cancer_pathology_data_sharing_test_kit 0.9.0

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

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+---
+:name: us_core_encounter
+:class_name: USCorev311EncounterSequence
+:version: v3.1.1
+:reformatted_version: v311
+:resource: Encounter
+:profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter
+:profile_name: US Core Encounter Profile
+:profile_version: 3.1.1
+:title: Encounter
+:short_description: Verify support for the server capabilities required by the US
+  Core Encounter Profile.
+:is_delayed: true
+:interactions:
+- :code: create
+  :expectation: MAY
+- :code: search-type
+  :expectation: SHALL
+- :code: read
+  :expectation: SHALL
+- :code: vread
+  :expectation: SHOULD
+- :code: update
+  :expectation: MAY
+- :code: patch
+  :expectation: MAY
+- :code: delete
+  :expectation: MAY
+- :code: history-instance
+  :expectation: SHOULD
+- :code: history-type
+  :expectation: MAY
+:operations: []
+:searches:
+- :names:
+  - patient
+  :expectation: SHALL
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :names:
+  - _id
+  :expectation: SHALL
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :names:
+  - identifier
+  :expectation: SHOULD
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHOULD
+  :names:
+  - class
+  - patient
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHOULD
+  :names:
+  - patient
+  - status
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHOULD
+  :names:
+  - patient
+  - type
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHALL
+  :names:
+  - date
+  - patient
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+:search_definitions:
+  :_id:
+    :paths:
+    - id
+    :full_paths:
+    - Encounter.id
+    :comparators: {}
+    :values: []
+    :type: http://hl7.org/fhirpath/System.String
+    :contains_multiple: false
+    :multiple_or: MAY
+  :identifier:
+    :paths:
+    - identifier
+    :full_paths:
+    - Encounter.identifier
+    :comparators: {}
+    :values: []
+    :type: Identifier
+    :contains_multiple: true
+    :multiple_or: MAY
+  :patient:
+    :paths:
+    - subject
+    :full_paths:
+    - Encounter.subject
+    :comparators: {}
+    :values: []
+    :type: Reference
+    :contains_multiple: false
+    :multiple_or: MAY
+  :class:
+    :paths:
+    - class
+    :full_paths:
+    - Encounter.class
+    :comparators: {}
+    :values: []
+    :type: Coding
+    :contains_multiple: false
+    :multiple_or: MAY
+  :status:
+    :paths:
+    - status
+    :full_paths:
+    - Encounter.status
+    :comparators: {}
+    :values:
+    - planned
+    - arrived
+    - triaged
+    - in-progress
+    - onleave
+    - finished
+    - cancelled
+    - entered-in-error
+    - unknown
+    :type: code
+    :contains_multiple: false
+    :multiple_or: MAY
+  :type:
+    :paths:
+    - type
+    :full_paths:
+    - Encounter.type
+    :comparators: {}
+    :values: []
+    :type: CodeableConcept
+    :contains_multiple: true
+    :multiple_or: MAY
+  :date:
+    :paths:
+    - period
+    :full_paths:
+    - Encounter.period
+    :comparators:
+      :eq: MAY
+      :ne: MAY
+      :gt: SHALL
+      :ge: SHALL
+      :lt: SHALL
+      :le: SHALL
+      :sa: MAY
+      :eb: MAY
+      :ap: MAY
+    :values: []
+    :type: Period
+    :contains_multiple: false
+    :multiple_or: MAY
+:include_params: []
+:revincludes:
+- Provenance:target
+:required_concepts: []
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements:
+  - :path: identifier
+  - :path: identifier.system
+  - :path: identifier.value
+  - :path: status
+  - :path: class
+  - :path: type
+  - :path: subject
+    :types:
+    - Reference
+  - :path: participant
+  - :path: participant.type
+  - :path: participant.period
+  - :path: participant.individual
+    :types:
+    - Reference
+  - :path: period
+  - :path: reasonCode
+  - :path: hospitalization
+  - :path: hospitalization.dischargeDisposition
+  - :path: location
+  - :path: location.location
+    :types:
+    - Reference
+:mandatory_elements:
+- Encounter.identifier.system
+- Encounter.identifier.value
+- Encounter.status
+- Encounter.statusHistory.status
+- Encounter.statusHistory.period
+- Encounter.class
+- Encounter.classHistory.class
+- Encounter.classHistory.period
+- Encounter.type
+- Encounter.subject
+- Encounter.diagnosis.condition
+- Encounter.location.location
+:bindings:
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/identifier-use
+  :path: identifier.use
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/encounter-status
+  :path: status
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/encounter-status
+  :path: statusHistory.status
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/encounter-location-status
+  :path: location.status
+:references:
+- :path: Encounter.identifier.assigner
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Encounter.subject
+  :profiles:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+- :path: Encounter.episodeOfCare
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/EpisodeOfCare
+- :path: Encounter.basedOn
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/ServiceRequest
+- :path: Encounter.participant.individual
+  :profiles:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner
+- :path: Encounter.appointment
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Appointment
+- :path: Encounter.reasonReference
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Condition
+  - http://hl7.org/fhir/StructureDefinition/Procedure
+  - http://hl7.org/fhir/StructureDefinition/Observation
+  - http://hl7.org/fhir/StructureDefinition/ImmunizationRecommendation
+- :path: Encounter.diagnosis.condition
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Condition
+  - http://hl7.org/fhir/StructureDefinition/Procedure
+- :path: Encounter.account
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Account
+- :path: Encounter.hospitalization.origin
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Location
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Encounter.hospitalization.destination
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Location
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Encounter.location.location
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Location
+- :path: Encounter.serviceProvider
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Encounter.partOf
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Encounter
+:tests:
+- :id: v101_us_core_v311_encounter_must_support_test
+  :file_name: encounter_must_support_test.rb
+:id: us_core_v311_encounter
+:file_name: encounter_group.rb
+:delayed_references:
+- :path: participant.individual
+  :resources:
+  - Practitioner

