From d049f895d40190dcc9160805fb3908f1ebe3cc66 Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Mon, 23 Oct 2023 12:15:06 -0400
Subject: [PATCH 1/7] FI-2233: step 1, clone Inferno::DSL::FHIRValidation to
 ::FHIRResourceValidation

---
 lib/inferno/dsl.rb                            |   4 +-
 lib/inferno/dsl/fhir_resource_validation.rb   | 285 ++++++++++++++++++
 .../dsl/fhir_resource_validation_spec.rb      | 206 +++++++++++++
 3 files changed, 494 insertions(+), 1 deletion(-)
 create mode 100644 lib/inferno/dsl/fhir_resource_validation.rb
 create mode 100644 spec/inferno/dsl/fhir_resource_validation_spec.rb

diff --git a/lib/inferno/dsl.rb b/lib/inferno/dsl.rb
index b50a9cb08..712425e87 100644
--- a/lib/inferno/dsl.rb
+++ b/lib/inferno/dsl.rb
@@ -1,6 +1,7 @@
 require_relative 'dsl/assertions'
 require_relative 'dsl/fhir_client'
 require_relative 'dsl/fhir_validation'
+require_relative 'dsl/fhir_resource_validation'
 require_relative 'dsl/http_client'
 require_relative 'dsl/results'
 require_relative 'dsl/runnable'
@@ -13,7 +14,8 @@ module DSL
       FHIRClient,
       HTTPClient,
       Results,
-      FHIRValidation
+      FHIRValidation,
+      FHIRResourceValidation
     ].freeze
 
