inferno_core 0.4.17 → 0.4.19

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 77e9c5d39c29db85f07321f5456cebad0fb4e285f0143533984d36500248fbd7
-  data.tar.gz: e22a7589dbb1bc4edd54ad3305526fdfeae4358fd992b2b23f5d69a8a8fa139c
+  metadata.gz: a9b06c0f0ce1702d3ba9662e4762e3174eb22527a19a3eb35a5ec0e01dbf57d3
+  data.tar.gz: 8c019f778c84c0926ef1705e256e0d3b27fd39a2c6af4f32bd8c4d1ad731ff84
 SHA512:
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-  data.tar.gz: 2f68462dee18ced89167e7327a3dd5fbb7d250adef866604e4590d5c891fcb695761127b46804125c9d165de859d0777dc74ccf4772ba5a1b9f2865f0dcda6f3
+  metadata.gz: 39690b392f9e9997081cc5d58ee93c249a15be3eaeecca3927619f4d116e00cd85cdecc8a91693385420bb7b7bc07398b05b636d9be94713b23ad52c99bc9161
+  data.tar.gz: f2970277134ae396003da04b2ba09c19cd3dc02f70e513cbdbeaf7a7e014561cbf742a95fc8ed40cec034a23723ad54ed823637989628dd0661fc467b49db11a

data/lib/inferno/apps/cli/main.rb

@@ -36,7 +36,7 @@ module Inferno
           command = "rerun \"#{command}\" --background"
         end
 
-        system command
+        exec command
       end
 
       desc 'suites', 'List available test suites'

data/lib/inferno/config/boot/suites.rb

@@ -25,5 +25,13 @@ Inferno::Application.boot(:suites) do
     end
 
     ObjectSpace.each_object(TracePoint, &:disable)
+
+    Inferno::Entities::TestSuite.descendants.each do |descendant|
+      # When ID not assigned in custom test suites, Runnable.id will return default ID
+      # equal to the custom test suite's parent class name
+      if descendant.id.blank? || descendant.id == 'Inferno::Entities::TestSuite'
+        raise StandardError, "Error initializing test suite #{descendant.name}: test suite ID is not set"
+      end
+    end
   end
 end

data/lib/inferno/dsl/fhir_client.rb

@@ -130,6 +130,78 @@ module Inferno
         end
       end
 
+      # Perform a FHIR vread interaction.
+      #
+      # @param resource_type [String, Symbol, Class]
+      # @param id [String]
+      # @param version_id [String]
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @return [Inferno::Entities::Request]
+      def fhir_vread(resource_type, id, version_id, client: :default, name: nil)
+        store_request_and_refresh_token(fhir_client(client), name) do
+          tcp_exception_handler do
+            fhir_client(client).vread(fhir_class_from_resource_type(resource_type), id, version_id)
+          end
+        end
+      end
+
+      # Perform a FHIR update interaction.
+      #
+      # @param resource [FHIR::Model]
+      # @param id [String]
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @return [Inferno::Entities::Request]
+      def fhir_update(resource, id, client: :default, name: nil)
+        store_request_and_refresh_token(fhir_client(client), name) do
+          tcp_exception_handler do
+            fhir_client(client).update(resource, id)
+          end
+        end
+      end
+
+      # Perform a FHIR patch interaction.
+      #
+      # @param resource_type [String, Symbol, Class]
+      # @param id [String]
+      # @param patchset [Array]
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @return [Inferno::Entities::Request]
+      def fhir_patch(resource_type, id, patchset, client: :default, name: nil)
+        store_request_and_refresh_token(fhir_client(client), name) do
+          tcp_exception_handler do
+            fhir_client(client).partial_update(fhir_class_from_resource_type(resource_type), id, patchset)
+          end
+        end
+      end
+
+      # Perform a FHIR history interaction.
+      #
+      # @param resource_type [String, Symbol, Class]
+      # @param id [String]
+      # @param client [Symbol]
+      # @param name [Symbol] Name for this request to allow it to be used by
+      #   other tests
+      # @return [Inferno::Entities::Request]
+      def fhir_history(resource_type = nil, id = nil, client: :default, name: nil)
+        store_request_and_refresh_token(fhir_client(client), name) do
+          tcp_exception_handler do
+            if id
+              fhir_client(client).resource_instance_history(fhir_class_from_resource_type(resource_type), id)
+            elsif resource_type
+              fhir_client(client).resource_history(fhir_class_from_resource_type(resource_type))
+            else
+              fhir_client(client).all_history
+            end
+          end
+        end
+      end
+
       # Perform a FHIR search interaction.
       #
       # @param resource_type [String, Symbol, Class]
@@ -139,7 +211,7 @@ module Inferno
       #   other tests
       # @param search_method [Symbol] Use `:post` to search via POST
       # @return [Inferno::Entities::Request]
-      def fhir_search(resource_type, client: :default, params: {}, name: nil, search_method: :get)
+      def fhir_search(resource_type = nil, client: :default, params: {}, name: nil, search_method: :get)
         search =
           if search_method == :post
             { body: params }
@@ -149,8 +221,12 @@ module Inferno
 
