cancer_pathology_data_sharing_test_kit 0.9.0

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/practitioner_role/metadata.yml

@@ -0,0 +1,44 @@
+---
+:name: us_pathology_related_practitioner_role
+:class_name: UsPathologyRelatedPractitionerRoleSequence
+:version: v1.0.1
+:reformatted_version: v101
+:resource: PractitionerRole
+:profile_url: http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-related-practitioner-role
+:profile_name: US Pathology Related Practitioner Roles
+:profile_version: 1.0.1
+:title: US Pathology Related Practitioner Roles
+:short_description: Verify support for the server capabilities required by the US
+  Pathology Related Practitioner Roles.
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements:
+  - :path: practitioner
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner
+  - :path: organization
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization
+  - :path: code
+  - :path: specialty
+  - :path: location
+    :types:
+    - Reference
+  - :path: telecom
+  - :path: telecom.system
+  - :path: telecom.value
+  - :path: endpoint
+    :types:
+    - Reference
+:mandatory_elements:
+- PractitionerRole.telecom.system
+- PractitionerRole.telecom.value
+- PractitionerRole.notAvailable.description
+:tests: []
+:id: v101_practitioner_role
+:file_name: practitioner_role_group.rb

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/practitioner_role/practitioner_role_must_support_test.rb

@@ -0,0 +1,45 @@
+require_relative '../../../must_support_test'
+require_relative '../../../group_metadata'
+
+module CancerPathologyDataSharingTestKit
+  module V101
+    class PractitionerRoleMustSupportTest < Inferno::Test
+      include CancerPathologyDataSharingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the Practitioner Role resources'
+      description %(
+        Report generators SHALL be capable of populating all must support data elements
+        defined in the [US Pathology ExchangeBundle profile](https://hl7.org/fhir/us/cancer-reporting/STU1.0.1/StructureDefinition-us-pathology-exchange-bundle.html)
+        and profiles it references. This test will look through the PractitionerRole resources
+        found in the provided report Bundles for the following must support elements:
+
+        * PractitionerRole.code
+        * PractitionerRole.endpoint
+        * PractitionerRole.location
+        * PractitionerRole.organization
+        * PractitionerRole.practitioner
+        * PractitionerRole.specialty
+        * PractitionerRole.telecom
+        * PractitionerRole.telecom.system
+        * PractitionerRole.telecom.value
+      )
+
+      id :cpds_v101_practitioner_role_must_support_test
+
+      def resource_type
+        'PractitionerRole'
+      end
+
+      def self.metadata
+        @metadata ||= GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      run do
+        all_resources = scratch[:cpds_resources]&.values&.map do |bundle_resources|
+          bundle_resources['PractitionerRole'] || []
+        end
+        perform_must_support_test(all_resources&.flatten)
+      end
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/practitioner_role/practitioner_role_validation_test.rb

@@ -0,0 +1,47 @@
+require_relative '../../../bundle_parse'
+require_relative '../../../validation_test'
+
+module CancerPathologyDataSharingTestKit
+  class PractitionerRoleValidationTest < Inferno::Test
+    include CancerPathologyDataSharingTestKit::ValidationTest
+    include CancerPathologyDataSharingTestKit::BundleParse
+
+    title 'PractitionerRole resources in the bundle(s) conforms to the US Pathology PractitionerRole profile'
+    description %(
+    This test verifies that any PractitionerRole resources from each bundle conforms to
+    the [US Pathology Related PractitionerRoles](http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-related-practitioner-role).
+
+    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.
+    )
+
+    id :cpds_practitioner_role_validation_test
+
+    def resource_type
+      'PractitionerRole'
+    end
+
+    output :dar_code_found, :dar_extension_found
+
+    run do
+      invalid_bundles = []
+      total_resources = 0
+      scratch[:cpds_resources].each do |bundle_id, bundle_resources|
+        resources = bundle_resources['PractitionerRole'] || []
+        total_resources += resources.length
+
+        profile_url = PE_BUNDLE_SLICE_RESOURCES['PractitionerRole']
+        invalid_bundles << bundle_id if perform_strict_validation_test('PractitionerRole', bundle_id, resources, profile_url, '1.0.1',
+                                                                       skip_if_empty: false)
+      end
+
+      skip_if total_resources.zero?,
+              "No #{resource_type} resources found in any of the given bundles"
+
+      check_for_errors(invalid_bundles)
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/service_request/metadata.yml