     EXTENDABLE_DSL_MODULES = [
diff --git a/lib/inferno/dsl/fhir_resource_validation.rb b/lib/inferno/dsl/fhir_resource_validation.rb
new file mode 100644
index 000000000..f4bd6cd31
--- /dev/null
+++ b/lib/inferno/dsl/fhir_resource_validation.rb
@@ -0,0 +1,285 @@
+require_relative '../ext/fhir_models'
+module Inferno
+  module DSL
+    # This module contains the methods needed to configure a validator to
+    # perform validation of FHIR resources. The actual validation is performed
+    # by an external FHIR validation service. Tests will typically rely on
+    # `assert_valid_resource` for validation rather than directly calling
+    # methods on a validator.
+    #
+    # @example
+    #
+    #   validator do
+    #     url 'http://example.com/validator'
+    #     exclude_message { |message| message.type == 'info' }
+    #     perform_additional_validation do |resource, profile_url|
+    #       if something_is_wrong
+    #         { type: 'error', message: 'something is wrong' }
+    #       else
+    #         { type: 'info', message: 'everything is ok' }
+    #       end
+    #     end
+    #   end
+    module FHIRResourceValidation
+      def self.included(klass)
+        klass.extend ClassMethods
+      end
+
+      # Perform validation, and add validation messages to the runnable
+      #
+      # @param resource [FHIR::Model]
+      # @param profile_url [String]
+      # @param validator [Symbol] the name of the validator to use
+      # @return [Boolean] whether the resource is valid
+      def resource_is_valid?(resource: self.resource, profile_url: nil, validator: :default)
+        find_validator(validator).resource_is_valid?(resource, profile_url, self)
+      end
+
+      # Find a particular validator. Looks through a runnable's parents up to
+      # the suite to find a validator with a particular name
+      def find_validator(validator_name)
+        self.class.find_validator(validator_name, suite_options)
+      end
+
+      class Validator
+        attr_reader :requirements
+
+        # @private
+        def initialize(requirements = nil, &)
+          instance_eval(&)
+          @requirements = requirements
+        end
+
+        # @private
+        def default_validator_url
+          ENV.fetch('VALIDATOR_URL')
+        end
+
+        # Set the url of the validator service
+        #
+        # @param validator_url [String]
+        def url(validator_url = nil)
+          @url = validator_url if validator_url
+
+          @url
+        end
+
+        # @private
+        def additional_validations
+          @additional_validations ||= []
+        end
+
+        # Perform validation steps in addition to FHIR validation.
+        #
+        # @example
+        #   perform_additional_validation do |resource, profile_url|
+        #     if something_is_wrong
+        #       { type: 'error', message: 'something is wrong' }
+        #     else
+        #       { type: 'info', message: 'everything is ok' }
+        #     end
+        #   end
+        # @yieldparam resource [FHIR::Model] the resource being validated
+        # @yieldparam profile_url [String] the profile the resource is being
+        #   validated against
+        # @yieldreturn [Array<Hash<Symbol, String>>,Hash<Symbol, String>] The
+        #   block should return a Hash or an Array of Hashes if any validation
+        #   messages should be added. The Hash must contain two keys: `:type`
+        #   and `:message`. `:type` can have a value of `'info'`, `'warning'`,
+        #   or `'error'`. A type of `'error'` means the resource is invalid.
+        #   `:message` contains the message string itself.
+        def perform_additional_validation(&block)
+          additional_validations << block
+        end
+
+        # @private
+        def additional_validation_messages(resource, profile_url)
+          additional_validations
+            .flat_map { |step| step.call(resource, profile_url) }
+            .select { |message| message.is_a? Hash }
+        end
+
+        # Filter out unwanted validation messages. Any messages for which the
+        # block evalutates to a truthy value will be excluded.
+        #
+        # @example
+        #   validator do
+        #     exclude_message { |message| message.type == 'info' }
+        #   end
+        # @yieldparam message [Inferno::Entities::Message]
+        def exclude_message(&block)
+          @exclude_message = block if block_given?
+          @exclude_message
+        end
+
+        # @see Inferno::DSL::FHIRResourceValidation#resource_is_valid?
+        def resource_is_valid?(resource, profile_url, runnable)
+          profile_url ||= FHIR::Definitions.resource_definition(resource.resourceType).url
+
+          begin
+            response = call_validator(resource, profile_url)
+          rescue StandardError => e
+            # This could be a complete failure to connect (validator isn't running)
+            # or a timeout (validator took too long to respond).
+            runnable.add_message('error', e.message)
+            raise Inferno::Exceptions::ErrorInValidatorException, "Unable to connect to validator at #{url}."
+          end
+          outcome = operation_outcome_from_validator_response(response.body, runnable)
+
+          message_hashes = message_hashes_from_outcome(outcome, resource, profile_url)
+
+          message_hashes
+            .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
+
+          unless response.status == 200
+            raise Inferno::Exceptions::ErrorInValidatorException,
+                  'Error occurred in the validator. Review Messages tab or validator service logs for more information.'
+          end
+
+          message_hashes
+            .none? { |message_hash| message_hash[:type] == 'error' }
+        rescue Inferno::Exceptions::ErrorInValidatorException
+          raise
+        rescue StandardError => e
+          runnable.add_message('error', e.message)
+          raise Inferno::Exceptions::ErrorInValidatorException,
+                'Error occurred in the validator. Review Messages tab or validator service logs for more information.'
+        end
+
+        # @private
+        def filter_messages(message_hashes)
+          message_hashes.reject! { |message| exclude_message.call(Entities::Message.new(message)) } if exclude_message
+        end
+
+        # @private
+        def message_hashes_from_outcome(outcome, resource, profile_url)
+          message_hashes = outcome.issue&.map { |issue| message_hash_from_issue(issue, resource) } || []
+
+          message_hashes.concat(additional_validation_messages(resource, profile_url))
+
+          filter_messages(message_hashes)
+
+          message_hashes
+        end
+
+        # @private
+        def message_hash_from_issue(issue, resource)
+          {
+            type: issue_severity(issue),
+            message: issue_message(issue, resource)
+          }
+        end
+
+        # @private
+        def issue_severity(issue)
+          case issue.severity
+          when 'warning'
+            'warning'
+          when 'information'
+            'info'
+          else
+            'error'
+          end
+        end
+
+        # @private
+        def issue_message(issue, resource)
+          location = if issue.respond_to?(:expression)
+                       issue.expression&.join(', ')
+                     else
+                       issue.location&.join(', ')
+                     end
+
+          location_prefix = resource.id ? "#{resource.resourceType}/#{resource.id}" : resource.resourceType
+
+          "#{location_prefix}: #{location}: #{issue&.details&.text}"
+        end
+
+        # Post a resource to the validation service for validating.
+        #
+        # @param resource [FHIR::Model]
+        # @param profile_url [String]
+        # @return [String] the body of the validation response
+        def validate(resource, profile_url)
+          call_validator(resource, profile_url).body
+        end
+
+        # @private
+        def call_validator(resource, profile_url)
+          Faraday.new(
+            url,
+            params: { profile: profile_url }
+          ).post('validate', resource.source_contents)
+        end
+
+        # @private
+        def operation_outcome_from_validator_response(response, runnable)
+          if response.start_with? '{'
+            FHIR::OperationOutcome.new(JSON.parse(response))
+          else
+            runnable.add_message('error', "Validator Response:\n#{response}")
+            raise Inferno::Exceptions::ErrorInValidatorException,
+                  'Validator response was an unexpected format. '\
+                  'Review Messages tab or validator service logs for more information.'
+          end
+        end
+      end
+
+      module ClassMethods
+        # @private
+        def fhir_validators
+          @fhir_validators ||= {}
+        end
+
+        # Define a validator
+        # @example
+        #   validator do
+        #     url 'http://example.com/validator'
+        #     exclude_message { |message| message.type == 'info' }
