Merge branch 'main' into add_json_files_to_gemspec

.env

@@ -3,6 +3,7 @@ VALIDATOR_URL=http://localhost/validatorapi
 REDIS_URL=redis://localhost:6379/0
 G10_VALIDATOR_URL=http://localhost/validatorapi
 FHIR_RESOURCE_VALIDATOR_URL=http://localhost/hl7validatorapi
+FHIRPATH_URL=http://localhost:6789
 
 # The base path where inferno will be hosted. Leave blank to host inferno at the
 # root of its host.

.env.test

@@ -1,3 +1,4 @@
 LOAD_DEV_SUITES=dev_*
 VALIDATOR_URL=https://example.com/validatorapi
 ASYNC_JOBS=false
+FHIRPATH_URL=https://example.com/fhirpath

CHANGELOG.md

@@ -1,3 +1,14 @@
+## 0.4.40
+* Update README content; fix broken links and improve generally. by @arscan in https://github.com/inferno-framework/inferno-core/pull/511
+* FI-2863: Added support for auth_info to fhir_client by @vanessuniq in https://github.com/inferno-framework/inferno-core/pull/512
+* FI-2865: FHIR Client Auth Info Refresh by @vanessuniq in https://github.com/inferno-framework/inferno-core/pull/513
+* FI-2910: Host JWKS for Client Assertion by @vanessuniq in https://github.com/inferno-framework/inferno-core/pull/515
+* FI-2857: Add auth input option by @AlyssaWang in https://github.com/inferno-framework/inferno-core/pull/514
+* FI-2990: Fix typo in Request Details Modal by @AlyssaWang in https://github.com/inferno-framework/inferno-core/pull/519
+* FI-2728: Prevent Test Runner from Crashing When Validator Response Contains Bad Characters by @vanessuniq in https://github.com/inferno-framework/inferno-core/pull/518
+* Fi-1930:  Custom Result Rollup by @vanessuniq in https://github.com/inferno-framework/inferno-core/pull/516
+* FI-2750:  Add FHIRPath Support by @vanessuniq in https://github.com/inferno-framework/inferno-core/pull/520
+
 ## 0.4.39
 * FI-2836: Fix double requests from suite endpoints by @Jammjammjamm in https://github.com/inferno-framework/inferno-core/pull/505
 * Bump braces from 3.0.2 to 3.0.3 by @dependabot in https://github.com/inferno-framework/inferno-core/pull/506

Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    inferno_core (0.4.39)
+    inferno_core (0.4.40)
       activesupport (~> 6.1.7.5)
       base62-rb (= 0.3.1)
       blueprinter (= 0.25.2)
@@ -106,7 +106,7 @@ GEM
     faraday-httpclient (1.0.1)
     faraday-multipart (1.0.4)
       multipart-post (~> 2)
-    faraday-net_http (1.0.1)
+    faraday-net_http (1.0.2)
     faraday-net_http_persistent (1.2.0)
     faraday-patron (1.0.0)
     faraday-rack (1.0.0)
@@ -156,7 +156,7 @@ GEM
     hansi (0.2.1)
     hashdiff (1.0.1)
     http-accept (1.7.0)
-    http-cookie (1.0.6)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     i18n (1.12.0)
       concurrent-ruby (~> 1.0)
@@ -170,7 +170,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0604)
+    mime-types-data (3.2024.0903)
     minitest (5.18.0)
     multi_json (1.15.0)
     multi_xml (0.7.1)
@@ -183,11 +183,11 @@ GEM
       mustermann (= 1.1.2)
     netrc (0.11.0)
     nio4r (2.7.3)
-    nokogiri (1.16.6-arm64-darwin)
+    nokogiri (1.16.7-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.6-x86_64-darwin)
+    nokogiri (1.16.7-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.6-x86_64-linux)
+    nokogiri (1.16.7-x86_64-linux)
       racc (~> 1.4)
     oauth2 (1.4.11)
       faraday (>= 0.17.3, < 3.0)
@@ -210,7 +210,7 @@ GEM
     public_suffix (4.0.7)
     puma (5.6.8)
       nio4r (~> 2.0)
-    racc (1.8.0)
+    racc (1.8.1)
     rack (2.2.9)
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
@@ -286,7 +286,7 @@ GEM
     strings-ansi (0.2.0)
     strscan (3.1.0)
     thor (1.2.2)
-    tilt (2.3.0)
+    tilt (2.4.0)
     tty-color (0.6.0)
     tty-markdown (0.7.2)
       kramdown (>= 1.16.2, < 3.0)

