Merge pull request #410 from onc-healthit/development

Version 2.9.0

.travis.yml

@@ -3,8 +3,6 @@ cache: bundler
 services:
   - docker
 before_install:
-  - gem update --system
-  - gem install bundler
   - docker-compose build
 before_script:
   - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter

Gemfile

@@ -10,14 +10,15 @@ gem 'colorize'
 gem 'data_mapper'
 gem 'dm-sqlite-adapter'
 gem 'fhir_client'
-gem 'json-jwt'
+gem 'jwt'
 gem 'kramdown'
 gem 'parser'
 gem 'pry'
 gem 'pry-byebug'
 gem 'rake'
 gem 'rb-readline'
 gem 'rest-client'
+gem 'rubyXL'
 gem 'selenium-webdriver'
 gem 'sinatra'
 gem 'sinatra-contrib'

Gemfile.lock

@@ -8,7 +8,6 @@ GEM
       tzinfo (~> 1.1)
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
-    aes_key_wrap (1.0.1)
     ast (2.4.0)
     backports (3.15.0)
     base62-rb (0.3.1)
@@ -17,7 +16,6 @@ GEM
     bcrypt (3.1.13)
     bcrypt-ruby (3.1.5)
       bcrypt (>= 3.1.3)
-    bindata (2.4.4)
     bitarray (1.2.0)
     bloomer (1.0.0)
       bitarray
@@ -121,10 +119,6 @@ GEM
       concurrent-ruby (~> 1.0)
     jaro_winkler (1.5.3)
     json (1.8.6)
-    json-jwt (1.11.0)
-      activesupport (>= 4.2)
-      aes_key_wrap
-      bindata
     json_pure (1.8.6)
     jwt (2.2.1)
     kramdown (2.1.0)
@@ -158,7 +152,7 @@ GEM
       byebug (~> 11.0)
       pry (~> 0.10)
     public_suffix (4.0.1)
-    rack (2.0.7)
+    rack (2.0.8)
     rack-protection (2.0.7)
       rack
     rack-test (1.1.0)
@@ -179,6 +173,9 @@ GEM
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 1.7)
     ruby-progressbar (1.10.1)
+    rubyXL (3.4.9)
+      nokogiri (>= 1.4.4)
+      rubyzip (>= 1.3.0)
     rubyzip (1.3.0)
     safe_yaml (1.0.5)
     selenium-webdriver (3.142.4)
@@ -235,7 +232,7 @@ DEPENDENCIES
   data_mapper
   dm-sqlite-adapter
   fhir_client
-  json-jwt
+  jwt
   kramdown
   minitest
   parser
@@ -246,6 +243,7 @@ DEPENDENCIES
   rb-readline
   rest-client
   rubocop
+  rubyXL
   selenium-webdriver
   simplecov
   sinatra

config.yml

@@ -37,14 +37,17 @@ include_extras: true
 
 badge_text: Community
 
+# Resource validator options: must be one of "internal" or "external". external_resource_validator_url is only used if resource_validator is set to external.
+resource_validator: internal
+external_resource_validator_url: http://validator_service:4567
+
 # module options: one or more must be set.  The first option in the list will be checked by default
 modules:
   - onc
   - smart
   - bdt
   - argonaut
   - uscore_v3.1.0
-  - bulk_data
 
 # preset fhir servers: optional. Minimally requires name, uri, module, optional inferno_uri, client_id, client_secret, scopes, instructions link
 presets:

docker-compose.yml

@@ -9,6 +9,8 @@ services:
       - bdt_service
   bdt_service:
     image: infernocommunity/inferno-bdt-service
+  validator_service:
+    image: infernocommunity/fhir-validator-wrapper
   nginx_server:
     image: nginx
     volumes:

generator/uscore/metadata_extractor.rb

@@ -5,10 +5,6 @@ module Generator
     module USCoreMetadataExtractor
       PROFILE_URIS = Inferno::ValidationUtil::US_CORE_R4_URIS
 