@@ -0,0 +1,75 @@
+---
+:name: us_pathology_service_request
+:class_name: UsPathologyServiceRequestSequence
+:version: v1.0.1
+:reformatted_version: v101
+:resource: ServiceRequest
+:profile_url: http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-service-request
+:profile_name: US Pathology Service Request
+:profile_version: 1.0.1
+:title: US Pathology Service Request
+:short_description: Verify support for the server capabilities required by the US
+  Pathology Service Request.
+:must_supports:
+  :extensions: []
+  :slices:
+  - :slice_id: ServiceRequest.category:us-core
+    :slice_name: us-core
+    :path: category
+    :discriminator:
+      :type: requiredBinding
+      :path: ''
+      :values:
+      - :system: http://snomed.info/sct
+        :code: '108252007'
+      - :system: http://snomed.info/sct
+        :code: '363679005'
+      - :system: http://snomed.info/sct
+        :code: '409063005'
+      - :system: http://snomed.info/sct
+        :code: '409073007'
+      - :system: http://snomed.info/sct
+        :code: '387713003'
+      - :system: http://snomed.info/sct
+        :code: '386053000'
+      - :system: http://snomed.info/sct
+        :code: '410606002'
+      - :system: http://hl7.org/fhir/us/core/CodeSystem/us-core-tags
+        :code: 'sdoh'
+  :elements:
+  - :path: identifier
+  - :path: basedOn
+    :types:
+    - Reference
+  - :path: status
+  - :path: intent
+  - :path: category
+  - :path: code
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+  - :path: encounter
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter
+  - :path: occurrencePeriod
+    :original_path: occurrence[x]
+  - :path: authoredOn
+  - :path: requester
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner
+:mandatory_elements:
+- ServiceRequest.status
+- ServiceRequest.intent
+- ServiceRequest.category
+- ServiceRequest.code
+- ServiceRequest.code.coding
+- ServiceRequest.subject
+:tests: []
+:id: v101_service_request
+:file_name: service_request_group.rb

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/service_request/service_request_must_support_test.rb

@@ -0,0 +1,52 @@
+require_relative '../../../must_support_test'
+require_relative '../../../group_metadata'
+
+module CancerPathologyDataSharingTestKit
+  module V101
+    class ServiceRequestMustSupportTest < Inferno::Test
+      include CancerPathologyDataSharingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the Service Request resources'
+      description %(
+        Report generators SHALL be capable of populating all must support data elements
+        defined in the [US Pathology ExchangeBundle profile](https://hl7.org/fhir/us/cancer-reporting/STU1.0.1/StructureDefinition-us-pathology-exchange-bundle.html)
+        and profiles it references. This test will look through the ServiceRequest resources
+        found in the provided report Bundles for the following must support elements:
+
+        * ServiceRequest.authoredOn
+        * ServiceRequest.basedOn
+        * ServiceRequest.category
+        * ServiceRequest.category:us-core
+        * ServiceRequest.code
+        * ServiceRequest.encounter
+        * ServiceRequest.identifier
+        * ServiceRequest.intent
+        * ServiceRequest.occurrencePeriod
+        * ServiceRequest.requester
+        * ServiceRequest.status
+        * ServiceRequest.subject
+      )
+
+      id :cpds_v101_service_request_must_support_test
+
+      def resource_type
+        'ServiceRequest'
+      end
+
+      def self.metadata
+        @metadata ||= GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:service_request_resources] ||= {}
+      end
+
+      run do
+        all_resources = scratch[:cpds_resources]&.values&.map do |bundle_resources|
+          bundle_resources['ServiceRequest'] || []
+        end
+        perform_must_support_test(all_resources&.flatten)
+      end
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/service_request/service_request_validation_test.rb

