Merge pull request #374 from onc-healthit/development

Version 2.8.0

.gitattributes

@@ -1,2 +1,3 @@
-lib/app/modules/uscore_v*/* linguist-generated=true
+lib/modules/uscore_v*/* linguist-generated=true
+lib/modules/bdt/* linguist-generated=true
 resources/terminology/validators/* linguist-generated=true

.gitignore

@@ -12,3 +12,4 @@ coverage
 tmp/*
 .vscode/*
 resources/terminology/*
+sequence_coverage.csv

.rubocop.yml

@@ -19,7 +19,7 @@ Style/SymbolArray:
 
 Metrics/LineLength:
   Exclude:
-    - 'lib/app/modules/**/*'
+    - 'lib/modules/**/*'
     - 'lib/app/helpers/browser_logic.rb'
 
 # Use code climate's metrics measurement rather than rubocop's

.rubocop_todo.yml

@@ -1,6 +1,6 @@
 # This configuration was generated by
 # `rubocop --auto-gen-config`
-# on 2019-09-26 15:38:33 -0400 using RuboCop version 0.74.0.
+# on 2019-11-05 10:58:04 -0500 using RuboCop version 0.74.0.
 # The point is for the user to remove these configuration records
 # one by one as the offenses are removed from the code base.
 # Note that changes in the inspected code, or installation of new
@@ -9,19 +9,13 @@
 # Offense count: 6
 Lint/EmptyWhen:
   Exclude:
-    - 'lib/app/modules/argonaut/argonaut_careplan_sequence.rb'
-    - 'lib/app/modules/argonaut/argonaut_diagnostic_report_sequence.rb'
-    - 'lib/app/modules/argonaut/argonaut_observation_sequence.rb'
-    - 'lib/app/modules/argonaut/argonaut_procedure_sequence.rb'
-    - 'lib/app/modules/argonaut/argonaut_vital_signs_observation_sequence.rb'
+    - 'lib/modules/argonaut/argonaut_careplan_sequence.rb'
+    - 'lib/modules/argonaut/argonaut_diagnostic_report_sequence.rb'
+    - 'lib/modules/argonaut/argonaut_observation_sequence.rb'
+    - 'lib/modules/argonaut/argonaut_procedure_sequence.rb'
+    - 'lib/modules/argonaut/argonaut_vital_signs_observation_sequence.rb'
     - 'lib/tasks/tasks.rake'
 
-# Offense count: 1
-# Configuration parameters: AllowComments.
-Lint/HandleExceptions:
-  Exclude:
-    - 'lib/app/sequence_base.rb'
-
 # Offense count: 1
 Lint/NonLocalExitFromIterator:
   Exclude:
@@ -33,20 +27,19 @@ Lint/ShadowingOuterLocalVariable:
     - 'lib/app/utils/terminology.rb'
     - 'lib/app/utils/valueset.rb'
 
-# Offense count: 32
+# Offense count: 36
 Metrics/CyclomaticComplexity:
   Max: 30
 
-# Offense count: 32
+# Offense count: 19
 Style/ClassVars:
   Exclude:
-    - 'lib/app/modules/onc_program/onc_ehr_launch_sequence.rb'
-    - 'lib/app/modules/onc_program/onc_standalone_launch_sequence.rb'
     - 'lib/app/sequence_base.rb'
     - 'lib/app/utils/logged_rest_client.rb'
-    - 'lib/app/utils/terminology.rb'
+    - 'lib/modules/onc_program/onc_ehr_launch_sequence.rb'
+    - 'lib/modules/onc_program/onc_standalone_launch_sequence.rb'
 
-# Offense count: 132
+# Offense count: 162
 Style/Documentation:
   Enabled: false
 
@@ -57,12 +50,11 @@ Style/GuardClause:
     - 'lib/app/utils/tls_tester.rb'
     - 'lib/app/utils/validation.rb'
 
-# Offense count: 3
+# Offense count: 1
 # Cop supports --auto-correct.
 Style/IfUnlessModifier:
   Exclude:
     - 'lib/app/models/testing_instance.rb'
-    - 'lib/app/utils/assertions.rb'
 
