Merge pull request #514 from onc-healthit/development

Version 2.11.0 Release

.codeclimate.yml

@@ -1,6 +1,7 @@
 version: "2"         # required to adjust maintainability checks
 exclude_patterns:
   - "!**/test/"
+  - "!db/**/*"
 checks:
   argument-count:
     enabled: true

.gitignore

@@ -14,3 +14,4 @@ tmp/*
 resources/terminology/*
 sequence_coverage.csv
 fhir-pgdata/
+umls.db

.rubocop.yml

@@ -7,6 +7,7 @@ AllCops:
     - 'vendor/**/*'
     - 'node_modules/**/*'
     - '.git/**/*'
+    - 'db/**/*'
 
 Layout/MultilineMethodCallIndentation:
   EnforcedStyle: 'indented'

.travis.yml

@@ -9,11 +9,12 @@ before_script:
   - chmod +x ./cc-test-reporter
   - ./cc-test-reporter before-build
 script:
+  - RACK_ENV=test bundle exec rake db:create db:schema:load
   - 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
+  - docker-compose run ruby_server ./bin/run_tests.sh 
   - bundle exec rubocop
 notifications:
   email:

Dockerfile

@@ -19,10 +19,13 @@ COPY config* /var/www/inferno/
 COPY Rakefile /var/www/inferno/
 COPY test /var/www/inferno/test
 COPY lib /var/www/inferno/lib
+COPY db /var/www/inferno/db
+COPY bin /var/www/inferno/bin
 
 ### Set up environment
 
 ENV APP_ENV=production
+ENV RACK_ENV=production
 EXPOSE 4567
 
-CMD ["bundle", "exec", "rackup", "-o", "0.0.0.0"]
+CMD ["./bin/run.sh"]

Gemfile

@@ -2,13 +2,12 @@
 
 source 'https://rubygems.org'
 
+gem 'activerecord', '~> 5.2'
 gem 'addressable'
 gem 'ast'
 gem 'base62-rb'
 gem 'bloomer'
 gem 'colorize'
-gem 'data_mapper'
-gem 'dm-sqlite-adapter'
 gem 'fhir_client'
 gem 'jwt'
 gem 'kramdown'
@@ -23,13 +22,15 @@ gem 'selenium-webdriver'
 gem 'sinatra'
 gem 'sinatra-contrib'
 gem 'sqlite3'
+gem 'standalone_migrations', '~> 6.0'
 gem 'thin'
 gem 'time_difference'
 
 group :test do
+  gem 'database_cleaner-active_record'
   gem 'minitest'
   gem 'rack-test'
-  gem 'rubocop', require: false
+  gem 'rubocop', '~> 0.80.0', require: false
   gem 'simplecov', require: false
   gem 'webmock'
 end