-      def profile_uri(profile)
-        "http://hl7.org/fhir/us/core/StructureDefinition/#{profile}"
-      end
-
       def search_param_path(resource, param)
         param = 'id' if param == '_id'
         "SearchParameter/us-core-#{resource.downcase}-#{param}"
@@ -27,6 +23,7 @@ def extract_metadata
         capability_statement_json = capability_statement('server')
         add_metadata_from_ig(metadata, ig_resource)
         add_metadata_from_resources(metadata, capability_statement_json['rest'][0]['resource'])
+        fix_metadata_errors(metadata)
         add_special_cases(metadata)
       end
 
@@ -53,8 +50,16 @@ def generate_unique_test_id_prefix(title)
         test_id_prefix
       end
 
+      def get_base_path(profile)
+        if profile.include? 'us/core/'
+          profile.split('us/core/').last
+        else
+          profile.split('fhir/').last
+        end
+      end
+
       def build_new_sequence(resource, profile)
-        base_path = profile.split('us/core/').last
+        base_path = get_base_path(profile)
         base_name = profile.split('StructureDefinition/').last
         profile_json = @resource_by_path[base_path]
         reformatted_version = ig_resource['version'].delete('.')
@@ -64,15 +69,15 @@ def build_new_sequence(resource, profile)
 
         # In case the profile doesn't start with US Core
         class_name = "USCore#{reformatted_version}#{class_name}" unless class_name.start_with? 'USCore'
-
         {
           name: base_name.tr('-', '_'),
           class_name: class_name,
           test_id_prefix: test_id_prefix,
           resource: resource['type'],
-          profile: profile_uri(base_name), # link in capability statement is incorrect,
+          profile: profile,
           title: profile_title,
           interactions: [],
+          operations: [],
           searches: [],
           search_param_descriptions: {},
           element_descriptions: {},
@@ -94,10 +99,11 @@ def add_metadata_from_resources(metadata, resources)
             add_basic_searches(resource, new_sequence)
             add_combo_searches(resource, new_sequence)
             add_interactions(resource, new_sequence)
+            add_operations(resource, new_sequence)
             add_include_search(resource, new_sequence)
             add_revinclude_targets(resource, new_sequence)
 
-            base_path = new_sequence[:profile].split('us/core/').last
+            base_path = get_base_path(supported_profile)
             profile_definition = @resource_by_path[base_path]
             add_must_support_elements(profile_definition, new_sequence)
             add_search_param_descriptions(profile_definition, new_sequence)
@@ -152,6 +158,17 @@ def add_interactions(resource, sequence)
         end
       end
 
+      def add_operations(resource, sequence)
+        operations = resource['operation']
+        operations&.each do |operation|
+          new_operation = {
+            operation: operation['name'],
+            expectation: operation['extension'][0]['valueCode']
+          }
+          sequence[:operations] << new_operation
+        end
+      end
+
       def add_include_search(resource, sequence)
         sequence[:include_params] = resource['searchInclude'] || []
       end
@@ -180,7 +197,7 @@ def add_must_support_elements(profile_definition, sequence)
               sequence[:must_supports] <<
                 {
                   type: 'element',
-                  path: path.gsub('[x]', type['code'].slice(0).capitalize + type['code'].slice(1..-1))
+                  path: path.gsub('[x]', capitalize_first_letter(type['code']))
                 }
             end
           else
@@ -196,13 +213,10 @@ def add_must_support_elements(profile_definition, sequence)
       def add_search_param_descriptions(profile_definition, sequence)
         sequence[:search_param_descriptions].each_key do |param|
           search_param_definition = @resource_by_path[search_param_path(sequence[:resource], param.to_s)]
-          path_parts = search_param_definition['xpath'].split('/f:')
-          if param.to_s != '_id'
-            path_parts[0] = sequence[:resource]
-            path = path_parts.join('.')
-          else
-            path = path_parts[0]
-          end
+          path = search_param_definition['expression']
+          path = path.gsub(/.where\((.*)/, '')
+          as_type = path.scan(/.as\((.*?)\)/).flatten.first
+          path = path.gsub(/.as\((.*?)\)/, capitalize_first_letter(as_type)) if as_type.present?
           profile_element = profile_definition['snapshot']['element'].select { |el| el['id'] == path }.first
           param_metadata = {
             path: path,
@@ -224,6 +238,8 @@ def add_search_param_descriptions(profile_definition, sequence)
             expectation = expectation_extension[index]['extension'].first['valueCode'] unless expectation_extension.nil?
             param_metadata[:comparators][comparator.to_sym] = expectation
           end
+          multiple_or_expectation = search_param_definition['_multipleOr']['extension'].first['valueCode']
+          param_metadata[:multiple_or] = multiple_or_expectation
           sequence[:search_param_descriptions][param] = param_metadata
         end
       end
@@ -285,6 +301,24 @@ def add_element_definitions(profile_definition, sequence)
         end
       end
 
