onc_certification_g10_test_kit 2.0.0.rc3 → 2.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/inferno/terminology/tasks/check_built_terminology.rb

@@ -4,9 +4,11 @@ module Inferno
   module Terminology
     module Tasks
       class CheckBuiltTerminology
-        MIME_TYPE_SYSTEMS = [
+        NON_UMLS_SYSTEMS = [
           'http://hl7.org/fhir/ValueSet/mimetypes',
-          'urn:ietf:bcp:13'
+          'urn:ietf:bcp:13',
+          'http://hl7.org/fhir/us/core/ValueSet/simple-language',
+          'urn:ietf:bcp:47'
         ].freeze
 
         def run
@@ -15,16 +17,16 @@ module Inferno
             return
           end
 
-          if only_mime_types_mismatch?
-            Inferno.logger.info <<~MIME
+          if only_non_umls_mismatch?
+            Inferno.logger.info <<~NON_UMLS
               Terminology built successfully.
 
-              Mime-type based terminology did not match, but this can be a
-              result of using a newer version of the `mime-types-data` gem and
-              does not necessarily reflect a problem with the terminology build.
-              The expected mime-types codes were generated with version
-              `mime-types-data` version `3.2021.0901`.
-            MIME
+              Some terminology not based on UMLS did not match, but this can be
+              a result of these terminologies having a different update schedule
+              than UMLS. As long as the actual number of codes is close to the
+              expected number, this does not does not reflect a problem with the
+              terminology build.
+            NON_UMLS
           else
             Inferno.logger.info 'Terminology build results different than expected.'
           end
@@ -61,8 +63,8 @@ module Inferno
           new_manifest.find { |value_set| value_set[:url] == url }
         end
 
-        def only_mime_types_mismatch?
-          mismatched_value_sets.all? { |value_set| MIME_TYPE_SYSTEMS.include? value_set[:url] }
+        def only_non_umls_mismatch?
+          mismatched_value_sets.all? { |value_set| NON_UMLS_SYSTEMS.include? value_set[:url] }
         end
 
         def mismatched_value_set_message(expected_value_set)

data/lib/onc_certification_g10_test_kit/bulk_data_authorization.rb

@@ -21,8 +21,9 @@ module ONCCertificationG10TestKit
 
     input :bulk_token_endpoint,
           title: 'Backend Services Token Endpoint',
-          description: 'The OAuth 2.0 Token Endpoint used by the Backend Services specification
-                        to provide bearer tokens.'
+          description: <<~DESCRIPTION
+            The OAuth 2.0 Token Endpoint used by the Backend Services specification to provide bearer tokens.
+          DESCRIPTION
     input :bulk_client_id,
           title: 'Bulk Data Client ID',
           description: 'Client ID provided at registration to the Inferno application.'
@@ -32,8 +33,10 @@ module ONCCertificationG10TestKit
           default: 'system/*.read'
     input :bulk_encryption_method,
           title: 'Encryption Method',
-          description: 'The server is required to suport either ES384 or RS384 encryption methods
-                        for JWT signature verification. Select which method to use.',
+          description: <<~DESCRIPTION,
+            The server is required to suport either ES384 or RS384 encryption methods for JWT signature verification.
+            Select which method to use.
+          DESCRIPTION
           type: 'radio',
           default: 'ES384',
           options: {

data/lib/onc_certification_g10_test_kit/bulk_data_group_export.rb

@@ -19,11 +19,12 @@ module ONCCertificationG10TestKit
           description: 'The Group ID associated with the group of patients to be exported.'
     input :bulk_timeout,
           title: 'Export Times Out after (1-600)',
-          description: 'While testing, Inferno waits for the server to complete the exporting task.
-          If the calculated totalTime is greater than the timeout value specified here,
-          Inferno bulk client stops testing. Please enter an integer for the maximum wait time in seconds.
-          If timeout is less than 1, Inferno uses default value 180.
-          If the timeout is greater than 600 (10 minutes), Inferno uses the maximum value 600.',
+          description: <<~DESCRIPTION,
+            While testing, Inferno waits for the server to complete the exporting task. If the calculated totalTime is
+            greater than the timeout value specified here, Inferno bulk client stops testing. Please enter an integer
+            for the maximum wait time in seconds. If timeout is less than 1, Inferno uses default value 180. If the
+              timeout is greater than 600 (10 minutes), Inferno uses the maximum value 600.
+          DESCRIPTION
           default: 180
 