         store_request_and_refresh_token(fhir_client(client), name) do
           tcp_exception_handler do
-            fhir_client(client)
-              .search(fhir_class_from_resource_type(resource_type), { search: })
+            if resource_type
+              fhir_client(client)
+                .search(fhir_class_from_resource_type(resource_type), { search: })
+            else
+              fhir_client(client).search_all({ search: })
+            end
           end
         end
       end

data/lib/inferno/dsl/fhir_validation.rb

@@ -116,17 +116,26 @@ module Inferno
         def resource_is_valid?(resource, profile_url, runnable)
           profile_url ||= FHIR::Definitions.resource_definition(resource.resourceType).url
 
-          outcome = FHIR::OperationOutcome.new(JSON.parse(validate(resource, profile_url)))
+          outcome, http_status = validate(resource, profile_url, runnable)
 
-          message_hashes = outcome.issue&.map { |issue| message_hash_from_issue(issue, resource) } || []
+          message_hashes = message_hashes_from_outcome(outcome, resource, profile_url)
 
-          message_hashes.concat(additional_validation_messages(resource, profile_url))
+          message_hashes
+            .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
 
-          filter_messages(message_hashes)
+          unless http_status == 200
+            raise Inferno::Exceptions::ErrorInValidatorException,
+                  'Error occurred in the validator. Review Messages tab or validator service logs for more information.'
+          end
 
           message_hashes
-            .each { |message_hash| runnable.add_message(message_hash[:type], message_hash[:message]) }
             .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
@@ -134,6 +143,17 @@ module Inferno
           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)
           {
@@ -171,12 +191,33 @@ module Inferno
         #
         # @param resource [FHIR::Model]
         # @param profile_url [String]
-        # @return [String] the body of the validation response
-        def validate(resource, profile_url)
-          Faraday.new(
-            url,
-            params: { profile: profile_url }
-          ).post('validate', resource.source_contents).body
+        # @param runnable [Inferno::Entities::Test]
+        # @return [[Array(FHIR::OperationOutcome, Number)] the validation response and HTTP status code
+        def validate(resource, profile_url, runnable)
+          begin
+            response = Faraday.new(
+              url,
+              params: { profile: profile_url }
+            ).post('validate', resource.source_contents)
+          rescue StandardError => e
+            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, response.status]
+        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: #{response}")
+            raise Inferno::Exceptions::ErrorInValidatorException,
+                  'Validator response was an unexpected format. '\
+                  'Review Messages tab or validator service logs for more information.'
+          end
         end
       end
 

data/lib/inferno/exceptions.rb

@@ -39,6 +39,16 @@ module Inferno
       end
     end
 
+    class ErrorInValidatorException < TestResultException
+      # This extends TestResultException instead of RuntimeError
+      # to bypass printing the stack trace in the UI.
+      # (The stack trace of this exception may not be useful,
+      # instead the message should point to where in the validator an error occurred)
+      def result
+        'error'
+      end
+    end
+
     class ParentNotLoadedException < RuntimeError
       def initialize(klass, id)
         super("No #{klass.name.demodulize} found with id '#{id}'")