at_home_in_vitro_test_kit 0.9.0

data/lib/at_home_in_vitro_test_kit/http_request_group/bundle_validator_request_group.rb

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+require_relative 'request_fhir_bundle_validation'
+require_relative 'request_fhir_bundle_entry_validation'
+require_relative 'request_receive_post'
+
+module AtHomeInVitroTestKit
+  class BundleValidatorRequestGroup< Inferno::TestGroup
+
+    title 'At-Home In-Vitro Test'
+    short_description 'Validate a FHIR Bundle and all of its nested resources.'
+    description %(
+    # Background
+  
+    The At-Home In-Vitro Test sequence verifies that
+    a At-Home In-Vitro FHIR Bundle and its entries, constructed either manually or by
+    a digital testing application, can be sent via a POST request and conforms to the resource profile
+    outlined in the [At-Home In-Vitro FHIR Implementation Guide](http://hl7.org/fhir/us/home-lab-report/ImplementationGuide/hl7.fhir.us.home-lab-report).
+  
+    # Testing Methodology
+    ## POST Request verification
+        
+    The first test in this sequence prepares the kit for POST request handling. The user will enter an input string identifier for this test session
+    and will be prompted with a message about the Inferno endpoint a POST request should be sent to. The request MUST include 'id=<INPUT VALUE>' as
+    a query parameter so the test kit can associate a POST with a particular testing session. The FHIR bundle MUST be sent as raw JSON in the body
+    of the POST request.
+
+    ## Bundle Validation
+  
+    The second test in this sequence verifies that the FHIR Bundle
+    received via POST request conforms to the specifications outlined in the
+    [At-Home In-Vitro Bundle Profile](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Bundle-at-home-in-vitro-test).
+  
+    According to the Profile description, a valid Bundle MUST contain the following elements:
+  
+    * identifier - Persistent identifier for the bundle
+    * type - fixed value code that identifies the bundle type ('message')
+    * timestamp - identifies time that the bundle was assembled
+    * entry:messageHeader - bundle entry and resource of type [MessageHeader](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/MessageHeader-at-home-in-vitro-test-results)
+  
+    While a MessageHeader entry is required for all bundles to conform, a bundle
+    may contain multiple entry resources that conform to other resource profiles outlined
+    in the IG.
+  
+    ## Entry Validation
+  
+    The third test in this sequence uses the FHIR Bundle
+    from the first test, and validates each entry resource against its
+    profile outlined in the IG. Entry types that can be validated (aside from MessageHeader) include
+    the following:
+  
+    * [Device](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Bundle-at-home-in-vitro-test)
+    * [DiagnosticSupport](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/DiagnosticReport-at-home-in-vitro-results)
+    * [Observation -At-Home In-Vitro Test Result](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Observation-at-home-in-vitro-test-result)
+    * [Observation -Pateint Question Answer](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Observation-patient-question-answer)
+    * [Patient](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Patient-at-home-in-vitro-test)
+    * [Specimen](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Specimen-at-home-in-vitro-test)
+    )
+    id :bundle_validator_request_group
+
+    run_as_group(true)
+
+    test from: :request_receive_post
+    test from: :request_fhir_bundle_validation
+    test from: :request_fhir_bundle_entry_validation
+  end
+end

data/lib/at_home_in_vitro_test_kit/http_request_group/request_fhir_bundle_entry_validation.rb

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+require_relative '../test_common/fhir_bundle_validation'
+
+module AtHomeInVitroTestKit
+    class RequestFhirBundleEntryValidation < Inferno::Test
+        include AtHomeInVitroTestKit::FhirBundleValidator
+      title 'FHIR Bundle Entry Validation'
+      description %(
+        Validate that the FHIR Bundle entries conform to their relative At-Home In-Vitro Test Report IG specifications.
+      )
+      id :request_fhir_bundle_entry_validation
+
+      uses_request :bundle
+
+      def fhir_resource
+        FHIR::Json.from_json(request.request_body)
+      end
+
+      run do
+        validate_bundle_entries(fhir_resource)
+      end
+    end
+end

data/lib/at_home_in_vitro_test_kit/http_request_group/request_fhir_bundle_validation.rb