@@ -0,0 +1,47 @@
+require_relative '../../../bundle_parse'
+require_relative '../../../validation_test'
+
+module CancerPathologyDataSharingTestKit
+  class ServiceRequestValidationTest < Inferno::Test
+    include CancerPathologyDataSharingTestKit::ValidationTest
+    include CancerPathologyDataSharingTestKit::BundleParse
+
+    title 'ServiceRequest resources in the bundle(s) conforms to the US Pathology ServiceRequest profile'
+    description %(
+    This test verifies that any ServiceRequest resources from each bundle conforms to
+    the [US Pathology Service Request](http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-service-request).
+
+    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.
+    )
+
+    id :cpds_service_request_validation_test
+
+    def resource_type
+      'ServiceRequest'
+    end
+
+    output :dar_code_found, :dar_extension_found
+
+    run do
+      invalid_bundles = []
+      total_resources = 0
+      scratch[:cpds_resources].each do |bundle_id, bundle_resources|
+        resources = bundle_resources['ServiceRequest'] || []
+        total_resources += resources.length
+
+        profile_url = PE_BUNDLE_SLICE_RESOURCES['ServiceRequest']
+        invalid_bundles << bundle_id if perform_strict_validation_test('ServiceRequest', bundle_id, resources, profile_url, '1.0.1',
+                                                                       skip_if_empty: false)
+      end
+
+      skip_if total_resources.zero?,
+              "No #{resource_type} resources found in any of the given bundles"
+
+      check_for_errors(invalid_bundles)
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/specimen/metadata.yml

@@ -0,0 +1,51 @@
+---
+:name: us_pathology_specimen
+:class_name: UsPathologySpecimenSequence
+:version: v1.0.1
+:reformatted_version: v101
+:resource: Specimen
+:profile_url: http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-specimen
+:profile_name: US Pathology Specimen
+:profile_version: 1.0.1
+:title: US Pathology Specimen
+:short_description: Verify support for the server capabilities required by the US
+  Pathology Specimen.
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements:
+  - :path: identifier
+  - :path: accessionIdentifier
+  - :path: status
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+  - :path: type
+  - :path: receivedTime
+  - :path: parent
+    :types:
+    - Reference
+  - :path: collection
+  - :path: collection.collector
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-related-practitioner-role
+  - :path: collection.collected[x]
+  - :path: collection.method
+  - :path: collection.bodySite
+  - :path: container
+  - :path: note
+:mandatory_elements:
+- Specimen.identifier
+- Specimen.accessionIdentifier
+- Specimen.type
+- Specimen.collection.collected[x]
+- Specimen.collection.method
+- Specimen.container
+- Specimen.container.identifier
+:tests: []
+:id: v101_specimen
+:file_name: specimen_group.rb

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/specimen/specimen_must_support_test.rb

@@ -0,0 +1,53 @@
+require_relative '../../../must_support_test'
+require_relative '../../../group_metadata'
+
+module CancerPathologyDataSharingTestKit
+  module V101
+    class SpecimenMustSupportTest < Inferno::Test
+      include CancerPathologyDataSharingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the Specimen resources'
+      description %(
+        Report generators SHALL be capable of populating all must support data elements
+        defined in the [US Pathology ExchangeBundle profile](https://hl7.org/fhir/us/cancer-reporting/STU1.0.1/StructureDefinition-us-pathology-exchange-bundle.html)
+        and profiles it references. This test will look through the Specimen resources
+        found in the provided report Bundles for the following must support elements:
+
+        * Specimen.accessionIdentifier
+        * Specimen.collection
+        * Specimen.collection.bodySite
+        * Specimen.collection.collected[x]
+        * Specimen.collection.collector
+        * Specimen.collection.method
+        * Specimen.container
+        * Specimen.identifier
+        * Specimen.note
+        * Specimen.parent
+        * Specimen.receivedTime
+        * Specimen.status
+        * Specimen.type
+      )
+
+      id :cpds_v101_specimen_must_support_test
+
+      def resource_type
+        'Specimen'
+      end
+
+      def self.metadata
+        @metadata ||= GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      def scratch_resources
+        scratch[:specimen_resources] ||= {}
+      end
+
+      run do
+        all_resources = scratch[:cpds_resources]&.values&.map do |bundle_resources|
+          bundle_resources['Specimen'] || []
+        end
+        perform_must_support_test(all_resources&.flatten)
+      end
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/specimen/specimen_validation_test.rb

