self.metadata
+        @metadata ||= YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true)[:groups].map do |raw_metadata|
+            Generator::GroupMetadata.new(raw_metadata)
+          end
+      end
+
+      validator do
+        url ENV.fetch('V700_BALLOT_VALIDATOR_URL', 'http://validator_service:4567')
+        message_filters = VALIDATION_MESSAGE_FILTERS + VERSION_SPECIFIC_MESSAGE_FILTERS
+
+        exclude_message do |message|
+
+          message_filters.any? { |filter| filter.match? message.message }
+        end
+
+        perform_additional_validation do |resource, profile_url|
+          ProvenanceValidator.validate(resource) if resource.instance_of?(FHIR::Provenance)
+        end
+      end
+
+      id :us_core_v700_ballot
+
+      input :url,
+        title: 'FHIR Endpoint',
+        description: 'URL of the FHIR endpoint'
+
+      suite_option :smart_app_launch_version,
+        title: 'SMART App Launch Version',
+        list_options: [
+          {
+            label: 'SMART App Launch 1.0.0',
+            value: USCoreOptions::SMART_1
+          },
+          {
+            label: 'SMART App Launch 2.0.0',
+            value: USCoreOptions::SMART_2
+          }
+        ]
+
+      group from: :us_core_smart_app_launch
+
+      group do
+        input :smart_credentials,
+          title: 'OAuth Credentials',
+          type: :oauth_credentials,
+          optional: true
+
+        fhir_client do
+          url :url
+          oauth_credentials :smart_credentials
+        end
+
+        title 'US Core FHIR API'
+        id :us_core_v700_ballot_fhir_api
+
+        config(
+          options: {
+            tag_requests: true
+          }
+        )
+
+        group from: :us_core_v700_ballot_capability_statement
+      
+        group from: :us_core_v700_ballot_patient
+        group from: :us_core_v700_ballot_allergy_intolerance
+        group from: :us_core_v700_ballot_care_plan
+        group from: :us_core_v700_ballot_care_team
+        group from: :us_core_v700_ballot_condition_encounter_diagnosis
+        group from: :us_core_v700_ballot_condition_problems_health_concerns
+        group from: :us_core_v700_ballot_coverage
+        group from: :us_core_v700_ballot_device
+        group from: :us_core_v700_ballot_diagnostic_report_note
+        group from: :us_core_v700_ballot_diagnostic_report_lab
+        group from: :us_core_v700_ballot_document_reference
+        group from: :us_core_v700_ballot_encounter
+        group from: :us_core_v700_ballot_goal
+        group from: :us_core_v700_ballot_immunization
+        group from: :us_core_v700_ballot_medication_dispense
+        group from: :us_core_v700_ballot_medication_request
+        group from: :us_core_v700_ballot_observation_lab
+        group from: :us_core_v700_ballot_observation_pregnancystatus
+        group from: :us_core_v700_ballot_observation_pregnancyintent
+        group from: :us_core_v700_ballot_observation_occupation
+        group from: :us_core_v700_ballot_respiratory_rate
+        group from: :us_core_v700_ballot_simple_observation
+        group from: :us_core_v700_ballot_treatment_intervention_preference
+        group from: :us_core_v700_ballot_care_experience_preference
+        group from: :us_core_v700_ballot_heart_rate
+        group from: :us_core_v700_ballot_body_temperature
+        group from: :us_core_v700_ballot_pediatric_weight_for_height
+        group from: :us_core_v700_ballot_pulse_oximetry
+        group from: :us_core_v700_ballot_smokingstatus
+        group from: :us_core_v700_ballot_observation_sexual_orientation
+        group from: :us_core_v700_ballot_head_circumference
+        group from: :us_core_v700_ballot_body_height
+        group from: :us_core_v700_ballot_bmi
+        group from: :us_core_v700_ballot_observation_screening_assessment
+        group from: :us_core_v700_ballot_average_blood_pressure
+        group from: :us_core_v700_ballot_blood_pressure
+        group from: :us_core_v700_ballot_observation_clinical_result
+        group from: :us_core_v700_ballot_pediatric_bmi_for_age
+        group from: :us_core_v700_ballot_head_circumference_percentile
+        group from: :us_core_v700_ballot_body_weight
+        group from: :us_core_v700_ballot_procedure
+        group from: :us_core_v700_ballot_questionnaire_response
+        group from: :us_core_v700_ballot_service_request
