inferno_core 0.4.30 → 0.4.32

checksums.yaml

@@ -1,7 +1,7 @@
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data/lib/inferno/apps/cli/templates/%library_name%.gemspec.tt

@@ -0,0 +1,26 @@
+Gem::Specification.new do |spec|
+  spec.name          = '<%= library_name %>'
+  spec.version       = '0.0.1'
+  spec.authors       = <%= authors %>
+  # spec.email         = ['TODO']
+  spec.date          = Time.now.utc.strftime('%Y-%m-%d')
+  spec.summary       = '<%= title_name %> Test Kit'
+  spec.description   = '<%= human_name %> Inferno test kit for FHIR'
+  # spec.homepage      = 'TODO'
+  spec.license       = 'Apache-2.0'
+  spec.add_runtime_dependency 'inferno_core', '~> <%= Inferno::VERSION %>'
+  spec.add_development_dependency 'database_cleaner-sequel', '~> 1.8'
+  spec.add_development_dependency 'factory_bot', '~> 6.1'
+  spec.add_development_dependency 'rspec', '~> 3.10'
+  spec.add_development_dependency 'webmock', '~> 3.11'
+  spec.required_ruby_version = Gem::Requirement.new('>= 3.1.2')
+  # spec.metadata['homepage_uri'] = spec.homepage
+  # spec.metadata['source_code_uri'] = 'TODO'
+  spec.files = [
+    Dir['lib/**/*.rb'],
+    Dir['lib/**/*.json'],
+    'LICENSE'
+  ].flatten
+
+  spec.require_paths = ['lib']
+end

data/lib/inferno/apps/cli/templates/Dockerfile.tt

@@ -0,0 +1,22 @@
+FROM ruby:3.1.2
+
+ENV INSTALL_PATH=/opt/inferno/
+ENV APP_ENV=production
+RUN mkdir -p $INSTALL_PATH
+
+WORKDIR $INSTALL_PATH
+
+ADD *.gemspec $INSTALL_PATH
+ADD Gemfile* $INSTALL_PATH
+RUN gem install bundler
+# The below RUN line is commented out for development purposes, because any change to the 
+# required gems will break the dockerfile build process.
+# If you want to run in Deploy mode, just run `bundle install` locally to update 
+# Gemfile.lock, and uncomment the following line.
+# RUN bundle config set --local deployment 'true'
+RUN bundle install
+
+ADD . $INSTALL_PATH
+
+EXPOSE 4567
+CMD ["bundle", "exec", "puma"]

data/lib/inferno/apps/cli/templates/Gemfile.tt

@@ -0,0 +1,9 @@
+# frozen_string_literal: true
+
+source "https://rubygems.org"
+
+gemspec
+
+group :development, :test do
+  gem 'debug'
+end

data/lib/inferno/apps/cli/templates/LICENSE.tt

@@ -0,0 +1,201 @@
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data/lib/inferno/apps/cli/templates/Procfile.tt

@@ -0,0 +1,2 @@
+web: bundle exec puma
+worker: bundle exec sidekiq -r ./worker.rb

data/lib/inferno/apps/cli/templates/README.md.tt

@@ -0,0 +1,39 @@
+# <%= title_name %> Test Kit
+
+<%= human_name %> [Inferno](https://github.com/inferno-community/inferno-core) Test Kit
+for FHIR testing.
+
+## Instructions for Developing Your Test Kit
+
+Refer to the Inferno documentation for information about [setting up
+your development environment and running your Test Kit](https://inferno-framework.github.io/docs/getting-started/).
+
+More information about what is included in this repository can be [found here](https://inferno-framework.github.io/docs/getting-started/repo-layout-and-organization.html).
+
+## Documentation
+- [Inferno documentation](https://inferno-framework.github.io/docs/)
+- [Ruby API documentation](https://inferno-framework.github.io/inferno-core/docs/)
+- [JSON API documentation](https://inferno-framework.github.io/inferno-core/api-docs/)
+
+## Example Inferno Test Kits
+
+A list of all Test Kits registered with the Inferno Team can be found on the [Test Kit Registry](https://inferno-framework.github.io/community/test-kits.html) page.
+
+## License
+Copyright <%= Time.now.year %> TODO
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not use
+this file except in compliance with the License. You may obtain a copy of the
+License at
+```
+http://www.apache.org/licenses/LICENSE-2.0
+```
+Unless required by applicable law or agreed to in writing, software distributed
+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
+CONDITIONS OF ANY KIND, either express or implied. See the License for the
+specific language governing permissions and limitations under the License.
+
+## Trademark Notice
+
+HL7, FHIR and the FHIR [FLAME DESIGN] are the registered trademarks of Health
+Level Seven International and their use does not constitute endorsement by HL7.

