auscvdrisk_inferno 0.1.0

data/lib/auscvdrisk/prepop/observations.rb

@@ -0,0 +1,433 @@
+require_relative '../helpers'
+
+module AusCVDRisk
+  module PrePopulation
+    class Observations < Inferno::TestGroup
+      include AusCVDRisk::Helpers
+
+      title 'Pre-population: Observations'
+      id :prepop_observations
+
+      test do
+        optional
+        title 'Server declares support for Observation patient search parameter'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          parameter_name = 'patient'
+
+          if check_search_parameter_support(capability_statement, resource_type, parameter_name)
+            pass "Server declares support for Observation search parameter: #{parameter_name}"
+          else
+            assert false, "Server does not declare support for required Observation search parameter: #{parameter_name}"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for Observation code search parameter'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          parameter_name = 'code'
+
+          if check_search_parameter_support(capability_statement, resource_type, parameter_name)
+            pass "Server declares support for Observation search parameter: #{parameter_name}"
+          else
+            assert false, "Server does not declare support for required Observation search parameter: #{parameter_name}"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for Observation status search parameter'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          parameter_name = 'status'
+
+          if check_search_parameter_support(capability_statement, resource_type, parameter_name)
+            pass "Server declares support for Observation search parameter: #{parameter_name}"
+          else
+            assert false, "Server does not declare support for required Observation search parameter: #{parameter_name}"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for Observation _count search parameter'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          parameter_name = '_count'
+
+          # Check for Observation resource specifically
+          if check_search_parameter_support(capability_statement, resource_type, parameter_name)
+            pass "Server declares support for Observation search parameter: #{parameter_name}"
+          end
+
+          # Check for global search parameters
+          if check_global_search_parameter_support(capability_statement, parameter_name)
+            pass "Server declares global support for _count search parameter"
+          else
+            assert false, "Server does not declare support for search parameter: #{parameter_name}"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for Observation _sort search parameter'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          parameter_name = '_sort'
+
+          # Check for Observation resource specifically
+          if check_search_parameter_support(capability_statement, resource_type, parameter_name)
+            pass "Server declares support for Observation search parameter: #{parameter_name}"
+          end
+
+          # Check for global search parameters
+          if check_global_search_parameter_support(capability_statement, parameter_name)
+            pass "Server declares global support for _count search parameter"
+          else
+            assert false, "Server does not declare support for search parameter: #{parameter_name}"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for Observation combined search parameters'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          required_params = %w[patient code status _count _sort]
+          combined_params = 'patient+code+status+_count+_sort'
+
+          if check_search_combination_support(capability_statement, resource_type, required_params)
+            pass "Server declares support for combined Observation search parameters: #{combined_params}"
+          else
+            assert false, "Server does not declare support for combined Observation search parameters: #{combined_params}"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Observation search with patient parameter is successful'
+
+        input :patient_id,
+              title: 'Patient ID',
+              description: 'ID of a patient resource on the server'
+
+        run do
+          skip_if patient_id.blank?, 'No patient ID provided'
+
+          search_params = "patient=#{patient_id}"
+
+          fhir_search(:observation, params: { patient: patient_id })
+
+          assert_response_status(200)
+          bundle = JSON.parse(response[:body])
+          verify_search_parameters_in_self_link(bundle, search_params)
+          pass 'Successfully searched for Observations with patient parameter'
+        end
+      end
+
+      test do
+        optional
+        title 'Observation search with code parameter is successful'
+
+        input :patient_id,
+              title: 'Patient ID',
+              description: 'ID of a patient resource on the server'
+
+        run do
+          skip_if patient_id.blank?, 'No patient ID provided'
+
+          # Using LOINC code for total cholesterol as an example
+          code = 'http://loinc.org|2093-3'
+          search_params = "code=#{code}&patient=#{patient_id}"
+
+          fhir_search(:observation, params: {
+            code: code,
+            patient: patient_id
+          })
+
+          assert_response_status(200)
+          bundle = JSON.parse(response[:body])
+          verify_search_parameters_in_self_link(bundle, search_params)
+          pass 'Successfully searched for Observations with code parameter'
+        end
+      end
+
+      test do
+        optional
+        title 'Observation search with status parameter is successful'
+
+        input :patient_id,
+              title: 'Patient ID',
+              description: 'ID of a patient resource on the server'
+
+        run do
+          skip_if patient_id.blank?, 'No patient ID provided'
+
+          status = 'final,amended,corrected'
+          search_params = "status=#{status}&patient=#{patient_id}"
+
+          fhir_search(:observation, params: {
+            status: status,
+            patient: patient_id
+          })
+
+          assert_response_status(200)
+          bundle = JSON.parse(response[:body])
+          verify_search_parameters_in_self_link(bundle, search_params)
+          pass 'Successfully searched for Observations with status parameter'
+        end
+      end
+
+      test do
+        optional
+        title 'Observation search with _count parameter is successful'
+
+        input :patient_id,