+        #     perform_additional_validation do |resource, profile_url|
+        #       if something_is_wrong
+        #         { type: 'error', message: 'something is wrong' }
+        #       else
+        #         { type: 'info', message: 'everything is ok' }
+        #       end
+        #     end
+        #   end
+        #
+        # @param name [Symbol] the name of the validator, only needed if you are
+        #   using multiple validators
+        # @param required_suite_options [Hash] suite options that must be
+        #   selected in order to use this validator
+        def validator(name = :default, required_suite_options: nil, &block)
+          current_validators = fhir_validators[name] || []
+
+          new_validator = Inferno::DSL::FHIRResourceValidation::Validator.new(required_suite_options, &block)
+
+          current_validators.reject! { |validator| validator.requirements == required_suite_options }
+          current_validators << new_validator
+
+          fhir_validators[name] = current_validators
+        end
+
+        # Find a particular validator. Looks through a runnable's parents up to
+        # the suite to find a validator with a particular name
+        def find_validator(validator_name, selected_suite_options = nil)
+          validators = fhir_validators[validator_name] ||
+                       Array.wrap(parent&.find_validator(validator_name, selected_suite_options))
+
+          validator =
+            if selected_suite_options.present?
+              validators.find do |possible_validator|
+                possible_validator.requirements.nil? || selected_suite_options >= possible_validator.requirements
+              end
+            else
+              validators.first
+            end
+
+          raise Exceptions::ValidatorNotFoundException, validator_name if validator.nil?
+
+          validator
+        end
+      end
+    end
+  end
+end
diff --git a/spec/inferno/dsl/fhir_resource_validation_spec.rb b/spec/inferno/dsl/fhir_resource_validation_spec.rb
new file mode 100644
index 000000000..8dd3a11b1
--- /dev/null
+++ b/spec/inferno/dsl/fhir_resource_validation_spec.rb
@@ -0,0 +1,206 @@
+RSpec.describe Inferno::DSL::FHIRResourceValidation do
+  let(:validation_url) { 'http://example.com' }
+  let(:profile_url) { 'PROFILE' }
+  let(:validator) do
+    Inferno::DSL::FHIRResourceValidation::Validator.new do
+      url 'http://example.com'
+    end
+  end
+  let(:runnable) do
+    Inferno::Entities::Test.new
+  end
+  let(:resource) { FHIR::Patient.new }
+
+  describe '#perform_additional_validation' do
+    before do
+      stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
+        .to_return(status: 200, body: FHIR::OperationOutcome.new.to_json)
+    end
+
+    context 'when the step does not return a hash' do
+      it 'does not add any messages to the runnable' do
+        validator.perform_additional_validation { 1 }
+        validator.perform_additional_validation { nil }
+
+        expect(validator.resource_is_valid?(resource, profile_url, runnable)).to be(true)
+        expect(runnable.messages).to eq([])
+      end
+    end
+
+    context 'when the step returns an hash' do
+      let(:extra_message) do
+        { type: 'info', message: 'INFO' }
+      end
+
+      it 'adds the messages to the runnable' do
+        validator.perform_additional_validation { extra_message }
+
+        expect(validator.resource_is_valid?(resource, profile_url, runnable)).to be(true)
+        expect(runnable.messages).to eq([extra_message])
+      end
+    end
+
+    context 'when the step returns an array of hashes' do
+      let(:extra_messages) do
+        [
+          { type: 'info', message: 'INFO' },
+          { type: 'warning', message: 'WARNING' }
+        ]
+      end
+
+      it 'adds the messages to the runnable' do
+        validator.perform_additional_validation { extra_messages }
+
+        expect(validator.resource_is_valid?(resource, profile_url, runnable)).to be(true)
+        expect(runnable.messages).to eq(extra_messages)
+      end
+    end
+
+    context 'when the step returns an error message' do
+      let(:extra_messages) do
+        [
+          { type: 'info', message: 'INFO' },
+          { type: 'error', message: 'ERROR' }
+        ]
+      end
+
+      it 'fails validation' do
+        validator.perform_additional_validation { extra_messages }
+
+        expect(validator.resource_is_valid?(resource, profile_url, runnable)).to be(false)
+        expect(runnable.messages).to eq(extra_messages)
+      end
+    end
+  end
+
+  describe '#resource_is_valid?' do
+    let(:resource_string) do
+      {
+        resourceType: 'Patient',
+        id: '0000',
+        _gender: {
+          extension: [
+            {
+              url: 'http: //hl7.org/fhir/StructureDefinition/data-absent-reason',
+              valueCode: 'unknown'
+            }
+          ]
+        }
+      }.to_json
+    end
+    let(:resource) { FHIR.from_contents(resource_string) }
+
+    context 'with invalid resource' do
+      let(:invalid_outcome) do
+        {
+          resourceType: 'OperationOutcome',
+          issue: [
+            {
+              severity: 'error',
+              code: 'processing',
+              diagnostics: 'Identifier.system must be an absolute reference, not a local reference',
+              location: [
+                'Patient.identifier[0]',
+                'Line 14, Col 10'
+              ]
+            }
+          ]
+        }.to_json
+      end
+
+      before do
+        stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
+          .with(body: resource_string)
+          .to_return(status: 200, body: invalid_outcome)
+      end
+
+      it 'includes resourceType/id in error message' do
+        result = validator.resource_is_valid?(resource, profile_url, runnable)
+
+        expect(result).to be(false)
+        expect(runnable.messages.first[:message]).to start_with("#{resource.resourceType}/#{resource.id}:")
+      end
+
+      it 'includes resourceType in error message if resource.id is nil' do
+        resource.id = nil
+        result = validator.resource_is_valid?(resource, profile_url, runnable)
+
+        expect(result).to be(false)
+        expect(runnable.messages.first[:message]).to start_with("#{resource.resourceType}:")
+      end
+    end
+
+    context 'with error from validator' do
+      let(:error_outcome) do
+        {
+          resourceType: 'OperationOutcome',
+          issue: [
+            {
+              severity: 'fatal',
+              code: 'structure',
+              diagnostics: 'Validator still warming up... Please wait',
+              details: {
+                text: 'Validator still warming up... Please wait'
+              }
+            }
+          ]
+        }.to_json
+      end
+
+      it 'throws ErrorInValidatorException when validator not ready yet' do
+        stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
+          .with(body: resource_string)
+          .to_return(status: 503, body: error_outcome)
+
+        expect do
+          validator.resource_is_valid?(resource, profile_url, runnable)
+        end.to raise_error(Inferno::Exceptions::ErrorInValidatorException)
+        expect(runnable.messages.first[:message]).to include('Validator still warming up... Please wait')
+      end
+
+      it 'throws ErrorInValidatorException for non-JSON response' do
+        stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
+          .with(body: resource_string)
+          .to_return(status: 500, body: '<html><body>Internal Server Error</body></html>')
+
+        expect do
+          validator.resource_is_valid?(resource, profile_url, runnable)
+        end.to raise_error(Inferno::Exceptions::ErrorInValidatorException)
+      end
+    end
+
+    it 'posts the resource with primitive extensions intact' do
+      stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
+        .with(body: resource_string)
+        .to_return(status: 200, body: FHIR::OperationOutcome.new.to_json)
+
+      expect(validator.resource_is_valid?(resource, profile_url, runnable)).to be(true)
+    end
+  end
+
+  describe '.find_validator' do
+    it 'finds the correct validator based on suite options' do
+      suite = OptionsSuite::Suite
+
+      v1_validator = suite.find_validator(:default, ig_version: '1')
+      v2_validator = suite.find_validator(:default, ig_version: '2')
+
+      expect(v1_validator.url).to eq('v1_validator')
+      expect(v2_validator.url).to eq('v2_validator')
+    end
+  end
+
+  describe '#find_validator' do
+    it 'finds the correct validator based on suite options' do
+      test_class = OptionsSuite::Suite.groups.first.tests.first
+      v1_test = test_class.new(suite_options: { ig_version: '1' })
+      v2_test = test_class.new(suite_options: { ig_version: '2' })
+
+      v1_validator = v1_test.find_validator(:default)
+      v2_validator = v2_test.find_validator(:default)
+
+      expect(v1_validator.url).to eq('v1_validator')
+      expect(v2_validator.url).to eq('v2_validator')
+    end
+  end
+end