@@ -0,0 +1,22 @@
+require_relative '../test_common/fhir_bundle_validation'
+
+module AtHomeInVitroTestKit
+    class RequestFhirBundleValidation < Inferno::Test
+        include AtHomeInVitroTestKit::FhirBundleValidator
+      title 'FHIR Bundle Validation'
+      description %(
+        Validate that the FHIR Bundle conforms to the At-Home In-Vitro Test Report IG specifications.
+      )
+      id :request_fhir_bundle_validation
+
+      uses_request :bundle
+
+      def fhir_resource
+        FHIR::Json.from_json(request.request_body);
+      end
+
+      run do
+        validate_bundle(fhir_resource)
+      end
+    end
+end

data/lib/at_home_in_vitro_test_kit/http_request_group/request_receive_post.rb

@@ -0,0 +1,35 @@
+require_relative '../test_common/fhir_bundle_validation'
+require 'inferno'
+
+module AtHomeInVitroTestKit
+    class RequestReceivePost < Inferno::Test
+        include AtHomeInVitroTestKit::FhirBundleValidator
+      title 'Receive FHIR Bundle via POST request.'
+      description %(
+        Confirm that App Server or Data Hub correctly passes a FHIR bundle to the At-Home In-Vitro test kit.
+      )
+      id :request_receive_post
+
+      input :session_id,
+            type: 'text',
+            description: 'Value used to identify test session. Whatever value is entered here MUST be included in the POST request as a query parameter.'
+
+      receives_request :bundle
+
+      run do
+        wait(
+            identifier: session_id,
+            message: %(
+                Make a request to this endpoint within the next 24 hours.
+
+                #{Inferno::Application['base_url']}/custom/at_home_test_kit/bundle?id=#{session_id}
+
+                If the test times out or is cancelled for any reason, rerunning the test group will restart the timeout.
+
+                Your request body MUST be your FHIR Bundle in raw json format. Testing will resume automatically after a valid POST is received.
+            ),
+            timeout: 86400
+        )
+      end
+    end
+end

data/lib/at_home_in_vitro_test_kit/manual_entry_group/bundle_validator_manual_entry.rb

@@ -0,0 +1,57 @@
+require_relative 'manual_fhir_bundle_validation'
+require_relative 'manual_fhir_bundle_entry_validation'
+
+module AtHomeInVitroTestKit
+  class BundleValidatorManualEntry < Inferno::TestGroup
+
+    title 'At-Home In-Vitro Manual Input Test'
+    short_description 'Validate a manually input FHIR Bundle and all of its nested resources.'
+    description %(
+      # Background
+
+      The At-Home In-Vitro Manual Input Test sequence verifies that
+      a At-Home In-Vitro FHIR Bundle and its entries, constructed either manually or by
+      a digital testing application, conforms to the resource profile
+      outlined in the [At-Home In-Vitro FHIR Implementation Guide](http://hl7.org/fhir/us/home-lab-report/ImplementationGuide/hl7.fhir.us.home-lab-report).
+
+      # Testing Methodology
+      ## Bundle Validation
+
+      The first test in this sequence verifies that the FHIR Bundle
+      taken from user input conforms to the specifications outlined in the
+      [At-Home In-Vitro Bundle Profile](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Bundle-at-home-in-vitro-test).
+
+      According to the Profile description, a valid Bundle MUST contain the following elements:
+
+      * identifier - Persistent identifier for the bundle
+      * type - fixed value code that identifies the bundle type ('message')
+      * timestamp - identifies time that the bundle was assembled
+      * entry:messageHeader - bundle entry and resource of type [MessageHeader](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/MessageHeader-at-home-in-vitro-test-results)
+
+      While as MessageHeader entry is required for all bundles to conform, a bundle
+      may contain multiple entry resources that conform to other resource profiles outlined
+      in the IG.
+
+      ## Entry Validation
+
+      The second test in this sequence uses the manualy input FHIR Bundle
+      from the first test, and validates each entry resource against its
+      profile outlined in the IG. Entry types that can be validated (aside from MessageHeader) include
+      the following:
+
+      * [Device](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Bundle-at-home-in-vitro-test)
+      * [DiagnosticSupport](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/DiagnosticReport-at-home-in-vitro-results)
+      * [Observation -At-Home In-Vitro Test Result](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Observation-at-home-in-vitro-test-result)
+      * [Observation -Pateint Question Answer](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Observation-patient-question-answer)
+      * [Patient](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Patient-at-home-in-vitro-test)
+      * [Specimen](http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Specimen-at-home-in-vitro-test)
+
+    )
+    id :bundle_validator_manual_entry
+
+    run_as_group(true)
+
+    test from: :manual_fhir_bundle_validation
+    test from: :manual_fhir_bundle_entry_validation
+  end
+end

