inferno_core 0.4.37 → 0.4.38

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5fad068333ba8fce867afba323937728da89231ded560129675318866059975a
-  data.tar.gz: d231cf80975b781b0584c5bb2b4677e1493eaba2fa6469ffca490e113d46ba08
+  metadata.gz: e2af0569e09addd1d815e42110f9813a875037b66a67871af0441a149b38c818
+  data.tar.gz: 4b526226bac3009548c7e70b75b59dc77e9c800700eed13e13846d30cbc79161
 SHA512:
-  metadata.gz: 34c983546c7ea05443d9edde97e59d9c9dab2e1848271eefb4f888ff58cafc1219541de91634250ae4831162689cdd9e1e8f043735bc0fe6e495c86eb3a1bf41
-  data.tar.gz: 2208622633268affb624426a91f4d6b7feed45cd7eac97dbad7c750c22169d7c08c5297fa96f8be86d13785faccf9966ad328b700528bcce0d2b8c6ba9cf97d1
+  metadata.gz: c0ab492c234d9a19ee06cca497a1e9714238bd1b7b0a2765b3647a49e0f3125a7a3b3f73e025e9741ec71b67c695d78258480d22aaf8974f8002b0354a0c0bdc
+  data.tar.gz: 241271ec1ef24731b06446dd442485fb8053f43504e3948a29077e26358b6b515102f41671336577c54b6705cb3858b7c59e0ac53819eadde5243ea98c16f8b2

data/lib/inferno/apps/cli/console.rb

@@ -4,6 +4,9 @@ module Inferno
       def run
         require_relative '../../../inferno'
 
+        ENV['ASYNC_JOBS'] = 'false'
+        ENV['INITIALIZE_VALIDATOR_SESSIONS'] = 'false'
+
         Inferno::Application.finalize!
         Pry.start
       end

data/lib/inferno/apps/cli/main.rb

@@ -11,6 +11,7 @@ module Inferno
     class Main < Thor
       desc 'console', 'Start an interactive console session with Inferno'
       def console
+        Migration.new.run(Logger::INFO)
         Console.new.run
       end
 
@@ -25,6 +26,7 @@ module Inferno
              type: :boolean,
              desc: 'Automatically restart Inferno when a file is changed.'
       def start
+        Migration.new.run(Logger::INFO)
         command = 'foreman start --env=/dev/null'
         if `gem list -i foreman`.chomp == 'false'
           puts "You must install foreman with 'gem install foreman' prior to running Inferno."

data/lib/inferno/apps/cli/migration.rb

@@ -3,9 +3,9 @@ require_relative '../../utils/migration'
 module Inferno
   module CLI
     class Migration
-      def run
+      def run(log_level = Logger::DEBUG)
         Inferno::Application.start(:logging)
-        Inferno::Application['logger'].level = Logger::DEBUG
+        Inferno::Application['logger'].level = log_level
 
         Utils::Migration.new.run
       end

data/lib/inferno/apps/cli/templates/.env.development

@@ -1,2 +1,2 @@
-VALIDATOR_URL=http://localhost/validatorapi
+FHIR_RESOURCE_VALIDATOR_URL=http://localhost/hl7validatorapi
 REDIS_URL=redis://localhost:6379/0

data/lib/inferno/apps/cli/templates/.env.production

@@ -1,2 +1,2 @@
 REDIS_URL=redis://redis:6379/0
-VALIDATOR_URL=http://validator_service:4567
+FHIR_RESOURCE_VALIDATOR_URL=http://hl7_validator_service:3500

data/lib/inferno/apps/cli/templates/.env.test

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

data/lib/inferno/apps/cli/templates/config/nginx.background.conf.tt

@@ -82,5 +82,21 @@ http {
 
       proxy_pass http://validator_service:4567/;
     }
+
+    location /hl7validatorapi/ {
+      proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+      proxy_set_header Host $http_host;
+      proxy_set_header X-Forwarded-Proto $scheme;
+      proxy_set_header X-Forwarded-Port $server_port;
+      proxy_redirect off;
+      proxy_set_header Connection '';
+      proxy_http_version 1.1;
+      chunked_transfer_encoding off;
+      proxy_buffering off;
+      proxy_cache off;
+      proxy_read_timeout 600s;
+
+      proxy_pass http://hl7_validator_service:3500/;
+    }
   }
 }

