inferno_core 0.0.8.pre2 → 0.1.1.pre

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: d08c713be3303b146a40a6316765e017d76a4213e3981c6121fd502e7eb4e577
+  metadata.gz: 70e3295132f61902fb03d7dcfc6fd3f8593b9cdfb5dd5079a1ae7fe92d6c165c
+  data.tar.gz: a3d26fbdbb272907f5f244d90971a5496466419d4204201cc21762bf6939f7ff
 SHA512:
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+  data.tar.gz: dd3664cc7873ffc8a998a04409632a3a53424b964e189bd5b0918cc8d372a76cdc161e1b0515a54012b43b6f787b79f60b1d1d2b1511ee97187a28c66efcbd6f

data/lib/inferno/apps/web/controllers/test_runs/create.rb

@@ -33,7 +33,8 @@ module Inferno
               session_data_repo.save(
                 test_session_id: test_session.id,
                 name: input[:name],
-                value: input[:value]
+                value: input[:value],
+                type: input[:type]
               )
             end
 

data/lib/inferno/apps/web/serializers/result.rb

@@ -16,6 +16,7 @@ module Inferno
         field :result_message, if: :field_present?
         field :created_at
         field :updated_at
+        field :optional?, name: :optional
 
         field :outputs do |result, _options|
           result.output_json.present? ? JSON.parse(result.output_json) : []

data/lib/inferno/apps/web/serializers/test.rb

@@ -4,10 +4,14 @@ module Inferno
       class Test < Serializer
         identifier :id
         field :title
+        field :short_title
         field :input_definitions, name: :inputs, extractor: HashValueExtractor, blueprint: Input
         field :output_definitions, name: :outputs, extractor: HashValueExtractor
         field :description
+        field :short_description
+        field :input_instructions
         field :user_runnable?, name: :user_runnable
+        field :optional?, name: :optional
       end
     end
   end

data/lib/inferno/apps/web/serializers/test_group.rb

@@ -5,10 +5,14 @@ module Inferno
         identifier :id
 
         field :title
+        field :short_title
         field :description
+        field :short_description
+        field :input_instructions
         field :test_count
         field :run_as_group?, name: :run_as_group
         field :user_runnable?, name: :user_runnable
+        field :optional?, name: :optional
 
         association :groups, name: :test_groups, blueprint: TestGroup
         association :tests, blueprint: Test

data/lib/inferno/apps/web/serializers/test_suite.rb

@@ -5,7 +5,10 @@ module Inferno
         view :summary do
           identifier :id
           field :title
+          field :short_title
           field :description
+          field :short_description
+          field :input_instructions
           field :test_count
         end
 

data/lib/inferno/db/migrations/001_create_initial_structure.rb

@@ -11,81 +11,81 @@ Sequel.migration do
     # end
 
     create_table :test_sessions do
-      column :id, String, primary_key: true, null: false
-      column :test_suite_id, String
+      column :id, String, primary_key: true, null: false, size: 36
+      column :test_suite_id, String, size: 255
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :test_runs do
-      column :id, String, primary_key: true, null: false
-      column :status, String
-      foreign_key :test_session_id, :test_sessions, index: true, type: String
+      column :id, String, primary_key: true, null: false, size: 36
+      column :status, String, size: 255
+      foreign_key :test_session_id, :test_sessions, index: true, type: String, size: 36, key: [:id]
       index [:test_session_id, :status] # Searching by unfinished test runs seems like it will be a likely query
 
-      column :test_suite_id, String, index: true
-      column :test_group_id, String, index: true
-      column :test_id, String, index: true
+      column :test_suite_id, String, index: true, size: 255
+      column :test_group_id, String, index: true, size: 255
+      column :test_id, String, index: true, size: 255
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :test_run_inputs do
-      column :id, String, primary_key: true, null: false
-      foreign_key :test_run_id, :test_runs, index: true, type: String
-      column :test_input_id, String
-      column :value, String
+      column :id, String, primary_key: true, null: false, size: 36
+      foreign_key :test_run_id, :test_runs, index: true, type: String, key: [:id]
+      column :test_input_id, String, size: 255
+      column :value, String, text: true
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :results do
-      column :id, String, primary_key: true, null: false
+      column :id, String, primary_key: true, null: false, size: 36
 
