Merge pull request #266 from onc-healthit/development

Version 2.4

.codeclimate.yml

@@ -0,0 +1,30 @@
+version: "2"         # required to adjust maintainability checks
+exclude_patterns:
+  - "!**/test/"
+checks:
+  argument-count:
+    enabled: true
+  complex-logic:
+    enabled: true
+  file-lines:
+    enabled: true
+  method-complexity:
+    enabled: true
+  method-count:
+    enabled: false
+  method-lines:
+    enabled: true
+  nested-control-flow:
+    enabled: true
+  return-statements:
+    enabled: false
+  similar-code:
+    enabled: false
+  identical-code:
+    enabled: true
+plugins:
+  rubocop:
+    enabled: true
+    channel: rubocop-0-67
+    config:
+      file: .rubocop.yml

.gitignore

@@ -11,4 +11,5 @@ data/*
 coverage
 tmp/*
 .vscode/*
-resources/terminology/*
+resources/terminology/*
+.ruby-version

.rubocop-windows.yml

@@ -0,0 +1,4 @@
+inherit_from: .rubocop.yml
+
+Layout/EndOfLine:
+  EnforcedStyle: crlf

.rubocop.yml

@@ -21,3 +21,25 @@ Metrics/LineLength:
   Exclude:
     - 'lib/app/modules/**/*'
     - 'lib/app/helpers/browser_logic.rb'
+
+# Use code climate's metrics measurement rather than rubocop's
+Metrics/AbcSize:
+  Enabled: false
+
+Metrics/BlockLength:
+  Enabled: false
+
+Metrics/ClassLength:
+  Enabled: false
+
+Metrics/MethodLength:
+  Enabled: false
+
+Metrics/ModuleLength:
+  Enabled: false
+
+Metrics/PerceivedComplexity:
+  Enabled: false
+
+Metrics/ParameterLists:
+  Enabled: false

.rubocop_todo.yml

@@ -32,49 +32,15 @@ Lint/UselessAssignment:
   Exclude:
     - 'lib/tasks/tasks.rake'
 
-# Offense count: 150
-Metrics/AbcSize:
-  Max: 176
-
-# Offense count: 38
-# Configuration parameters: CountComments, ExcludedMethods.
-# ExcludedMethods: refine
-Metrics/BlockLength:
-  Max: 388
-
 # Offense count: 3
 # Configuration parameters: CountBlocks.
 Metrics/BlockNesting:
   Max: 4
 
-# Offense count: 60
-# Configuration parameters: CountComments.
-Metrics/ClassLength:
-  Max: 594
-
 # Offense count: 38
 Metrics/CyclomaticComplexity:
   Max: 33
 
-# Offense count: 140
-# Configuration parameters: CountComments, ExcludedMethods.
-Metrics/MethodLength:
-  Max: 142
-
-# Offense count: 1
-# Configuration parameters: CountComments.
-Metrics/ModuleLength:
-  Max: 199
-
-# Offense count: 2
-# Configuration parameters: CountKeywordArgs.
-Metrics/ParameterLists:
-  Max: 10
-
-# Offense count: 19
-Metrics/PerceivedComplexity:
-  Max: 32
-
 # Offense count: 33
 Style/ClassVars:
   Exclude:

.travis.yml

@@ -4,16 +4,23 @@ services:
 rvm:
   - 2.5
   - 2.6
+before_install:
+  - gem update --system
+  - gem install bundler
+  - docker-compose build
+before_script:
+  - curl -L https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64 > ./cc-test-reporter
+  - chmod +x ./cc-test-reporter
+  - ./cc-test-reporter before-build
 script:
   - bundle exec rake
+  # For unknown reasons, the test-reporter fails when using docker if run in an
+  # after_script section
+  - ./cc-test-reporter after-build -t simplecov --exit-code $TRAVIS_TEST_RESULT
   - docker-compose run ruby_server bundle exec rake
   - bundle exec rubocop
 notifications:
   email:
     recipients:
       - inferno@groups.mitre.org
     on_failure: change
-before_install:
-  - gem update --system
-  - gem install bundler
-  - docker-compose build

Dockerfile

@@ -2,7 +2,7 @@ FROM ruby:2.5
 
 # Install gems into a temporary directory
 COPY Gemfile* ./
-RUN bundle install
+RUN gem install bundler && bundle install
 
 # Expose the port
 EXPOSE 4567

Gemfile

@@ -12,6 +12,7 @@ gem 'fhir_client'
 gem 'json-jwt'
 gem 'kramdown'
 gem 'pry'
+gem 'pry-byebug'
 gem 'rack-test'
 gem 'rake'
 gem 'rb-readline'