+        group from: :us_core_v700_ballot_location
+        group from: :us_core_v700_ballot_organization
+        group from: :us_core_v700_ballot_practitioner
+        group from: :us_core_v700_ballot_practitioner_role
+        group from: :us_core_v700_ballot_provenance
+        group from: :us_core_v700_ballot_related_person
+        group from: :us_core_v700_ballot_specimen
+        group from: :us_core_v400_clinical_notes_guidance
+        group from: :us_core_311_data_absent_reason
+      end
+
+      group from: :us_core_v700_ballot_smart_granular_scopes,
+            required_suite_options: USCoreOptions::SMART_2_REQUIREMENT
+      
+    end
+  end
+end

data/lib/us_core_test_kit/generator/granular_scope_group_generator.rb

@@ -0,0 +1,127 @@
+require_relative 'naming'
+require_relative '../custom_groups/smart_scopes_constants'
+
+module USCoreTestKit
+  class Generator
+    class GranularScopeGroupGenerator
+      class << self
+        def generate(ig_metadata, base_output_dir)
+          return unless ['6', '7'].include? ig_metadata.ig_version[1]
+
+          [1, 2].each do |group_number|
+            new(ig_metadata, base_output_dir, group_number).generate
+          end
+        end
+      end
+
+      attr_accessor :ig_metadata, :base_output_dir, :group_number
+
+      def initialize(ig_metadata, base_output_dir, group_number)
+        self.ig_metadata = ig_metadata
+        self.base_output_dir = base_output_dir
+        self.group_number = group_number
+      end
+
+      def template
+        @template ||= File.read(File.join(__dir__, 'templates', 'granular_scope_group.rb.erb'))
+      end
+
+      def output
+        @output ||= ERB.new(template).result(binding)
+      end
+
+      def base_output_file_name
+        "#{class_name.underscore}.rb"
+      end
+
+      def base_metadata_file_name
+        "metadata.yml"
+      end
+
+      def class_name
+        "GranularScopes#{group_number}Group"
+      end
+
+      def module_name
+        "USCore#{ig_metadata.reformatted_version.upcase}"
+      end
+
+      def title
+        "#US Core FHIR API w/Granular Scopes #{group_number}"
+      end
+
+      def short_description
+        # TODO
+      end
+
+      def output_file_name
+        File.join(base_output_dir, base_output_file_name)
+      end
+
+      def group_dir
+        File.join(base_output_dir, 'granular_scope_tests')
+      end
+
+      def group_id
+        "us_core_#{ig_metadata.reformatted_version}_smart_granular_scopes_#{group_number}"
+      end
+
+      def generate
+        FileUtils.mkdir_p(group_dir)
+        File.open(output_file_name, 'w') { |f| f.write(output) }
+        ig_metadata.granular_scope_groups <<
+          {
+            id: group_id,
+            file_name: base_output_file_name
+          }
+      end
+
+      def group_id_list
+        @group_id_list ||=
+          ig_metadata
+            .granular_scope_resource_type_groups
+            .values
+            .flatten
+            .map { |group| group[:id] }
+            .select { |id| id.include? "scope_#{group_number}" }
+      end
+
+      def group_file_list
+        @group_file_list ||=
+          ig_metadata.granular_scope_resource_type_groups
+            .values
+            .flatten
+            .select { |group| group[:file_name].include? "scope#{group_number}" }
+            .map do |group|
+              name_without_suffix = group[:file_name].delete_suffix('.rb')
+              "./#{name_without_suffix}"
+            end
+      end
+
+      def search_param_name_string
+        required_searches
+          .map { |search| search[:names].join(' + ') }
+          .map { |names| "* #{names}" }
+          .join("\n")
+      end
+
+      def scopes_string
+        SmartScopesConstants.const_get("SMART_GRANULAR_SCOPES_GROUP#{group_number}")
+          .dig(ig_metadata.reformatted_version)
+          .map { |scope| scope.delete_prefix 'patient/' }
+          .map { |scope| "* `#{scope}`" }
+          .join("\n")
+      end
+
+      def description
+        <<~DESCRIPTION
+          The tests in this group repeat all of the searches from the US Core
+          FHIR API tests, and verify that the resources returned are filtered
+          based on the following granular scopes:
+
+          #{scopes_string}
+        DESCRIPTION
+      end
+    end
+  end
+end