FI-1247: Remove suites (#12)

* WIP reorganize inferno

* wip

* working

* require runnables to require their imported runnables

* make bin/console work when used as gem

* update config for puma

* update suite loading

* remove real suites

* add initial gemspec

* add missing require to fixture suite

* correct dry-system version

* only use in-memory db until db config is updated

* add factories to gem

* rename console command

* make db configurable in suite repos

* fix rack config

* update logging path

* ignore coverage for migrations

* update gemspec

* update readme and package-lock.json

.dockerignore

@@ -1,5 +1,4 @@
 /db/*.db
-/public/assets*
 /tmp
 .env.local
 .env.*.local
@@ -14,8 +13,9 @@
 .idea
 
 /coverage
+/data
 /docs/yard
-.yardoc
+/.yardoc
 /node_modules
 /.git
 /.github

.env.development

@@ -1,2 +1,4 @@
+LOAD_DEV_SUITES=true
+LOAD_UI_SUITES=true
 VALIDATOR_URL=https://inferno.healthit.gov/validatorapi
 JS_HOST=http://localhost:3000

.env.test

@@ -1 +1,2 @@
+LOAD_DEV_SUITES=true
 VALIDATOR_URL=https://example.com/validatorapi

.gitignore

@@ -1,5 +1,10 @@
+/data/*.db
 /db/*.db
-/public/assets*
+/lib/inferno/public/assets*
+/lib/inferno/public/*.js
+/lib/inferno/public/*.LICENSE.txt
+/lib/inferno/public/*.png
+!/lib/inferno/public/logo*.png
 /tmp
 .env.local
 .env.*.local

.rubocop.yml

@@ -13,16 +13,15 @@ AllCops:
 Layout/LineLength:
   Max: 120
   Exclude:
-    - 'dev_suites/onc_program/**/*'
-    - 'suites/ips/**/*'
-    - 'dev_suites/smart_scheduling_links/**/*'
+    - 'ui_suites/onc_program/**/*'
+    - 'ui_suites/smart_scheduling_links/**/*'
 
 Layout/MultilineMethodCallIndentation:
   EnforcedStyle: 'indented'
 
 Lint/EmptyBlock:
   Exclude:
-    - 'dev_suites/onc_program/**/*'
+    - 'ui_suites/onc_program/**/*'
 
 Style/BlockComments:
   Exclude:

CHANGELOG.md

@@ -0,0 +1,3 @@
+# 0.0.1
+
+* Initial gem release

Gemfile

@@ -2,7 +2,7 @@ source 'https://rubygems.org'
 
 ruby '2.7.2'
 
-gem 'dry-system', '~> 0.17', require: 'dry/system/container'
+gem 'dry-system', '0.18.1'
 
 gem 'sqlite3'
 gem 'sequel'
@@ -13,7 +13,7 @@ gem 'hanami-router', '~> 1.3'
 gem 'oj'
 gem 'puma'
 
-gem 'activesupport', require: 'active_support/all'
+gem 'activesupport'
 gem 'dotenv'
 gem 'fhir_client'
 gem 'rake'

Gemfile.lock

@@ -237,7 +237,7 @@ DEPENDENCIES
   codecov
   database_cleaner-sequel
   dotenv
-  dry-system (~> 0.17)
+  dry-system (= 0.18.1)
   factory_bot
   faraday
   fhir_client