data/lib/inferno/apps/cli/templates/Rakefile.tt

@@ -0,0 +1,15 @@
+begin
+  require 'rspec/core/rake_task'
+  RSpec::Core::RakeTask.new(:spec)
+  task default: :spec
+rescue LoadError # rubocop:disable Lint/SuppressedException
+end
+
+namespace :db do
+  desc 'Apply changes to the database'
+  task :migrate do
+    require 'inferno/config/application'
+    require 'inferno/utils/migration'
+    Inferno::Utils::Migration.new.run
+  end
+end

data/lib/inferno/apps/cli/templates/config/database.yml.tt

@@ -0,0 +1,18 @@
+development:
+  adapter: sqlite
+  database: data/inferno_development.db
+  max_connections: 10
+  # user:
+  # password:
+  # host:
+  # port:
+
+production:
+  adapter: sqlite
+  database: data/inferno_production.db
+  max_connections: 10
+
+test:
+  adapter: sqlite
+  database: ':memory:'
+  max_connections: 10

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

@@ -0,0 +1,86 @@
+# this sets the user nginx will run as,
+#and the number of worker processes
+user nobody nogroup;
+worker_processes  2;
+#user www-data;
+#worker_processes auto;
+
+# setup where nginx will log errors to
+# and where the nginx process id resides
+error_log  /var/log/nginx/error.log;
+pid        /var/run/nginx.pid;
+
+events {
+  worker_connections  1024;
+  # set to on if you have more than 1 worker_processes
+  accept_mutex on;
+}
+
+http {
+  include       /etc/nginx/mime.types;
+
+  default_type application/octet-stream;
+  access_log /tmp/nginx.access.log combined;
+
+  # use the kernel sendfile
+  # sendfile        on;  # this causes over-caching because modified timestamps lost in VM
+  # prepend http headers before sendfile()
+  tcp_nopush     on;
+
+  keepalive_timeout  600;
+  tcp_nodelay        on;
+
+  gzip  on;
+  gzip_vary on;
+  gzip_min_length 500;
+
+  gzip_disable "MSIE [1-6]\.(?!.*SV1)";
+  gzip_types text/plain text/xml text/css
+     text/comma-separated-values
+     text/javascript application/x-javascript
+     application/atom+xml image/x-icon;
+
+  # configure the virtual host
+  server {
+    # replace with your domain name
+    # server_name inferno-server;
+
+    # port to listen for requests on
+    listen 80;
+
+    # maximum accepted body size of client request
+    client_max_body_size 4G;
+    # the server will close connections after this time
+    keepalive_timeout 600;
+
+    location /validator {
+      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_pass http://fhir_validator_app;
+    }
+
+    location /validatorapi/ {
+      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_pass http://validator_service:4567/;
+    }
+  }
+}

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

@@ -0,0 +1,101 @@
+# this sets the user nginx will run as,
+#and the number of worker processes
+user nobody nogroup;
+worker_processes  2;
+#user www-data;
+#worker_processes auto;
+
+# setup where nginx will log errors to
+# and where the nginx process id resides
+error_log  /var/log/nginx/error.log;
+pid        /var/run/nginx.pid;
+
+events {
+  worker_connections  1024;
+  # set to on if you have more than 1 worker_processes
+  accept_mutex on;
+}
+
+http {
+  include       /etc/nginx/mime.types;
+
+  default_type application/octet-stream;
+  access_log /tmp/nginx.access.log combined;
+
+  # use the kernel sendfile
+  # sendfile        on;  # this causes over-caching because modified timestamps lost in VM
+  # prepend http headers before sendfile()
+  tcp_nopush     on;
+
+  keepalive_timeout  600;
+  tcp_nodelay        on;
+
+  gzip  on;
+  gzip_vary on;
+  gzip_min_length 500;
+
+  gzip_disable "MSIE [1-6]\.(?!.*SV1)";
+  gzip_types text/plain text/xml text/css
+     text/comma-separated-values
+     text/javascript application/x-javascript
+     application/atom+xml image/x-icon;
+
+  # configure the virtual host
+  server {
+    # replace with your domain name
+    # server_name inferno-server;
+
+    # port to listen for requests on
+    listen 80;
+
+    # maximum accepted body size of client request
+    client_max_body_size 4G;
+    # the server will close connections after this time
+    keepalive_timeout 600;
+
+    location / {
+      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_pass http://inferno:4567;
+    }
+
+    location /validator {
+      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_pass http://fhir_validator_app;
+    }
+
+    location /validatorapi/ {
+      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_pass http://validator_service:4567/;
+    }
+  }
+}