+      def fix_metadata_errors(metadata)
+        # Procedure's date search param definition says Procedure.occurenceDateTime even though Procedure doesn't have an occurenceDateTime
+        procedure_sequence = metadata[:sequences].find { |sequence| sequence[:resource] == 'Procedure' }
+        procedure_sequence[:search_param_descriptions][:date][:path] = 'Procedure.performed'
+
+        goal_sequence = metadata[:sequences].find { |sequence| sequence[:resource] == 'Goal' }
+        goal_sequence[:search_param_descriptions][:'target-date'][:path] = 'Goal.target.dueDate'
+        goal_sequence[:search_param_descriptions][:'target-date'][:type] = 'date'
+
+        # add the ge comparator - the metadata is missing it for some reason
+        metadata[:sequences].each do |sequence|
+          sequence[:search_param_descriptions].each do |_param, description|
+            param_comparators = description[:comparators]
+            param_comparators[:ge] = param_comparators[:le] if param_comparators.key? :le
+          end
+        end
+      end
+
       def add_special_cases(metadata)
         category_first_profiles = [
           PROFILE_URIS[:lab_results]
@@ -320,6 +354,10 @@ def set_first_search(sequence, params)
         sequence[:searches].delete(search)
         sequence[:searches].unshift(search)
       end
+
+      def capitalize_first_letter(str)
+        str.slice(0).capitalize + str.slice(1..-1)
+      end
     end
   end
 end

generator/uscore/templates/module.yml.erb

@@ -7,21 +7,18 @@ test_sets:
   ad_hoc_testing:
     view: default
     tests:
-      - name: Discovery
+      - name: SMART App Launch
         sequences:
-        - UsCoreR4CapabilityStatementSequence
         - SMARTDiscoverySequence
-        run_all: true
-      - name: Authorization and Authentication
-        sequences:
         - DynamicRegistrationSequence
         - ManualRegistrationSequence
         - StandaloneLaunchSequence
         - EHRLaunchSequence
-      - name: US Core R4 Patient Based Profiles
+      - name: US Core v3.1.0 Profiles
         run_all: true
-        sequences:<% non_delayed_sequences.each do |sequence| %>
+        sequences:
+        - UsCoreR4CapabilityStatementSequence
+        - USCore310PatientSequence<% non_delayed_sequences.each do |sequence| %>
         - <%=sequence[:class_name]%><% end %>
-        - R4ProvenanceSequence
         - USCoreR4ClinicalNotesSequence<% delayed_sequences.each do |sequence| %>
         - <%=sequence[:class_name]%><% end %>

generator/uscore/templates/unit_tests/authorization_unit_test.rb.erb

@@ -15,6 +15,10 @@ describe 'unauthorized search test' do
 
   it 'skips if the <%= resource_type %> search interaction is not supported' do
     @instance.server_capabilities.destroy
+    Inferno::Models::ServerCapabilities.create(
+      testing_instance_id: @instance.id,
+      capabilities: FHIR::CapabilityStatement.new.to_json
+    )
     @instance.reload
     exception = assert_raises(Inferno::SkipException) { @sequence.run_test(@test) }
 

generator/uscore/templates/unit_tests/resource_read_unit_test.rb.erb

@@ -10,6 +10,10 @@ describe '<%= resource_type %> read test' do
 
   it 'skips if the <%= resource_type %> read interaction is not supported' do
     @instance.server_capabilities.destroy
+    Inferno::Models::ServerCapabilities.create(
+      testing_instance_id: @instance.id,
+      capabilities: FHIR::CapabilityStatement.new.to_json
+    )
     @instance.reload
     exception = assert_raises(Inferno::SkipException) { @sequence.run_test(@test) }