update for inferno_core 0.0.5 (#1)

.env

@@ -1,2 +1,3 @@
 JS_HOST=""
-VALIDATOR_URL=http://validator_service/validatorapi
+VALIDATOR_URL=http://validator_service:4567
+REDIS_URL=redis://redis:6379/0

.env.test

@@ -1 +1,2 @@
 VALIDATOR_URL=https://example.com/validatorapi
+ASYNC_JOBS=false

.gitignore

@@ -1,4 +1,6 @@
 /data/*.db
+/data/redis/*.rdb
+/data/redis/*.aof
 /tmp
 .env.local
 .env.*.local

Dockerfile

@@ -10,7 +10,6 @@ ADD lib/ips/version.rb $INSTALL_PATH/lib/ips/version.rb
 ADD *.gemspec $INSTALL_PATH
 ADD Gemfile* $INSTALL_PATH
 RUN gem install bundler
-RUN bundle config set --local deployment 'true'
 RUN bundle install
 
 ADD . $INSTALL_PATH

Gemfile.lock

@@ -1,26 +1,27 @@
 PATH
   remote: .
   specs:
-    ips_test_kit (0.0.1)
-      inferno_core (>= 0.0.3)
+    ips_test_kit (0.0.2)
+      inferno_core (= 0.0.5)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.1.3.2)
+    activesupport (6.1.4)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
       tzinfo (~> 2.0)
       zeitwerk (~> 2.3)
-    addressable (2.7.0)
+    addressable (2.8.0)
       public_suffix (>= 2.0.2, < 5.0)
     bcp47 (0.3.3)
       i18n
     blueprinter (0.25.2)
     byebug (11.1.3)
     coderay (1.1.3)
     concurrent-ruby (1.1.9)
+    connection_pool (2.2.5)
     crack (0.4.5)
       rexml
     database_cleaner (1.99.0)
@@ -40,10 +41,10 @@ GEM
     dry-container (0.8.0)
       concurrent-ruby (~> 1.0)
       dry-configurable (~> 0.1, >= 0.1.3)
-    dry-core (0.6.0)
+    dry-core (0.7.1)
       concurrent-ruby (~> 1.0)
     dry-equalizer (0.3.0)
-    dry-inflector (0.2.0)
+    dry-inflector (0.2.1)
     dry-logic (1.2.0)
       concurrent-ruby (~> 1.0)
       dry-core (~> 0.5, >= 0.5)
@@ -68,19 +69,25 @@ GEM
       dry-logic (~> 1.0, >= 1.0.2)
     factory_bot (6.2.0)
       activesupport (>= 5.0.0)
-    faraday (1.4.2)
+    faraday (1.7.0)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
       faraday-excon (~> 1.1)
+      faraday-httpclient (~> 1.0.1)
       faraday-net_http (~> 1.0)
       faraday-net_http_persistent (~> 1.1)
+      faraday-patron (~> 1.0)
+      faraday-rack (~> 1.0)
       multipart-post (>= 1.2, < 3)
       ruby2_keywords (>= 0.0.4)
     faraday-em_http (1.0.0)
     faraday-em_synchrony (1.0.0)
     faraday-excon (1.1.0)
+    faraday-httpclient (1.0.1)
     faraday-net_http (1.0.1)
-    faraday-net_http_persistent (1.1.0)
+    faraday-net_http_persistent (1.2.0)
+    faraday-patron (1.0.0)
+    faraday-rack (1.0.0)
     fhir_client (4.0.6)
       activesupport (>= 3)
       addressable (>= 2.3)
@@ -92,21 +99,21 @@ GEM
       rack (>= 1.5)
       rest-client (~> 2.0)
       tilt (>= 1.1)
-    fhir_dstu2_models (1.0.11)
+    fhir_dstu2_models (1.1.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.10.4)
-    fhir_models (4.1.2)
+      nokogiri (>= 1.11.4)
+    fhir_models (4.2.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.10.4)
-    fhir_stu3_models (3.0.2)
+      nokogiri (>= 1.11.4)
+    fhir_stu3_models (3.1.0)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
-      nokogiri (>= 1.10.4)
+      nokogiri (>= 1.11.4)
     hanami-controller (1.3.3)
       hanami-utils (~> 1.3)
       rack (~> 2.0)
@@ -127,13 +134,14 @@ GEM
     i18n (1.8.10)
       concurrent-ruby (~> 1.0)
     ice_nine (0.11.2)
-    inferno_core (0.0.3)
+    inferno_core (0.0.5)
       activesupport (~> 6.1)
       blueprinter (= 0.25.2)
       dotenv (~> 2.7)
       dry-system (= 0.18.1)
       faraday (~> 1.2)
       fhir_client (~> 4.0)
+      fhir_models (~> 4.2.0)
       hanami-controller (~> 1.3)
       hanami-router (~> 1.3)
       oj (~> 3.11)
@@ -142,41 +150,43 @@ GEM
       puma (~> 5.3)
       rake (~> 13.0)
       sequel (~> 5.42)
+      sidekiq (~> 6.2.1)
       sqlite3 (~> 1.4)
     jwt (2.2.3)
     method_source (1.0.0)
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2021.0225)
+    mime-types-data (3.2021.0704)
     minitest (5.14.4)
     multi_json (1.15.0)
     multi_xml (0.6.0)
     multipart-post (2.1.1)
     netrc (0.11.0)
-    nio4r (2.5.7)
-    nokogiri (1.11.7-x86_64-darwin)
+    nio4r (2.5.8)
+    nokogiri (1.12.2-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.11.7-x86_64-linux)
+    nokogiri (1.12.2-x86_64-linux)
       racc (~> 1.4)
     oauth2 (1.4.7)
       faraday (>= 0.8, < 2.0)
       jwt (>= 1.0, < 3.0)
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    oj (3.11.6)
+    oj (3.13.1)
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
     pry-byebug (3.8.0)
       byebug (~> 11.0)
       pry (~> 0.10)
     public_suffix (4.0.6)
-    puma (5.3.2)
+    puma (5.4.0)
       nio4r (~> 2.0)
     racc (1.5.2)
     rack (2.2.3)
-    rake (13.0.3)
+    rake (13.0.6)
+    redis (4.4.0)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
@@ -196,8 +206,12 @@ GEM
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.10.0)
     rspec-support (3.10.2)
-    ruby2_keywords (0.0.4)
-    sequel (5.45.0)
+    ruby2_keywords (0.0.5)
+    sequel (5.47.0)
+    sidekiq (6.2.1)
+      connection_pool (>= 2.2.2)
+      rack (~> 2.0)
+      redis (>= 4.2.0)
     sqlite3 (1.4.2)
     tilt (2.0.10)
     transproc (1.1.1)