     output :requires_access_token, :status_output, :bulk_download_url
@@ -56,9 +57,30 @@ module ONCCertificationG10TestKit
     test do
       title 'Bulk Data Server declares support for Group export operation in CapabilityStatement'
       description <<~DESCRIPTION
-        The Bulk Data Server SHALL declare support for Group/[id]/$export operation in its server CapabilityStatement
+        This test verifies that the Bulk Data Server declares support for
+        Group/[id]/$export operation in its server CapabilityStatement.
+
+        Given flexibility in the FHIR specification for declaring constrained
+        OperationDefinitions, this test only verifies that the server declares
+        any operation on the Group resource.  It does not verify that it
+        declares the standard group export OperationDefinition provided in the
+        Bulk Data specification, nor does it attempt to resolve any non-standard
+        OperationDefinitions to verify if it is a constrained version of the
+        standard OperationDefintion.
+
+        This test will provide a warning if no operations are declared at
+        `Group/[id]/$export`, via the
+        `CapabilityStatement.rest.resource.operation.name` element.  It will
+        also provide an informational message if an operation on the Group
+        resource exists, but does not point to the standard OperationDefinition
+        canonical URL:
+        http://hl7.org/fhir/uv/bulkdata/OperationDefinition/group-export
+
+        Additionally, this test provides a warning if the bulk data server does
+        not include the following URL in its `CapabilityStatement.instantiates`
+        element: http://hl7.org/fhir/uv/bulkdata/CapabilityStatement/bulk-data
+
       DESCRIPTION
-      # link 'http://hl7.org/fhir/uv/bulkdata/STU1/OperationDefinition-group-export.html'
 
       run do
         fhir_get_capability_statement(client: :bulk_server)
@@ -67,18 +89,39 @@ module ONCCertificationG10TestKit
         assert_valid_json(request.response_body)
         capability_statement = FHIR.from_contents(request.response_body)
 
-        has_export_operation = capability_statement&.rest&.any? do |rest|
-          rest.resource&.any? do |resource|
-            resource.type == 'Group' &&
-              resource.respond_to?(:operation) &&
-              resource.operation&.find do |operation|
-                operation.definition&.match(%r{^http://hl7.org/fhir/uv/bulkdata/OperationDefinition/group-export(\|\S+)?})
-              end
+        warning do
+          has_instantiates = capability_statement&.instantiates&.any? do |canonical|
+            canonical.match(%r{^http://hl7.org/fhir/uv/bulkdata/CapabilityStatement/bulk-data(\|\S+)?$})
+          end
+          assert has_instantiates,
+                 'Server did not declare conformance to the Bulk Data IG by including ' \
+                 "'http://hl7.org/fhir/uv/bulkdata/CapabilityStatement/bulk-data' in " \
+                 " CapabilityStatement.instantiates element (#{capability_statement&.instantiates})"
+        end
+
+        group_resource_capabilities = nil
+
+        capability_statement&.rest&.each do |rest|
+          group_resource_capabilities = rest.resource&.find do |resource|
+            resource.type == 'Group'
           end
         end
 
-        assert has_export_operation,
-               'Server CapabilityStatement did not declare support for export operation in Group resource'
+        assert group_resource_capabilities.respond_to?(:operation) && group_resource_capabilities.operation&.any?,
+               'Server CapabilityStatement did not declare support for any operations on the Group resource'
+
+        has_export_operation = group_resource_capabilities.operation&.any? do |operation|
+          name_match = (operation.name == 'export')
+          if name_match && !operation.definition&.match(%r{^http://hl7.org/fhir/uv/bulkdata/OperationDefinition/group-export(\|\S+)?$})
+            info('Server CapabilityStatement does not include export operation with definition http://hl7.org/fhir/uv/bulkdata/OperationDefinition/group-export')
+          end
+          name_match
+        end
+        warning do
+          assert has_export_operation,
+                 'Server CapabilityStatement did not declare support for an operation named "export" in the Group ' \
+                 ' resource (operation.name should be "export")'
+        end
       end
     end
 