From 1f5b4672fd743be75c15e699d3a7c7d2a1cc900c Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Tue, 24 Oct 2023 12:42:40 -0400
Subject: [PATCH 2/7] reapply changed from PoC

---
 lib/inferno/dsl/fhir_resource_validation.rb | 64 ++++++++++++++++++---
 1 file changed, 56 insertions(+), 8 deletions(-)

diff --git a/lib/inferno/dsl/fhir_resource_validation.rb b/lib/inferno/dsl/fhir_resource_validation.rb
index f4bd6cd31..0fb08dd65 100644
--- a/lib/inferno/dsl/fhir_resource_validation.rb
+++ b/lib/inferno/dsl/fhir_resource_validation.rb
@@ -64,6 +64,15 @@ def url(validator_url = nil)
           @url
         end
 
+        # Set the IGs that the validator will need to load
+        # Example: ["hl7.fhir.us.core#4.0.0"]
+        # @param igs [Array<String>]
+        def igs(validator_igs = nil)
+          @igs = validator_igs if validator_igs
+
+          @igs
+        end
+
         # @private
         def additional_validations
           @additional_validations ||= []
@@ -124,7 +133,7 @@ def resource_is_valid?(resource, profile_url, runnable)
             runnable.add_message('error', e.message)
             raise Inferno::Exceptions::ErrorInValidatorException, "Unable to connect to validator at #{url}."
           end
-          outcome = operation_outcome_from_validator_response(response.body, runnable)
+          outcome = operation_outcome_from_validator_response(response, runnable)
 
           message_hashes = message_hashes_from_outcome(outcome, resource, profile_url)
 
@@ -195,6 +204,31 @@ def issue_message(issue, resource)
           "#{location_prefix}: #{location}: #{issue&.details&.text}"
         end
 
+        # @private
+        def wrap_resource_for_hl7_wrapper(resource, profile_url)
+          wrapped_resource = {
+            cliContext: {
+              # TODO: these should be configurable as well
+              sv: '4.0.1',
+              # displayWarnings: true,  # -display-issues-are-warnings
+              # txServer: nil,          # -tx n/a
+              igs: @igs || [],
+              # NOTE: this profile must be part of a loaded IG,
+              # otherwise the response is an HTTP 500 with no content
+              profiles: [profile_url]
+            },
+            filesToValidate: [
+              {
+                fileName: 'manually_entered_file.json',
+                fileContent: resource.to_json,
+                fileType: 'json'
+              }
+            ],
+            sessionId: @session_id
+          }
+          wrapped_resource.to_json
+        end
+
         # Post a resource to the validation service for validating.
         #
         # @param resource [FHIR::Model]
@@ -206,18 +240,32 @@ def validate(resource, profile_url)
 