data/lib/inferno/apps/cli/templates/config/puma.rb.tt

@@ -0,0 +1,2 @@
+environment ENV.fetch('APP_ENV', 'development')
+port ENV.fetch('INFERNO_PORT', 4567)

data/lib/inferno/apps/cli/templates/config.ru.tt

@@ -0,0 +1,11 @@
+require 'inferno'
+
+use Rack::Static,
+    urls: Inferno::Utils::StaticAssets.static_assets_map,
+    root: Inferno::Utils::StaticAssets.inferno_path
+
+Inferno::Application.finalize!
+
+use Inferno::Utils::Middleware::RequestLogger
+
+run Inferno::Web.app

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

@@ -0,0 +1,30 @@
+version: '3'
+services:
+  validator_service:
+    image: infernocommunity/fhir-validator-service
+    # Update this path to match your directory structure
+    volumes:
+      - ./<%= ig_path %>:/home/igs
+  fhir_validator_app:
+    image: infernocommunity/fhir-validator-app
+    depends_on:
+      - validator_service
+    environment:
+      EXTERNAL_VALIDATOR_URL: http://localhost/validatorapi
+      VALIDATOR_BASE_PATH: /validator
+  nginx:
+    image: nginx
+    volumes:
+      - ./config/nginx.background.conf:/etc/nginx/nginx.conf
+    ports:
+      - "80:80"
+    command: [nginx, '-g', 'daemon off;']
+    depends_on:
+      - fhir_validator_app
+  redis:
+    image: redis
+    ports:
+      - "6379:6379"
+    volumes:
+      - ./data/redis:/data
+    command: redis-server --appendonly yes

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

@@ -0,0 +1,35 @@
+version: '3'
+services:
+  inferno:
+    build:
+      context: ./
+    volumes:
+      - ./data:/opt/inferno/data
+    depends_on:
+      - validator_service
+  worker:
+    build:
+      context: ./
+    volumes:
+      - ./data:/opt/inferno/data
+    command: bundle exec sidekiq -r ./worker.rb
+    depends_on:
+      - redis
+  validator_service:
+    extends:
+      file: docker-compose.background.yml
+      service: validator_service
+  fhir_validator_app:
+    extends:
+      file: docker-compose.background.yml
+      service: fhir_validator_app
+  nginx:
+    extends:
+      file: docker-compose.background.yml
+      service: nginx
+    volumes:
+      - ./config/nginx.conf:/etc/nginx/nginx.conf
+  redis:
+    extends:
+      file: docker-compose.background.yml
+      service: redis

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

@@ -0,0 +1,44 @@
+module <%= module_name %>
+  class PatientGroup < Inferno::TestGroup
+    title 'Patient Tests'
+    description 'Verify that the server makes Patient resources available'
+    id :patient_group
+
+    test do
+      title 'Server returns requested Patient resource from the Patient read interaction'
+      description %(
+        Verify that Patient resources can be read from the server.
+      )
+
+      input :patient_id,
+            title: 'Patient ID'
+
+      # Named requests can be used by other tests
+      makes_request :patient
+
+      run do
+        fhir_read(:patient, patient_id, name: :patient)
+
+        assert_response_status(200)
+        assert_resource_type(:patient)
+        assert resource.id == patient_id,
+               "Requested resource with id #{patient_id}, received resource with id #{resource.id}"
+      end
+    end
+
+    test do
+      title 'Patient resource is valid'
+      description %(
+        Verify that the Patient resource returned from the server is a valid FHIR resource.
+      )
+      # This test will use the response from the :patient request in the
+      # previous test
+      uses_request :patient
+
+      run do
+        assert_resource_type(:patient)
+        assert_valid_resource
+      end
+    end
+  end
+end