data/lib/inferno/apps/cli/templates/config/nginx.conf.tt

@@ -97,5 +97,21 @@ http {
 
       proxy_pass http://validator_service:4567/;
     }
+
+    location /hl7validatorapi/ {
+      proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
+      proxy_set_header Host $http_host;
+      proxy_set_header X-Forwarded-Proto $scheme;
+      proxy_set_header X-Forwarded-Port $server_port;
+      proxy_redirect off;
+      proxy_set_header Connection '';
+      proxy_http_version 1.1;
+      chunked_transfer_encoding off;
+      proxy_buffering off;
+      proxy_cache off;
+      proxy_read_timeout 600s;
+
+      proxy_pass http://hl7_validator_service:3500/;
+    }
   }
 }

data/lib/inferno/apps/cli/templates/docker-compose.background.yml.tt

@@ -1,5 +1,16 @@
 version: '3'
 services:
+  hl7_validator_service:
+    image: infernocommunity/inferno-resource-validator
+    environment:
+      # Defines how long validator sessions last if unused, in minutes:
+      # Negative values mean sessions never expire, 0 means sessions immediately expire
+      SESSION_CACHE_DURATION: -1
+    volumes:
+      - ./<%= ig_path %>:/app/igs
+      # To let the service share your local FHIR package cache,
+      # uncomment the below line
+      # - ~/.fhir:/home/ktor/.fhir
   validator_service:
     image: infernocommunity/fhir-validator-service
     # Update this path to match your directory structure

data/lib/inferno/apps/cli/templates/docker-compose.yml.tt

@@ -15,6 +15,10 @@ services:
     command: bundle exec sidekiq -r ./worker.rb
     depends_on:
       - redis
+  hl7_validator_service:
+    extends:
+      file: docker-compose.background.yml
+      service: hl7_validator_service
   validator_service:
     extends:
       file: docker-compose.background.yml

data/lib/inferno/apps/cli/templates/lib/%library_name%/igs/README.md

@@ -0,0 +1,21 @@
+# Note on this IGs folder
+
+There are three reasons why it would be necessary to put an IG package.tgz in this folder. If none of these apply, you do not need to put any files here, or can consider removing any existing files to make it clear they are unused.
+
+## 1. Generated Test Suites
+Some test kits use a "generator" to automatically generate the contents of a test suite for an IG. The IG files are required every time the test suites need to be regenerated. Examples of test kits that use this approach are the US Core Test Kit and CARIN IG for Blue Button® Test Kit.
+
+
+## 2. Non-published IG
+If your IG, or the specific version of the IG you want to test against, is not published, then the validator service needs to load the IG from file in order to be able to validate resources with it. The IG must be referenced in the `fhir_resource_validator` block in the test suite definition by filename, ie:
+
+```ruby
+      fhir_resource_validator do
+        igs 'igs/filename.tgz'
+
+        ...
+      end
+```
+
+## 3. Inferno Validator UI
+The Inferno Validator UI is configured to auto-load any IGs present in the igs folder and include them in all validations. In general, the Inferno team is currently leaving IGs in this folder even if not otherwise necessary to make it easy to re-enable the validator UI.

data/lib/inferno/apps/cli/templates/lib/%library_name%.rb.tt

@@ -22,8 +22,13 @@ module <%= module_name %>
     end
 
     # All FHIR validation requsets will use this FHIR validator
-    validator do
-      url ENV.fetch('VALIDATOR_URL')
+    fhir_resource_validator do
+      # igs 'identifier#version' # Use this method for published IGs/versions
+      # igs 'igs/filename.tgz'   # Use this otherwise
+
+      exclude_message do |message|
+        message.message.match?(/\A\S+: \S+: URL value '.*' does not resolve/)
+      end
     end
 
