us_core_test_kit 0.2.4 → 0.3.1

data/lib/us_core_test_kit/generated/v5.0.1/smokingstatus/smokingstatus_reference_resolution_test.rb

@@ -0,0 +1,38 @@
+require_relative '../../../reference_resolution_test'
+require_relative '../resource_list'
+
+module USCoreTestKit
+  module USCoreV501
+    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 external references provided within elements
+        marked as 'MustSupport', if any are available.  Elements which may provide
+        external references include:
+
+        * Observation.subject
+      )
+
+      id :us_core_v501_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/v5.0.1/smokingstatus/smokingstatus_validation_test.rb

@@ -0,0 +1,40 @@
+require_relative '../../../validation_test'
+
+module USCoreTestKit
+  module USCoreV501
+    class SmokingstatusValidationTest < Inferno::Test
+      include USCoreTestKit::ValidationTest
+
+      id :us_core_v501_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).
+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[:smokingstatus_resources] ||= {}
+      end
+
+      run do
+        perform_validation_test(scratch_resources[:all] || [],
+                                'http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus',
+                                '5.0.1',
+                                skip_if_empty: true)
+      end
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v5.0.1/smokingstatus_group.rb

@@ -0,0 +1,96 @@
+require_relative 'smokingstatus/smokingstatus_patient_code_search_test'
+require_relative 'smokingstatus/smokingstatus_patient_category_date_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_status_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 USCoreV501
+    class SmokingstatusGroup < Inferno::TestGroup
+      title 'Observation Smoking Status Tests'
+      short_description 'Verify support for the server capabilities required by the US Core Smoking Status Observation Profile.'
+      description %(
+  # Background
+
+The US Core Observation Smoking Status 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 v5.0.1 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 + code
+* patient + category + date
+* patient + category
+
+### 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
+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_v501_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_v501_smokingstatus_patient_code_search_test
+      test from: :us_core_v501_smokingstatus_patient_category_date_search_test
+      test from: :us_core_v501_smokingstatus_patient_code_date_search_test
+      test from: :us_core_v501_smokingstatus_patient_category_search_test
+      test from: :us_core_v501_smokingstatus_patient_category_status_search_test
+      test from: :us_core_v501_smokingstatus_read_test
+      test from: :us_core_v501_smokingstatus_provenance_revinclude_search_test
+      test from: :us_core_v501_smokingstatus_validation_test
+      test from: :us_core_v501_smokingstatus_must_support_test
+      test from: :us_core_v501_smokingstatus_reference_resolution_test
+    end
+  end
+end

data/lib/us_core_test_kit/generated/v5.0.1/us_core_test_suite.rb

@@ -0,0 +1,134 @@
+require 'inferno/dsl/oauth_credentials'
+require_relative '../../version'
+require_relative '../../custom_groups/v5.0.1/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_encounter_diagnosis_group'
+require_relative 'condition_problems_health_concerns_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_request_group'
+require_relative 'observation_lab_group'
+require_relative 'observation_sdoh_assessment_group'
+require_relative 'respiratory_rate_group'
+require_relative 'observation_social_history_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 'blood_pressure_group'
+require_relative 'observation_imaging_group'
+require_relative 'observation_clinical_test_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 'organization_group'
+require_relative 'practitioner_group'
+require_relative 'provenance_group'
+require_relative 'related_person_group'
+
+module USCoreTestKit
+  module USCoreV501
+    class USCoreTestSuite < Inferno::TestSuite
+      title 'US Core v5.0.1'
+      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('V501_VALIDATOR_URL', 'http://validator_service:4567')
+        exclude_message do |message|
+          VALIDATION_MESSAGE_FILTERS.any? { |filter| filter.match? message.message }
+        end
+      end
+
+      id :us_core_v501
+
+      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_v501_capability_statement
+  
+      group from: :us_core_v501_patient
+      group from: :us_core_v501_allergy_intolerance
+      group from: :us_core_v501_care_plan
+      group from: :us_core_v501_care_team
+      group from: :us_core_v501_condition_encounter_diagnosis
+      group from: :us_core_v501_condition_problems_health_concerns
+      group from: :us_core_v501_device
+      group from: :us_core_v501_diagnostic_report_note
+      group from: :us_core_v501_diagnostic_report_lab
+      group from: :us_core_v501_document_reference
+      group from: :us_core_v501_encounter
+      group from: :us_core_v501_goal
+      group from: :us_core_v501_immunization
+      group from: :us_core_v501_medication_request
+      group from: :us_core_v501_observation_lab
+      group from: :us_core_v501_observation_sdoh_assessment
+      group from: :us_core_v501_respiratory_rate
+      group from: :us_core_v501_observation_social_history
+      group from: :us_core_v501_heart_rate
+      group from: :us_core_v501_body_temperature
+      group from: :us_core_v501_pediatric_weight_for_height
+      group from: :us_core_v501_pulse_oximetry
+      group from: :us_core_v501_smokingstatus
+      group from: :us_core_v501_observation_sexual_orientation
+      group from: :us_core_v501_head_circumference
+      group from: :us_core_v501_body_height
+      group from: :us_core_v501_bmi
+      group from: :us_core_v501_blood_pressure
+      group from: :us_core_v501_observation_imaging
+      group from: :us_core_v501_observation_clinical_test
+      group from: :us_core_v501_pediatric_bmi_for_age
+      group from: :us_core_v501_head_circumference_percentile
+      group from: :us_core_v501_body_weight
+      group from: :us_core_v501_procedure
+      group from: :us_core_v501_questionnaire_response
+      group from: :us_core_v501_service_request
+      group from: :us_core_v501_organization
+      group from: :us_core_v501_practitioner
+      group from: :us_core_v501_provenance
+      group from: :us_core_v501_related_person
+      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