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

@@ -0,0 +1,53 @@
+require_relative '<%= library_name %>/patient_group'
+
+module <%= module_name %>
+  class Suite < Inferno::TestSuite
+    id :<%= test_suite_id %>
+    title '<%= title_name %> Test Suite'
+    description 'Inferno <%= human_name.downcase %> test suite for FHIR'
+
+    # These inputs will be available to all tests in this suite
+    input :url,
+          title: 'FHIR Server Base Url'
+
+    input :credentials,
+          title: 'OAuth Credentials',
+          type: :oauth_credentials,
+          optional: true
+
+    # All FHIR requests in this suite will use this FHIR client
+    fhir_client do
+      url :url
+      oauth_credentials :credentials
+    end
+
+    # All FHIR validation requsets will use this FHIR validator
+    validator do
+      url ENV.fetch('VALIDATOR_URL')
+    end
+
+    # Tests and TestGroups can be defined inline
+    group do
+      id :capability_statement
+      title 'Capability Statement'
+      description 'Verify that the server has a CapabilityStatement'
+
+      test do
+        id :capability_statement_read
+        title 'Read CapabilityStatement'
+        description 'Read CapabilityStatement from /metadata endpoint'
+
+        run do
+          fhir_get_capability_statement
+
+          assert_response_status(200)
+          assert_resource_type(:capability_statement)
+        end
+      end
+    end
+
+    # Tests and TestGroups can be written in separate files and then included
+    # using their id
+    group from: :patient_group
+  end
+end

data/lib/inferno/apps/cli/templates/run.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+docker compose build
+docker compose up

data/lib/inferno/apps/cli/templates/setup.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+docker compose pull
+docker compose build
+docker compose run inferno bundle exec inferno migrate

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

@@ -0,0 +1,105 @@
+RSpec.describe <%= module_name %>::PatientGroup do
+  let(:suite) { Inferno::Repositories::TestSuites.new.find('<%= test_suite_id %>') }
+  let(:group) { suite.groups[1] }
+  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' }]) }
+
+  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)
+    inputs.each do |name, value|
+      session_data_repo.save(test_session_id: test_session.id, name: name, value: value, type: 'text')
+    end
+    Inferno::TestRunner.new(test_session: test_session, test_run: test_run).run(runnable)
+  end
+
+  describe 'read test' do
+    let(:test) { group.tests.first }
+    let(:patient_id) { 'abc123' }
+
+    it 'passes if a Patient was received' do
+      resource = FHIR::Patient.new(id: patient_id)
+      stub_request(:get, "#{url}/Patient/#{patient_id}")
+        .to_return(status: 200, body: resource.to_json)
+
+      result = run(test, url: url, patient_id: patient_id)
+
+      expect(result.result).to eq('pass')
+    end
+
+    it 'fails if a 200 is not received' do
+      resource = FHIR::Patient.new(id: patient_id)
+      stub_request(:get, "#{url}/Patient/#{patient_id}")
+        .to_return(status: 201, body: resource.to_json)
+
+      result = run(test, url: url, patient_id: patient_id)
+
+      expect(result.result).to eq('fail')
+      expect(result.result_message).to match(/200/)
+    end
+
+    it 'fails if a Patient is not received' do
+      resource = FHIR::Condition.new(id: patient_id)
+      stub_request(:get, "#{url}/Patient/#{patient_id}")
+        .to_return(status: 200, body: resource.to_json)
+
+      result = run(test, url: url, patient_id: patient_id)
+
+      expect(result.result).to eq('fail')
+      expect(result.result_message).to match(/Patient/)
+    end
+
+    it 'fails if the id received does not match the one requested' do
+      resource = FHIR::Patient.new(id: '456')
+      stub_request(:get, "#{url}/Patient/#{patient_id}")
+        .to_return(status: 200, body: resource.to_json)
+
+      result = run(test, url: url, patient_id: patient_id)
+
+      expect(result.result).to eq('fail')
+      expect(result.result_message).to match(/resource with id/)
+    end
+  end
+
+  describe 'validation test' do
+    let(:test) { group.tests.last }
+
+    it 'passes if the resource is valid' do
+      stub_request(:post, "#{ENV.fetch('VALIDATOR_URL')}/validate")
+        .with(query: hash_including({}))
+        .to_return(status: 200, body: FHIR::OperationOutcome.new.to_json)
+
+      resource = FHIR::Patient.new
+      repo_create(
+        :request,
+        name: :patient,
+        test_session_id: test_session.id,
+        response_body: resource.to_json
+      )
+
+      result = run(test)
+
+      expect(result.result).to eq('pass')
+    end
+
+    it 'fails if the resource is not valid' do
+      stub_request(:post, "#{ENV.fetch('VALIDATOR_URL')}/validate")
+        .with(query: hash_including({}))
+        .to_return(status: 200, body: error_outcome.to_json)
+
+      resource = FHIR::Patient.new
+      repo_create(
+        :request,
+        name: :patient,
+        test_session_id: test_session.id,
+        response_body: resource.to_json
+      )
+
+      result = run(test)
+
+      expect(result.result).to eq('fail')
+    end
+  end
+end

