cancer_registry_reporting_test_kit 0.9.0

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/secondary_condition/metadata.yml

@@ -0,0 +1,102 @@
+---
+:name: mcode_secondary_cancer_condition
+:class_name: McodeSecondaryCancerConditionSequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: Condition
+:profile_url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-secondary-cancer-condition
+:profile_name: Secondary Cancer Condition Profile
+:profile_version: 3.0.0
+:title: Condition Secondary Cancer
+:short_description: Verify support for the server capabilities required by the Secondary
+  Cancer Condition Profile.
+:must_supports:
+  :extensions:
+  - :id: Condition.extension:assertedDate
+    :path: extension
+    :url: http://hl7.org/fhir/StructureDefinition/condition-assertedDate
+  - :id: Condition.extension:histologyMorphologyBehavior
+    :path: extension
+    :url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-histology-morphology-behavior
+  - :id: Condition.extension:relatedPrimaryCancerCondition
+    :path: extension
+    :url: http://hl7.org/fhir/StructureDefinition/condition-related
+  - :id: Condition.bodySite.extension:locationQualifier
+    :path: bodySite.extension
+    :url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-body-location-qualifier
+  - :id: Condition.bodySite.extension:lateralityQualifier
+    :path: bodySite.extension
+    :url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-laterality-qualifier
+  :slices:
+  - :slice_id: Condition.category:us-core
+    :slice_name: us-core
+    :path: category
+    :discriminator:
+      :type: requiredBinding
+      :path: ''
+      :values:
+      - :system: http://terminology.hl7.org/CodeSystem/condition-category
+        :code: problem-list-item
+      - :system: http://terminology.hl7.org/CodeSystem/condition-category
+        :code: encounter-diagnosis
+  - :slice_id: Condition.category:sdoh
+    :slice_name: sdoh
+    :path: category
+    :discriminator:
+      :type: patternCodeableConcept
+      :path: ''
+      :code: sdoh
+      :system: http://hl7.org/fhir/us/core/CodeSystem/us-core-tags
+  :elements:
+  - :path: clinicalStatus
+  - :path: verificationStatus
+  - :path: category
+  - :path: code
+  - :path: bodySite
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient
+  - :path: onsetDateTime
+    :original_path: onset[x]
+  - :path: abatementDateTime
+    :original_path: abatement[x]
+  - :path: recordedDate
+  - :path: stage
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-stage
+:mandatory_elements:
+- Condition.category
+- Condition.code
+- Condition.subject
+:tests: []
+:id: ccrr_v100_mcode_secondary_cancer_condition
+:file_name: mcode_secondary_cancer_condition_group.rb
+:searches:
+- :expectation: SHALL
+  :names:
+  - patient
+  - category
+:search_definitions:
+  :patient:
+    :paths:
+    - subject
+    :full_paths:
+    - Condition.subject
+    :comparators: {}
+    :values: []
+    :type: Reference
+    :contains_multiple: false
+    :multiple_or: MAY
+  :category:
+    :paths:
+    - category
+    :full_paths:
+    - Condition.category
+    :comparators: {}
+    :type: CodeableConcept
+    :contains_multiple: true
+    :multiple_or: MAY

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/secondary_condition/secondary_cancer_condition_must_support_test.rb

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+# frozen_string_literal: true
+
+require_relative '../../../must_support_test'
+
+module CancerRegistryReportingTestKit
+  class SecondaryCancerConditionMustSupportTest < Inferno::Test
+    include CancerRegistryReportingTestKit::MustSupportTest
+
+    title 'All must support elements are provided in the mCODE Secondary Cancer Condition resources returned'
+    description %(
+      CCRR EHRs SHALL be capable of populating all data elements as
+      part of the query results. This test will look through the Condition resources
+      found previously for the following must support elements:
+
+      * Condition.abatement[x]
+      * Condition.bodySite
+      * Condition.bodySite.extension:locationQualifier
+      * Condition.bodySite.extension:lateralityQualifier
+      * Condition.category
+      * Condition.code
+      * Condition.clinicalStatus
+      * Condition.extension:assertedDate
+      * Condition.extension:histologyMorphologyBehavior
+      * Condition.verificationStatus
+      * Condition.recordedDate
+      * Condition.onset[x]
+      * Condition.subject
+      * Condition.stage
+      * Condition.stage.assessment
+    )
+
+    id :ccrr_secondary_cancer_condition_must_support_test
+
+    def resource_type
+      'Condition'
+    end
+
+    def self.metadata
+      @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+    end
+
+    def scratch_resources
+      scratch[:secondary_condition_resources] ||= {}
+    end
+
+    run do
+      perform_must_support_test(all_scratch_resources)
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/secondary_condition/secondary_cancer_condition_search_test.rb