data/lib/at_home_in_vitro_test_kit/manual_entry_group/manual_fhir_bundle_entry_validation.rb

@@ -0,0 +1,22 @@
+require_relative '../test_common/fhir_bundle_validation'
+
+module AtHomeInVitroTestKit
+    class ManualFhirBundleEntryValidation < Inferno::Test
+        include AtHomeInVitroTestKit::FhirBundleValidator
+      title 'FHIR Bundle Entry Validation'
+      description %(
+        Validate that the FHIR Bundle entries conform to their relative At-Home In-Vitro Test Report IG specifications.
+      )
+      id :manual_fhir_bundle_entry_validation
+      input :fhir_bundle
+
+      def fhir_resource
+        resource = FHIR::Json.from_json(fhir_bundle);
+        resource
+      end
+
+      run do
+        validate_bundle_entries(fhir_resource)
+      end
+    end
+end

data/lib/at_home_in_vitro_test_kit/manual_entry_group/manual_fhir_bundle_validation.rb

@@ -0,0 +1,24 @@
+require_relative '../test_common/fhir_bundle_validation'
+
+module AtHomeInVitroTestKit
+    class ManualFhirBundleValidation < Inferno::Test
+        include AtHomeInVitroTestKit::FhirBundleValidator
+      title 'FHIR Bundle Validation'
+      description %(
+        Validate that the FHIR Bundle conforms to the At-Home In-Vitro Test Report IG specification.
+      )
+      id :manual_fhir_bundle_validation
+      input :fhir_bundle,
+            type: 'textarea',
+            description: 'At-Home In-Vitro Bundle'
+
+      def fhir_resource
+        resource = FHIR::Json.from_json(fhir_bundle);
+        resource
+      end
+
+      run do
+        validate_bundle(fhir_resource)
+      end
+    end
+end

data/lib/at_home_in_vitro_test_kit/test_common/fhir_bundle_validation.rb

@@ -0,0 +1,14 @@
+
+module AtHomeInVitroTestKit
+    module FhirBundleValidator
+        def validate_bundle(resource)
+
+            assert_resource_type(:bundle, resource: resource)
+            assert_valid_resource(resource: resource, profile_url: 'http://hl7.org/fhir/us/home-lab-report/StructureDefinition/Bundle-at-home-in-vitro-test')
+        end
+
+        def validate_bundle_entries(resource)
+            assert_valid_bundle_entries(bundle: resource, resource_types: {})
+        end
+    end
+end

data/lib/at_home_in_vitro_test_kit/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module AtHomeInVitroTestKit
+    VERSION = '0.9.0'
+end