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

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+---
+:name: us_core_patient
+:class_name: USCorev311PatientSequence
+:version: v3.1.1
+:reformatted_version: v311
+:resource: Patient
+:profile_url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+:profile_name: US Core Patient Profile
+:profile_version: 3.1.1
+:title: Patient
+:short_description: Verify support for the server capabilities required by the US
+  Core Patient Profile.
+:is_delayed: false
+:interactions:
+- :code: create
+  :expectation: MAY
+- :code: search-type
+  :expectation: SHALL
+- :code: read
+  :expectation: SHALL
+- :code: vread
+  :expectation: SHOULD
+- :code: update
+  :expectation: MAY
+- :code: patch
+  :expectation: MAY
+- :code: delete
+  :expectation: MAY
+- :code: history-instance
+  :expectation: SHOULD
+- :code: history-type
+  :expectation: MAY
+:operations: []
+:searches:
+- :names:
+  - _id
+  :expectation: SHALL
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :names:
+  - identifier
+  :expectation: SHALL
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :names:
+  - name
+  :expectation: SHALL
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHOULD
+  :names:
+  - birthdate
+  - family
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHOULD
+  :names:
+  - family
+  - gender
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHALL
+  :names:
+  - birthdate
+  - name
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+- :expectation: SHALL
+  :names:
+  - gender
+  - name
+  :names_not_must_support_or_mandatory: []
+  :must_support_or_mandatory: true
+:search_definitions:
+  :_id:
+    :paths:
+    - id
+    :full_paths:
+    - Patient.id
+    :comparators: {}
+    :values: []
+    :type: http://hl7.org/fhirpath/System.String
+    :contains_multiple: false
+    :multiple_or: MAY
+  :identifier:
+    :paths:
+    - identifier
+    :full_paths:
+    - Patient.identifier
+    :comparators: {}
+    :values: []
+    :type: Identifier
+    :contains_multiple: true
+    :multiple_or: MAY
+  :name:
+    :paths:
+    - name
+    :full_paths:
+    - Patient.name
+    :comparators: {}
+    :values: []
+    :type: HumanName
+    :contains_multiple: true
+    :multiple_or: MAY
+  :birthdate:
+    :paths:
+    - birthDate
+    :full_paths:
+    - Patient.birthDate
+    :comparators:
+      :eq: MAY
+      :ne: MAY
+      :gt: MAY
+      :ge: MAY
+      :lt: MAY
+      :le: MAY
+      :sa: MAY
+      :eb: MAY
+      :ap: MAY
+    :values: []
+    :type: date
+    :contains_multiple: false
+    :multiple_or: MAY
+  :family:
+    :paths:
+    - name.family
+    :full_paths:
+    - Patient.name.family
+    :comparators: {}
+    :values: []
+    :type: string
+    :contains_multiple: false
+    :multiple_or: MAY
+  :gender:
+    :paths:
+    - gender
+    :full_paths:
+    - Patient.gender
+    :comparators: {}
+    :values: []
+    :type: code
+    :contains_multiple: false
+    :multiple_or: MAY
+:include_params: []
+:revincludes:
+- Provenance:target
+:required_concepts: []
+:must_supports:
+  :extensions:
+  - :id: Patient.extension:race
+    :path: extension
+    :url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-race
+  - :id: Patient.extension:ethnicity
+    :path: extension
+    :url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity
+  - :id: Patient.extension:birthsex
+    :path: extension
+    :url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex
+  :slices: []
+  :elements:
+  - :path: identifier
+  - :path: identifier.system
+  - :path: identifier.value
+  - :path: name
+  - :path: name.family
+  - :path: name.given
+  - :path: telecom
+  - :path: telecom.system
+  - :path: telecom.value
+  - :path: telecom.use
+  - :path: gender
+  - :path: birthDate
+  - :path: address
+  - :path: address.line
+  - :path: address.city
+  - :path: address.state
+  - :path: address.postalCode
+  - :path: address.period.end
+    :uscdi_only: true
+  - :path: communication
+  - :path: communication.language
+  - :path: name.period.end
+    :uscdi_only: true
+  - :path: name.use
+    :fixed_value: old
+    :uscdi_only: true
+  - :path: address.use
+    :fixed_value: old
+    :uscdi_only: true
+  :choices:
+  - :paths:
+    - address.period.end
+    - address.use
+    :uscdi_only: true
+  - :paths:
+    - name.period.end
+    - name.use
+    :uscdi_only: true
+:mandatory_elements:
+- Patient.identifier
+- Patient.identifier.system
+- Patient.identifier.value
+- Patient.name
+- Patient.telecom.system
+- Patient.telecom.value
+- Patient.gender
+- Patient.communication.language
+- Patient.link.other
+- Patient.link.type
+:bindings:
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/identifier-use
+  :path: identifier.use
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/name-use
+  :path: name.use
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/contact-point-system
+  :path: telecom.system
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/contact-point-use
+  :path: telecom.use
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/administrative-gender
+  :path: gender
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/address-use
+  :path: address.use
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/address-type
+  :path: address.type
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/administrative-gender
+  :path: contact.gender
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/ValueSet/link-type
+  :path: link.type
+- :type: Coding
+  :strength: required
+  :system: http://hl7.org/fhir/us/core/ValueSet/omb-race-category
+  :path: value
+  :extensions:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-race
+  - ombCategory
+- :type: Coding
+  :strength: required
+  :system: http://hl7.org/fhir/us/core/ValueSet/detailed-race
+  :path: value
+  :extensions:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-race
+  - detailed
+- :type: Coding
+  :strength: required
+  :system: http://hl7.org/fhir/us/core/ValueSet/omb-ethnicity-category
+  :path: value
+  :extensions:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity
+  - ombCategory
+- :type: Coding
+  :strength: required
+  :system: http://hl7.org/fhir/us/core/ValueSet/detailed-ethnicity
+  :path: value
+  :extensions:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity
+  - detailed
+- :type: code
+  :strength: required
+  :system: http://hl7.org/fhir/us/core/ValueSet/birthsex
+  :path: value
+  :extensions:
+  - http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex
+:references:
+- :path: Patient.identifier.assigner
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Patient.contact.organization
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Patient.generalPractitioner
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Organization
+  - http://hl7.org/fhir/StructureDefinition/Practitioner
+  - http://hl7.org/fhir/StructureDefinition/PractitionerRole
+- :path: Patient.managingOrganization
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Organization
+- :path: Patient.link.other
+  :profiles:
+  - http://hl7.org/fhir/StructureDefinition/Patient
+  - http://hl7.org/fhir/StructureDefinition/RelatedPerson
+:tests:
+- :id: v101_us_core_v311_patient_must_support_test
+  :file_name: patient_must_support_test.rb
+:id: us_core_v311_patient
+:file_name: patient_group.rb
+:delayed_references: []