 # Offense count: 1
 Style/MixinUsage:
@@ -79,12 +71,13 @@ Style/MutableConstant:
 
 # Offense count: 1
 # Cop supports --auto-correct.
-# Configuration parameters: AllowAsExpressionSeparator.
-Style/Semicolon:
+# Configuration parameters: EnforcedStyle, AllowInnerSlashes.
+# SupportedStyles: slashes, percent_r, mixed
+Style/RegexpLiteral:
   Exclude:
-    - 'test/unit/sequence_validation_test.rb'
+    - 'test/test_helper.rb'
 
-# Offense count: 1064
+# Offense count: 542
 # Cop supports --auto-correct.
 # Configuration parameters: AutoCorrect, AllowHeredoc, AllowURI, URISchemes, IgnoreCopDirectives, IgnoredPatterns.
 # URISchemes: http, https

.travis.yml

@@ -1,4 +1,5 @@
 language: ruby
+cache: bundler
 services:
   - docker
 before_install:

Gemfile

@@ -3,6 +3,7 @@
 source 'https://rubygems.org'
 
 gem 'addressable'
+gem 'ast'
 gem 'base62-rb'
 gem 'bloomer'
 gem 'colorize'
@@ -11,6 +12,7 @@ gem 'dm-sqlite-adapter'
 gem 'fhir_client'
 gem 'json-jwt'
 gem 'kramdown'
+gem 'parser'
 gem 'pry'
 gem 'pry-byebug'
 gem 'rake'

Gemfile.lock

@@ -117,11 +117,11 @@ GEM
     http-accept (1.7.0)
     http-cookie (1.0.3)
       domain_name (~> 0.5)
-    i18n (1.6.0)
+    i18n (1.7.0)
       concurrent-ruby (~> 1.0)
     jaro_winkler (1.5.3)
     json (1.8.6)
-    json-jwt (1.10.2)
+    json-jwt (1.11.0)
       activesupport (>= 4.2)
       aes_key_wrap
       bindata
@@ -228,6 +228,7 @@ PLATFORMS
 
 DEPENDENCIES
   addressable
+  ast
   base62-rb
   bloomer
   colorize
@@ -237,6 +238,7 @@ DEPENDENCIES
   json-jwt
   kramdown
   minitest
+  parser
   pry
   pry-byebug
   rack-test

README.md

@@ -21,7 +21,7 @@ Docker is the recommended installation method for Windows devices and can also b
 2. Download the [latest release of the `inferno` project](https://github.com/onc-healthit/inferno/releases) to your local computer on a directory of your choice.
 3. Open a terminal in the directory where the project was downloaded (above).
 4. Run the command `docker-compose up` to start the server. This will automatically build the Docker image and launch both the ruby server (using unicorn) and an NGINX web server.
-5. Navigate to http://localhost:8080 to find the running application.
+5. Navigate to http://localhost:4567 to find the running application.
 
 If the docker image gets out of sync with the underlying system, such as when new dependencies are added to the application, you need to run `docker-compose up --build` to rebuild the containers.
 

Rakefile

@@ -15,6 +15,7 @@ end
 Rake::TestTask.new(:test) do |t|
   t.libs << 'test'
   t.pattern = 'test/**/*_test.rb'
+  t.test_files = Dir.glob('lib/modules/*/test/*_test.rb')
   t.verbose = true
   t.warning = false
 end

config.yml

@@ -40,11 +40,11 @@ badge_text: Community
 # module options: one or more must be set.  The first option in the list will be checked by default
 modules:
   - onc
-  - onc_r4
   - smart
+  - bdt
   - argonaut
-  - uscore_v3.0.0
-  - uscore_v3.0.1
+  - uscore_v3.1.0
+  - bulk_data
 