Gemfile.lock

@@ -22,6 +22,7 @@ GEM
     bloomer (1.0.0)
       bitarray
       msgpack
+    byebug (11.0.1)
     childprocess (1.0.1)
       rake (< 13.0)
     coderay (1.1.2)
@@ -152,6 +153,9 @@ GEM
     pry (0.12.2)
       coderay (~> 1.1.0)
       method_source (~> 0.9.0)
+    pry-byebug (3.7.0)
+      byebug (~> 11.0)
+      pry (~> 0.10)
     psych (3.1.0)
     public_suffix (3.0.3)
     rack (2.0.7)
@@ -233,6 +237,7 @@ DEPENDENCIES
   json-jwt
   kramdown
   pry
+  pry-byebug
   rack-test
   rake
   rb-readline
@@ -246,3 +251,6 @@ DEPENDENCIES
   thin
   time_difference
   webmock
+
+BUNDLED WITH
+   2.0.2

README.md

@@ -1,6 +1,6 @@
-<img src="https://github.com/siteadmin/inferno/blob/master/public/images/inferno_logo.png" width="300px" />
+<img src="https://github.com/onc-healthit/inferno/blob/master/public/images/inferno_logo.png" width="300px" />
 
-[![Build Status](https://travis-ci.org/siteadmin/inferno.svg?branch=master)](https://travis-ci.org/siteadmin/inferno)
+[![Build Status](https://travis-ci.org/onc-healthit/inferno.svg?branch=master)](https://travis-ci.org/onc-healthit/inferno)
 
 Inferno is an open source tool that tests whether patients can access their health data through a standard interface.
 It makes HTTP(S) requests to test your server's conformance to authentication, authorization, and FHIR content standards and reports the results back to you.
@@ -9,7 +9,7 @@ This application creates test clients that exercise the range of requirements of
 
 ## Using Inferno
 
-If you are new to FHIR or SMART-on-FHIR, you may want to review the [Inferno Quick Start Guide](https://github.com/siteadmin/inferno/wiki/Quick-Start-Guide).
+If you are new to FHIR or SMART-on-FHIR, you may want to review the [Inferno Quick Start Guide](https://github.com/onc-healthit/inferno/wiki/Quick-Start-Guide).
 
 ## Installation and Deployment
 
@@ -18,14 +18,14 @@ If you are new to FHIR or SMART-on-FHIR, you may want to review the [Inferno Qui
 Docker is the recommended installation method for Windows devices and can also be used on Linux and MacOS hosts.
 
 1. Install [Docker](https://www.docker.com/) for the host platform as well as the [docker-compose](https://docs.docker.com/compose/install/) tool (which may be included in the distribution, as is the case for Windows and MacOS).
-2. Download the [latest release of the `inferno` project](https://github.com/siteadmin/inferno/releases) to your local computer on a directory of your choice.
+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.
 
 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.
 
-Check out the [Troubleshooting Documentation](https://github.com/siteadmin/inferno/wiki/Troubleshooting) for help.
+Check out the [Troubleshooting Documentation](https://github.com/onc-healthit/inferno/wiki/Troubleshooting) for help.
 