README.md

@@ -89,7 +89,7 @@ GET http://localhost:4567/api/test_sessions/TEST_SESSION_ID/results
 ```
 
 ## Development
-To get to an interactive console, run `bundle exec bin/console`
+To get to an interactive console, run `bundle exec bin/inferno-console`
 
 ## License
 Copyright 2021 The MITRE Corporation

Rakefile

@@ -8,7 +8,7 @@ end
 namespace :db do
   desc 'Apply changes to the database'
   task :migrate do
-    require_relative 'config/application'
+    require_relative 'lib/inferno/app/config/application'
 
     Inferno::Application.start(:db)
   end

bin/inferno-console

@@ -0,0 +1,8 @@
+#!/usr/bin/env ruby
+
+require 'pry'
+require_relative '../lib/inferno'
+
+Inferno::Application.finalize!
+
+Pry.start

config.ru

@@ -1,6 +1,6 @@
-require_relative 'config/application'
+require_relative 'lib/inferno'
 
-use Rack::Static, urls: ['/public']
+use Rack::Static, urls: ['/public'], root: 'lib/inferno'
 
 Inferno::Application.finalize!
 

config/database.yml

@@ -1,6 +1,6 @@
 development:
   adapter: sqlite
-  database: db/inferno_development.db
+  database: data/inferno_development.db
   max_connections: 10
   # user:
   # password:
@@ -9,7 +9,7 @@ development:
 
 production:
   adapter: sqlite
-  database: db/inferno_production.db
+  database: ':memory:'
   max_connections: 10
 
 test:

dev_suites/demo_ig_stu1/demo_suite.rb

@@ -1,3 +1,5 @@
+require_relative 'groups/demo_group'
+
 module DemoIG_STU1 # rubocop:disable Naming/ClassAndModuleCamelCase
   class DemoSuite < Inferno::TestSuite
     title 'Demonstration Suite'

dev_suites/infrastructure_test/external_inner_group.rb

@@ -1,3 +1,5 @@
+require_relative 'external_test1'
+
 module InfrastructureTest
   class ExternalInnerGroup < Inferno::TestGroup
     id 'external_inner_group'

dev_suites/infrastructure_test/external_outer_group.rb

@@ -1,3 +1,5 @@
+require_relative 'external_inner_group'
+
 module InfrastructureTest
   class ExternalOuterGroup < Inferno::TestGroup
     id 'external_outer_group'

dev_suites/infrastructure_test/infrastructure_test.rb

@@ -1,3 +1,5 @@
+require_relative 'external_outer_group'
+
 module InfrastructureTest
   class Suite < Inferno::TestSuite
     id 'infra_test'

inferno_core.gemspec

@@ -0,0 +1,64 @@
+# frozen_string_literal: true
+
+require_relative 'lib/inferno/version'
+require 'rake'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'inferno_core'
+  spec.version       = Inferno::VERSION
+  spec.authors       = ['Stephen MacVicar', 'Robert Scanlon', 'Chase Zhou']
+  spec.email         = ['inferno@groups.mitre.org']
+  spec.date          = Time.now.utc.strftime('%Y-%m-%d')
+  spec.summary       = 'Inferno Core is an open source tool for testing data exchanges enabled by the FHIR standand'
+  spec.description   = 'Inferno Core is an open source tool for testing data exchanges enabled by the FHIR standand'
+  spec.homepage      = 'https://github.com/inferno_community/inferno-core'
+  spec.license       = 'Apache 2.0'
+  spec.add_runtime_dependency 'activesupport'
+  spec.add_runtime_dependency 'blueprinter'
+  spec.add_runtime_dependency 'dotenv'
+  spec.add_runtime_dependency 'dry-system', '0.18.1'
+  spec.add_runtime_dependency 'faraday'
+  spec.add_runtime_dependency 'fhir_client'
+  spec.add_runtime_dependency 'hanami-controller', '~> 1.3'
+  spec.add_runtime_dependency 'hanami-router', '~> 1.3'
+  spec.add_runtime_dependency 'oj'
+  spec.add_runtime_dependency 'pry'
+  spec.add_runtime_dependency 'pry-byebug'
+  spec.add_runtime_dependency 'puma'
+  spec.add_runtime_dependency 'rake'
+  spec.add_runtime_dependency 'sequel'
+  spec.add_runtime_dependency 'sqlite3'
+  spec.add_development_dependency 'codecov'
+  spec.add_development_dependency 'database_cleaner-sequel'
+  spec.add_development_dependency 'factory_bot'
+  spec.add_development_dependency 'rack-test'
+  spec.add_development_dependency 'rspec'
+  spec.add_development_dependency 'rubocop', '~> 1.9'
+  spec.add_development_dependency 'rubocop-rake'
+  spec.add_development_dependency 'rubocop-rspec'
+  spec.add_development_dependency 'rubocop-sequel'
+  spec.add_development_dependency 'simplecov'
+  spec.add_development_dependency 'webmock'
+  spec.add_development_dependency 'yard'