     # Tests and TestGroups can be defined inline

data/lib/inferno/apps/cli/templates/spec/%library_name%/patient_group_spec.rb.tt

@@ -4,7 +4,26 @@ RSpec.describe <%= module_name %>::PatientGroup do
   let(:session_data_repo) { Inferno::Repositories::SessionData.new }
   let(:test_session) { repo_create(:test_session, test_suite_id: '<%= test_suite_id %>') }
   let(:url) { 'http://example.com/fhir' }
-  let(:error_outcome) { FHIR::OperationOutcome.new(issue: [{ severity: 'error' }]) }
+  let(:success_outcome) do
+    {
+      outcomes: [{
+        issues: []
+      }],
+      sessionId: ''
+    }
+  end
+  let(:error_outcome) do
+    {
+      outcomes: [{
+        issues: [{
+          location: 'Patient.identifier[0]',
+          message: 'Identifier.system must be an absolute reference, not a local reference',
+          level: 'ERROR'
+        }]
+      }],
+      sessionId: ''
+    }
+  end
 
   def run(runnable, inputs = {})
     test_run_params = { test_session_id: test_session.id }.merge(runnable.reference_hash)
@@ -67,9 +86,9 @@ RSpec.describe <%= module_name %>::PatientGroup do
     let(:test) { group.tests.last }
 
     it 'passes if the resource is valid' do
-      stub_request(:post, "#{ENV.fetch('VALIDATOR_URL')}/validate")
+      stub_request(:post, "#{ENV.fetch('FHIR_RESOURCE_VALIDATOR_URL')}/validate")
         .with(query: hash_including({}))
-        .to_return(status: 200, body: FHIR::OperationOutcome.new.to_json)
+        .to_return(status: 200, body: success_outcome.to_json)
 
       resource = FHIR::Patient.new
       repo_create(
@@ -79,13 +98,13 @@ RSpec.describe <%= module_name %>::PatientGroup do
         response_body: resource.to_json
       )
 
-      result = run(test)
+      result = run(test, url: url)
 
       expect(result.result).to eq('pass')
     end
 
     it 'fails if the resource is not valid' do
-      stub_request(:post, "#{ENV.fetch('VALIDATOR_URL')}/validate")
+      stub_request(:post, "#{ENV.fetch('FHIR_RESOURCE_VALIDATOR_URL')}/validate")
         .with(query: hash_including({}))
         .to_return(status: 200, body: error_outcome.to_json)
 
@@ -97,7 +116,7 @@ RSpec.describe <%= module_name %>::PatientGroup do
         response_body: resource.to_json
       )
 
-      result = run(test)
+      result = run(test, url: url)
 
       expect(result.result).to eq('fail')
     end

data/lib/inferno/config/boot/sidekiq.rb

@@ -5,6 +5,11 @@ Inferno::Application.register_provider(:sidekiq) do
     if Inferno::Application['async_jobs']
       Sidekiq.configure_server do |config|
         config.redis = { url: ENV.fetch('REDIS_URL', 'redis://127.0.0.1:6379/0') }
+
+        config.capsule('validator_sessions') do |cap|
+          cap.concurrency = ENV.fetch('VALIDATOR_SESSIONS_CONCURRENCY', '1').to_i
+          cap.queues = ['validator_sessions']
+        end
       end
     end
   end

data/lib/inferno/config/boot/validator.rb

@@ -8,6 +8,8 @@ Inferno::Application.register_provider(:validator) do
 
     next if ENV['APP_ENV'] == 'test'
 
+    next if ENV.fetch('INITIALIZE_VALIDATOR_SESSIONS', 'true').casecmp?('false')
+
     Inferno::Repositories::TestSuites.new.all.each do |suite|
       suite.fhir_validators.each do |name, validators|
         validators.each_with_index do |validator, index|

data/lib/inferno/dsl/resume_test_route.rb

@@ -1,4 +1,4 @@
-require_relative 'suite_endpoint'
+require 'hanami/controller'
 
 module Inferno
   module DSL
@@ -6,47 +6,58 @@ module Inferno
     # an incoming request.
     # @private
     # @see Inferno::DSL::Runnable#resume_test_route
-    class ResumeTestRoute < SuiteEndpoint
-      # The incoming request
-      #
-      # @return [Inferno::Entities::Request]
-      def request
-        @request ||= Inferno::Entities::Request.from_hanami_request(req)
+    class ResumeTestRoute < Hanami::Action
+      include Import[
+                requests_repo: 'inferno.repositories.requests',
+                results_repo: 'inferno.repositories.results',
+                test_runs_repo: 'inferno.repositories.test_runs',
+                tests_repo: 'inferno.repositories.tests'
+              ]
+
+      def self.call(...)
+        new.call(...)
       end
 