data/lib/inferno/apps/cli/templates/spec/spec_helper.rb.tt

@@ -0,0 +1,141 @@
+# Hide deprecation warnings
+$VERBOSE = nil
+
+ENV['APP_ENV'] ||= 'test'
+
+require 'database_cleaner/sequel'
+require 'pry'
+require 'pry-byebug'
+
+require 'webmock/rspec'
+WebMock.disable_net_connect!
+
+require 'factory_bot'
+
+# This file was generated by the `rspec --init` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# The generated `.rspec` file contains `--require spec_helper` which will cause
+# this file to always be loaded, without a need to explicitly require it in any
+# files.
+#
+# Given that it is always loaded, you are encouraged to keep this file as
+# light-weight as possible. Requiring heavyweight dependencies from this file
+# will add to the boot time of your test suite on EVERY test run, even for an
+# individual file that may not need all of that loaded. Instead, consider making
+# a separate helper file that requires the additional dependencies and performs
+# the additional setup, and require it from the spec files that actually need
+# it.
+#
+# The `.rspec` file also contains a few flags that are not defaults but that
+# users commonly want.
+#
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # This option will default to `true` in RSpec 4. It makes the `description`
+    # and `failure_message` of custom matchers include text for helper methods
+    # defined using `chain`, e.g.:
+    #     be_bigger_than(2).and_smaller_than(4).description
+    #     # => "be bigger than 2 and smaller than 4"
+    # ...rather than:
+    #     # => "be bigger than 2"
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  # rspec-mocks config goes here. You can use an alternate test double
+  # library (such as bogus or mocha) by changing the `mock_with` option here.
+  config.mock_with :rspec do |mocks|
+    # Prevents you from mocking or stubbing a method that does not exist on
+    # a real object. This is generally recommended, and will default to
+    # `true` in RSpec 4.
+    mocks.verify_partial_doubles = true
+  end
+
+  # Allows RSpec to persist some state between runs in order to support
+  # the `--only-failures` and `--next-failure` CLI options. We recommend
+  # you configure your source control system to ignore this file.
+  config.example_status_persistence_file_path = 'spec/examples.txt'
+
+  # Limits the available syntax to the non-monkey patched syntax that is
+  # recommended. For more details, see:
+  #   - http://myronmars.to/n/dev-blog/2012/06/rspecs-new-expectation-syntax
+  #   - http://teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
+  #   - http://myronmars.to/n/dev-blog/2014/05/notable-changes-in-rspec-3#new__config_option_to_disable_rspeccore_monkey_patching
+  config.disable_monkey_patching!
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = 'doc'
+  end
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = :random
+
+  # Seed global randomization in this process using the `--seed` CLI option.
+  # Setting this allows you to use `--seed` to deterministically reproduce
+  # test failures related to randomization by passing the same `--seed` value
+  # as the one that triggered the failure.
+  Kernel.srand config.seed
+
+  # These two settings work together to allow you to limit a spec run
+  # to individual examples or groups you care about by tagging them with
+  # `:focus` metadata. When nothing is tagged with `:focus`, all examples
+  # get run.
+  config.filter_run :focus
+  config.run_all_when_everything_filtered = true
+
+  # This setting enables warnings. It's recommended, but in many cases may
+  # be too noisy due to issues in dependencies.
+  # config.warnings = false
+
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  # config.profile_examples = 10
+
+  config.before(:suite) do
+    DatabaseCleaner.strategy = :transaction
+    DatabaseCleaner.clean_with(:truncation)
+  end
+
+  config.around do |example|
+    DatabaseCleaner.cleaning { example.run }
+  end
+
+  config.include FactoryBot::Syntax::Methods
+
+  config.before(:suite) do
+    FactoryBot.find_definitions
+  end
+end
+
+require 'inferno/config/application'
+require 'inferno/utils/migration'
+Inferno::Utils::Migration.new.run
+
+require 'inferno'
+Inferno::Application.finalize!
+
+require Inferno::SpecSupport::FACTORY_BOT_SUPPORT_PATH
+
+FactoryBot.definition_file_paths = [
+  Inferno::SpecSupport::FACTORY_PATH
+]
+
+RSpec::Matchers.define_negated_matcher :exclude, :include
+
+FHIR.logger = Inferno::Application['logger']
+
+DatabaseCleaner[:sequel].strategy = :truncation
+DatabaseCleaner[:sequel].db = Inferno::Application['db.connection']