+              title: 'Patient ID',
+              description: 'ID of a patient resource on the server'
+
+        run do
+          skip_if patient_id.blank?, 'No patient ID provided'
+
+          count = 5
+          search_params = "_count=#{count}&patient=#{patient_id}"
+
+          fhir_search(:observation, params: {
+            _count: count,
+            patient: patient_id
+          })
+
+          assert_response_status(200)
+          bundle = JSON.parse(response[:body])
+          verify_search_parameters_in_self_link(bundle, search_params)
+
+          # Verify that no more than _count resources are returned
+          if bundle['entry']
+            assert bundle['entry'].length <= count, "Server returned more than #{count} resources despite _count parameter"
+          end
+
+          pass 'Successfully searched for Observations with _count parameter'
+        end
+      end
+
+      test do
+        optional
+        title 'Observation search with _sort parameter is successful'
+
+        input :patient_id,
+              title: 'Patient ID',
+              description: 'ID of a patient resource on the server'
+
+        run do
+          skip_if patient_id.blank?, 'No patient ID provided'
+
+          sort = '-date'
+          search_params = "_sort=#{sort}&patient=#{patient_id}"
+
+          fhir_search(:observation, params: {
+            _sort: sort,
+            patient: patient_id
+          })
+
+          assert_response_status(200)
+          bundle = JSON.parse(response[:body])
+          verify_search_parameters_in_self_link(bundle, search_params)
+
+          # Check if entries are sorted by date in descending order
+          if bundle['entry'] && bundle['entry'].length > 1
+            dates = bundle['entry'].map do |entry|
+              next unless entry['resource']['resourceType'] == 'Observation'
+              entry['resource']['effectiveDateTime'] ||
+                (entry['resource']['effectivePeriod'] && entry['resource']['effectivePeriod']['start']) ||
+                entry['resource']['issued']
+            end.compact
+
+            if dates.length > 1
+              is_sorted = dates.each_cons(2).all? { |a, b| a >= b }
+              assert is_sorted, 'Observations are not properly sorted by date in descending order'
+            end
+          end
+
+          pass 'Successfully searched for Observations with _sort parameter'
+        end
+      end
+
+      test do
+        optional
+        title 'Observation search with combined parameters is successful'
+
+        input :patient_id,
+              title: 'Patient ID',
+              description: 'ID of a patient resource on the server'
+
+        run do
+          skip_if patient_id.blank?, 'No patient ID provided'
+
+          # Using LOINC code for total cholesterol as an example
+          code = 'http://loinc.org|2093-3'
+          status = 'final'
+          count = 5
+          sort = '-date'
+
+          search_params = "code=#{code}&status=#{status}&_count=#{count}&_sort=#{sort}&patient=#{patient_id}"
+
+          fhir_search(:observation, params: {
+            code: code,
+            status: status,
+            _count: count,
+            _sort: sort,
+            patient: patient_id
+          })
+
+          assert_response_status(200)
+          bundle = JSON.parse(response[:body])
+          verify_search_parameters_in_self_link(bundle, search_params)
+
+          # Verify that no more than _count resources are returned
+          if bundle['entry']
+            assert bundle['entry'].length <= count, "Server returned more than #{count} resources despite _count parameter"
+
+            # Check if entries are sorted by date in descending order
+            if bundle['entry'].length > 1
+              dates = bundle['entry'].map do |entry|
+                next unless entry['resource']['resourceType'] == 'Observation'
+                entry['resource']['effectiveDateTime'] ||
+                  (entry['resource']['effectivePeriod'] && entry['resource']['effectivePeriod']['start']) ||
+                  entry['resource']['issued']
+              end.compact
+
+              if dates.length > 1
+                is_sorted = dates.each_cons(2).all? { |a, b| a >= b }
+                assert is_sorted, 'Observations are not properly sorted by date in descending order'
+              end
+            end
+          end
+
+          pass 'Successfully searched for Observations with combined parameters'
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for CVD Risk Sitting Blood Pressure profile '
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          profile_url = 'https://www.cvdcheck.org.au/fhir/StructureDefinition/CVDRiskSittingBloodPressure'
+
+          has_profile = check_capability_statement_for_profile(capability_statement, resource_type, profile_url)
+
+          if has_profile
+            pass "Server declares support for CVD Risk Sitting Blood Pressure profile"
+          else
+            assert false, "CapabilityStatement does not declare support for CVD Risk Sitting Blood Pressure profile, but this is a SHOULD requirement"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for AU Core Smoking Status profile '
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          profile_url = 'http://hl7.org.au/fhir/core/StructureDefinition/au-core-smokingstatus'
+
+          has_profile = check_capability_statement_for_profile(capability_statement, resource_type, profile_url)
+
+          if has_profile
+            pass "Server declares support for AU Core Smoking Status profile"
+          else
+            assert false, "CapabilityStatement does not declare support for AU Core Smoking Status profile, but this is a SHOULD requirement"
+          end
+        end
+      end
+
+      test do
+        optional
+        title 'Server declares support for AU Core Pathology Result profile '
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+          capability_statement = resource
+
+          resource_type = 'Observation'
+          profile_url = 'http://hl7.org.au/fhir/core/StructureDefinition/au-core-diagnosticresult-path'
+
+          has_profile = check_capability_statement_for_profile(capability_statement, resource_type, profile_url)
+
+          if has_profile
+            pass "Server declares support for AU Core Pathology Result profile"
+          else
+            assert false, "CapabilityStatement does not declare support for AU Core Pathology Result profile, but this is a SHOULD requirement"
+          end
+        end
+      end
+    end
+  end
+end