docker-compose.background.yml

@@ -36,3 +36,7 @@ services:
       # To let the service share your local FHIR package cache,
       # uncomment the below line
       # - ~/.fhir:/home/ktor/.fhir
+  fhirpath:
+    image: infernocommunity/fhirpath-service
+    ports:
+      - "6789:6789"

lib/inferno/dsl.rb

@@ -2,6 +2,7 @@
 require_relative 'dsl/fhir_client'
 require_relative 'dsl/fhir_validation'
 require_relative 'dsl/fhir_resource_validation'
+require_relative 'dsl/fhirpath_evaluation'
 require_relative 'dsl/http_client'
 require_relative 'dsl/results'
 require_relative 'dsl/runnable'
@@ -18,6 +19,7 @@ module DSL
       Results,
       FHIRValidation,
       FHIRResourceValidation,
+      FhirpathEvaluation,
       Messages
     ].freeze
 

lib/inferno/dsl/fhirpath_evaluation.rb

@@ -0,0 +1,121 @@
+module Inferno
+  module DSL
+    # This module contains the methods needed to perform FHIRPath evaluations
+    # on FHIR resources/elements. The actual evaluation is typically performed by an external
+    # FHIRPath evaluation service.
+    #
+    # Tests can leverage the evaluation functionality by  calling `evaluate_fhirpath` to retrieve
+    # results of FHIRPath expressions.
+    #
+    # @example
+    #
+    #   results = evaluate_fhirpath(resource: patient_resource, path: 'Patient.name.given')
+    #
+    # results will be an array representing the result of evaluating the given
+    # expression against the given root element.  Each "result" in the returned
+    # array will be in the form
+    # `{ "type": "[FHIR datatype of the result]", "element": "[result value of the FHIRPath expression]" }`.
+    # @note the `element` field can either be a primitive value (string, boolean, etc.) or a FHIR::Model.
+    module FhirpathEvaluation
+      def self.included(klass)
+        klass.extend ClassMethods
+      end
+
+      # Evaluates a fhirpath expression for a given FHIR resource
+      #
+      # @param resource [FHIR::Model] the root FHIR resource to use when evaluating the fhirpath expression.
+      # @param path [String] The FHIRPath expression to evaluate.
+      # @param url [String] the url of the fhirpath service to use.
+      # @return [Array<Hash>] An array of hashes representing the result of evaluating the given expression against
+      #   the given root resource.
+      def evaluate_fhirpath(resource:, path:, url: nil)
+        self.class.evaluator(url).evaluate_fhirpath(resource, path, self)
+      end
+
+      class Evaluator
+        # @private
+        def initialize(url = nil)
+          url(url)
+        end
+
+        # @private
+        def default_fhirpath_url
+          ENV.fetch('FHIRPATH_URL')
+        end
+
+        # Set/Get the url of the fhirpath service
+        #
+        # @param fhirpath_url [String]
+        # @return [String]
+        def url(fhirpath_url = nil)
+          @url ||= fhirpath_url || default_fhirpath_url
+        end
+
+        # Evaluates a fhirpath expression for a given FHIR resource
+        #
+        # @param fhir_resource [FHIR::Model] the root FHIR resource to use when evaluating the fhirpath expression.
+        # @param fhirpath_expression [String] The FHIRPath expression to evaluate.
+        # @param runnable [Inferno::Test] to add any error message that occurs.
+        # @return [Array<Hash>] An array hashes representing the result of evaluating the given expression against
+        #   the given root resource. Each "result" in the returned array will be in the form
+        #   `{ "type": "[FHIR datatype of the result]", "element": "[result value of the FHIRPath expression]" }`.
+        # @note the `element` field can either be a primitive value (string, boolean, etc.) or a FHIR::Model.
+        def evaluate_fhirpath(fhir_resource, fhirpath_expression, runnable)
+          begin
+            response = call_fhirpath_service(fhir_resource, fhirpath_expression)
+          rescue StandardError => e
+            # This could be a complete failure to connect (fhirpath service isn't running)
+            # or a timeout (fhirpath service took too long to respond).
+            runnable.add_message('error', e.message)
+            raise Inferno::Exceptions::ErrorInFhirpathException, "Unable to connect to FHIRPath service at #{url}."
+          end
+
+          sanitized_body = remove_invalid_characters(response.body)
+          return transform_fhirpath_results(JSON.parse(sanitized_body)) if response.status.to_s.start_with? '2'
+
+          runnable.add_message('error', "FHIRPath service Response: HTTP #{response.status}\n#{sanitized_body}")
+          raise Inferno::Exceptions::ErrorInFhirpathException,
+                'FHIRPath service call failed. Review Messages tab for more information.'
+        rescue JSON::ParserError
+          runnable.add_message('error', "Invalid FHIRPath service response format:\n#{sanitized_body}")
+          raise Inferno::Exceptions::ErrorInFhirpathException,
+                'Error occurred in the FHIRPath service. Review Messages tab for more information.'
+        end
+
+        # @private
+        def transform_fhirpath_results(fhirpath_results)
+          fhirpath_results.each do |result|
+            klass = FHIR.const_get(result['type'])
+            result['element'] = klass.new(result['element'])
+          rescue NameError
+            next
+          end
+          fhirpath_results
+        end
+
+        def call_fhirpath_service(fhir_resource, fhirpath_expression)
+          Faraday.new(
+            url,
+            request: { timeout: 600 }
+          ).post(
+            "evaluate?path=#{fhirpath_expression}",
+            fhir_resource.to_json,
+            content_type: 'application/json'
+          )
+        end
+
+        # @private
+        def remove_invalid_characters(string)
+          string.gsub(/[^[:print:]\r\n]+/, '')
+        end
+      end
+
+      module ClassMethods
+        # @private
+        def evaluator(url = nil)
+          @evaluator ||= Inferno::DSL::FhirpathEvaluation::Evaluator.new(url)
+        end
+      end
+    end
+  end
+end