data/lib/inferno/apps/cli/templates/worker.rb.tt

@@ -0,0 +1,3 @@
+require 'inferno'
+
+Inferno::Application.finalize!

data/lib/inferno/apps/web/controllers/test_session_form_post_controller.rb

@@ -0,0 +1,39 @@
+module Inferno
+  module Web
+    module Controllers
+      class TestSessionFormPostController < Hanami::Action
+        def self.call(...)
+          new.call(...)
+        end
+
+        def handle(req, res)
+          test_suite_id = req.params[:test_suite_id]
+
+          test_suite = Inferno::Repositories::TestSuites.new.find(test_suite_id)
+          halt 404, "Unable to find test suite with id #{test_suite_id}" if test_suite.nil?
+
+          params = { test_suite_id: }
+          suite_option_keys = test_suite.suite_options.map(&:id)
+          options = req.params.to_h.slice(*suite_option_keys)
+
+          params[:suite_options] = options.map { |key, value| { id: key, value: } } if options.present?
+
+          repo = Inferno::Repositories::TestSessions.new
+          session = repo.create(params)
+
+          preset_id = req.params[:preset_id]
+
+          if preset_id.present?
+            preset = Inferno::Repositories::Presets.new.find(preset_id)
+
+            halt 422, "Unable to find preset with id #{preset_id} for test suite #{test_suite_id}" if preset.nil?
+
+            repo.apply_preset(session, preset_id)
+          end
+
+          res.redirect_to "#{Inferno::Application['base_url']}/#{test_suite_id}/#{session.id}"
+        end
+      end
+    end
+  end
+end

data/lib/inferno/apps/web/router.rb

@@ -72,6 +72,8 @@ module Inferno
 
       get '/test_sessions/:id', to: Inferno::Web::Controllers::TestSessions::ClientShow, as: :client_session_show
       get '/:test_suite_id/:id', to: Inferno::Web::Controllers::TestSessions::ClientShow, as: :client_suite_session_show
+
+      post '/:test_suite_id', to: Inferno::Web::Controllers::TestSessionFormPostController, as: :session_form_post
     end
 
     Router = # rubocop:disable Naming/ConstantName

data/lib/inferno/dsl/configurable.rb

@@ -177,6 +177,11 @@ module Inferno
           inputs[identifier]&.type
         end
 
+        # @private
+        def input_optional?(identifier)
+          inputs[identifier]&.optional
+        end
+
         ### Output Configuration ###
 