README.md

@@ -14,5 +14,7 @@ these tests so that you don't have to configure ruby locally.
 - Clone this repo.
 - Run `docker-compose build` in this repo.
 - Run `docker-compose pull` in this repo.
+- Run `docker-compose run inferno bundle exec rake db:migrate` to set up the
+  database.
 - Run `docker-compose up` in this repo.
 - Navigate to `http://localhost:4567`. The IPS test suite will be available.

Rakefile

@@ -4,3 +4,12 @@ begin
   task default: :spec
 rescue LoadError # rubocop:disable Lint/SuppressedException
 end
+
+namespace :db do
+  desc 'Apply changes to the database'
+  task :migrate do
+    require 'inferno'
+
+    Inferno::Application.start(:db)
+  end
+end

docker-compose.yml

@@ -13,3 +13,16 @@ services:
     image: infernocommunity/fhir-validator-service
     volumes:
       - ./lib/ips/igs:/home/igs
+  redis:
+    image: redis
+    volumes:
+      - ./data/redis:/data
+    command: redis-server --appendonly yes
+  worker:
+    build:
+      context: ./
+    volumes:
+      - ./data:/opt/inferno/data
+    command: bundle exec sidekiq -r ./worker.rb
+    depends_on:
+      - redis

ips_test_kit.gemspec

@@ -11,8 +11,8 @@ Gem::Specification.new do |spec|
   spec.summary       = 'A collection of tests for the International Patient Summary FHIR Implementation Guide'
   spec.description   = 'A collection of tests for the International Patient Summary FHIR Implementation Guide'
   spec.homepage      = 'https://github.com/inferno_community/ips-test-kit'
-  spec.license       = 'Apache 2.0'
-  spec.add_runtime_dependency 'inferno_core', '>= 0.0.3'
+  spec.license       = 'Apache-2.0'
+  spec.add_runtime_dependency 'inferno_core', '0.0.5'
   spec.add_development_dependency 'database_cleaner-sequel', '~> 1.8'
   spec.add_development_dependency 'factory_bot', '~> 6.1'
   spec.add_development_dependency 'rspec', '~> 3.10'