data/lib/auscvdrisk/suite.rb

@@ -0,0 +1,57 @@
+require_relative 'metadata'
+require_relative 'context'
+require_relative 'prepop/demographics'
+require_relative 'prepop/diagnoses'
+require_relative 'prepop/medications'
+require_relative 'prepop/observations'
+require_relative 'write_back'
+
+module AusCVDRisk
+  class Suite < Inferno::TestSuite
+    id :auscvdrisk_server
+    title 'Aus CVD Risk-i Server Test Suite'
+    description <<~DESCRIPTION
+      Tests conformance against the requirements for implementing a FHIR service that supports the 
+      Aus CVD Risk-i Calculator application.
+    DESCRIPTION
+
+    # These inputs will be available to all tests in this suite
+    input :url,
+          title: 'FHIR Server Base Url'
+
+    input :credentials,
+          title: 'OAuth Credentials',
+          type: :oauth_credentials,
+          optional: true
+
+    input :patient_id
+
+    # All FHIR requests in this suite will use this FHIR client
+    fhir_client do
+      url :url
+      oauth_credentials :credentials if credentials.present?
+      headers 'Prefer' => 'handling=strict'
+    end
+
+    # All FHIR validation requests will use this FHIR validator
+    fhir_resource_validator do
+      igs 'hl7.fhir.au.core#1.0.0', 'igs/auscvdrisk-Iteration3.tgz'
+
+      cli_context do
+        txServer 'https://tx.dev.hl7.org.au/fhir'
+        snomedCT '32506021000036107'
+      end
+
+      exclude_message do |message|
+        message.message.match?(/\A\S+: \S+: URL value '.*' does not resolve/)
+      end
+    end
+
+    group from: :context
+    group from: :prepop_demographics
+    group from: :prepop_diagnoses
+    group from: :prepop_medications
+    group from: :prepop_observations
+    group from: :write_back
+  end
+end