@@ -71,6 +71,20 @@ module USCoreTestKit
         group_metadata.resource
       end
 
+      def search_validation_resource_type
+        text = "#{resource_type} resources"
+        if resource_type == 'Condition' && group_metadata.reformatted_version == 'v501'
+          case profile_url
+          when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-encounter-diagnosis'
+            text.concat(' with category `encounter-diagnosis`')
+          when 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition-problems-health-concerns'
+            text.concat(' with category `problem-list-item | health-concern`')
+          end
+        end
+
+        text
+      end
+
       def profile_name
         group_metadata.profile_name
       end
@@ -79,6 +93,11 @@ module USCoreTestKit
         group_metadata.profile_url
       end
 
+
+      def optional?
+        resource_type == 'QuestionnaireResponse'
+      end
+
       def generate
         add_special_tests
         File.open(output_file_name, 'w') { |f| f.write(output) }
@@ -88,7 +107,7 @@ module USCoreTestKit
       end
 
       def add_special_tests
-        return unless group_metadata.reformatted_version == 'v400'
+        return if group_metadata.reformatted_version == 'v311'
 
         case group_metadata.resource
         when 'Device'
@@ -149,7 +168,7 @@ module USCoreTestKit
 
         ### Search Validation
         Inferno will retrieve up to the first 20 bundle pages of the reply for
-        #{resource_type} resources and save them for subsequent tests. Each of
+        #{search_validation_resource_type} 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,

data/lib/us_core_test_kit/generator/group_metadata.rb

@@ -9,6 +9,7 @@ module USCoreTestKit
         :resource,
         :profile_url,
         :profile_name,
+        :profile_version,
         :title,
         :short_description,
         :interactions,
@@ -28,14 +29,16 @@ module USCoreTestKit
         :delayed_references
       ].freeze
 
-      NON_USCDI_RESOURCES = [
-        'Encounter',
-        'Location',
-        'Organization',
-        'Practitioner',
-        'PractitionerRole',
-        'Provenance'
-      ].freeze
+      NON_USCDI_RESOURCES = {
+        'Encounter' => ['v311', 'v400'],
+        'Location' => ['v311', 'v400', 'v501'],
+        'Organization' => ['v311', 'v400', 'v501'],
+        'Practitioner' => ['v311', 'v400', 'v501'],
+        'PractitionerRole' => ['v311', 'v400', 'v501'],
+        'Provenance' => ['v311', 'v400', 'v501'],
+        'RelatedPerson' => ['v501']
+      }.freeze
+
 
       ATTRIBUTES.each { |name| attr_accessor name }
 
@@ -58,7 +61,7 @@ module USCoreTestKit
       end
 
       def non_uscdi_resource?
-        NON_USCDI_RESOURCES.include? resource
+        NON_USCDI_RESOURCES.key?(resource) && NON_USCDI_RESOURCES[resource].include?(reformatted_version)
       end
 
       def add_test(id:, file_name:)

data/lib/us_core_test_kit/generator/group_metadata_extractor.rb

@@ -32,6 +32,7 @@ module USCoreTestKit
             resource: resource,
             profile_url: profile_url,
             profile_name: profile_name,
+            profile_version: profile_version,
             title: title,
             short_description: short_description,
             interactions: interactions,
@@ -69,9 +70,13 @@ module USCoreTestKit
 
             any_must_support_slices = must_supports[:slices].any? do |slice|
               # only handle type slices because that is all we need for now
+              # for a slice like Observation.effective[x]:effectiveDateTime, the search parameter's expression could be
+              # either Observation.effective or Observation.effectiveDateTime.
               if slice[:discriminator] && slice[:discriminator][:type] == 'type'
                 full_must_support_path = "#{resource}.#{slice[:path].sub('[x]', slice[:discriminator][:code])}"
-                full_paths.include?(full_must_support_path)
+                base_must_support_path = "#{resource}.#{slice[:path].sub('[x]', '')}"
+
+                full_paths.intersection([full_must_support_path,base_must_support_path]).present?
               else
                 false
               end
@@ -92,9 +97,14 @@ module USCoreTestKit
 