lib/ips/document_operation.rb

@@ -54,7 +54,7 @@ class DocumentOperation < Inferno::TestGroup
 
         composition = resource
         references_in_composition = []
-        walk_resource(composition) do |value, meta, _path|
+        composition.each_element do |value, meta, _path|
           next if meta['type'] != 'Reference'
           next if value.reference.blank?
 

lib/ips/version.rb

@@ -1,3 +1,3 @@
 module IPS
-  VERSION = '0.0.1'.freeze
+  VERSION = '0.0.2'.freeze
 end

spec/ips/condition_spec.rb

@@ -1,15 +1,18 @@
 RSpec.describe IPS::Condition do
   let(:suite) { Inferno::Repositories::TestSuites.new.find('ips') }
   let(:group) { suite.groups[1].groups[21] }
+  let(:session_data_repo) { Inferno::Repositories::SessionData.new }
   let(:test_session) { repo_create(:test_session, test_suite_id: 'ips') }
   let(:url) { 'http://example.com/fhir' }
   let(:error_outcome) { FHIR::OperationOutcome.new(issue: [{ severity: 'error' }]) }
 
   def run(runnable, inputs = {})
     test_run_params = { test_session_id: test_session.id }.merge(runnable.reference_hash)
     test_run = Inferno::Repositories::TestRuns.new.create(test_run_params)
-    Inferno::TestRunner.new(test_session: test_session, test_run: test_run).run(runnable, inputs)
-    Inferno::Repositories::TestRuns.new.results_for_test_run(test_run.id)
+    inputs.each do |name, value|
+      session_data_repo.save(test_session_id: test_session.id, name: name, value: value)
+    end
+    Inferno::TestRunner.new(test_session: test_session, test_run: test_run).run(runnable)
   end
 
   describe 'read test' do
@@ -21,7 +24,7 @@ def run(runnable, inputs = {})
       stub_request(:get, "#{url}/Condition/#{condition_id}")
         .to_return(status: 200, body: resource.to_json)
 
-      result = run(test, url: url, condition_id: condition_id).first
+      result = run(test, url: url, condition_id: condition_id)
 
       expect(result.result).to eq('pass')
     end
@@ -31,7 +34,7 @@ def run(runnable, inputs = {})
       stub_request(:get, "#{url}/Condition/#{condition_id}")
         .to_return(status: 201, body: resource.to_json)
 
-      result = run(test, url: url, condition_id: condition_id).first
+      result = run(test, url: url, condition_id: condition_id)
 
       expect(result.result).to eq('fail')
       expect(result.result_message).to match(/200/)
@@ -42,7 +45,7 @@ def run(runnable, inputs = {})
       stub_request(:get, "#{url}/Condition/#{condition_id}")
         .to_return(status: 200, body: resource.to_json)
 
-      result = run(test, url: url, condition_id: condition_id).first
+      result = run(test, url: url, condition_id: condition_id)
 
       expect(result.result).to eq('fail')
       expect(result.result_message).to match(/Condition/)
@@ -53,7 +56,7 @@ def run(runnable, inputs = {})
       stub_request(:get, "#{url}/Condition/#{condition_id}")
         .to_return(status: 200, body: resource.to_json)
 
-      result = run(test, url: url, condition_id: condition_id).first
+      result = run(test, url: url, condition_id: condition_id)
 
       expect(result.result).to eq('fail')
       expect(result.result_message).to match(/resource with id/)
@@ -76,7 +79,7 @@ def run(runnable, inputs = {})
         response_body: resource.to_json
       )
 
-      result = run(test).first
+      result = run(test)
 
       expect(result.result).to eq('pass')
     end
@@ -94,7 +97,7 @@ def run(runnable, inputs = {})
         response_body: resource.to_json
       )
 
-      result = run(test).first
+      result = run(test)
 
       expect(result.result).to eq('fail')
     end