cancer_registry_reporting_test_kit 0.9.0

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/procedure/procedure_must_support_test.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require_relative '../../../../must_support_test'
+require_relative '../../../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class ProcedureMustSupportTest < Inferno::Test
+      include CancerRegistryReportingTestKit::MustSupportTest
+
+      title 'US Core Procedure profile must support element coverage'
+      description %(
+        This test looks across all instances
+        associated with the [US Core Procedure profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure|5.0.1)
+        found in the provided report Bundles and verifies that they
+        contain populated examples of the following must support elements
+        defined in the profile:
+
+        * Procedure.code
+        * Procedure.performedDateTime
+        * Procedure.status
+        * Procedure.subject
+      )
+
+      id :ccrr_v100_procedure_must_support_test
+
+      def resource_type
+        'Procedure'
+      end
+
+      def self.metadata
+        @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:procedure_resources] ||= {}
+      end
+
+      run do
+        perform_must_support_test(all_scratch_resources)
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/procedure/procedure_validation_test.rb

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+require_relative '../../../../validation_test'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class ProcedureValidationTest < Inferno::Test
+      include CancerRegistryReportingTestKit::ValidationTest
+
+      id :ccrr_v100_procedure_validation_test
+      title 'US Core Procedure profile conformance'
+      description %(
+        This test verifies that Procedure instances
+        found in the Procedures sections of the provided reports conform to the
+        [US Core Procedure profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure|5.0.1).
+      )
+      
+
+      def resource_type
+        'Procedure'
+      end
+
+      def scratch_resources
+        scratch[:procedure_resources] ||= {}
+      end
+
+      run do
+        perform_validation_test(scratch_resources[:all] || [],
+                                'http://hl7.org/fhir/us/core/StructureDefinition/us-core-procedure',
+                                '5.0.1',
+                                skip_if_empty: true)
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/service_request/metadata.yml

@@ -0,0 +1,26 @@
+---
+:name: ServiceRequest
+:class_name: ServicerequestSequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: ServiceRequest
+:profile_url: http://hl7.org/fhir/StructureDefinition/ServiceRequest
+:profile_name: Base ServiceRequest
+:profile_version: 4.0.1
+:title: Base ServiceRequest
+:short_description: Verify support for the server capabilities required by the Base
+  ServiceRequest.
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements: []
+:mandatory_elements:
+- ServiceRequest.status
+- ServiceRequest.intent
+- ServiceRequest.subject
+:tests:
+- :id: ccrr_v100_service_request_must_support_test
+  :file_name: service_request_must_support_test.rb
+- :id: ccrr_v100_service_request_validation_test
+  :file_name: service_request_validation_test.rb
+:id: ccrr_v100_service_request

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/service_request/service_request_must_support_test.rb

@@ -0,0 +1,41 @@
+# frozen_string_literal: true
+
+require_relative '../../../../must_support_test'
+require_relative '../../../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class ServiceRequestMustSupportTest < Inferno::Test
+      include CancerRegistryReportingTestKit::MustSupportTest
+
+      title 'Base ServiceRequest profile must support element coverage'
+      description %(
+        This test looks across all instances
+        associated with the [Base ServiceRequest profile](http://hl7.org/fhir/StructureDefinition/ServiceRequest|4.0.1)
+        found in the provided report Bundles and verifies that they
+        contain populated examples of the following must support elements
+        defined in the profile:
+
+
+      )
+
+      id :ccrr_v100_service_request_must_support_test
+
+      def resource_type
+        'ServiceRequest'
+      end
+
+      def self.metadata
+        @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:service_request_resources] ||= {}
+      end
+
+      run do
+        perform_must_support_test(all_scratch_resources)
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/service_request/service_request_validation_test.rb

