Merge pull request #301 from onc-healthit/development

Version 2.6.0

.gitignore

@@ -12,4 +12,3 @@ coverage
 tmp/*
 .vscode/*
 resources/terminology/*
-.ruby-version

.ruby-version

@@ -0,0 +1 @@
+2.5.6

.tool-versions

@@ -0,0 +1 @@
+ruby 2.5.6

.travis.yml

@@ -1,9 +1,6 @@
 language: ruby
 services:
   - docker
-rvm:
-  - 2.5
-  - 2.6
 before_install:
   - gem update --system
   - gem install bundler

Dockerfile

@@ -1,8 +1,28 @@
-FROM ruby:2.5
+FROM ruby:2.5.6
 
-# Install gems into a temporary directory
-COPY Gemfile* ./
-RUN gem install bundler && bundle install
+WORKDIR /var/www/inferno
 
-# Expose the port
+### Install dependencies
+
+COPY Gemfile* /var/www/inferno/
+RUN gem install bundler
+# Throw an error if Gemfile & Gemfile.lock are out of sync
+RUN bundle config --global frozen 1
+RUN bundle install
+
+### Install Inferno
+
+RUN mkdir data
+COPY public /var/www/inferno/public
+COPY resources /var/www/inferno/resources
+COPY config* /var/www/inferno/
+COPY Rakefile /var/www/inferno/
+COPY test /var/www/inferno/test
+COPY lib /var/www/inferno/lib
+
+### Set up environment
+
+ENV APP_ENV=production
 EXPOSE 4567
+
+CMD ["bundle", "exec", "rackup", "-o", "0.0.0.0"]

Gemfile

@@ -13,17 +13,19 @@ gem 'json-jwt'
 gem 'kramdown'
 gem 'pry'
 gem 'pry-byebug'
-gem 'rack-test'
 gem 'rake'
 gem 'rb-readline'
 gem 'rest-client'
-gem 'rubocop', require: false
 gem 'selenium-webdriver'
 gem 'sinatra'
 gem 'sinatra-contrib'
 gem 'sqlite3'
 gem 'thin'
 gem 'time_difference'
-gem 'webmock'
 
-gem 'simplecov', require: false, group: :test
+group :test do
+  gem 'rack-test'
+  gem 'rubocop', require: false
+  gem 'simplecov', require: false
+  gem 'webmock'
+end

README.md

@@ -1,4 +1,4 @@
-<img src="https://github.com/onc-healthit/inferno/blob/master/public/images/inferno_logo.png" width="300px" />
+<img src="https://raw.githubusercontent.com/onc-healthit/inferno/master/public/images/inferno_logo.png" width="300px" />
 
 [![Build Status](https://travis-ci.org/onc-healthit/inferno.svg?branch=master)](https://travis-ci.org/onc-healthit/inferno)
 
@@ -82,7 +82,7 @@ bundle exec rake test
 ## Inspecting and Exporting Tests
 
 Tests are written to be easily understood, even by those who aren't familiar with Ruby.  They can be
-viewed directly [in this repository](https://github.com/onc-healthit/inferno/tree/master/lib/app/sequences).
+viewed directly [in this repository](https://github.com/onc-healthit/inferno/tree/master/lib/app/modules).
 
 Tests contain metadata that provide additional details and traceability to standards.  The active tests and related metadata can be exported into CSV format and saved to a file named `testlist.csv` with the following command:
 

config.yml

@@ -5,9 +5,6 @@ app_name: Inferno
 # There are a few exceptions, such as "/" and "/landing".
 base_path: "inferno"
 
-# Show or hide tutorials
-show_tutorial: true
-
 # Useful during development to purge the database on each reload
 purge_database_on_reload: false
 

docker-compose.yml

@@ -1,19 +1,12 @@
 version: '3'
 services:
-  # the main ruby server
   ruby_server:
-    # build the image from ./Dockerfile (this installs the dependencies into the image)
     build:
       context: ./
-    # map the project directory into the running container
     volumes:
-      - .:/var/www/inferno
-    # expose the internal application to direct HTTP requests
-    #ports:
-    #  - "4567:8080"
-    # run the application
-    working_dir: /var/www/inferno
-    command: rackup -o 0.0.0.0
+      - ./config.yml:/var/www/inferno/config.yml
+    ports:
+     - "4567:8080"
   nginx_server:
     image: nginx
     volumes:
@@ -24,4 +17,4 @@ services:
     links:
       - ruby_server:ruby_server
     depends_on:
-      - ruby_server
+      - ruby_server

generators/uscore-r4/generator.rb

@@ -6,9 +6,17 @@
 require 'net/http'
 require 'fhir_models'
 require_relative './metadata_extractor'
+require_relative '../../lib/app/utils/validation'
 
