v1.0.3

README.md

@@ -40,7 +40,7 @@ And run the following commands from the terminal:
 git clone https://github.com/siteadmin/inferno
 cd inferno
 bundle install
-rackup
+bundle exec rackup
 ```
 
 Inferno can then be accessed at http://localhost:4567 in a web browser.

config.yml

@@ -34,3 +34,6 @@ logging_enabled: true
 
 # Automatically Run Conformance Sequence on new server create
 autorun_conformance: false
+
+# Include extra tests: true or false
+include_extras: true

lib/app/endpoint.rb

@@ -14,6 +14,7 @@ class Endpoint < Sinatra::Base
       Inferno::DEFAULT_SCOPES = settings.default_scopes
       Inferno::ENVIRONMENT = settings.environment
       Inferno::PURGE_ON_RELOAD = settings.purge_database_on_reload
+      Inferno::EXTRAS = settings.include_extras
 
       if settings.logging_enabled
         Inferno.logger = if settings.log_to_file

lib/app/models/resource_reference.rb

@@ -1,13 +1,14 @@
+# frozen_string_literal: true
+
 module Inferno
   module Models
     class ResourceReference
       include DataMapper::Resource
-      property :id, String, key: true, default: proc { SecureRandom.uuid}
+      property :id, String, key: true, default: proc { SecureRandom.uuid }
       property :resource_type, String
       property :resource_id, String
 
       belongs_to :testing_instance
     end
   end
 end
-

lib/app/models/testing_instance.rb

@@ -86,9 +86,11 @@ def patient_id
       end
 
       def patient_id= patient_id
+        return if patient_id.to_s == self.patient_id.to_s
 
         existing_patients = self.resource_references.select{|ref| ref.resource_type == 'Patient'}
-        self.resource_references.each(&:destroy)
+        # Use destroy directly (instead of on each, so we don't have to reload)
+        self.resource_references.destroy
         self.save!
 
         self.resource_references << ResourceReference.new({
@@ -113,7 +115,9 @@ def save_supported_resources(conformance)
                      'MedicationStatement',
                      'MedicationOrder',
                      'Observation',
-                     'Procedure']
+                     'Procedure',
+                     'DocumentReference',
+                     'Provenance']
 
         supported_resources = conformance.rest.first.resource.select{ |r| resources.include? r.type}.reduce({}){|a,k| a[k.type] = k; a}
 
@@ -162,6 +166,19 @@ def conformance_supported?(resource, methods = [])
           end
         end
       end
+
+      def post_resource_references(resource_type: nil, resource_id: nil)
+        self.resource_references.each do |ref|
+          if (ref.resource_type == resource_type) && (ref.resource_id == resource_id)
+            ref.destroy
+          end
+        end
+        self.resource_references << ResourceReference.new({resource_type: resource_type,
+                                                          resource_id: resource_id})
+        self.save!
+        # Ensure the instance resource references are accurate
+        self.reload
+      end
     end
   end
 end

lib/app/sequence_base.rb

@@ -15,12 +15,12 @@ class SequenceBase
       include Inferno::WebDriver
 
       STATUS = {
-          pass: 'pass',
-          fail: 'fail',
-          error: 'error',
-          todo: 'todo',
-          wait: 'wait',
-          skip: 'skip'
+        pass: 'pass',
+        fail: 'fail',
+        error: 'error',
+        todo: 'todo',
+        wait: 'wait',
+        skip: 'skip'
       }
 
       @@test_index = 0
@@ -31,6 +31,7 @@ class SequenceBase
       @@descriptions = {}
       @@details = {}
       @@requires = {}
+      @@conformance_supports = {}
       @@defines = {}
       @@test_metadata = {}
 
@@ -226,6 +227,11 @@ def self.requires(*requires)
         @@requires[self.sequence_name] || []
       end
 
+      def self.conformance_supports(*supports)
+        @@conformance_supports[self.sequence_name] = supports unless supports.empty?
+        @@conformance_supports[self.sequence_name] || []
+      end
+
       def self.missing_requirements(instance, recurse = false)
 
         return [] unless @@requires.key?(self.sequence_name)
@@ -306,7 +312,7 @@ def self.optional?