Gemfile.lock

@@ -1,90 +1,65 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.4.3)
+    actionpack (5.2.4.4)
+      actionview (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
+      rack (~> 2.0, >= 2.0.8)
+      rack-test (>= 0.6.3)
+      rails-dom-testing (~> 2.0)
+      rails-html-sanitizer (~> 1.0, >= 1.0.2)
+    actionview (5.2.4.4)
+      activesupport (= 5.2.4.4)
+      builder (~> 3.1)
+      erubi (~> 1.4)
+      rails-dom-testing (~> 2.0)
+      rails-html-sanitizer (~> 1.0, >= 1.0.3)
+    activemodel (5.2.4.4)
+      activesupport (= 5.2.4.4)
+    activerecord (5.2.4.4)
+      activemodel (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
+      arel (>= 9.0)
+    activesupport (5.2.4.4)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
+    arel (9.0.0)
     ast (2.4.0)
     backports (3.15.0)
     base62-rb (0.3.1)
     bcp47 (0.3.3)
       i18n
-    bcrypt (3.1.13)
-    bcrypt-ruby (3.1.5)
-      bcrypt (>= 3.1.3)
     bitarray (1.2.0)
     bloomer (1.0.0)
       bitarray
       msgpack
+    builder (3.2.4)
     byebug (11.0.1)
     childprocess (2.0.0)
       rake (< 13.0)
     coderay (1.1.2)
     colorize (0.8.1)
-    concurrent-ruby (1.1.6)
+    concurrent-ruby (1.1.7)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
+    crass (1.0.6)
     daemons (1.3.1)
-    data_mapper (1.2.0)
-      dm-aggregates (~> 1.2.0)
-      dm-constraints (~> 1.2.0)
-      dm-core (~> 1.2.0)
-      dm-migrations (~> 1.2.0)
-      dm-serializer (~> 1.2.0)
-      dm-timestamps (~> 1.2.0)
-      dm-transactions (~> 1.2.0)
-      dm-types (~> 1.2.0)
-      dm-validations (~> 1.2.0)
-    data_objects (0.10.17)
-      addressable (~> 2.1)
+    database_cleaner (1.8.5)
+    database_cleaner-active_record (1.8.0)
+      activerecord
+      database_cleaner (~> 1.8.0)
     date_time_precision (0.8.1)
-    dm-aggregates (1.2.0)
-      dm-core (~> 1.2.0)
-    dm-constraints (1.2.0)
-      dm-core (~> 1.2.0)
-    dm-core (1.2.1)
-      addressable (~> 2.3)
-    dm-do-adapter (1.2.0)
-      data_objects (~> 0.10.6)
-      dm-core (~> 1.2.0)
-    dm-migrations (1.2.0)
-      dm-core (~> 1.2.0)
-    dm-serializer (1.2.2)
-      dm-core (~> 1.2.0)
-      fastercsv (~> 1.5)
-      json (~> 1.6)
-      json_pure (~> 1.6)
-      multi_json (~> 1.0)
-    dm-sqlite-adapter (1.2.0)
-      dm-do-adapter (~> 1.2.0)
-      do_sqlite3 (~> 0.10.6)
-    dm-timestamps (1.2.0)
-      dm-core (~> 1.2.0)
-    dm-transactions (1.2.0)
-      dm-core (~> 1.2.0)
-    dm-types (1.2.2)
-      bcrypt-ruby (~> 3.0)
-      dm-core (~> 1.2.0)
-      fastercsv (~> 1.5)
-      json (~> 1.6)
-      multi_json (~> 1.0)
-      stringex (~> 1.4)
-      uuidtools (~> 2.1)
-    dm-validations (1.2.0)
-      dm-core (~> 1.2.0)
-    do_sqlite3 (0.10.17)
-      data_objects (= 0.10.17)
     docile (1.3.2)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
+    erubi (1.10.0)
     eventmachine (1.2.7)
     faraday (0.15.4)
       multipart-post (>= 1.2, < 3)
-    fastercsv (1.5.5)
     fhir_client (4.0.3)
       activesupport (>= 3)
       addressable (>= 2.3)
@@ -101,7 +76,7 @@ GEM
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
       nokogiri (>= 1.10.4)
-    fhir_models (4.1.0)
+    fhir_models (4.1.1)
       bcp47 (>= 0.3)
       date_time_precision (>= 0.8)
       mime-types (>= 3.0)
@@ -117,18 +92,20 @@ GEM
       domain_name (~> 0.5)
     i18n (1.8.5)
       concurrent-ruby (~> 1.0)
-    jaro_winkler (1.5.3)
-    json (1.8.6)
-    json_pure (1.8.6)
+    jaro_winkler (1.5.4)
+    json (2.3.1)
     jwt (2.2.1)
     kramdown (2.3.0)
       rexml
+    loofah (2.7.0)
+      crass (~> 1.0.2)
+      nokogiri (>= 1.5.9)
     method_source (0.9.2)
     mime-types (3.3.1)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2020.0512)
+    mime-types-data (3.2020.1104)
     mini_portile2 (2.4.0)
-    minitest (5.14.1)
+    minitest (5.14.2)
     msgpack (1.3.1)
     multi_json (1.13.1)
     multi_xml (0.6.0)
@@ -143,8 +120,8 @@ GEM
       multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (>= 1.2, < 3)
-    parallel (1.17.0)
-    parser (2.6.4.1)
+    parallel (1.20.1)
+    parser (2.7.1.3)
       ast (~> 2.4.0)
     pry (0.12.2)
       coderay (~> 1.1.0)
@@ -158,6 +135,17 @@ GEM
       rack
     rack-test (1.1.0)
       rack (>= 1.0, < 3)
+    rails-dom-testing (2.0.3)
+      activesupport (>= 4.2.0)
+      nokogiri (>= 1.6)
+    rails-html-sanitizer (1.3.0)
+      loofah (~> 2.3)
+    railties (5.2.4.4)
+      actionpack (= 5.2.4.4)
+      activesupport (= 5.2.4.4)
+      method_source
+      rake (>= 0.8.7)
+      thor (>= 0.19.0, < 2.0)
     rainbow (3.0.0)
     rake (12.3.3)
     rb-readline (0.5.5)
@@ -167,11 +155,12 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     rexml (3.2.4)
-    rubocop (0.74.0)
+    rubocop (0.80.1)
       jaro_winkler (~> 1.5.1)
       parallel (~> 1.10)
-      parser (>= 2.6)
+      parser (>= 2.7.0.1)
       rainbow (>= 2.2.2, < 4.0)
+      rexml
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 1.7)
     ruby-progressbar (1.10.1)
@@ -201,22 +190,25 @@ GEM
       sinatra (= 2.0.7)
       tilt (~> 2.0)
     sqlite3 (1.4.1)
-    stringex (1.5.1)
+    standalone_migrations (6.0.0)
+      activerecord (>= 4.2.7, < 6.1.0, != 5.2.3.rc1, != 5.2.3)
+      railties (>= 4.2.7, < 6.1.0, != 5.2.3.rc1, != 5.2.3)
+      rake (>= 10.0)
     thin (1.7.2)
       daemons (~> 1.0, >= 1.0.9)
       eventmachine (~> 1.0, >= 1.0.4)
       rack (>= 1, < 3)
+    thor (1.0.1)
     thread_safe (0.3.6)
     tilt (2.0.10)
     time_difference (0.7.0)
       activesupport (~> 5.1)
-    tzinfo (1.2.7)
+    tzinfo (1.2.8)
       thread_safe (~> 0.1)
     unf (0.1.4)
       unf_ext
     unf_ext (0.0.7.6)
-    unicode-display_width (1.6.0)
-    uuidtools (2.1.5)
+    unicode-display_width (1.6.1)
     webmock (3.7.6)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
@@ -226,13 +218,13 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
+  activerecord (~> 5.2)
   addressable
   ast
   base62-rb
   bloomer
   colorize
-  data_mapper
-  dm-sqlite-adapter
+  database_cleaner-active_record
   fhir_client
   jwt
   kramdown
@@ -244,13 +236,14 @@ DEPENDENCIES
   rake
   rb-readline
   rest-client
-  rubocop
+  rubocop (~> 0.80.0)
   rubyXL
   selenium-webdriver
   simplecov
   sinatra
   sinatra-contrib
   sqlite3
+  standalone_migrations (~> 6.0)
   thin
   time_difference
   webmock