-OUT_PATH = '../../lib/app/modules'
-RESOURCE_PATH = '../../resources/us_core_r4/'
+OUT_PATH = File.expand_path('../../lib/app/modules', __dir__)
+RESOURCE_PATH = File.expand_path('../../resources/us_core_r4', __dir__)
+
+PROFILE_URIS = Inferno::ValidationUtil::US_CORE_R4_URIS
+
+def validation_profile_uri(sequence)
+  profile_uri = PROFILE_URIS.key(sequence[:profile])
+  "Inferno::ValidationUtil::US_CORE_R4_URIS[:#{profile_uri}]" if profile_uri
+end
 
 def run
   redownload_files = (ARGV&.first == '-d')
@@ -31,8 +39,15 @@ def generate_search_validators(metadata)
 end
 
 def generate_tests(metadata)
+  # first isolate the profiles that don't have patient searches
+  mark_delayed_sequences(metadata)
+
   metadata[:sequences].each do |sequence|
     puts "Generating test #{sequence[:name]}"
+
+    # read reference if sequence contains no search sequences
+    create_read_test(sequence) if sequence[:delayed_sequence]
+
     # authorization test
     create_authorization_test(sequence)
 
@@ -52,6 +67,7 @@ def generate_tests(metadata)
       .each do |interaction|
         # specific edge cases
         interaction[:code] = 'history' if interaction[:code] == 'history-instance'
+        next if interaction[:code] == 'read' && sequence[:delayed_sequence]
 
         create_interaction_test(sequence, interaction)
       end
@@ -62,25 +78,52 @@ def generate_tests(metadata)
   end
 end
 
+def mark_delayed_sequences(metadata)
+  metadata[:sequences].each do |sequence|
+    sequence[:delayed_sequence] = sequence[:resource] != 'Patient' && sequence[:searches].none? { |search| search[:names].include? 'patient' }
+  end
+  metadata[:delayed_sequences] = metadata[:sequences].select { |seq| seq[:delayed_sequence] }
+  metadata[:non_delayed_sequences] = metadata[:sequences].reject { |seq| seq[:delayed_sequence] }
+end
+
+def find_first_search(sequence)
+  sequence[:searches].find { |search_param| search_param[:expectation] == 'SHALL' } ||
+    sequence[:searches].find { |search_param| search_param[:expectation] == 'SHOULD' }
+end
+
 def generate_sequence(sequence)
   puts "Generating #{sequence[:name]}\n"
   file_name = OUT_PATH + '/us_core_r4/' + sequence[:name].downcase + '_sequence.rb'
 
-  template = ERB.new(File.read('./templates/sequence.rb.erb'))
+  template = ERB.new(File.read(File.join(__dir__, 'templates/sequence.rb.erb')))
   output =   template.result_with_hash(sequence)
   FileUtils.mkdir_p(OUT_PATH + '/us_core_r4') unless File.directory?(OUT_PATH + '/us_core_r4')
   File.write(file_name, output)
 end
 
+def create_read_test(sequence)
+  read_test = {
+    tests_that: "Can read #{sequence[:resource]} from the server",
+    index: sequence[:tests].length + 1,
+    link: 'https://build.fhir.org/ig/HL7/US-Core-R4/CapabilityStatement-us-core-server.html'
+  }
+
+  read_test[:test_code] = %(
+        #{sequence[:resource].downcase}_id = @instance.resource_references.find { |reference| reference.resource_type == '#{sequence[:resource]}' }&.resource_id
+        skip 'No #{sequence[:resource]} references found from the prior searches' if #{sequence[:resource].downcase}_id.nil?
+        @#{sequence[:resource].downcase} = fetch_resource('#{sequence[:resource]}', #{sequence[:resource].downcase}_id)
+        @resources_found = !@#{sequence[:resource].downcase}.nil?)
+  sequence[:tests] << read_test
+end
+
 def create_authorization_test(sequence)
   authorization_test = {
     tests_that: "Server rejects #{sequence[:resource]} search without authorization",
     index: sequence[:tests].length + 1,
     link: 'http://www.fhir.org/guides/argonaut/r2/Conformance-server.html'
   }
 
-  first_search = sequence[:searches].find { |search_param| search_param[:expectation] == 'SHALL' } ||
-                 sequence[:searches].find { |search_param| search_param[:expectation] == 'SHOULD' }
+  first_search = find_first_search(sequence)
   return if first_search.nil?
 
   authorization_test[:test_code] = %(
@@ -98,10 +141,17 @@ def create_search_test(sequence, search_param)
   search_test = {
     tests_that: "Server returns expected results from #{sequence[:resource]} search by #{search_param[:names].join('+')}",
     index: sequence[:tests].length + 1,
-    link: 'https://build.fhir.org/ig/HL7/US-Core-R4/CapabilityStatement-us-core-server.html'
+    link: 'https://build.fhir.org/ig/HL7/US-Core-R4/CapabilityStatement-us-core-server.html',
+    optional: search_param[:expectation] != 'SHALL'
   }
 