data/lib/at_home_in_vitro_test_kit.rb

@@ -0,0 +1,45 @@
+require_relative 'at_home_in_vitro_test_kit/manual_entry_group/bundle_validator_manual_entry'
+require_relative 'at_home_in_vitro_test_kit/http_request_group/bundle_validator_request_group'
+module AtHomeInVitroTestKit
+  require 'inferno'
+  class Suite < Inferno::TestSuite
+    id :at_home_test_kit
+    title 'At-Home In-Vitro Test Kit'
+    description 'An Inferno Test Kit used for validating At-Home In-Vitro FHIR Bundles and their entry resources.'
+
+    # All FHIR validation requsets will use this FHIR validator
+    validator do
+
+      url ENV.fetch('VALIDATOR_URL', 'http://validator_service:4567')
+
+      exclude_message do |message|
+        (message.type == 'warning' &&
+        message.message.match?(/Global Profile reference .* could not be resolved, so has not been checked/)) || 
+        (message.type == 'info' && message.message.match?(/.* This element does not match any known slice defined in the profile .*/))
+      end
+      
+    end
+
+    resume_test_route :post, '/bundle' do |request|
+      request.query_parameters["id"]
+    end
+
+    links [
+      {
+        label: 'Report Issue',
+        url: 'https://github.com/inferno-framework/at-home-in-vitro-test-kit/issues'
+      },
+      {
+        label: 'Open Source',
+        url: 'https://github.com/inferno-framework/at-home-in-vitro-test-kit/'
+      },
+      {
+        label: 'At-Home In-Vitro Test Report IG',
+        url: 'http://hl7.org/fhir/us/home-lab-report/STU1/'
+      }
+    ]
+
+    group from: :bundle_validator_request_group
+    group from: :bundle_validator_manual_entry
+  end
+end

metadata

@@ -0,0 +1,128 @@
+--- !ruby/object:Gem::Specification
+name: at_home_in_vitro_test_kit
+version: !ruby/object:Gem::Version
+  version: 0.9.0
+platform: ruby
+authors:
+- Inferno Team
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2023-05-04 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: inferno_core
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.4.4
+- !ruby/object:Gem::Dependency
+  name: database_cleaner-sequel
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: factory_bot
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '6.1'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.10'
+- !ruby/object:Gem::Dependency
+  name: webmock
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.11'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.11'
+description: Inferno tests for the At Home In Vitro IG
+email:
+- inferno@groups.mitre.org
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE
+- lib/at_home_in_vitro_test_kit.rb
+- lib/at_home_in_vitro_test_kit/examples/Bundle-bundle-at-home-in-vitro-test-results-p-noelle.json
+- lib/at_home_in_vitro_test_kit/examples/Bundle-bundle-at-home-in-vitro-test-results-s-trevor.json
+- lib/at_home_in_vitro_test_kit/http_request_group/bundle_validator_request_group.rb
+- lib/at_home_in_vitro_test_kit/http_request_group/request_fhir_bundle_entry_validation.rb
+- lib/at_home_in_vitro_test_kit/http_request_group/request_fhir_bundle_validation.rb
+- lib/at_home_in_vitro_test_kit/http_request_group/request_receive_post.rb
+- lib/at_home_in_vitro_test_kit/manual_entry_group/bundle_validator_manual_entry.rb
+- lib/at_home_in_vitro_test_kit/manual_entry_group/manual_fhir_bundle_entry_validation.rb
+- lib/at_home_in_vitro_test_kit/manual_entry_group/manual_fhir_bundle_validation.rb
+- lib/at_home_in_vitro_test_kit/test_common/fhir_bundle_validation.rb
+- lib/at_home_in_vitro_test_kit/version.rb
+homepage: https://github.com/inferno-framework/inferno-template
+licenses:
+- Apache-2.0
+metadata:
+  homepage_uri: https://github.com/inferno-framework/inferno-template
+  source_code_uri: https://github.com/inferno-framework/at-home-in-vitro-test-kit
+post_install_message:
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.1.2
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.3.7
+signing_key:
+specification_version: 4
+summary: Inferno tests for the At Home In Vitro IG
+test_files: []