 
       def self.preconditions(description, &block)
         @@preconditions[self.sequence_name] = {
-            block: block,
+          block: block,
             description: description
         }
       end
@@ -460,11 +466,11 @@ def warning
       def get_resource_by_params(klass, params = {})
         assert !params.empty?, "No params for search"
         options = {
-            :search => {
-                :flag => false,
-                :compartment => nil,
-                :parameters => params
-            }
+          :search => {
+            :flag => false,
+              :compartment => nil,
+              :parameters => params
+          }
         }
         @client.search(klass, options)
       end
@@ -510,16 +516,14 @@ def validate_search_reply(klass, reply)
       end
 
       def save_resource_ids_in_bundle(klass, reply)
-
         return if reply.try(:resource).try(:entry).nil?
 
         entries = reply.resource.entry.select{ |entry| entry.resource.class == klass }
 
         entries.each do |entry|
-          @instance.resource_references << Models::ResourceReference.new({resource_type: klass.name.split(':').last, resource_id: entry.resource.id})
+          @instance.post_resource_references(resource_type: klass.name.split(':').last,
+                                             resource_id: entry.resource.id)
         end
-
-        @instance.save!
       end
 
       def validate_read_reply(resource, klass)
@@ -617,61 +621,64 @@ def self.sequences_overview
       end
 
       def self.sequences_groups
-        [{
+        groups = [{
           name: 'Discovery',
           overview: %(
-            This is a description of the discovery group
+            Sequences related to discovering servers and learning about their capabilities.
           ),
           sequences: [ConformanceSequence],
           run_all: false
         },
-        {
-          name: 'Authentication and Authorization',
-          overview: %(
-
-
-
-          ),
-          sequences: [
-            DynamicRegistrationSequence,
-            ManualRegistrationSequence,
-            StandaloneLaunchSequence,
-            EHRLaunchSequence,
-            OpenIDConnectSequence,
-            TokenRefreshSequence
-          ],
-          run_all: false
-        },
-        {
-          name: 'Argonaut Profile Conformance',
-          overview: %(
-
-
-
-          ),
-          sequences: [
-            ArgonautPatientSequence,
-            ArgonautAllergyIntoleranceSequence,
-            ArgonautCarePlanSequence,
-            ArgonautCareTeamSequence,
-            ArgonautConditionSequence,
-            ArgonautDeviceSequence,
-            ArgonautDiagnosticReportSequence,
-            ArgonautObservationSequence,
-            ArgonautGoalSequence,
-            ArgonautImmunizationSequence,
-            ArgonautMedicationStatementSequence,
-            ArgonautMedicationOrderSequence,
-            ArgonautProcedureSequence,
-            ArgonautSmokingStatusSequence,
-            ArgonautVitalSignsSequence
-          ],
-          run_all: true
-        }]
-
-
+                  {
+                    name: 'Authentication and Authorization',
+                    overview: %(Tests for Authentication and Authorization.  Primarily in regards to SMART-on-FHIR),
+                    sequences: [
+                      DynamicRegistrationSequence,
+                      ManualRegistrationSequence,
+                      StandaloneLaunchSequence,
+                      EHRLaunchSequence,
+                      OpenIDConnectSequence,
+                      TokenRefreshSequence
+                    ],
+                    run_all: false
+                  },
+                  {
+                    name: 'Argonaut Profile Conformance',
+                    overview: %(Tests related the the Arognauts Data Query Implementation Guide),
+                    sequences: [
+                      ArgonautPatientSequence,
+                      ArgonautAllergyIntoleranceSequence,
+                      ArgonautCarePlanSequence,
+                      ArgonautCareTeamSequence,
+                      ArgonautConditionSequence,
+                      ArgonautDeviceSequence,
+                      ArgonautDiagnosticReportSequence,
+                      ArgonautObservationSequence,
+                      ArgonautGoalSequence,
+                      ArgonautImmunizationSequence,
+                      ArgonautMedicationStatementSequence,
+                      ArgonautMedicationOrderSequence,
+                      ArgonautProcedureSequence,
+                      ArgonautSmokingStatusSequence,
+                      ArgonautVitalSignsSequence
+                    ],
+                    run_all: true
+                  }]
+
+        if Inferno::EXTRAS
+          groups << {
+            name: 'Additional Resources',
+            overview: %(
+              Tests for resources corresponding to [Draft USCDI v1](https://www.healthit.gov/sites/default/files/draft-uscdi.pdf) that are not represeted in the Argonaut Data Query Implementation Guide.