-  is_first_search = search_test[:index] == 2 # if first search - fix this check later
+  is_first_search = search_param == find_first_search(sequence)
+  save_resource_ids_in_bundle_arguments = [
+    "versioned_resource_class('#{sequence[:resource]}')",
+    'reply',
+    validation_profile_uri(sequence)
+  ].compact.join(', ')
+
   search_test[:test_code] =
     if is_first_search
       %(#{get_search_params(search_param[:names], sequence)}
@@ -116,7 +166,8 @@ def create_search_test(sequence, search_param)
 
         @#{sequence[:resource].downcase} = reply.try(:resource).try(:entry).try(:first).try(:resource)
         @#{sequence[:resource].downcase}_ary = reply&.resource&.entry&.map { |entry| entry&.resource }
-        save_resource_ids_in_bundle(versioned_resource_class('#{sequence[:resource]}'), reply)
+        save_resource_ids_in_bundle(#{save_resource_ids_in_bundle_arguments})
+        save_delayed_sequence_references(@#{sequence[:resource].downcase})
         validate_search_reply(versioned_resource_class('#{sequence[:resource]}'), reply, search_params))
     else
       %(
@@ -216,7 +267,7 @@ def create_resource_profile_test(sequence)
   }
   test[:test_code] = %(
         skip 'No resources appear to be available for this patient. Please use patients with more information.' unless @resources_found
-        test_resources_against_profile('#{sequence[:resource]}'))
+        test_resources_against_profile('#{sequence[:resource]}'#{', ' + validation_profile_uri(sequence) if validation_profile_uri(sequence)}))
 
   sequence[:tests] << test
 end
@@ -259,6 +310,8 @@ def get_value_path_by_type(type)
     '.code'
   when 'HumanName'
     '.family'
+  when 'Address'
+    '.city'
   else
     ''
   end
@@ -334,14 +387,13 @@ def get_comparator_searches(search_params, sequence)
 def search_param_constants(search_parameters, sequence)
   return "patient: @instance.patient_id, category: 'assess-plan'" if search_parameters == ['patient', 'category'] && sequence[:resource] == 'CarePlan'
   return "patient: @instance.patient_id, status: 'active'" if search_parameters == ['patient', 'status'] && sequence[:resource] == 'CareTeam'
-  return "patient: @instance.patient_id, name: 'Boston'" if search_parameters == ['name'] && (['Location', 'Organization'].include? sequence[:resource])
   return "'_id': @instance.patient_id" if search_parameters == ['_id'] && sequence[:resource] == 'Patient'
-  return "patient: @instance.patient_id, code: '72166-2'" if search_parameters == ['patient', 'code'] && sequence[:profile] == 'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-smokingstatus.json'
-  return "patient: @instance.patient_id, category: 'laboratory'" if search_parameters == ['patient', 'category'] && sequence[:profile] == 'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-observation-lab.json'
-  return "patient: @instance.patient_id, code: '77606-2'" if search_parameters == ['patient', 'code'] && sequence[:profile] == 'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-pediatric-weight-for-height.json'
-  return "patient: @instance.patient_id, code: '59576-9'" if search_parameters == ['patient', 'code'] && sequence[:profile] == 'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-pediatric-bmi-for-age.json'
-  return "patient: @instance.patient_id, category: 'LAB'" if search_parameters == ['patient', 'category'] && sequence[:profile] == 'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-diagnosticreport-lab.json'
-  return "patient: @instance.patient_id, code: 'LP29684-5'" if search_parameters == ['patient', 'category'] && sequence[:profile] == 'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-diagnosticreport-note.json'
+  return "patient: @instance.patient_id, code: '72166-2'" if search_parameters == ['patient', 'code'] && sequence[:profile] == PROFILE_URIS[:smoking_status]
+  return "patient: @instance.patient_id, category: 'laboratory'" if search_parameters == ['patient', 'category'] && sequence[:profile] == PROFILE_URIS[:lab_results]
+  return "patient: @instance.patient_id, code: '77606-2'" if search_parameters == ['patient', 'code'] && sequence[:profile] == PROFILE_URIS[:pediatric_weight_height]
+  return "patient: @instance.patient_id, code: '59576-9'" if search_parameters == ['patient', 'code'] && sequence[:profile] == PROFILE_URIS[:pediatric_bmi_age]
+  return "patient: @instance.patient_id, category: 'LAB'" if search_parameters == ['patient', 'category'] && sequence[:profile] == PROFILE_URIS[:diagnostic_report_lab]
+  return "patient: @instance.patient_id, code: 'LP29684-5'" if search_parameters == ['patient', 'category'] && sequence[:profile] == PROFILE_URIS[:diagnostic_report_note]
 end
 
 def create_search_validation(sequence)
@@ -418,7 +470,7 @@ def validate_resource_item(resource, property, value)
 def generate_module(module_info)
   file_name = OUT_PATH + '/us_core_module.yml'
 