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+require_relative '../../../../validation_test'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class ServiceRequestValidationTest < Inferno::Test
+      include CancerRegistryReportingTestKit::ValidationTest
+
+      id :ccrr_v100_service_request_validation_test
+      title 'Base ServiceRequest profile conformance'
+      description %(
+        This test verifies that ServiceRequest instances
+        found in the Plan of Treatment sections of the provided reports conform to the
+        [Base ServiceRequest profile](http://hl7.org/fhir/StructureDefinition/ServiceRequest|4.0.1).
+      )
+      
+
+      def resource_type
+        'ServiceRequest'
+      end
+
+      def scratch_resources
+        scratch[:service_request_resources] ||= {}
+      end
+
+      run do
+        perform_validation_test(scratch_resources[:all] || [],
+                                'http://hl7.org/fhir/StructureDefinition/ServiceRequest',
+                                '4.0.1',
+                                skip_if_empty: true)
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/smokingstatus/metadata.yml

@@ -0,0 +1,58 @@
+---
+:name: us_core_smokingstatus
+:class_name: UsCoreSmokingstatusSequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: Observation
+:profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus
+:profile_name: US Core Smoking Status Observation Profile
+:profile_version: 5.0.1
+:title: Observation US Core Smoking Status
+:short_description: Verify support for the server capabilities required by the US
+  Core Smoking Status Observation Profile.
+:must_supports:
+  :extensions: []
+  :slices:
+  - :slice_id: Observation.category:SocialHistory
+    :slice_name: SocialHistory
+    :path: category
+    :discriminator:
+      :type: patternCodeableConcept
+      :path: ''
+      :code: social-history
+      :system: http://terminology.hl7.org/CodeSystem/observation-category
+  - :slice_id: Observation.effective[x]:effectiveDateTime
+    :slice_name: effectiveDateTime
+    :path: effective[x]
+    :discriminator:
+      :type: type
+      :code: DateTime
+  - :slice_id: Observation.value[x]:valueCodeableConcept
+    :slice_name: valueCodeableConcept
+    :path: value[x]
+    :discriminator:
+      :type: type
+      :code: CodeableConcept
+  :elements:
+  - :path: status
+  - :path: category
+  - :path: code
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+:mandatory_elements:
+- Observation.status
+- Observation.category
+- Observation.code
+- Observation.subject
+- Observation.effective[x]
+- Observation.value[x]
+- Observation.component.code
+:tests:
+- :id: ccrr_v100_smokingstatus_must_support_test
+  :file_name: smokingstatus_must_support_test.rb
+- :id: ccrr_v100_smokingstatus_validation_test
+  :file_name: smokingstatus_validation_test.rb
+:id: ccrr_v100_smokingstatus

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/smokingstatus/smokingstatus_must_support_test.rb

@@ -0,0 +1,47 @@
+# frozen_string_literal: true
+
+require_relative '../../../../must_support_test'
+require_relative '../../../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class SmokingstatusMustSupportTest < Inferno::Test
+      include CancerRegistryReportingTestKit::MustSupportTest
+
+      title 'US Core Smoking Status Observation profile must support element coverage'
+      description %(
+        This test looks across all instances
+        associated with the [US Core Smoking Status Observation profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus|5.0.1)
+        found in the provided report Bundles and verifies that they
+        contain populated examples of the following must support elements
+        defined in the profile:
+
+        * Observation.category
+        * Observation.category:SocialHistory
+        * Observation.code
+        * Observation.effective[x]:effectiveDateTime
+        * Observation.status
+        * Observation.subject
+        * Observation.value[x]:valueCodeableConcept
+      )
+
+      id :ccrr_v100_smokingstatus_must_support_test
+
+      def resource_type
+        'Observation'
+      end
+
+      def self.metadata
+        @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:smokingstatus_resources] ||= {}
+      end
+
+      run do
+        perform_must_support_test(all_scratch_resources)
+      end
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/hdea_suite/generated/v1.0.0/smokingstatus/smokingstatus_validation_test.rb