@@ -0,0 +1,47 @@
+require_relative '../../../bundle_parse'
+require_relative '../../../validation_test'
+
+module CancerPathologyDataSharingTestKit
+  class SpecimenValidationTest < Inferno::Test
+    include CancerPathologyDataSharingTestKit::ValidationTest
+    include CancerPathologyDataSharingTestKit::BundleParse
+
+    title 'Specimen resources in the bundle(s) conforms to the US Pathology Specimen profile'
+    description %(
+    This test verifies there is at least one of the Specimen resource returned from each bundle and that it conforms to
+    the [US Pathology Specimen](http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-specimen).
+
+    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.
+    )
+
+    id :cpds_specimen_validation_test
+
+    def resource_type
+      'Specimen'
+    end
+
+    output :dar_code_found, :dar_extension_found
+
+    run do
+      invalid_bundles = []
+      total_resources = 0
+      scratch[:cpds_resources].each do |bundle_id, bundle_resources|
+        resources = bundle_resources['Specimen'] || []
+        total_resources += resources.length
+
+        profile_url = PE_BUNDLE_SLICE_RESOURCES['Specimen']
+        invalid_bundles << bundle_id if perform_strict_validation_test('Specimen', bundle_id, resources, profile_url, '1.0.1',
+                                                                       restriction: 'at_least_one')
+      end
+
+      skip_if total_resources.zero?,
+              "No #{resource_type} resources found in any of the given bundles"
+
+      check_for_errors(invalid_bundles)
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/us_pathology_diagnostic_report/diagnostic_report_validation_test.rb

@@ -0,0 +1,47 @@
+require_relative '../../../bundle_parse'
+require_relative '../../../validation_test'
+
+module CancerPathologyDataSharingTestKit
+  class DiagnosticReportValidationTest < Inferno::Test
+    include CancerPathologyDataSharingTestKit::ValidationTest
+    include CancerPathologyDataSharingTestKit::BundleParse
+
+    title 'DiagnosticReport resource in each bundle conforms to the US Pathology Diagnostic Report profile'
+    description %(
+    This test verifies that there is exactly one DiagnosticReport resource returned from each bundle and that it conforms to
+    the [US Pathology Diagnostic Report](http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-diagnostic-report).
+
+    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.
+    )
+
+    id :cpds_diagnostic_report_validation_test
+
+    def resource_type
+      'DiagnosticReport'
+    end
+
+    output :dar_code_found, :dar_extension_found
+
+    run do
+      invalid_bundles = []
+      total_resources = 0
+      scratch[:cpds_resources].each do |bundle_id, bundle_resources|
+        resources = bundle_resources['DiagnosticReport'] || []
+        total_resources += resources.length
+
+        profile_url = PE_BUNDLE_SLICE_RESOURCES['DiagnosticReport']
+        invalid_bundles << bundle_id if perform_strict_validation_test('DiagnosticReport', bundle_id, resources, profile_url, '1.0.1',
+                                                                       restriction: 'exactly_one')
+      end
+
+      skip_if total_resources.zero?,
+              "No #{resource_type} resources found in any of the given bundles"
+
+      check_for_errors(invalid_bundles)
+    end
+  end
+end