lib/inferno/entities/test_group.rb

@@ -10,6 +10,7 @@ class TestGroup
       extend DSL::HTTPClient::ClassMethods
       extend DSL::Runnable
       include DSL::FHIRValidation
+      include DSL::FhirpathEvaluation
       include DSL::Results
       include DSL::Assertions
       include DSL::Messages

lib/inferno/entities/test_suite.rb

@@ -16,6 +16,7 @@ class TestSuite
       extend DSL::HTTPClient::ClassMethods
       include DSL::FHIRValidation
       include DSL::FHIRResourceValidation
+      include DSL::FhirpathEvaluation
       include DSL::Results
       include DSL::Assertions
       include DSL::Messages

lib/inferno/exceptions.rb

@@ -64,6 +64,25 @@ def initialize(validator_name)
       end
     end
 
+    class FhirpathNotFoundException < RuntimeError
+      def initialize(fhirpath_name)
+        super("No '#{fhirpath_name}' FHIRPath evaluator found")
+      end
+    end
+
+    # ErrorInFhirpathException is used when an exception occurred in
+    # calling the FHIRPath service, for example a connection timeout
+    # or an unexpected response format.
+    # Note: This class extends TestResultException instead of RuntimeError
+    # to bypass printing the stack trace in the UI, since
+    # the stack trace of this exception is not likely be useful.
+    # Instead the message should point to where in the fhirpath evaluator an error occurred.
+    class ErrorInFhirpathException < TestResultException
+      def result
+        'error'
+      end
+    end
+
     class RequiredInputsNotFound < RuntimeError
       def initialize(missing_inputs)
         super("Missing the following required inputs: #{missing_inputs.join(', ')}")

lib/inferno/version.rb

@@ -1,4 +1,4 @@
 module Inferno
   # Standard patterns for gem versions: https://guides.rubygems.org/patterns/
-  VERSION = '0.4.39'.freeze
+  VERSION = '0.4.40'.freeze
 end