-  template = ERB.new(File.read('./templates/module.yml.erb'))
+  template = ERB.new(File.read(File.join(__dir__, 'templates/module.yml.erb')))
   output = template.result_with_hash(module_info)
 
   File.write(file_name, output)

generators/uscore-r4/metadata_extractor.rb

@@ -1,19 +1,23 @@
 # frozen_string_literal: true
 
 class MetadataExtractor
-  CAPABILITY_STATEMENT_URI = 'https://build.fhir.org/ig/HL7/US-Core-R4/CapabilityStatement-us-core-server.json'
+  CAPABILITY_STATEMENT_URI = 'https://www.hl7.org/fhir/us/core/CapabilityStatement-us-core-server.json'
 
   def profile_uri(profile)
-    "https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-#{profile}.json"
+    "http://hl7.org/fhir/us/core/StructureDefinition/#{profile}"
+  end
+
+  def profile_json_uri(profile)
+    "https://www.hl7.org/fhir/us/core/StructureDefinition-#{profile}.json"
   end
 
   def search_param_uri(resource, param)
     param = 'id' if param == '_id'
-    "https://build.fhir.org/ig/HL7/US-Core-R4/SearchParameter-us-core-#{resource.downcase}-#{param}.json"
+    "https://www.hl7.org/fhir/us/core/SearchParameter-us-core-#{resource.downcase}-#{param}.json"
   end
 
   def get_json_from_uri(uri)
-    filename = RESOURCE_PATH + uri.split('/').last
+    filename = File.join(RESOURCE_PATH, uri.split('/').last)
     unless File.exist?(filename)
       puts "Downloading #{uri}\n"
       json_result = Net::HTTP.get(URI(uri))
@@ -33,7 +37,7 @@ def extract_metadata
 
   def build_new_sequence(resource, profile)
     base_name = profile.split('StructureDefinition/')[1]
-    profile_json = get_json_from_uri(profile_uri(base_name))
+    profile_json = get_json_from_uri(profile_json_uri(base_name))
     profile_title = profile_json['title'].gsub(/US\s*Core\s*/, '').gsub(/\s*Profile/, '').strip
     {
       name: base_name.tr('-', '_'),
@@ -44,6 +48,7 @@ def build_new_sequence(resource, profile)
         .gsub('UsCore', 'USCoreR4') + 'Sequence',
       resource: resource['type'],
       profile: profile_uri(base_name), # link in capability statement is incorrect,
+      profile_json: profile_json_uri(base_name),
       title: profile_title,
       interactions: [],
       searches: [],
@@ -67,7 +72,7 @@ def extract_metadata_from_resources(resources)
         add_combo_searches(resource, new_sequence)
         add_interactions(resource, new_sequence)
 
-        profile_definition = get_json_from_uri(new_sequence[:profile])
+        profile_definition = get_json_from_uri(new_sequence[:profile_json])
         add_must_support_elements(profile_definition, new_sequence)
         add_search_param_descriptions(profile_definition, new_sequence)
         add_element_definitions(profile_definition, new_sequence)
@@ -203,9 +208,9 @@ def add_element_definitions(profile_definition, sequence)
 
   def add_special_cases
     category_first_profiles = [
-      'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-diagnosticreport-lab.json',
-      'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-observation-lab.json',
-      'https://build.fhir.org/ig/HL7/US-Core-R4/StructureDefinition-us-core-diagnosticreport-note.json'
+      PROFILE_URIS[:diagnostic_report_lab],
+      PROFILE_URIS[:lab_results],
+      PROFILE_URIS[:diagnostic_report_note]
     ]
 
     # search by patient first

generators/uscore-r4/templates/module.yml.erb

@@ -18,9 +18,10 @@ test_sets:
         - ManualRegistrationSequence
         - StandaloneLaunchSequence
         - EHRLaunchSequence
-      - name: US Core R4
+      - name: US Core R4 Patient Based Profiles
         run_all: true
-        sequences:<% sequences.each do |sequence| %>
+        sequences:<% non_delayed_sequences.each do |sequence| %>
         - <%=sequence[:classname]%><% end %>
         - R4ProvenanceSequence
-        - USCoreR4ClinicalNotesSequence
+        - USCoreR4ClinicalNotesSequence<% delayed_sequences.each do |sequence| %>
+        - <%=sequence[:classname]%><% end %>