@@ -0,0 +1,35 @@
+# frozen_string_literal: true
+
+require_relative '../../../../validation_test'
+
+module CancerRegistryReportingTestKit
+  module HDEAV100
+    class SmokingstatusValidationTest < Inferno::Test
+      include CancerRegistryReportingTestKit::ValidationTest
+
+      id :ccrr_v100_smokingstatus_validation_test
+      title 'US Core Smoking Status Observation profile conformance'
+      description %(
+        This test verifies that Observation instances
+        found in the Social History sections of the provided reports conform to the
+        [US Core Smoking Status Observation profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-smokingstatus|5.0.1).
+      )
+      
+
+      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/cancer_registry_reporting_test_kit/hdea_suite.rb

@@ -0,0 +1,80 @@
+# frozen_string_literal: true
+
+require 'inferno/dsl/oauth_credentials'
+require_relative 'version'
+
+require_relative 'hdea_suite/bundle_resources_group'
+
+module CancerRegistryReportingTestKit
+  module CCRRV100
+    class HDEASuite < Inferno::TestSuite
+      id :ccrr_v100_report_generation
+      title 'Cancer Registry Reporting Health Data Exchange App (HDEA) Test Suite'
+      short_title 'HDEA Cancer Registry Reporting'
+      description File.read(File.join(__dir__, 'docs', 'hdea_suite_description.md'))
+      links [
+        {
+          label: 'Report Issue',
+          url: 'https://github.com/inferno-framework/cancer-registry-reporting-test-kit/issues/'
+        },
+        {
+          label: 'Open Source',
+          url: 'https://github.com/inferno-framework/cancer-registry-reporting-test-kit/'
+        },
+        {
+          label: 'Download',
+          url: 'https://github.com/inferno-framework/cancer-registry-reporting-test-kit/releases'
+        },
+        {
+          label: 'Implementation Guide',
+          url: 'https://hl7.org/fhir/us/central-cancer-registry-reporting/STU1/'
+        }
+      ]
+
+      GENERAL_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\[\d*\]: Constraint failed: 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
+        /\A\S+: \S+: URL value '.*' does not resolve/,
+        %r{Observation.component\[\d+\].value.ofType\(Quantity\): The code provided \(http://unitsofmeasure.org#L/min\)
+        was not found in the value set 'Vital Signs Units'} # Known issue with the Pulse Oximetry Profile
+      ].freeze
+      VALIDATION_MESSAGE_FILTERS = GENERAL_MESSAGE_FILTERS
+
+      def self.metadata
+        @metadata ||= YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true)[:groups].map do |raw_metadata|
+          HdeaGenerator::GroupMetadata.new(raw_metadata)
+        end
+      end
+
+      fhir_resource_validator do
+        igs 'hl7.fhir.us.central-cancer-registry-reporting#1.0.0'
+        message_filters = VALIDATION_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
+
+      input :reports,
+            title: 'Cancer Reports',
+            description: %(
+              A comma-Separated list of one or more FHIR Central Cancer Registry Reporting Content Bundles
+              in JSON format generated by the system under test.
+            ),
+            type: 'textarea'
+
+      group from: :ccrr_report_resources
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/igs/README.md

@@ -0,0 +1,21 @@
+# Note on this IGs folder
+
+There are three reasons why it would be necessary to put an IG package.tgz in this folder. If none of these apply, you do not need to put any files here, or can consider removing any existing files to make it clear they are unused.
+
+## 1. Generated Test Suites
+Some test kits use a "generator" to automatically generate the contents of a test suite for an IG. The IG files are required every time the test suites need to be regenerated. Examples of test kits that use this approach are the US Core Test Kit and CARIN IG for Blue Button® Test Kit.
+
+
+## 2. Non-published IG
+If your IG, or the specific version of the IG you want to test against, is not published, then the validator service needs to load the IG from file in order to be able to validate resources with it. The IG must be referenced in the `fhir_resource_validator` block in the test suite definition by filename, ie:
+
+```ruby
+      fhir_resource_validator do
+        igs 'igs/filename.tgz'
+
+        ...
+      end
+```
+
+## 3. Inferno Validator UI
+The Inferno Validator UI is configured to auto-load any IGs present in the igs folder and include them in all validations. In general, the Inferno team is currently leaving IGs in this folder even if not otherwise necessary to make it easy to re-enable the validator UI.