@@ -0,0 +1,70 @@
+# frozen_string_literal: true
+
+require_relative '../../../search_test'
+require_relative '../../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  class SecondaryCancerConditionSearchTest < Inferno::Test
+    include CancerRegistryReportingTestKit::SearchTest
+
+    title 'Server returns valid results for Condition search by patient + category'
+    description %(
+        A server SHALL support searching by
+        patient + category on the Condition resource. This test
+        will pass if resources are returned and match the search criteria. If
+        none are returned, the test is skipped.
+
+        Because this is the first search of the sequence, resources in the
+        response will be used for subsequent tests.
+
+        Additionally, this test will check that GET and POST search methods
+        return the same number of results.
+
+        [CCRR Capability Statement](https://hl7.org/fhir/us/central-cancer-registry-reporting/STU1/CapabilityStatement-central-cancer-registry-reporting-ehr.html)
+
+        [mCODE Query Support](https://hl7.org/fhir/us/mcode/conformance-general.html#support-querying-mcode-conforming-resources)
+
+      )
+
+    id :ccrr_secondary_cancer_condition_search_test
+    input :patient_ids,
+          title: 'Patient IDs',
+          description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements.'
+
+    input :secondary_condition_category,
+          title: 'Secondary Cancer Condition category',
+          description: %(
+            `Condition.category` value that distinguishes Secondary Cancer Condition instances. Used as a search
+            parameter value when searching to identify Condition instances to check for conformance to the Secondary
+            Cancer Condition profile.
+          ),
+          optional: true
+
+    def self.properties
+      @properties ||= USCoreTestKit::SearchTestProperties.new(
+        first_search: true,
+        resource_type: 'Condition',
+        search_param_names: %w[patient category],
+        test_post_search: true
+      )
+    end
+
+    def self.metadata
+      @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+    end
+
+    def scratch_resources
+      scratch[:secondary_condition_resources] ||= {}
+    end
+
+    run do
+      skip_if secondary_condition_category.blank?,
+              'Provide a cateogry search value for Secondary Cancer Conditions in the ' \
+              '**Secondary Cancer Condition category** input to run these tests.'
+
+      # manual params must be in the same order as the param names
+      @manual_search_params = [secondary_condition_category]
+      run_search_test
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/secondary_condition/secondary_cancer_condition_validation_test.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+require_relative '../../../validation_test'
+
+module CancerRegistryReportingTestKit
+  class SecondaryCancerConditionValidationTest < Inferno::Test
+    include CancerRegistryReportingTestKit::ValidationTest
+
+    id :ccrr_secondary_cancer_condition_validation_test
+    title 'Condition resources returned during previous tests conform to the mCODE Secondary Cancer Condition Profile'
+    description %(
+        This test verifies resources returned from the first search conform to
+        the [mCODE Secondary Cancer Condition Profile](http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-secondary-cancer-condition).
+        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.
+
+      )
+
+    def resource_type
+      'Condition'
+    end
+
+    def scratch_resources
+      scratch[:secondary_condition_resources] ||= {}
+    end
+
+    run do
+      perform_validation_test(scratch_resources[:all] || [],
+                              'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-secondary-cancer-condition',
+                              '3.0.0',
+                              skip_if_empty: true)
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_distant_metastases_category/metadata.yml

@@ -0,0 +1,65 @@
+---
+:name: mcode_tnm_distant_metastases_category
+:class_name: McodeTnmDistantMetastasesCategorySequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: Observation
+:profile_url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-distant-metastases-category
+:profile_name: TNM Distant Metastases Category Profile
+:profile_version: 3.0.0
+:title: Observation TNM Distant Metastases Category
+:short_description: Verify support for the server capabilities required by the TNM
+  Distant Metastases Category Profile.
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements:
+  - :path: status
+  - :path: code
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient
+  - :path: focus
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-primary-cancer-condition
+  - :path: effective[x]
+  - :path: value[x]
+  - :path: method
+:mandatory_elements:
+- Observation.status
+- Observation.code
+- Observation.method
+- Observation.component.code
+:tests: []
+:id: ccrr_v100_mcode_tnm_distant_metastases_category
+:file_name: mcode_tnm_distant_metastases_category_group.rb
+:searches:
+- :expectation: SHALL
+  :names:
+  - patient
+  - code
+:search_definitions:
+  :patient:
+    :paths:
+    - subject
+    :full_paths:
+    - Observation.subject
+    :comparators: {}
+    :values: []
+    :type: Reference
+    :contains_multiple: false
+    :multiple_or: MAY
+  :code:
+    :paths:
+    - code
+    :full_paths:
+    - Observation.code
+    :comparators: {}
+    :type: CodeableConcept
+    :contains_multiple: true
+    :multiple_or: MAY
+