 ### Native Installation
 
@@ -39,7 +39,7 @@ And run the following commands from the terminal:
 
 ```sh
 # MacOS or Linux
-git clone https://github.com/siteadmin/inferno
+git clone https://github.com/onc-healthit/inferno
 cd inferno
 bundle install
 bundle exec rackup
@@ -59,7 +59,7 @@ Inferno can also be deployed onto a server to test many different instances of t
 
 Deployment on a remote server can be done by using a modified form of the Docker containers provided (see above) or by direct installation on the remote host.
 
-Please see the file [deployment-configuration.md](https://github.com/siteadmin/inferno/blob/master/deployment-configuration.md) for details.
+Please see the file [deployment-configuration.md](https://github.com/onc-healthit/inferno/blob/master/deployment-configuration.md) for details.
 
 ### Reference Implementation
 
@@ -82,7 +82,7 @@ bundle exec rake test
 ## Inspecting and Exporting Tests
 
 Tests are written to be easily understood, even by those who aren't familiar with Ruby.  They can be
-viewed directly [in this repository](https://github.com/siteadmin/inferno/tree/master/lib/app/modules).
+viewed directly [in this repository](https://github.com/onc-healthit/inferno/tree/master/lib/app/sequences).
 
 Tests contain metadata that provide additional details and traceability to standards.  The active tests and related metadata can be exported into CSV format and saved to a file named `testlist.csv` with the following command:
 
@@ -134,7 +134,7 @@ bundle exec rake inferno:generate_script[https://my-server.org/data,onc]
 * The `confidential_client` field is a boolean and must be provided as `true` or `false`
 
 ## Using with Continuous Integration Systems
-Instructions and examples are available in the [Continuous Integration Section of the Wiki](https://github.com/siteadmin/inferno/wiki/Using-with-Continuous-Integration-Systems).
+Instructions and examples are available in the [Continuous Integration Section of the Wiki](https://github.com/onc-healthit/inferno/wiki/Using-with-Continuous-Integration-Systems).
 
 ## Contact Us
 The Inferno development team can be reached by email at inferno@groups.mitre.org.  Inferno also has a dedicated [HL7 FHIR chat channel](https://chat.fhir.org/#narrow/stream/153-inferno).

config.yml

@@ -57,20 +57,20 @@ presets:
     inferno_uri: https://inferno.healthit.gov
     client_id: vkPKDPcTIEMaw5Uf-DdUUtNMFMZaX0
     client_secret: LS1nY3JFU3FDeEs0cWoxQWF6TVJFNU05RmZZNGZhZ2Vwb2JYWjdSWWJGakwwNTZ2Vng=
-    instructions: https://github.com/siteadmin/inferno/wiki/SITE-Preset-Instructions
+    instructions: https://github.com/onc-healthit/inferno/wiki/SITE-Preset-Instructions
   site_test_healthit_gov:
     name: SITE DSTU2 FHIR Sandbox
     uri: https://fhir.sitenv.org/secure/fhir
     module: onc
     inferno_uri: https://infernotest.healthit.gov
     client_id: TrToU5piE-dJ1g6PBG1elFV4r9KLmH
     client_secret: ckFqb1ZhbmFMQS13WDE0c1dTLWxSdGRLSE8yUXpWNS1vSnd6azNrMmU3Y0JPdDRja3U=
-    instructions: https://github.com/siteadmin/inferno/wiki/SITE-Preset-Instructions
+    instructions: https://github.com/onc-healthit/inferno/wiki/SITE-Preset-Instructions
   site_local:
     name: SITE DSTU2 FHIR Sandbox
     uri: https://fhir.sitenv.org/secure/fhir
     module: onc
     inferno_uri: http://localhost:4567
     client_id: Yg0o6sJ8I8CfVVyHz1eA0m8jv6sXwe
     client_secret: UDVrTXlna0NvcGRQZ1VhMkZaZzQ0R1FxVGdtTWxFMXVoT3pPd1VRMUN4MFVkV25Gejk=
-    instructions: https://github.com/siteadmin/inferno/wiki/SITE-Preset-Instructions
+    instructions: https://github.com/onc-healthit/inferno/wiki/SITE-Preset-Instructions

deployment-configuration.md

@@ -23,7 +23,7 @@ It is important to open port `80` for HTTP  and port `22` for SSH if you need to
 "Review and Launch" button, click next button until you get to the Security Groups option. Ensure 80 is accessible from anywhere and 22 is
 available from an IP range from which you will connect. Below is an example:
 
-![Security Groups Configuration](https://raw.githubusercontent.com/siteadmin/inferno/master/deployment-files/security-groups.png "Security Groups Configuration")
+![Security Groups Configuration](https://raw.githubusercontent.com/onc-healthit/inferno/master/deployment-files/security-groups.png "Security Groups Configuration")
 
 After this step is done, launch the instance.  Obtain your instance's IP or host name from the AWS console. Point a web browser to the instance using the IP address or host name.
 
@@ -70,7 +70,7 @@ Now, issue the following commands to setup Inferno.
      sudo apt-get install git ruby-bundler ruby-dev
      sudo apt-get install sqlite3 libsqlite3-dev
      sudo apt-get install build-essential patch zlib1g-dev liblzma-dev
-     git clone https://github.com/siteadmin/inferno.git
+     git clone https://github.com/onc-healthit/inferno.git
      cd  inferno
      bundle install
 
@@ -183,7 +183,7 @@ This section describes how to setup the tool using Apache2 using Passenger.
     sudo apt-get install apache2 git ruby-bundler ruby-dev
     sudo apt-get install sqlite3 libsqlite3-dev
     sudo apt-get install build-essential patch zlib1g-dev liblzma-dev
-    git clone https://github.com/siteadmin/inferno.git
+    git clone https://github.com/onc-healthit/inferno.git
     cd  inferno
     bundle install