@@ -161,7 +204,7 @@ module ONCCertificationG10TestKit
         start = Time.now
 
         loop do
-          get(polling_url, headers: { authorization: "Bearer #{bearer_token}" })
+          get(polling_url, headers: { authorization: "Bearer #{bearer_token}", accept: 'application/json' })
 
           retry_after_val = request.response_header('retry-after')&.value.to_i
 

data/lib/onc_certification_g10_test_kit/bulk_data_group_export_validation.rb

@@ -17,14 +17,18 @@ module ONCCertificationG10TestKit
           optional: true
     input :bulk_patient_ids_in_group,
           title: 'Patient IDs in exported Group',
-          description: 'Comma separated list of every Patient ID that is in the specified Group. This information is
-          provided by the system under test to verify that data returned matches expectations. Leave blank to not
-          verify Group inclusion.'
+          description: <<~DESCRIPTION
+            Comma separated list of every Patient ID that is in the specified Group. This information is provided by
+            the system under test to verify that data returned matches expectations. Leave blank to not verify Group
+            inclusion.
+          DESCRIPTION
     input :bulk_device_types_in_group,
           title: 'Implantable Device Type Codes in exported Group',
-          description: 'Comma separated list of every Implantable Device type that is in the specified Group. This
-          information is provided by the system under test to verify that data returned matches expectations. Leave
-          blank to verify all Device resources against the Implantable Device profile.',
+          description: <<~DESCRIPTION,
+            Comma separated list of every Implantable Device type that is in the specified Group. This information is
+            provided by the system under test to verify that data returned matches expectations. Leave blank to verify
+            all Device resources against the Implantable Device profile.
+          DESCRIPTION
           optional: true
 
     test from: :tls_version_test do

data/lib/onc_certification_g10_test_kit/bulk_export_validation_tester.rb

@@ -13,23 +13,26 @@ module ONCCertificationG10TestKit
 
     def observation_metadata
       [
-        USCoreTestKit::PediatricBmiForAgeGroup.metadata,
-        USCoreTestKit::PediatricWeightForHeightGroup.metadata,
-        USCoreTestKit::ObservationLabGroup.metadata,
-        USCoreTestKit::PulseOximetryGroup.metadata,
-        USCoreTestKit::SmokingstatusGroup.metadata,
-        USCoreTestKit::HeadCircumferenceGroup.metadata,
-        USCoreTestKit::BpGroup.metadata,
-        USCoreTestKit::BodyheightGroup.metadata,
-        USCoreTestKit::BodytempGroup.metadata,
-        USCoreTestKit::BodyweightGroup.metadata,
-        USCoreTestKit::HeartrateGroup.metadata,
-        USCoreTestKit::ResprateGroup.metadata
+        USCoreTestKit::USCoreV311::PediatricBmiForAgeGroup.metadata,
+        USCoreTestKit::USCoreV311::PediatricWeightForHeightGroup.metadata,
+        USCoreTestKit::USCoreV311::ObservationLabGroup.metadata,
+        USCoreTestKit::USCoreV311::PulseOximetryGroup.metadata,
+        USCoreTestKit::USCoreV311::SmokingstatusGroup.metadata,
+        USCoreTestKit::USCoreV311::HeadCircumferenceGroup.metadata,
+        USCoreTestKit::USCoreV311::BpGroup.metadata,
+        USCoreTestKit::USCoreV311::BodyheightGroup.metadata,
+        USCoreTestKit::USCoreV311::BodytempGroup.metadata,
+        USCoreTestKit::USCoreV311::BodyweightGroup.metadata,
+        USCoreTestKit::USCoreV311::HeartrateGroup.metadata,
+        USCoreTestKit::USCoreV311::ResprateGroup.metadata
       ]
     end
 
     def diagnostic_metadata
-      [USCoreTestKit::DiagnosticReportLabGroup.metadata, USCoreTestKit::DiagnosticReportNoteGroup.metadata]
+      [
+        USCoreTestKit::USCoreV311::DiagnosticReportLabGroup.metadata,
+        USCoreTestKit::USCoreV311::DiagnosticReportNoteGroup.metadata
+      ]
     end
 
     def determine_metadata
@@ -37,17 +40,21 @@ module ONCCertificationG10TestKit
       return diagnostic_metadata if resource_type == 'DiagnosticReport'
 
       if resource_type == 'Location' || resource_type == 'Medication'
-        return Array.wrap(USCoreTestKit::USCoreTestSuite.metadata.find do |meta|
+        return Array.wrap(USCoreTestKit::USCoreV311::USCoreTestSuite.metadata.find do |meta|
                             meta.resource == resource_type
                           end)
       end
-      ["USCoreTestKit::#{resource_type}Group".constantize.metadata]
+      ["USCoreTestKit::USCoreV311::#{resource_type}Group".constantize.metadata]
     end
 
     def metadata_list
       @metadata_list ||= determine_metadata
     end
 
+    def resources_from_all_files
+      @resources_from_all_files ||= {}
+    end
+
     def patient_ids_seen
       scratch[:patient_ids_seen] ||= []
     end
@@ -58,7 +65,7 @@ module ONCCertificationG10TestKit
       headers
     end
 