-      foreign_key :test_run_id, :test_runs, index: true, type: String
-      foreign_key :test_session_id, :test_sessions, index: true, type: String
+      foreign_key :test_run_id, :test_runs, index: true, type: String, size: 36, key: [:id]
+      foreign_key :test_session_id, :test_sessions, index: true, type: String, size: 36, key: [:id]
 
-      column :result, String
-      column :result_message, String
+      column :result, String, size: 255
+      column :result_message, String, text: true
 
-      column :test_suite_id, String
-      column :test_group_id, String
-      column :test_id, String
+      column :test_suite_id, String, size: 255
+      column :test_group_id, String, size: 255
+      column :test_id, String, size: 255
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :result_inputs do
-      column :id, String, primary_key: true, null: false
-      foreign_key :result_id, :results, index: true, type: String
-      column :test_input_id, String
-      column :value, String
+      column :id, String, primary_key: true, null: false, size: 36
+      foreign_key :result_id, :results, index: true, type: String, size: 36, key: [:id]
+      column :test_input_id, String, size: 255
+      column :value, String, text: true
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :result_outputs do
-      column :id, String, primary_key: true, null: false
-      foreign_key :result_id, :results, index: true, type: String
-      column :test_output_id, String
-      column :value, String
+      column :id, String, primary_key: true, null: false, size: 36
+      foreign_key :result_id, :results, index: true, type: String, size: 36, key: [:id]
+      column :test_output_id, String, size: 255
+      column :value, String, text: true
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :result_prompt_values do
-      column :id, String, primary_key: true, null: false
+      column :id, String, primary_key: true, null: false, size: 36
 
-      foreign_key :result_id, :results, index: true, type: String
+      foreign_key :result_id, :results, index: true, type: String, size: 36, key: [:id]
 
-      column :test_prompt_id, String, null: false
-      column :value, String, null: false
+      column :test_prompt_id, String, null: false, size: 255
+      column :value, String, null: false, text: true
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
@@ -93,10 +93,10 @@ Sequel.migration do
 
     create_table :messages do
       primary_key :index
-      column :id, String, index: true, null: false
-      foreign_key :result_id, :results, index: true, type: String
-      column :type, String
-      column :message, String
+      column :id, String, index: true, null: false, size: 36
+      foreign_key :result_id, :results, index: true, type: String, size: 36, key: [:id]
+      column :type, String, size: 255
+      column :message, String, text: true
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
@@ -104,40 +104,41 @@ Sequel.migration do
 
     create_table :requests do
       primary_key :index
-      column :id, String, index: true, null: false
-      column :verb, String
-      column :url, String
-      column :direction, String
+      column :id, String, null: false, size: 36
+      column :verb, String, size: 255
+      column :url, String, text: true
+      column :direction, String, size: 255
       column :status, Integer
-      column :name, String
+      column :name, String, size: 255
       column :request_body, String, text: true
       column :response_body, String, text: true # It would be nice if we could store this on disk
+      index [:id], unique: true
 
       # Requires requests to be a part of tests now.
-      foreign_key :result_id, :results, index: true, type: String
-      foreign_key :test_session_id, :test_sessions, index: true, type: String
-      index [:test_session_id, :name], concurrently: true
+      foreign_key :result_id, :results, index: true, type: String, size: 36, key: [:id]
+      foreign_key :test_session_id, :test_sessions, index: true, type: String, size: 36, key: [:id]
+      index [:test_session_id, :name]
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :headers do
-      column :id, String, index: true, null: false
-      foreign_key :request_id, :requests, index: true, type: String
-      column :type, String # request / response
-      column :name, String
-      column :value, String
+      column :id, String, index: true, null: false, size: 36
+      foreign_key :request_id, :requests, index: true, type: Integer, key: [:index]
+      column :type, String, size: 255 # request / response
+      column :name, String, size: 255
+      column :value, String, text: true
 
       column :created_at, DateTime, null: false
       column :updated_at, DateTime, null: false
     end
 
     create_table :session_data do
-      column :id, String, index: true, null: false
-      foreign_key :test_session_id, :test_sessions, index: true, type: String
-      column :name, String
-      column :value, String
+      column :id, String, index: true, null: false, size: 255
+      foreign_key :test_session_id, :test_sessions, index: true, type: String, size: 36, key: [:id]
+      column :name, String, size: 255
+      column :value, String, text: true
       index [:test_session_id, :name]
     end
   end