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/us_pathology_diagnostic_report/metadata.yml

@@ -0,0 +1,77 @@
+---
+:name: us_pathology_diagnostic_report
+:class_name: UsPathologyDiagnosticReportSequence
+:version: v1.0.1
+:reformatted_version: v101
+:resource: DiagnosticReport
+:profile_url: http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-diagnostic-report
+:profile_name: US Pathology Diagnostic Report
+:profile_version: 1.0.1
+:title: DiagnosticReport US Pathology Diagnostic Report
+:short_description: Verify support for the server capabilities required by the US
+  Pathology Diagnostic Report.
+:must_supports:
+  :extensions: []
+  :slices:
+  - :slice_id: DiagnosticReport.category:us-core
+    :slice_name: us-core
+    :path: category
+    :discriminator:
+      :type: requiredBinding
+      :path: ''
+      :values:
+      - :system: http://loinc.org
+        :code: LP29684-5
+      - :system: http://loinc.org
+        :code: LP29708-2
+      - :system: http://loinc.org
+        :code: LP7839-6
+  :elements:
+  - :path: status
+  - :path: category
+  - :path: code
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+  - :path: encounter
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter
+  - :path: effectiveDateTime
+    :original_path: effective[x]
+  - :path: issued
+  - :path: performer
+    :types:
+    - Reference
+  - :path: resultsInterpreter
+    :types:
+    - Reference
+  - :path: specimen
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/cancer-reporting/StructureDefinition/us-pathology-specimen
+  - :path: result
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-clinical-test
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-imaging
+  - :path: media
+  - :path: media.link
+    :types:
+    - Reference
+  - :path: presentedForm
+:mandatory_elements:
+- DiagnosticReport.status
+- DiagnosticReport.category
+- DiagnosticReport.code
+- DiagnosticReport.subject
+- DiagnosticReport.media.link
+:tests: []
+:id: v101_us_pathology_diagnostic_report
+:file_name: us_pathology_diagnostic_report_group.rb

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/us_pathology_diagnostic_report/us_pathology_diagnostic_report_must_support_test.rb

@@ -0,0 +1,51 @@
+require_relative '../../../must_support_test'
+require_relative '../../../group_metadata'
+
+module CancerPathologyDataSharingTestKit
+  module V101
+    class UsPathologyDiagnosticReportMustSupportTest < Inferno::Test
+      include CancerPathologyDataSharingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the US Pathology Diagnostic Report resources'
+      description %(
+        Report generators SHALL be capable of populating all must support data elements
+        defined in the [US Pathology ExchangeBundle profile](https://hl7.org/fhir/us/cancer-reporting/STU1.0.1/StructureDefinition-us-pathology-exchange-bundle.html)
+        and profiles it references. This test will look through the DiagnosticReport resources
+        found in the provided report Bundles for the following must support elements:
+
+        * DiagnosticReport.category
+        * DiagnosticReport.category:us-core
+        * DiagnosticReport.code
+        * DiagnosticReport.effectiveDateTime
+        * DiagnosticReport.encounter
+        * DiagnosticReport.issued
+        * DiagnosticReport.media
+        * DiagnosticReport.media.link
+        * DiagnosticReport.performer
+        * DiagnosticReport.presentedForm
+        * DiagnosticReport.result
+        * DiagnosticReport.resultsInterpreter
+        * DiagnosticReport.specimen
+        * DiagnosticReport.status
+        * DiagnosticReport.subject
+      )
+
+      id :cpds_v101_us_pathology_diagnostic_report_must_support_test
+
+      def resource_type
+        'DiagnosticReport'
+      end
+
+      def self.metadata
+        @metadata ||= GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+      end
+
+      run do
+        all_resources = scratch[:cpds_resources]&.values&.map do |bundle_resources|
+          bundle_resources['DiagnosticReport'] || []
+        end
+        perform_must_support_test(all_resources&.flatten)
+      end
+    end
+  end
+end