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_distant_metastases_category/tnm_distant_metastases_category_must_support_test.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require_relative '../../../must_support_test'
+
+module CancerRegistryReportingTestKit
+  class TNMDistantMetastasesCategoryMustSupportTest < Inferno::Test
+    include CancerRegistryReportingTestKit::MustSupportTest
+
+    title 'All must support elements are provided in the mCODE TNM Distant Metastases Category Observation resources returned'
+    description %(
+      CCRR EHRs SHALL be capable of populating all data elements as
+      part of the query results. This test will look through the Observation resources
+      found previously for the following must support elements:
+
+      * Observation.category
+      * Observation.code
+      * Observation.effective[x]
+      * Observation.focus
+      * Observation.method
+      * Observation.performer
+      * Observation.status
+      * Observation.subject
+      * Observation.value[x]
+    )
+
+    id :ccrr_tnm_distant_metastases_category_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[:tnm_distant_metastases_category_resources] ||= {}
+    end
+
+    run do
+      perform_must_support_test(all_scratch_resources)
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_distant_metastases_category/tnm_distant_metastases_category_search_test.rb

@@ -0,0 +1,69 @@
+# frozen_string_literal: true
+
+require_relative '../../../search_test'
+require_relative '../../../hdea_generator/group_metadata'
+
+module CancerRegistryReportingTestKit
+  class TNMDistantMetastasesCategorySearchTest < Inferno::Test
+    include CancerRegistryReportingTestKit::SearchTest
+
+    title 'Server returns valid results for Observation search by patient + code'
+    description %(
+        A server SHALL support searching by
+        patient + code on the Observation resource. This test
+        will pass if resources are returned and match the search criteria. If
+        none are returned, the test is skipped.
+
+        Because this is the first search of the sequence, resources in the
+        response will be used for subsequent tests.
+
+        Additionally, this test will check that GET and POST search methods
+        return the same number of results.
+      )
+
+    id :ccrr_tnm_distant_metastases_category_search_test
+    input :patient_ids,
+          title: 'Patient IDs',
+          description: 'Comma separated list of patient IDs that in sum contain all MUST SUPPORT elements'
+
+    input :tnm_distant_metastases_category_code,
+          title: 'TNM Distant Metastases Category code',
+          description: %(
+            `Observation.code` value that distinguishes TNM Distant Metastases Category instances from
+            other Observations. Used as a search parameter value when searching for Observation instances
+            to check for conformance to the TNM Distant Metastases Category Observation profile.
+          ),
+          optional: true
+
+    def self.properties
+      @properties ||= CancerRegistryReportingTestKit::SearchTestProperties.new(
+        first_search: true,
+        fixed_value_search: false,
+        resource_type: 'Observation',
+        search_param_names: %w[patient code],
+        possible_status_search: true,
+        token_search_params: ['code'],
+        test_reference_variants: true,
+        test_post_search: false
+      )
+    end
+
+    def self.metadata
+      @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(File.join(__dir__, 'metadata.yml'), aliases: true))
+    end
+
+    def scratch_resources
+      scratch[:tnm_distant_metastases_category_resources] ||= {}
+    end
+
+    run do
+      skip_if tnm_distant_metastases_category_code.blank?,
+              'Provide a code search value for TNM Distant Metastases Categories in the ' \
+              '**TNM Distant Metastases Category code** input to run these tests.'
+
+      # manual params must be in the same order as the param names
+      @manual_search_params = [tnm_distant_metastases_category_code]
+      run_search_test
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_distant_metastases_category/tnm_distant_metastases_category_validation_test.rb

@@ -0,0 +1,39 @@
+# frozen_string_literal: true
+
+require_relative '../../../validation_test'
+
+module CancerRegistryReportingTestKit
+  class TNMDistantMetastasesCategoryValidationTest < Inferno::Test
+    include CancerRegistryReportingTestKit::ValidationTest
+
+    id :ccrr_tnm_distant_metastases_category_validation_test
+    title 'Observation resources returned during previous tests conform to the mCODE TNM Distant Metastases Category profile'
+    description %(
+        This test verifies resources returned from the first search conform to
+        the [mCODE TNM Distant Metastases Category Profile](https://hl7.org/fhir/us/mcode/STU3/StructureDefinition-mcode-tnm-distant-metastases-category.html).
+        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.
+
+      )
+
+    def resource_type
+      'Observation'
+    end
+
+    def scratch_resources
+      scratch[:tnm_distant_metastases_category_resources] ||= {}
+    end
+
+    run do
+      perform_validation_test(scratch_resources[:all] || [],
+                              'http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-distant-metastases-category',
+                              '3.0.0',
+                              skip_if_empty: true)
+    end
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_distant_metastases_category_group.rb