data/lib/inferno/db/migrations/002_add_wait_support.rb

@@ -1,7 +1,7 @@
 Sequel.migration do
   change do
-    add_column :test_runs, :identifier, String, text: true
+    add_column :test_runs, :identifier, String, text: true, size: 255
     add_column :test_runs, :wait_timeout, DateTime
-    add_index :test_runs, [:status, :identifier, :wait_timeout, :updated_at], concurrently: true
+    add_index :test_runs, [:status, :identifier, :wait_timeout, :updated_at]
   end
 end

data/lib/inferno/db/migrations/003_update_session_data.rb

@@ -4,15 +4,15 @@ Sequel.migration do
     drop_table :result_inputs
 
     set_column_type :session_data, :value, String, text: true
-    drop_index :session_data, [:test_session_id, :name], concurrently: true
-    add_index :session_data, [:test_session_id, :name], unique: true, concurrently: true
-    drop_index :session_data, :id, concurrently: true
-    add_index :session_data, :id, unique: true, concurrently: true
+    drop_index :session_data, [:test_session_id, :name]
+    add_index :session_data, [:test_session_id, :name], unique: true
+    drop_index :session_data, :id
+    add_index :session_data, :id, unique: true
 
     add_column :results, :input_json, String, text: true
     add_column :results, :output_json, String, text: true
-    add_index :results, [:test_session_id, :test_id], concurrently: true
-    add_index :results, [:test_session_id, :test_group_id], concurrently: true
-    add_index :results, [:test_session_id, :test_suite_id], concurrently: true
+    add_index :results, [:test_session_id, :test_id]
+    add_index :results, [:test_session_id, :test_group_id]
+    add_index :results, [:test_session_id, :test_suite_id]
   end
 end

data/lib/inferno/db/migrations/004_add_request_results_table.rb

@@ -2,8 +2,8 @@ Sequel.migration do
   change do
     create_table :requests_results do
       # using results_id instead of result_id to avoid ambiguous column error
-      foreign_key :results_id, :results, index: true, type: String, null: false
-      foreign_key :requests_id, :requests, index: true, type: String, null: false
+      foreign_key :results_id, :results, index: true, type: String, null: false, size: 36, key: [:id]
+      foreign_key :requests_id, :requests, index: true, type: Integer, null: false, size: 36, key: [:index]
     end
   end
 end

data/lib/inferno/db/migrations/005_add_updated_at_index_to_results.rb

@@ -1,5 +1,5 @@
 Sequel.migration do
   change do
-    add_index :results, [:test_run_id, :updated_at], concurrently: true
+    add_index :results, [:test_run_id, :updated_at]
   end
 end

data/lib/inferno/db/migrations/006_remove_unused_tables.rb

@@ -0,0 +1,38 @@
+Sequel.migration do
+  change do
+    drop_table :result_outputs
+    drop_table :result_prompt_values
+
+    alter_table(:test_sessions) { set_column_not_null :test_suite_id }
+
+    alter_table(:results) do
+      set_column_not_null :test_run_id
+      set_column_not_null :test_session_id
+    end
+
+    alter_table(:messages) do
+      set_column_not_null :result_id
+      set_column_not_null :type
+      set_column_not_null :message
+    end
+
+    alter_table(:requests) do
+      set_column_not_null :verb
+      set_column_not_null :url
+      set_column_not_null :direction
+      set_column_not_null :result_id
+      set_column_not_null :test_session_id
+    end
+
+    alter_table(:headers) do
+      set_column_not_null :request_id
+      set_column_not_null :type
+      set_column_not_null :name
+    end
+
+    alter_table(:session_data) do
+      set_column_not_null :test_session_id
+      set_column_not_null :name
+    end
+  end
+end

data/lib/inferno/db/schema.rb

@@ -6,7 +6,7 @@ Sequel.migration do
     
     create_table(:test_sessions) do
       String :id, :size=>255, :null=>false
-      String :test_suite_id, :size=>255
+      String :test_suite_id, :size=>255, :null=>false
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
       