-    def stream_ndjson(endpoint, headers, process_chunk_line, process_response)
+    def stream_ndjson(endpoint, headers, process_chunk_line, process_response) # rubocop:disable Metrics/CyclomaticComplexity
       hanging_chunk = String.new
 
       process_body = proc { |chunk|
@@ -74,6 +81,24 @@ module ONCCertificationG10TestKit
 
       stream(process_body, endpoint, headers: headers)
 
+      max_redirect = 5
+
+      while [301, 302, 303, 307].include?(response[:status]) &&
+            request.response_header('location')&.value.present? &&
+            max_redirect.positive?
+
+        max_redirect -= 1
+
+        redirect_url = request.response_header('location')&.value
+
+        # handle relative redirects
+        redirect_url = URI.parse(endpoint).merge(redirect_url).to_s unless redirect_url.start_with?('http')
+
+        redirect_headers = headers.reject { |key, _value| key == :authorization }
+
+        stream(process_body, redirect_url, headers: redirect_headers)
+      end
+
       process_chunk_line.call(hanging_chunk)
       process_response.call(response)
     end
@@ -105,6 +130,7 @@ module ONCCertificationG10TestKit
         @metadata = meta
         @missing_elements = nil
         @missing_slices = nil
+        @missing_extensions = nil
         begin
           perform_must_support_test(resources[meta.profile_url])
         rescue Inferno::Exceptions::PassException
@@ -152,8 +178,9 @@ module ONCCertificationG10TestKit
       }
 
       stream_ndjson(url, build_headers(requires_access_token), process_line, process_headers)
-      validate_conformance(resources)
-
+      resources_from_all_files.merge!(resources) do |_key, all_resources, file_resources|
+        all_resources | file_resources
+      end
       line_count
     end
 
@@ -169,11 +196,14 @@ module ONCCertificationG10TestKit
         skip message
       end
 
+      @resources_from_all_files = {}
       success_count = 0
       file_list.each do |file|
         success_count += check_file_request(file['url'])
       end
 
+      validate_conformance(resources_from_all_files)
+
       pass "Successfully validated #{success_count} #{resource_type} resource(s)."
     end
   end

data/lib/onc_certification_g10_test_kit/configuration_checker.rb

@@ -55,7 +55,7 @@ module ONCCertificationG10TestKit
           success_messages << "* `#{url}`: #{actual_value_set[:count]} codes"
         elsif actual_value_set.nil?
           error_messages << "* `#{url}`: Not loaded"
-        elsif terminology_checker.class::MIME_TYPE_SYSTEMS.include? url
+        elsif terminology_checker.class::NON_UMLS_SYSTEMS.include? url
           warning_messages <<
             "* `#{url}`: Expected codes: #{expected_value_set[:count]} Actual codes: #{actual_value_set[:count]}"
         else
@@ -74,10 +74,11 @@ module ONCCertificationG10TestKit
 
       if warning_messages.present?
         warning_message = <<~WARNING
-          Mime-type based terminology did not exactly match. This can be the
-          result of using a slightly different version of the `mime-types-data`
-          gem and does not reflect a problem with the terminology build as long
-          as the expected and actual number of codes are close to each other.
+          Some terminology not based on UMLS did not match, but this can be a
+          result of these terminologies having a different update schedule than
+          UMLS. As long as the actual number of codes is close to the expected
+          number, this does not does not reflect a problem with the terminology
+          build.
         WARNING
         messages << {
           type: 'warning',

data/lib/onc_certification_g10_test_kit/multi_patient_api.rb

@@ -36,6 +36,17 @@ module ONCCertificationG10TestKit
     id :multi_patient_api
     run_as_group
 
+    input_order :bulk_server_url,
+                :bulk_token_endpoint,
+                :bulk_client_id,
+                :bulk_scope,
+                :bulk_encryption_method,
+                :group_id,
+                :bulk_patient_ids_in_group,
+                :bulk_device_types_in_group,
+                :lines_to_validate,
+                :bulk_timeout
+
     group from: :bulk_data_authorization
     group from: :bulk_data_group_export
     group from: :bulk_data_group_export_validation