@@ -0,0 +1,74 @@
+# frozen_string_literal: true
+
+require_relative 'tnm_distant_metastases_category/tnm_distant_metastases_category_search_test'
+require_relative 'tnm_distant_metastases_category/tnm_distant_metastases_category_must_support_test'
+require_relative 'tnm_distant_metastases_category/tnm_distant_metastases_category_validation_test'
+
+module CancerRegistryReportingTestKit
+  class EHRTNMDistantMetastasesCategoryTests < Inferno::TestGroup
+    title 'mCODE TNM Distant Metastases Category'
+    description %(
+      # Background
+      The mCODE TNM Distant Metastases Category group verifies that the system under test is
+      able to provide correct responses for TNM Distant Metastases Category Observation queries. These queries
+      return resources conforming to the [mCODE TNM Distant Metastases Category Profile](https://hl7.org/fhir/us/mcode/STU3/StructureDefinition-mcode-tnm-distant-metastases-category.html)
+      as specified in the mCODE v3.0.0 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
+
+      ### Search Parameters
+      The first search uses values from the **Patient IDs** and
+      **TNM Distant Metastases Category code** inputs as provided by the tester.
+      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 first
+      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 [mCODE TNM Distant Metastases Category Profile](https://hl7.org/fhir/us/mcode/STU3/StructureDefinition-mcode-tnm-distant-metastases-category.html).
+      Each element is checked against terminology 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.
+    )
+
+    id :ccrr_ehr_tnm_distant_metastases_category
+    run_as_group
+
+    def self.metadata
+      @metadata ||= HdeaGenerator::GroupMetadata.new(YAML.load_file(
+                                                       File.join(__dir__, 'tnm_distant_metastases_category',
+                                                                 'metadata.yml'), aliases: true
+                                                     ))
+    end
+    test from: :ccrr_tnm_distant_metastases_category_search_test
+    test from: :ccrr_tnm_distant_metastases_category_validation_test
+    test from: :ccrr_tnm_distant_metastases_category_must_support_test
+  end
+end

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_primary_tumor_category/metadata.yml

@@ -0,0 +1,64 @@
+---
+:name: mcode_tnm_primary_tumor_category
+:class_name: McodeTnmPrimaryTumorCategorySequence
+:version: v1.0.0
+:reformatted_version: v100
+:resource: Observation
+:profile_url: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-primary-tumor-category
+:profile_name: TNM Primary Tumor Category Profile
+:profile_version: 3.0.0
+:title: Observation TNM Primary Tumor Category
+:short_description: Verify support for the server capabilities required by the TNM
+  Primary Tumor Category Profile.
+:must_supports:
+  :extensions: []
+  :slices: []
+  :elements:
+  - :path: status
+  - :path: code
+  - :path: subject
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-cancer-patient
+  - :path: focus
+    :types:
+    - Reference
+    :target_profiles:
+    - http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-primary-cancer-condition
+  - :path: effective[x]
+  - :path: value[x]
+  - :path: method
+:mandatory_elements:
+- Observation.status
+- Observation.code
+- Observation.method
+- Observation.component.code
+:tests: []
+:id: ccrr_v100_mcode_tnm_primary_tumor_category
+:file_name: mcode_tnm_primary_tumor_category_group.rb
+:searches:
+- :expectation: SHALL
+  :names:
+  - patient
+  - code
+:search_definitions:
+  :patient:
+    :paths:
+    - subject
+    :full_paths:
+    - Observation.subject
+    :comparators: {}
+    :values: []
+    :type: Reference
+    :contains_multiple: false
+    :multiple_or: MAY
+  :code:
+    :paths:
+    - code
+    :full_paths:
+    - Observation.code
+    :comparators: {}
+    :type: CodeableConcept
+    :contains_multiple: true
+    :multiple_or: MAY

data/lib/cancer_registry_reporting_test_kit/ehr_suite/mcode_data_access_resources/tnm_primary_tumor_category/tnm_primary_tumor_category_must_support_test.rb

@@ -0,0 +1,44 @@
+# frozen_string_literal: true
+
+require_relative '../../../must_support_test'
+
+module CancerRegistryReportingTestKit
+  class TNMPrimaryTumorCategoryMustSupportTest < Inferno::Test
+    include CancerRegistryReportingTestKit::MustSupportTest
+
+    title 'All must support elements are provided in the TNM Primary Tumor Category Observation resources returned'
+    description %(
+      CCRR EHRs SHALL be capable of populating all data elements as
+      part of the query results. This test will look through the Observation resources
+      found previously for the following must support elements:
+
+      * Observation.category
+      * Observation.code
+      * Observation.effective[x]
+      * Observation.focus
+      * Observation.method
+      * Observation.performer
+      * Observation.status
+      * Observation.subject
+      * Observation.value[x]
+    )
+
+    id :ccrr_tnm_primary_tumor_category_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[:tnm_primary_tumor_category_resources] ||= {}
+    end
+
+    run do
+      perform_must_support_test(all_scratch_resources)
+    end
+  end
+end