         # @private
         def call_validator(resource, profile_url)
-          Faraday.new(
-            url,
-            params: { profile: profile_url }
-          ).post('validate', resource.source_contents)
+          request_body = wrap_resource_for_hl7_wrapper(resource, profile_url)
+          response = Faraday.new(
+            url
+          ).post('validate', request_body, content_type: 'application/json')
+        end
+
+        # @private
+        def operation_outcome_from_hl7_wrapped_response(response)
+          res = JSON.parse(response)
+
+          @session_id = res['sessionId']
+
+          # assume for now that one resource -> one request
+          issues = res['outcomes'][0]['issues']&.map do |i|
+            { severity: i['level'].downcase, expression: i['location'], details: { text: i['message'] } }
+          end
+          # this is circuitous, ideally we would map this response directly to message_hashes
+          FHIR::OperationOutcome.new(issue: issues)
         end
 
         # @private
         def operation_outcome_from_validator_response(response, runnable)
-          if response.start_with? '{'
-            FHIR::OperationOutcome.new(JSON.parse(response))
+          if response.body.start_with? '{'
+            operation_outcome_from_hl7_wrapped_response(response.body)
           else
-            runnable.add_message('error', "Validator Response:\n#{response}")
+            runnable.add_message('error', "Validator Response: HTTP #{response.status}\n#{response.body}")
             raise Inferno::Exceptions::ErrorInValidatorException,
                   'Validator response was an unexpected format. '\
                   'Review Messages tab or validator service logs for more information.'

From 1e898f2abf3e0c00f83cae7df3ee640314aa3e8a Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Wed, 25 Oct 2023 12:36:03 -0400
Subject: [PATCH 3/7] update unit tests

---
 lib/inferno/dsl.rb                            |   3 +-
 lib/inferno/dsl/fhir_resource_validation.rb   |   2 +-
 .../dsl/fhir_resource_validation_spec.rb      | 134 ++++++++----------
 3 files changed, 65 insertions(+), 74 deletions(-)

diff --git a/lib/inferno/dsl.rb b/lib/inferno/dsl.rb
index 712425e87..8730d6ca6 100644
--- a/lib/inferno/dsl.rb
+++ b/lib/inferno/dsl.rb
@@ -14,8 +14,7 @@ module DSL
       FHIRClient,
       HTTPClient,
       Results,
-      FHIRValidation,
-      FHIRResourceValidation
+      FHIRValidation
     ].freeze
 
     EXTENDABLE_DSL_MODULES = [
diff --git a/lib/inferno/dsl/fhir_resource_validation.rb b/lib/inferno/dsl/fhir_resource_validation.rb
index 0fb08dd65..3b4b74bf9 100644
--- a/lib/inferno/dsl/fhir_resource_validation.rb
+++ b/lib/inferno/dsl/fhir_resource_validation.rb
@@ -241,7 +241,7 @@ def validate(resource, profile_url)
         # @private
         def call_validator(resource, profile_url)
           request_body = wrap_resource_for_hl7_wrapper(resource, profile_url)
-          response = Faraday.new(
+          Faraday.new(
             url
           ).post('validate', request_body, content_type: 'application/json')
         end
diff --git a/spec/inferno/dsl/fhir_resource_validation_spec.rb b/spec/inferno/dsl/fhir_resource_validation_spec.rb
index 8dd3a11b1..13382cc21 100644
--- a/spec/inferno/dsl/fhir_resource_validation_spec.rb
+++ b/spec/inferno/dsl/fhir_resource_validation_spec.rb
@@ -13,8 +13,18 @@
 
   describe '#perform_additional_validation' do
     before do
-      stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
-        .to_return(status: 200, body: FHIR::OperationOutcome.new.to_json)
+      stub_request(:post, "#{validation_url}/validate")
+        .to_return(status: 200, body: {
+          outcomes: [{
+            fileInfo: {
+              fileName: 'manually_entered_file.json',
+              fileContent: resource.to_json,
+              fileType: 'json'
+            },
+            issues: []
+          }],
+          sessionId: '5c7f903b-7e46-4e83-bdc9-0248ad2ba5f5'
+        }.to_json)
     end
 
     context 'when the step does not return a hash' do
@@ -88,93 +98,75 @@
         }
       }.to_json
     end
-    let(:resource) { FHIR.from_contents(resource_string) }
+    let(:resource2) { FHIR.from_contents(resource_string) }
+
+    let(:wrapped_resource_string) do
+      {
+        cliContext: {
+          sv: '4.0.1',
+          igs: [],
+          profiles: [profile_url]
+        },
+        filesToValidate: [
+          {
+            fileName: 'manually_entered_file.json',
+            fileContent: resource2.to_json,
+            fileType: 'json'
+          }
+        ],
+        sessionId: nil
+      }.to_json
+    end
 