+  spec.required_ruby_version = Gem::Requirement.new('>= 2.7.0')
+  spec.metadata['homepage_uri'] = spec.homepage
+  spec.metadata['source_code_uri'] = 'https://github.com/inferno_community/inferno-core'
+  spec.metadata['changelog_uri'] = 'https://github.com/inferno_community/inferno-core/CHANGELOG.md'
+  spec.files = [
+    'lib/inferno.rb',
+    'LICENSE.txt',
+    Dir['lib/inferno/**/*.rb'],
+    'bin/inferno-console',
+    Dir['lib/inferno/public/*.png'],
+    Dir['lib/inferno/public/*.ico'],
+    Dir['lib/inferno/public/*.js'],
+    'lib/inferno/public/bundle.js.LICENSE.txt',
+    'lib/inferno/public/assets.json',
+    'spec/support/factory_bot.rb',
+    Dir['spec/support/factories/**.*.rb']
+  ].flatten
+
+  spec.bindir        = 'bin'
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib', 'spec']
+end

lib/inferno.rb

@@ -1,2 +1,15 @@
+require 'active_support/all'
+require 'dotenv'
+require 'dry/system/container'
+require 'sequel'
+require_relative 'inferno/config/application'
+require_relative 'inferno/dsl'
+require_relative 'inferno/entities'
+require_relative 'inferno/exceptions'
+require_relative 'inferno/repositories'
+require_relative 'inferno/spec_support'
+require_relative 'inferno/test_runner'
+require_relative 'inferno/version'
+
 module Inferno
 end

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

@@ -2,7 +2,8 @@
 
 module Inferno
   module Web
-    client_page = ERB.new(File.read(File.join(Inferno::Application.root, 'apps', 'web', 'index.html.erb'))).result
+    client_page = ERB.new(File.read(File.join(Inferno::Application.root, 'lib', 'inferno', 'apps', 'web',
+                                              'index.html.erb'))).result
 
     Router = Hanami::Router.new(namespace: Inferno::Web::Controllers) do
       namespace 'api' do

config/application.rb → lib/inferno/config/application.rb

@@ -2,21 +2,21 @@
 
 module Inferno
   class Application < Dry::System::Container
+    ::Inferno::Import = injector
+
     use :env, inferrer: -> { ENV.fetch('APP_ENV', :development).to_sym }
 
     configure do |config|
-      config.root = File.expand_path('..', __dir__)
+      config.root = File.expand_path('../../..', __dir__)
       config.default_namespace = 'inferno'
-      config.system_dir = 'config'
-      config.bootable_dirs = [File.join('config', 'boot')]
+      config.system_dir = File.join('lib', 'inferno', 'config')
+      config.bootable_dirs = [File.join('lib', 'inferno', 'config', 'boot')]
 
-      config.auto_register = ['lib', 'apps']
+      config.auto_register = 'lib'
     end
 
     Application.register('js_host', ENV.fetch('JS_HOST', ''))
 
-    load_paths!('lib', 'apps')
+    load_paths!('lib')
   end
-
-  Import = Application.injector
 end

lib/inferno/config/boot.rb

@@ -0,0 +1,5 @@
+ENV['APP_ENV'] ||= 'development'
+
+root_path = Dir.pwd
+
+Dotenv.load(File.join(root_path, '.env'), File.join(root_path, ".env.#{ENV['APP_ENV']}"))

config/boot/db.rb → lib/inferno/config/boot/db.rb

@@ -6,7 +6,7 @@
 
     Sequel::Model.plugin :json_serializer
 
-    config_path = File.expand_path('database.yml', File.join(Inferno::Application.root, 'config'))
+    config_path = File.expand_path('database.yml', File.join(Dir.pwd, 'config'))
     config = YAML.load_file(config_path)[ENV['APP_ENV']]
       .merge(logger: Inferno::Application['logger'])
     connection = Sequel.connect(config)
@@ -17,7 +17,7 @@
 
   start do
     Sequel.extension :migration
-    migration_path = File.join(Inferno::Application.root, 'db', 'migrations')
+    migration_path = File.join(Inferno::Application.root, 'lib', 'inferno', 'db', 'migrations')
     Sequel::Migrator.run(Inferno::Application['db.connection'], migration_path)
   end
 end

config/boot/logging.rb → lib/inferno/config/boot/logging.rb

@@ -2,7 +2,7 @@
   init do
     logger =
       if Inferno::Application.env == :test
-        log_file_directory = File.join(Inferno::Application.root, 'tmp')
+        log_file_directory = File.join(Dir.pwd, 'tmp')
         FileUtils.mkdir_p(log_file_directory)
         log_file_path = File.join(log_file_directory, 'test.log')
         log_file = File.open(log_file_path, File::WRONLY | File::APPEND | File::CREAT)