@@ -15,8 +15,8 @@ Sequel.migration do
     
     create_table(:session_data, :ignore_index_errors=>true) do
       String :id, :size=>255, :null=>false
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255
-      String :name, :size=>255
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255, :null=>false
+      String :name, :size=>255, :null=>false
       String :value, :text=>true
       
       index [:id], :unique=>true
@@ -48,8 +48,8 @@ Sequel.migration do
     
     create_table(:results, :ignore_index_errors=>true) do
       String :id, :size=>255, :null=>false
-      foreign_key :test_run_id, :test_runs, :type=>String, :size=>255
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255
+      foreign_key :test_run_id, :test_runs, :type=>String, :size=>255, :null=>false
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255, :null=>false
       String :result, :size=>255
       String :result_message, :size=>255
       String :test_suite_id, :size=>255
@@ -73,9 +73,9 @@ Sequel.migration do
     create_table(:messages, :ignore_index_errors=>true) do
       primary_key :index
       String :id, :size=>255, :null=>false
-      foreign_key :result_id, :results, :type=>String, :size=>255
-      String :type, :size=>255
-      String :message, :size=>255
+      foreign_key :result_id, :results, :type=>String, :size=>255, :null=>false
+      String :type, :size=>255, :null=>false
+      String :message, :size=>255, :null=>false
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
       
@@ -86,55 +86,29 @@ Sequel.migration do
     create_table(:requests, :ignore_index_errors=>true) do
       primary_key :index
       String :id, :size=>255, :null=>false
-      String :verb, :size=>255
-      String :url, :size=>255
-      String :direction, :size=>255
+      String :verb, :size=>255, :null=>false
+      String :url, :size=>255, :null=>false
+      String :direction, :size=>255, :null=>false
       Integer :status
       String :name, :size=>255
       String :request_body, :text=>true
       String :response_body, :text=>true
-      foreign_key :result_id, :results, :type=>String, :size=>255
-      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255
+      foreign_key :result_id, :results, :type=>String, :size=>255, :null=>false
+      foreign_key :test_session_id, :test_sessions, :type=>String, :size=>255, :null=>false
+      String :"[:test_session_id, :name]"
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false
       
       index [:id]
       index [:result_id]
       index [:test_session_id]
-      index [:test_session_id, :name]
-    end
-    
-    create_table(:result_outputs, :ignore_index_errors=>true) do
-      String :id, :size=>255, :null=>false
-      foreign_key :result_id, :results, :type=>String, :size=>255
-      String :test_output_id, :size=>255
-      String :value, :size=>255
-      DateTime :created_at, :null=>false
-      DateTime :updated_at, :null=>false
-      
-      primary_key [:id]
-      
-      index [:result_id]
-    end
-    
-    create_table(:result_prompt_values, :ignore_index_errors=>true) do
-      String :id, :size=>255, :null=>false
-      foreign_key :result_id, :results, :type=>String, :size=>255
-      String :test_prompt_id, :size=>255, :null=>false
-      String :value, :size=>255, :null=>false
-      DateTime :created_at, :null=>false
-      DateTime :updated_at, :null=>false
-      
-      primary_key [:id]
-      
-      index [:result_id]
     end
     
     create_table(:headers, :ignore_index_errors=>true) do
       String :id, :size=>255, :null=>false
-      foreign_key :request_id, :requests, :type=>String, :size=>255
-      String :type, :size=>255
-      String :name, :size=>255
+      foreign_key :request_id, :requests, :type=>String, :size=>255, :null=>false
+      String :type, :size=>255, :null=>false
+      String :name, :size=>255, :null=>false
       String :value, :size=>255
       DateTime :created_at, :null=>false
       DateTime :updated_at, :null=>false

data/lib/inferno/dsl/configurable.rb

@@ -65,20 +65,23 @@ module Inferno
           inputs.dig(identifier, :name) || identifier
         end
 
+        def input_type(identifier)
+          inputs.dig(identifier, :type)
+        end
+
         ### Output Configuration ###
 
         def outputs
           configuration[:outputs] ||= {}
         end
 
-        def add_output(identifier)
-          return if output_config_exists?(identifier)
-
-          outputs[identifier] = default_output_config(identifier)
+        def add_output(identifier, new_config = {})
+          existing_config = output_config(identifier) || {}
+          outputs[identifier] = default_output_config(identifier).merge(existing_config, new_config)
         end
 
         def default_output_config(identifier)
-          { name: identifier }
+          { name: identifier, type: 'text' }
         end
 
         def output_config_exists?(identifier)
@@ -93,6 +96,10 @@ module Inferno
           outputs.dig(identifier, :name) || identifier
         end
 