     context 'with invalid resource' do
       let(:invalid_outcome) do
         {
-          resourceType: 'OperationOutcome',
-          issue: [
-            {
-              severity: 'error',
-              code: 'processing',
-              diagnostics: 'Identifier.system must be an absolute reference, not a local reference',
-              location: [
-                'Patient.identifier[0]',
-                'Line 14, Col 10'
-              ]
-            }
-          ]
+          outcomes: [{
+            fileInfo: {
+              fileName: 'manually_entered_file.json',
+              fileContent: resource_string.to_json,
+              fileType: 'json'
+            },
+            issues: [{
+              source: 'InstanceValidator',
+              line: 4,
+              col: 4,
+              location: 'Patient.identifier[0]',
+              message: 'Identifier.system must be an absolute reference, not a local reference',
+              messageId: 'Type_Specific_Checks_DT_Identifier_System',
+              type: 'CODEINVALID',
+              level: 'ERROR',
+              html: 'Identifier.system must be an absolute reference, not a local reference',
+              display: 'ERROR: Patient.identifier[0]: Identifier.system must be an absolute reference, ',
+              error: true
+            }]
+          }],
+          sessionId: 'b8cf5547-1dc7-4714-a797-dc2347b93fe2'
         }.to_json
       end
 
       before do
-        stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
-          .with(body: resource_string)
+        stub_request(:post, "#{validation_url}/validate")
+          .with(body: wrapped_resource_string)
           .to_return(status: 200, body: invalid_outcome)
       end
 
       it 'includes resourceType/id in error message' do
-        result = validator.resource_is_valid?(resource, profile_url, runnable)
+        result = validator.resource_is_valid?(resource2, profile_url, runnable)
 
         expect(result).to be(false)
-        expect(runnable.messages.first[:message]).to start_with("#{resource.resourceType}/#{resource.id}:")
-      end
-
-      it 'includes resourceType in error message if resource.id is nil' do
-        resource.id = nil
-        result = validator.resource_is_valid?(resource, profile_url, runnable)
-
-        expect(result).to be(false)
-        expect(runnable.messages.first[:message]).to start_with("#{resource.resourceType}:")
-      end
-    end
-
-    context 'with error from validator' do
-      let(:error_outcome) do
-        {
-          resourceType: 'OperationOutcome',
-          issue: [
-            {
-              severity: 'fatal',
-              code: 'structure',
-              diagnostics: 'Validator still warming up... Please wait',
-              details: {
-                text: 'Validator still warming up... Please wait'
-              }
-            }
-          ]
-        }.to_json
-      end
-
-      it 'throws ErrorInValidatorException when validator not ready yet' do
-        stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
-          .with(body: resource_string)
-          .to_return(status: 503, body: error_outcome)
-
-        expect do
-          validator.resource_is_valid?(resource, profile_url, runnable)
-        end.to raise_error(Inferno::Exceptions::ErrorInValidatorException)
-        expect(runnable.messages.first[:message]).to include('Validator still warming up... Please wait')
-      end
-
-      it 'throws ErrorInValidatorException for non-JSON response' do
-        stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
-          .with(body: resource_string)
-          .to_return(status: 500, body: '<html><body>Internal Server Error</body></html>')
-
-        expect do
-          validator.resource_is_valid?(resource, profile_url, runnable)
-        end.to raise_error(Inferno::Exceptions::ErrorInValidatorException)
+        expect(runnable.messages.first[:message]).to start_with("#{resource2.resourceType}/#{resource2.id}:")
       end
     end
 
-    it 'posts the resource with primitive extensions intact' do
-      stub_request(:post, "#{validation_url}/validate?profile=#{profile_url}")
-        .with(body: resource_string)
-        .to_return(status: 200, body: FHIR::OperationOutcome.new.to_json)
+    it 'throws ErrorInValidatorException for non-JSON response' do
+      stub_request(:post, "#{validation_url}/validate")
+        .with(body: wrapped_resource_string)
+        .to_return(status: 500, body: '<html><body>Internal Server Error</body></html>')
 
-      expect(validator.resource_is_valid?(resource, profile_url, runnable)).to be(true)
+      expect do
+        validator.resource_is_valid?(resource2, profile_url, runnable)
+      end.to raise_error(Inferno::Exceptions::ErrorInValidatorException)
     end
   end
 

From 431e1ff8456f78a58de44df451bf097e158b8fed Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Fri, 27 Oct 2023 10:15:54 -0400
Subject: [PATCH 4/7] wire everything up