         # The output configuration for this runnable.

data/lib/inferno/repositories/validator_sessions.rb

@@ -27,7 +27,7 @@ module Inferno
                     suite_options:,
                     validator_name: }
         ).insert(
-          id: "#{validator_session_id}_#{validator_name}",
+          id: SecureRandom.uuid,
           validator_session_id:,
           test_suite_id:,
           validator_name:,

data/lib/inferno/test_runner.rb

@@ -73,6 +73,8 @@ module Inferno
       result = begin
         raise Exceptions::CancelException, 'Test cancelled by user' if test_run_is_cancelling
 
+        check_inputs(test, test_instance, inputs)
+
         test_instance.load_named_requests
         test_instance.instance_eval(&test.block)
         'pass'
@@ -112,6 +114,16 @@ module Inferno
       test_result
     end
 
+    def check_inputs(test, _test_instance, inputs)
+      inputs.each do |key, value|
+        optional = test.config.input_optional?(key)
+        if value.nil? && !optional
+          raise Exceptions::SkipException,
+                "Input '#{test.config.input_name(key)}' is nil, skipping test."
+        end
+      end
+    end
+
     def run_group(group, scratch)
       group_inputs_with_values = group.available_inputs.map do |_input_identifier, input|
         {

data/lib/inferno/version.rb

@@ -1,4 +1,4 @@
 module Inferno
   # Standard patterns for gem versions: https://guides.rubygems.org/patterns/
-  VERSION = '0.4.30'.freeze
+  VERSION = '0.4.32'.freeze
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: inferno_core
 version: !ruby/object:Gem::Version
-  version: 0.4.30
+  version: 0.4.32
 platform: ruby
 authors:
 - Stephen MacVicar
@@ -10,7 +10,7 @@ authors:
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-03-08 00:00:00.000000000 Z
+date: 2024-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport
@@ -551,6 +551,28 @@ files:
 - lib/inferno/apps/cli/suite.rb
 - lib/inferno/apps/cli/suite_input_template.rb
 - lib/inferno/apps/cli/suites.rb
+- lib/inferno/apps/cli/templates/%library_name%.gemspec.tt
+- lib/inferno/apps/cli/templates/Dockerfile.tt
+- lib/inferno/apps/cli/templates/Gemfile.tt
+- lib/inferno/apps/cli/templates/LICENSE.tt
+- lib/inferno/apps/cli/templates/Procfile.tt
+- lib/inferno/apps/cli/templates/README.md.tt
+- lib/inferno/apps/cli/templates/Rakefile.tt
+- lib/inferno/apps/cli/templates/config.ru.tt
+- lib/inferno/apps/cli/templates/config/database.yml.tt
+- lib/inferno/apps/cli/templates/config/nginx.background.conf.tt
+- lib/inferno/apps/cli/templates/config/nginx.conf.tt
+- lib/inferno/apps/cli/templates/config/puma.rb.tt
+- lib/inferno/apps/cli/templates/docker-compose.background.yml.tt
+- lib/inferno/apps/cli/templates/docker-compose.yml.tt
+- lib/inferno/apps/cli/templates/lib/%library_name%.rb.tt
+- lib/inferno/apps/cli/templates/lib/%library_name%/igs/put_ig_package_dot_tgz_here
+- lib/inferno/apps/cli/templates/lib/%library_name%/patient_group.rb.tt
+- lib/inferno/apps/cli/templates/run.sh
+- lib/inferno/apps/cli/templates/setup.sh
+- lib/inferno/apps/cli/templates/spec/%library_name%/patient_group_spec.rb.tt
+- lib/inferno/apps/cli/templates/spec/spec_helper.rb.tt
+- lib/inferno/apps/cli/templates/worker.rb.tt
 - lib/inferno/apps/web/application.rb
 - lib/inferno/apps/web/controllers/controller.rb
 - lib/inferno/apps/web/controllers/requests/show.rb
@@ -558,6 +580,7 @@ files:
 - lib/inferno/apps/web/controllers/test_runs/destroy.rb
 - lib/inferno/apps/web/controllers/test_runs/results/index.rb
 - lib/inferno/apps/web/controllers/test_runs/show.rb
+- lib/inferno/apps/web/controllers/test_session_form_post_controller.rb
 - lib/inferno/apps/web/controllers/test_sessions/client_show.rb
 - lib/inferno/apps/web/controllers/test_sessions/create.rb
 - lib/inferno/apps/web/controllers/test_sessions/last_test_run.rb