data/lib/auscvdrisk/version.rb

@@ -0,0 +1,3 @@
+module AusCVDRisk
+  VERSION = '0.1.0'.freeze
+end

data/lib/auscvdrisk/write_back.rb

@@ -0,0 +1,89 @@
+require_relative 'helpers'
+
+module AusCVDRisk
+  class WriteBack < Inferno::TestGroup
+    include AusCVDRisk::Helpers
+
+    title 'Result write-back'
+    id :write_back
+
+    test do
+      optional
+      title 'Server declares support for CVD Risk Result profile '
+
+      run do
+        fhir_get_capability_statement
+
+        assert_response_status(200)
+        assert_resource_type(:capability_statement)
+        capability_statement = resource
+
+        resource_type = 'Observation'
+        profile_url = 'https://www.cvdcheck.org.au/fhir/StructureDefinition/CVDRiskResult'
+
+        has_profile = check_capability_statement_for_profile(capability_statement, resource_type, profile_url)
+
+        assert has_profile, "CapabilityStatement does not declare support for CVD Risk Result profile"
+      end
+    end
+
+    test do
+      optional
+      title 'Server supports creating CVD Risk Result resources'
+
+      input :patient_id,
+            title: 'Patient ID',
+            description: 'ID of a patient resource on the server'
+
+      run do
+        skip_if patient_id.blank?, 'No patient ID provided'
+
+        # Create a minimal CVD Risk Result resource
+        cvd_risk_result = FHIR::Observation.new(
+          status: 'final',
+          code: {
+            coding: [
+              {
+                system: 'http://loinc.org',
+                code: '79423-0',
+                display: 'Cardiovascular disease 5 year risk score'
+              }
+            ],
+            text: 'CVD Risk Score'
+          },
+          subject: {
+            reference: "Patient/#{patient_id}"
+          },
+          valueQuantity: {
+            value: 10.5,
+            unit: '%',
+            system: 'http://unitsofmeasure.org',
+            code: '%'
+          },
+          effectiveDateTime: Time.now.strftime('%Y-%m-%dT%H:%M:%S%:z'),
+          meta: {
+            profile: ['https://www.cvdcheck.org.au/fhir/StructureDefinition/CVDRiskResult']
+          }
+        )
+
+        fhir_create(cvd_risk_result)
+
+        # Check if creation was successful (201) or already exists (200)
+        assert [200, 201].include?(response[:status]),
+               "Expected response status to be 200 or 201, but was #{response[:status]}"
+
+        # If we got a 201 Created, verify we can read the resource back
+        if response[:status] == 201
+          # Extract the ID from the Location header or the resource
+          created_id = resource&.id
+          assert created_id.present?, 'Created resource does not have an ID'
+
+          # Try to read the created resource
+          fhir_read(:observation, created_id)
+          assert_response_status(200)
+          assert_resource_type(:observation)
+        end
+      end
+    end
+  end
+end

data/lib/auscvdrisk.rb

@@ -0,0 +1 @@
+require_relative 'auscvdrisk/suite'

metadata

@@ -0,0 +1,65 @@
+--- !ruby/object:Gem::Specification
+name: auscvdrisk_inferno
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Australian e-Health Research Centre, CSIRO
+bindir: bin
+cert_chain: []
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: inferno_core
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.6.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.6.2
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/auscvdrisk.rb
+- lib/auscvdrisk/context.rb
+- lib/auscvdrisk/helpers.rb
+- lib/auscvdrisk/igs/.keep
+- lib/auscvdrisk/igs/README.md
+- lib/auscvdrisk/igs/auscvdrisk-Iteration3.tgz
+- lib/auscvdrisk/igs/put_ig_package_dot_tgz_here
+- lib/auscvdrisk/metadata.rb
+- lib/auscvdrisk/prepop/demographics.rb
+- lib/auscvdrisk/prepop/diagnoses.rb
+- lib/auscvdrisk/prepop/medications.rb
+- lib/auscvdrisk/prepop/observations.rb
+- lib/auscvdrisk/suite.rb
+- lib/auscvdrisk/version.rb
+- lib/auscvdrisk/write_back.rb
+licenses: []
+metadata:
+  inferno_test_kit: 'true'
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.3.6
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.6.7
+specification_version: 4
+summary: Aus CVD Risk-i Test Kit
+test_files: []