---
 docker-compose.background.yml               |  7 ++++
 lib/inferno/dsl.rb                          |  3 +-
 lib/inferno/dsl/fhir_resource_validation.rb | 43 ++-------------------
 lib/inferno/entities/test_suite.rb          |  1 +
 4 files changed, 14 insertions(+), 40 deletions(-)

diff --git a/docker-compose.background.yml b/docker-compose.background.yml
index 33e8ff536..5647e552e 100644
--- a/docker-compose.background.yml
+++ b/docker-compose.background.yml
@@ -28,3 +28,10 @@ services:
     volumes:
       - ./data/redis:/data
     command: redis-server --appendonly yes
+  # hl7_validator_service:
+  #   image: markiantorno/validator-wrapper
+  #   # Update this path to match your directory structure
+  #   volumes:
+  #     - ./igs:/home/igs
+  #   ports:
+  #     - "3500:3500"
\ No newline at end of file
diff --git a/lib/inferno/dsl.rb b/lib/inferno/dsl.rb
index 8730d6ca6..712425e87 100644
--- a/lib/inferno/dsl.rb
+++ b/lib/inferno/dsl.rb
@@ -14,7 +14,8 @@ module DSL
       FHIRClient,
       HTTPClient,
       Results,
-      FHIRValidation
+      FHIRValidation,
+      FHIRResourceValidation
     ].freeze
 
     EXTENDABLE_DSL_MODULES = [
diff --git a/lib/inferno/dsl/fhir_resource_validation.rb b/lib/inferno/dsl/fhir_resource_validation.rb
index 3b4b74bf9..87a01bfcb 100644
--- a/lib/inferno/dsl/fhir_resource_validation.rb
+++ b/lib/inferno/dsl/fhir_resource_validation.rb
@@ -25,22 +25,6 @@ def self.included(klass)
         klass.extend ClassMethods
       end
 
-      # Perform validation, and add validation messages to the runnable
-      #
-      # @param resource [FHIR::Model]
-      # @param profile_url [String]
-      # @param validator [Symbol] the name of the validator to use
-      # @return [Boolean] whether the resource is valid
-      def resource_is_valid?(resource: self.resource, profile_url: nil, validator: :default)
-        find_validator(validator).resource_is_valid?(resource, profile_url, self)
-      end
-
-      # Find a particular validator. Looks through a runnable's parents up to
-      # the suite to find a validator with a particular name
-      def find_validator(validator_name)
-        self.class.find_validator(validator_name, suite_options)
-      end
-
       class Validator
         attr_reader :requirements
 
@@ -242,7 +226,8 @@ def validate(resource, profile_url)
         def call_validator(resource, profile_url)
           request_body = wrap_resource_for_hl7_wrapper(resource, profile_url)
           Faraday.new(
-            url
+            url,
+            request: { timeout: 600 }
           ).post('validate', request_body, content_type: 'application/json')
         end
 
@@ -281,7 +266,7 @@ def fhir_validators
 
         # Define a validator
         # @example
-        #   validator do
+        #   fhir_resource_validator do
         #     url 'http://example.com/validator'
         #     exclude_message { |message| message.type == 'info' }
         #     perform_additional_validation do |resource, profile_url|
@@ -297,7 +282,7 @@ def fhir_validators
         #   using multiple validators
         # @param required_suite_options [Hash] suite options that must be
         #   selected in order to use this validator
-        def validator(name = :default, required_suite_options: nil, &block)
+        def fhir_resource_validator(name = :default, required_suite_options: nil, &block)
           current_validators = fhir_validators[name] || []
 
           new_validator = Inferno::DSL::FHIRResourceValidation::Validator.new(required_suite_options, &block)
@@ -307,26 +292,6 @@ def validator(name = :default, required_suite_options: nil, &block)
 
           fhir_validators[name] = current_validators
         end
-
-        # Find a particular validator. Looks through a runnable's parents up to
-        # the suite to find a validator with a particular name
-        def find_validator(validator_name, selected_suite_options = nil)
-          validators = fhir_validators[validator_name] ||
-                       Array.wrap(parent&.find_validator(validator_name, selected_suite_options))
-
-          validator =
-            if selected_suite_options.present?
-              validators.find do |possible_validator|
-                possible_validator.requirements.nil? || selected_suite_options >= possible_validator.requirements
-              end
-            else
-              validators.first
-            end
-
-          raise Exceptions::ValidatorNotFoundException, validator_name if validator.nil?
-
-          validator
-        end
       end
     end
   end
diff --git a/lib/inferno/entities/test_suite.rb b/lib/inferno/entities/test_suite.rb
index 20af6108b..64f3225ca 100644
--- a/lib/inferno/entities/test_suite.rb
+++ b/lib/inferno/entities/test_suite.rb
@@ -13,6 +13,7 @@ class TestSuite
       extend DSL::FHIRClient::ClassMethods
       extend DSL::HTTPClient::ClassMethods
       include DSL::FHIRValidation
+      include DSL::FHIRResourceValidation
 
       class << self
         extend Forwardable

From 8ff081bda7e6a89a0a332f89b54e0cda0d95352e Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Mon, 6 Nov 2023 16:06:13 -0500
Subject: [PATCH 5/7] added commented-out nginx conf for hl7 validator endpoint