README.md

@@ -42,6 +42,7 @@ And run the following commands from the terminal:
 git clone https://github.com/onc-healthit/inferno
 cd inferno
 bundle install
+bundle exec rake db:create db:schema:load
 bundle exec rackup
 ```
 
@@ -61,6 +62,26 @@ Deployment on a remote server can be done by using a modified form of the Docker
 
 Please see the file [deployment-configuration.md](https://github.com/onc-healthit/inferno/blob/master/deployment-configuration.md) for details.
 
+#### Upgrading Inferno
+
+If an Inferno update makes changes to the database schema, migrations will have
+to be run when updating. Run migrations with:
+
+```sh
+bundle exec rake db:migrate
+```
+
+The above will migrate the development database. To migrate a production or test
+database, use:
+
+```sh
+RACK_ENV=production bundle exec rake db:migrate
+RACK_ENV=test bundle exec rake db:migrate
+```
+
+If you are using the provided inferno docker image, migrations will be run
+automatically.
+
 ### Reference Implementation
 
 While it is recommended that users install Inferno locally, a reference implementation of Inferno is hosted at https://inferno.healthit.gov
@@ -76,6 +97,7 @@ Inferno has been tested on the latest versions of Chrome, Firefox, Safari, and E
 Inferno contains a robust set of self-tests to ensure that the test clients conform to the specification and performs as intended.  To run these tests, execute the following command:
 
 ```sh
+RACK_ENV=test bundle exec rake db:create db:schema:load
 bundle exec rake test
 ```
 

Rakefile

@@ -2,6 +2,9 @@
 
 require 'rake/testtask'
 require 'rubocop/rake_task'
+require 'standalone_migrations'
+
+StandaloneMigrations::Tasks.load_tasks
 
 task :default do
   ENV['RACK_ENV'] = 'test'