+        def output_type(identifier)
+          outputs.dig(identifier, :type)
+        end
+
         ### Request Configuration ###
 
         def requests

data/lib/inferno/dsl/fhir_client.rb

@@ -72,7 +72,7 @@ module Inferno
       # @param headers [Hash] custom headers for this operation
       # @return [Inferno::Entities::Request]
       def fhir_operation(path, body: nil, client: :default, name: nil, headers: {})
-        store_request('outgoing', name) do
+        store_request_and_refresh_token(fhir_client(client), name) do
           operation_headers = fhir_client(client).fhir_headers
           operation_headers.merge!('Content-Type' => 'application/fhir+json') if body.present?
           operation_headers.merge!(headers) if headers.present?
@@ -88,7 +88,7 @@ module Inferno
       #   other tests
       # @return [Inferno::Entities::Request]
       def fhir_get_capability_statement(client: :default, name: nil)
-        store_request('outgoing', name) do
+        store_request_and_refresh_token(fhir_client(client), name) do
           fhir_client(client).conformance_statement
           fhir_client(client).reply
         end
@@ -103,7 +103,7 @@ module Inferno
       #   other tests
       # @return [Inferno::Entities::Request]
       def fhir_read(resource_type, id, client: :default, name: nil)
-        store_request('outgoing', name) do
+        store_request_and_refresh_token(fhir_client(client), name) do
           fhir_client(client).read(fhir_class_from_resource_type(resource_type), id)
         end
       end
@@ -124,21 +124,73 @@ module Inferno
           else
             { parameters: params }
           end
-        store_request('outgoing', name) do
+
+        store_request_and_refresh_token(fhir_client(client), name) do
           fhir_client(client)
             .search(fhir_class_from_resource_type(resource_type), { search: search })
         end
       end
 
+      # Perform a FHIR delete 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_delete(resource_type, id, client: :default, name: nil)
+        store_request('outgoing', name) do
+          fhir_client(client).destroy(fhir_class_from_resource_type(resource_type), id)
+        end
+      end
+
       # @todo Make this a FHIR class method? Something like
       #   FHIR.class_for(resource_type)
-      # @private
+      # @api private
       def fhir_class_from_resource_type(resource_type)
         FHIR.const_get(resource_type.to_s.camelize)
       end
 
+      # This method wraps a request to automatically refresh its access token if
+      # expired. It's combined with `store_request` so that all of the fhir
+      # request methods don't have to be wrapped twice.
+      # @api private
+      def store_request_and_refresh_token(client, name, &block)
+        store_request('outgoing', name) do
+          perform_refresh(client) if client.need_to_refresh? && client.able_to_refresh?
+          block.call
+        end
+      end
+
+      # @api private
+      def perform_refresh(client)
+        credentials = client.oauth_credentials
+
+        post(
+          credentials.token_url,
+          body: credentials.oauth2_refresh_params,
+          headers: credentials.oauth2_refresh_headers
+        )
+
+        return if request.status != 200
+
+        credentials.update_from_response_body(request)
+
+        if credentials.name.present?
+          Inferno::Repositories::SessionData.new.save(
+            name: credentials.name,
+            value: credentials,
+            type: 'oauth_credentials',
+            test_session_id: test_session_id
+          )
+        end
+      rescue StandardError => e
+        Inferno::Application[:logger].error "Unable to refresh token: #{e.message}"
+      end
+
       module ClassMethods
-        # @private
+        # @api private
         def fhir_client_definitions
           @fhir_client_definitions ||= {}
         end

data/lib/inferno/dsl/fhir_client_builder.rb

@@ -1,4 +1,5 @@
 require 'fhir_client'
+require_relative '../ext/fhir_client'
 
 module Inferno
   module DSL
@@ -15,6 +16,7 @@ module Inferno
           client.additional_headers = headers if headers
           client.default_json
           client.set_bearer_token bearer_token if bearer_token
+          oauth_credentials&.add_to_client(client)
         end
       end
 
@@ -48,6 +50,20 @@ module Inferno
           end
       end
 
+      # Define OAuth credentials for a client. These can allow a client to
+      # automatically refresh its access token when it expires.
+      #
+      # @param oauth_credentials [Inferno::DSL::OAuthCredentials, Symbol]
+      # @return [void]
+      def oauth_credentials(oauth_credentials = nil)
+        @oauth_credentials ||=
+          if oauth_credentials.is_a? Symbol
+            runnable.send(oauth_credentials)
+          else
+            oauth_credentials
+          end
+      end
+
       # Define custom headers for a client
       #
       # @param headers [Hash]