---
 config/nginx.background.conf  | 18 ++++++++++++++++++
 docker-compose.background.yml |  6 +++---
 2 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/config/nginx.background.conf b/config/nginx.background.conf
index f89747207..f69287fd1 100644
--- a/config/nginx.background.conf
+++ b/config/nginx.background.conf
@@ -82,5 +82,23 @@ http {
 
       proxy_pass http://validator_service:4567/;
     }
+
+# To enable the HL7 Validator Wrapper, both the section below and
+# the section in docker-compose.background.yml need to be uncommented
+#    location /hl7validatorapi/ {
+#      proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+#      proxy_set_header Host $http_host;
+#      proxy_set_header X-Forwarded-Proto $scheme;
+#      proxy_set_header X-Forwarded-Port $server_port;
+#      proxy_redirect off;
+#      proxy_set_header Connection '';
+#      proxy_http_version 1.1;
+#      chunked_transfer_encoding off;
+#      proxy_buffering off;
+#      proxy_cache off;
+#      proxy_read_timeout 600s;
+#
+#      proxy_pass http://hl7_validator_service:3500/;
+#    }
   }
 }
diff --git a/docker-compose.background.yml b/docker-compose.background.yml
index 5647e552e..c03de0b16 100644
--- a/docker-compose.background.yml
+++ b/docker-compose.background.yml
@@ -28,10 +28,10 @@ services:
     volumes:
       - ./data/redis:/data
     command: redis-server --appendonly yes
+  # To enable the HL7 Validator Wrapper, both the section below and
+  # the section in nginx.background.conf need to be uncommented
   # hl7_validator_service:
   #   image: markiantorno/validator-wrapper
   #   # Update this path to match your directory structure
   #   volumes:
-  #     - ./igs:/home/igs
-  #   ports:
-  #     - "3500:3500"
\ No newline at end of file
+  #     - ./igs:/home/igs
\ No newline at end of file

From f274aeed9f57b1d9eb0cd743a93845f27f469cd9 Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Fri, 10 Nov 2023 13:56:28 -0500
Subject: [PATCH 6/7] review feedback

---
 .env                                        | 1 +
 lib/inferno/dsl/fhir_resource_validation.rb | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.env b/.env
index 99ea9dc05..fa0d6327f 100644
--- a/.env
+++ b/.env
@@ -2,6 +2,7 @@
 VALIDATOR_URL=http://localhost/validatorapi
 REDIS_URL=redis://localhost:6379/0
 G10_VALIDATOR_URL=http://localhost/validatorapi
+FHIR_RESOURCE_VALIDATOR_URL=http://localhost/hl7validatorapi
 
 # The base path where inferno will be hosted. Leave blank to host inferno at the
 # root of its host.
diff --git a/lib/inferno/dsl/fhir_resource_validation.rb b/lib/inferno/dsl/fhir_resource_validation.rb
index 87a01bfcb..3d9d5bb03 100644
--- a/lib/inferno/dsl/fhir_resource_validation.rb
+++ b/lib/inferno/dsl/fhir_resource_validation.rb
@@ -36,7 +36,7 @@ def initialize(requirements = nil, &)
 
         # @private
         def default_validator_url
-          ENV.fetch('VALIDATOR_URL')
+          ENV.fetch('FHIR_RESOURCE_VALIDATOR_URL')
         end
 
         # Set the url of the validator service
@@ -203,7 +203,7 @@ def wrap_resource_for_hl7_wrapper(resource, profile_url)
             },
             filesToValidate: [
               {
-                fileName: 'manually_entered_file.json',
+                fileName: "#{resource.resourceType}/#{resource.id}.json",
                 fileContent: resource.to_json,
                 fileType: 'json'
               }

From 106656d8cc69714f758d9a39356760196afb3ecb Mon Sep 17 00:00:00 2001
From: Dylan Hall <dehall@mitre.org>
Date: Fri, 10 Nov 2023 14:28:06 -0500
Subject: [PATCH 7/7] update tests with new validator filename format

---
 spec/inferno/dsl/fhir_resource_validation_spec.rb | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/spec/inferno/dsl/fhir_resource_validation_spec.rb b/spec/inferno/dsl/fhir_resource_validation_spec.rb
index 13382cc21..e039452bb 100644
--- a/spec/inferno/dsl/fhir_resource_validation_spec.rb
+++ b/spec/inferno/dsl/fhir_resource_validation_spec.rb
@@ -17,7 +17,7 @@
         .to_return(status: 200, body: {
           outcomes: [{
             fileInfo: {
-              fileName: 'manually_entered_file.json',
+              fileName: 'Patient/id.json',
               fileContent: resource.to_json,
               fileType: 'json'
             },
@@ -109,7 +109,7 @@
         },
         filesToValidate: [
           {
-            fileName: 'manually_entered_file.json',
+            fileName: 'Patient/0000.json',
             fileContent: resource2.to_json,
             fileType: 'json'
           }
@@ -123,7 +123,7 @@
         {
           outcomes: [{
             fileInfo: {
-              fileName: 'manually_entered_file.json',
+              fileName: 'Patient/0000.json',
               fileContent: resource_string.to_json,
               fileType: 'json'
             },