+            ),
+            sequences: [
+                DocumentReferenceSequence,
+                ProvenanceSequence
+              ]
+          }
+        end
+        groups
       end
-
     end
 
     Dir[File.join(__dir__, 'sequences', '*_sequence.rb')].each { |file| require file }

lib/app/sequences/01_conformance_sequence.rb

@@ -57,7 +57,6 @@ class ConformanceSequence < SequenceBase
         metadata {
           id '01'
           link 'https://www.hl7.org/fhir/security.html'
-          optional
           desc %(
             All exchange of production data should be secured with TLS/SSL v1.2.
           )

lib/app/sequences/02_dynamic_registration_sequence.rb

@@ -31,7 +31,6 @@ class DynamicRegistrationSequence < SequenceBase
         metadata {
           id '01'
           link 'https://www.hl7.org/fhir/security.html'
-          optional
           desc %(
             The client registration endpoint MUST be protected by a transport layer security.
           )

lib/app/sequences/03_patient_standalone_launch_sequence.rb

@@ -18,7 +18,6 @@ class StandaloneLaunchSequence < SequenceBase
         metadata {
           id '01'
           link 'http://www.hl7.org/fhir/smart-app-launch/'
-          optional
           desc %(
             The client registration endpoint MUST be protected by a transport layer security.
           )
@@ -88,7 +87,6 @@ class StandaloneLaunchSequence < SequenceBase
         metadata {
           id '04'
           link 'http://www.hl7.org/fhir/smart-app-launch/'
-          optional
           desc %(
             Apps must assure that sensitive information (authentication secrets, authorization codes, tokens) is transmitted ONLY to authenticated servers, over TLS-secured channels.
           )

lib/app/sequences/04_provider_ehr_launch_sequence.rb

@@ -50,7 +50,6 @@ class EHRLaunchSequence < SequenceBase
         metadata {
           id '03'
           link 'http://www.hl7.org/fhir/smart-app-launch/'
-          optional
           desc %(
             Apps MUST assure that sensitive information (authentication secrets, authorization codes, tokens) is transmitted ONLY to authenticated servers, over TLS-secured channels.
             opaque identifier for the launch in the launch querystring parameter.
@@ -116,7 +115,6 @@ class EHRLaunchSequence < SequenceBase
         metadata {
           id '06'
           link 'http://www.hl7.org/fhir/smart-app-launch/'
-          optional
           desc %(
             Apps MUST assure that sensitive information (authentication secrets, authorization codes, tokens) is transmitted ONLY to authenticated servers, over TLS-secured channels.
           )

lib/app/sequences/06_token_introspection_sequence.rb

@@ -17,7 +17,6 @@ class TokenIntrospectionSequence < SequenceBase
         metadata {
           id '01'
           link 'https://tools.ietf.org/html/rfc7662'
-          optional
           desc %(
             The server MUST support Transport Layer Security (TLS) 1.2.
           )

lib/app/sequences/08a_argonaut_patient_sequence.rb

@@ -9,6 +9,7 @@ class ArgonautPatientSequence < SequenceBase
       test_id_prefix 'ARPA'
 
       requires :token, :patient_id
+      conformance_supports :Patient
 
       test 'Server rejects patient read without proper authorization' do
 
@@ -225,7 +226,7 @@ class ArgonautPatientSequence < SequenceBase
             All servers SHOULD make available the vread and history-instance interactions for the Argonaut Profiles the server chooses to support.          )
         }
 
-        skip_if_not_supported(:Patient, [:history])
+         
 
         validate_history_reply(@patient, FHIR::DSTU2::Patient)
 
@@ -242,7 +243,7 @@ class ArgonautPatientSequence < SequenceBase
           )
         }
 
-        skip_if_not_supported(:Patient, [:vread])
+         
 
         validate_vread_reply(@patient, FHIR::DSTU2::Patient)