 # preset fhir servers: optional. Minimally requires name, uri, module, optional inferno_uri, client_id, client_secret, scopes, instructions link
 presets:
@@ -54,6 +54,7 @@ presets:
     module: onc
     inferno_uri: https://inferno.healthit.gov
     client_id: vkPKDPcTIEMaw5Uf-DdUUtNMFMZaX0
+    confidential_client: true
     client_secret: LS1nY3JFU3FDeEs0cWoxQWF6TVJFNU05RmZZNGZhZ2Vwb2JYWjdSWWJGakwwNTZ2Vng=
     instructions: https://github.com/onc-healthit/inferno/wiki/SITE-Preset-Instructions
   site_test_healthit_gov:
@@ -62,6 +63,7 @@ presets:
     module: onc
     inferno_uri: https://infernotest.healthit.gov
     client_id: TrToU5piE-dJ1g6PBG1elFV4r9KLmH
+    confidential_client: true
     client_secret: ckFqb1ZhbmFMQS13WDE0c1dTLWxSdGRLSE8yUXpWNS1vSnd6azNrMmU3Y0JPdDRja3U=
     instructions: https://github.com/onc-healthit/inferno/wiki/SITE-Preset-Instructions
   site_local:
@@ -70,5 +72,23 @@ presets:
     module: onc
     inferno_uri: http://localhost:4567
     client_id: Yg0o6sJ8I8CfVVyHz1eA0m8jv6sXwe
+    confidential_client: true
     client_secret: UDVrTXlna0NvcGRQZ1VhMkZaZzQ0R1FxVGdtTWxFMXVoT3pPd1VRMUN4MFVkV25Gejk=
     instructions: https://github.com/onc-healthit/inferno/wiki/SITE-Preset-Instructions
+  standalone_bulk_server_local:
+    name: SMART Bulk Server Tests
+    module: bdt
+    uri: https://bulk-data.smarthealthit.org/eyJlcnIiOiIiLCJwYWdlIjoxMDAwLCJkdXIiOjEwLCJ0bHQiOjE1LCJtIjoxLCJzdHUiOjR9/fhir
+    inferno_uri: http://localhost:4567
+    bulk_url: https://bulk-data.smarthealthit.org/eyJlcnIiOiIiLCJwYWdlIjoxMDAwLCJkdXIiOjEwLCJ0bHQiOjE1LCJtIjoxLCJzdHUiOjR9/fhir
+    bulk_token_endpoint: https://bulk-data.smarthealthit.org/auth/token
+    bulk_requires_auth: true
+    bulk_client_id: eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCIsImtpZCI6InJlZ2lzdHJhdGlvbi10b2tlbiJ9.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.dkqFAJreUXIfBTESdygmiOBhtepzgcDNJWqI2662m4Q
+    bulk_public_key: "{'kty':'EC','crv':'P-384','x':'tVzDWQ5qM1ekRkO9acV2OrDW_JyeS6baDrXPs9vPOGOxa5z55CWtpwg_BDyOYt8n','y':'hpXICZMNezD1oMNakOqlGNh3WQgCdKfQUpDNlhx_dKQo0ymMPeXKxisMmVqWOk-L','key_ops':['verify'],'ext':true,'kid':'c9529a0aaefa5ea659d65c4939eca976','alg':'ES384'}"
+    bulk_private_key: "{'kty':'EC','crv':'P-384','d':'m9gJqGah8C8-vmos5-6bp902TPFGHvctUIzGd22LPyE6o5D2WEU1mWEm74lEeybP','x':'tVzDWQ5qM1ekRkO9acV2OrDW_JyeS6baDrXPs9vPOGOxa5z55CWtpwg_BDyOYt8n','y':'hpXICZMNezD1oMNakOqlGNh3WQgCdKfQUpDNlhx_dKQo0ymMPeXKxisMmVqWOk-L','key_ops':['sign'],'ext':true,'kid':'c9529a0aaefa5ea659d65c4939eca976','alg':'ES384'}"
+    bulk_fastest_resource: Patient
+    bulk_system_export_endpoint: /$export
+    bulk_patient_export_endpoint: /Patient/$export
+    bulk_group_export_endpoint: /Group/5/$export
+    # A UI for this launch configuration can be accessed at:
+    # https://bulk-data.smarthealthit.org/?auth_type=jwks&jwks=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&page=1000&stu=4

docker-compose.yml

@@ -5,16 +5,16 @@ services:
       context: ./
     volumes:
       - ./config.yml:/var/www/inferno/config.yml
-    ports:
-     - "4567:8080"
+    depends_on:
+      - bdt_service
+  bdt_service:
+    image: infernocommunity/inferno-bdt-service
   nginx_server:
     image: nginx
     volumes:
       - ./deployment-files/nginx.conf:/etc/nginx/nginx.conf:ro
     ports:
-      - "8080:80"
+      - "4567:80"
     command: [nginx, '-g', 'daemon off;']
-    links:
-      - ruby_server:ruby_server
     depends_on:
-      - ruby_server
+      - ruby_server