       CATEGORY_FIRST_PROFILES = [
         'http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan',
-        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
         'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-lab',
-        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note'
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-sdoh-assessment',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-social-history',
+        'http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-survey'
       ]
 
       def category_first_profile?
@@ -109,6 +119,8 @@ module USCoreTestKit
           ['patient', 'code']
         elsif resource == 'MedicationRequest'
           ['patient', 'intent']
+        elsif resource == 'CareTeam'
+          ['patient', 'status']
         else
           ['patient']
         end
@@ -169,8 +181,18 @@ module USCoreTestKit
         profile.title.gsub('  ', ' ')
       end
 
+      def profile_version
+        profile.version
+      end
+
       def title
-        profile.title.gsub(/US\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
+        title = profile.title.gsub(/US\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
+
+        if (Naming.resources_with_multiple_profiles.include?(resource)) && !title.start_with?(resource) && version != 'v3.1.1'
+          title = resource + ' ' + title.split(resource).map(&:strip).join(' ')
+        end
+
+        title
       end
 
       def short_description
@@ -241,7 +263,7 @@ module USCoreTestKit
 
       def must_support_metadata_extractor
         @must_support_metadata_extractor ||=
-          MustSupportMetadataExtractor.new(profile_elements, profile, resource)
+          MustSupportMetadataExtractor.new(profile_elements, profile, resource, ig_resources)
       end
 
       def must_supports

data/lib/us_core_test_kit/generator/ig_loader.rb

@@ -1,5 +1,6 @@
 require 'active_support/all'
 require 'fhir_models'
+require 'pathname'
 require 'rubygems/package'
 require 'zlib'
 require_relative 'ig_resources'
@@ -7,10 +8,10 @@ require_relative 'ig_resources'
 module USCoreTestKit
   class Generator
     class IGLoader
-      attr_accessor :base_ig_directory
+      attr_accessor :ig_file_name
 
-      def initialize(base_ig_directory)
-        self.base_ig_directory = base_ig_directory
+      def initialize(ig_file_name)
+        self.ig_file_name = ig_file_name
       end
 
       def ig_resources
@@ -23,7 +24,9 @@ module USCoreTestKit
       end
 
       def load_ig
-        tar = Gem::Package::TarReader.new(Zlib::GzipReader.open(File.join(base_ig_directory, 'package.tgz')))
+        tar = Gem::Package::TarReader.new(
+          Zlib::GzipReader.open(ig_file_name)
+        )
 
         tar.each do |entry|
           next if entry.directory?
@@ -49,7 +52,11 @@ module USCoreTestKit
       end
 
       def load_standalone_resources
-        Dir.glob(File.join(base_ig_directory, '*.json')).each do |file_path|
+        ig_directory = ig_file_name.chomp('.tgz')
+
+        return ig_resources unless File.exist? ig_directory
+
+        Dir.glob(File.join(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

@@ -8,7 +8,8 @@ module USCoreTestKit
 
       def initialize(ig_resources)
         self.ig_resources = ig_resources
-        add_vital_signs_profiles
+        add_missing_supported_profiles
+        remove_extra_supported_profiles
         self.metadata = IGMetadata.new
       end
 
@@ -26,10 +27,11 @@ module USCoreTestKit
         ig_resources.capability_statement.rest.first.resource
       end
 
-      # 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
-        if ig_resources.ig.version == "3.1.1"
+      def add_missing_supported_profiles
+        case ig_resources.ig.version
+        when '3.1.1'
+          # The US Core v3.1.1 Server Capability Statement does not list support for the
+          # required vital signs profiles, so they need to be added
           ig_resources.capability_statement.rest.first.resource
             .find { |resource| resource.type == 'Observation' }
             .supportedProfile.concat [
@@ -40,9 +42,24 @@ module USCoreTestKit
               'http://hl7.org/fhir/StructureDefinition/heartrate',
               'http://hl7.org/fhir/StructureDefinition/resprate'
             ]
+        when '5.0.1'
+          # The US Core v5.0.1 Server Capability Statement does not have supported-profile for Encounter
+          ig_resources.capability_statement.rest.first.resource
+            .find { |resource| resource.type == 'Encounter' }
+            .supportedProfile.concat [
+              'http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter'
+            ]
         end
       end
 
+      def remove_extra_supported_profiles
+        ig_resources.capability_statement.rest.first.resource
+            .find { |resource| resource.type == 'Observation' }
+            .supportedProfile.delete_if do |profile_url|
+              SpecialCases::PROFILES_TO_EXCLUDE.include?(profile_url)
+            end
+      end
+
       def add_metadata_from_resources
         metadata.groups =
           resources_in_capability_statement.flat_map do |resource|

data/lib/us_core_test_kit/generator/ig_resources.rb

@@ -32,7 +32,8 @@ module USCoreTestKit
       end
 
       def search_param_by_resource_and_name(resource, name)
-        normalized_name = name.to_s == '_id' ? 'id' : name.to_s
+        # remove '_' from search parameter name, such as _id or _tag
+        normalized_name = normalized_name = name.to_s.delete_prefix('_')
 
         resources_by_type['SearchParameter']
           .find { |param| param.id == "us-core-#{resource.downcase}-#{normalized_name}" }