       # @private
-      def test_run_identifier
-        @test_run_identifier ||= instance_exec(request, &test_run_identifier_block)
+      def test_run_identifier_block
+        self.class.singleton_class.instance_variable_get(:@test_run_identifier_block)
       end
 
       # @private
       def tags
-        self.class.singleton_class.instance_variable_get(:@tags) || []
+        self.class.singleton_class.instance_variable_get(:@tags)
       end
 
       # @private
-      def update_result
-        results_repo.update_result(result.id, new_result)
+      def result
+        self.class.singleton_class.instance_variable_get(:@result)
       end
 
       # @private
-      def make_response
-        res.redirect_to redirect_route(test_run, test)
+      def find_test_run(test_run_identifier)
+        test_runs_repo.find_latest_waiting_by_identifier(test_run_identifier)
       end
 
       # @private
-      def name
-        test.config.request_name(test.incoming_request_name)
+      def find_waiting_result(test_run)
+        results_repo.find_waiting_result(test_run_id: test_run.id)
       end
 
       # @private
-      def test_run_identifier_block
-        self.class.singleton_class.instance_variable_get(:@test_run_identifier_block)
+      def update_result(waiting_result)
+        results_repo.update_result(waiting_result.id, result)
       end
 
       # @private
-      def new_result
-        self.class.singleton_class.instance_variable_get(:@new_result)
+      def persist_request(request, test_run, waiting_result, test)
+        requests_repo.create(
+          request.to_hash.merge(
+            test_session_id: test_run.test_session_id,
+            result_id: waiting_result.id,
+            name: test.config.request_name(test.incoming_request_name),
+            tags:
+          )
+        )
       end
 
       # @private
@@ -54,10 +65,38 @@ module Inferno
         "#{Application['base_url']}/test_sessions/#{test_run.test_session_id}##{resume_ui_at_id(test_run, test)}"
       end
 
+      # @private
+      def find_test(waiting_result)
+        tests_repo.find(waiting_result.test_id)
+      end
+
       # @private
       def resume_ui_at_id(test_run, test)
         test_run.test_suite_id || test_run.test_group_id || test.parent.id
       end
+
+      # @private
+      def handle(req, res)
+        request = Inferno::Entities::Request.from_hanami_request(req)
+
+        test_run_identifier = instance_exec(request, &test_run_identifier_block)
+
+        test_run = find_test_run(test_run_identifier)
+
+        halt 500, "Unable to find test run with identifier '#{test_run_identifier}'." if test_run.nil?
+
+        test_runs_repo.mark_as_no_longer_waiting(test_run.id)
+
+        waiting_result = find_waiting_result(test_run)
+        test = find_test(waiting_result)
+
+        update_result(waiting_result)
+        persist_request(request, test_run, waiting_result, test)
+
+        Jobs.perform(Jobs::ResumeTestRun, test_run.id)
+
+        res.redirect_to redirect_route(test_run, test)
+      end
     end
   end
 end

data/lib/inferno/dsl/runnable.rb

@@ -343,7 +343,7 @@ module Inferno
         route_class = Class.new(ResumeTestRoute) do |klass|
           klass.singleton_class.instance_variable_set(:@test_run_identifier_block, block)
           klass.singleton_class.instance_variable_set(:@tags, tags)
-          klass.singleton_class.instance_variable_set(:@new_result, result)
+          klass.singleton_class.instance_variable_set(:@result, result)
         end
 
         route(method, path, route_class)

data/lib/inferno/dsl/suite_endpoint.rb

@@ -244,7 +244,7 @@ module Inferno
 
       # @private
       def resume_test_run?
-        find_result&.result != 'waiting'
+        find_result&.result != 'wait'
       end
 
       # @private

data/lib/inferno/jobs/invoke_validator_session.rb

@@ -2,6 +2,7 @@ module Inferno
   module Jobs
     class InvokeValidatorSession
       include Sidekiq::Worker
+      sidekiq_options queue: 'validator_sessions'
 
       def perform(suite_id, validator_name, validator_index)
         suite = Inferno::Repositories::TestSuites.new.find suite_id