data/lib/cancer_pathology_data_sharing_test_kit/report_generation_suite/exchange_bundle/patient/patient_must_support_test.rb

@@ -0,0 +1,58 @@
+require_relative '../../../must_support_test'
+require_relative '../../../group_metadata'
+
+module CancerPathologyDataSharingTestKit
+  module V101
+    class PatientMustSupportTest < Inferno::Test
+      include CancerPathologyDataSharingTestKit::MustSupportTest
+
+      title 'All must support elements are provided in the US Core Patient 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 Patient resources
+        found in the provided report Bundles for the following must support elements:
+
+        * Patient.address
+        * Patient.address.city
+        * Patient.address.line
+        * Patient.address.postalCode
+        * Patient.address.state
+        * Patient.birthDate
+        * Patient.communication
+        * Patient.communication.language
+        * Patient.extension:birthsex
+        * Patient.extension:ethnicity
+        * Patient.extension:race
+        * Patient.gender
+        * Patient.identifier
+        * Patient.identifier.system
+        * Patient.identifier.value
+        * Patient.name
+        * Patient.name.family
+        * Patient.name.given
+        * Patient.telecom
+        * Patient.telecom.system
+        * Patient.telecom.use
+        * Patient.telecom.value
+      )
+
+      id :cpds_v101_us_core_v311_patient_must_support_test
+
+      def resource_type
+        'Patient'
+      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['Patient'] || []
+        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/patient/patient_validation_test.rb

@@ -0,0 +1,47 @@
+require_relative '../../../bundle_parse'
+require_relative '../../../validation_test'
+
+module CancerPathologyDataSharingTestKit
+  class PatientValidationTest < Inferno::Test
+    include CancerPathologyDataSharingTestKit::ValidationTest
+    include CancerPathologyDataSharingTestKit::BundleParse
+
+    title 'Patient resource in each bundle conforms to the US Core Patient profile'
+    description %(
+    This test verifies that there is exactly one Patient resource returned from each bundle and that it conforms to
+    the [US Core Patient Profile](http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient).
+
+    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_patient_validation_test
+
+    def resource_type
+      'Patient'
+    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['Patient'] || []
+        total_resources += resources.length
+
+        profile_url = PE_BUNDLE_SLICE_RESOURCES['Patient']
+        invalid_bundles << bundle_id if perform_strict_validation_test('Patient', bundle_id, resources, profile_url, '5.0.1',
+                                                                       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