Reverting local changes loaded to the central repo

Author: Tomasz Gubala

.gitignore

@@ -13,9 +13,14 @@
 !/log/.keep
 !/tmp/.keep
 
+# Ignore uploaded files in development
+/storage/*
+!/storage/.keep
+
 /node_modules
 /yarn-error.log
 
+/public/assets
 .byebug_history
 
 # Ignore gemsects
@@ -34,3 +39,6 @@
 # Dont add production JWT key into git
 /config/jwt/prod.pem
 /config/jwt/prod-dev.pem
+
+# Ignore master key for decrypting credentials and more.
+/config/master.key

.gitlab-ci.yml

@@ -1,4 +1,4 @@
-image: cyfronet/ruby-2.4.1-node-chrome
+image: cyfronet/ruby-2.5.3-node-chrome
 
 services:
   - postgres
@@ -22,7 +22,7 @@ test:
   - google-chrome --version
   - ruby -v
   - which ruby
-  - gem install bundler --no-ri --no-rdoc
+  - gem install bundler
   - bundle install --path vendor --jobs $(nproc)  "${FLAGS[@]}"
   - cp config/database.yml.gitlab-ci config/database.yml
   - bundle exec rake db:create RAILS_ENV=test
@@ -35,7 +35,7 @@ integration:
   - google-chrome --version
   - ruby -v
   - which ruby
-  - gem install bundler --no-ri --no-rdoc
+  - gem install bundler
   - bundle install --path vendor --jobs $(nproc)  "${FLAGS[@]}"
   - cp config/database.yml.gitlab-ci config/database.yml
   - bundle exec rake db:create RAILS_ENV=test
@@ -47,15 +47,15 @@ rubocop:
   stage: test
   script:
     - ruby -v
-    - gem install bundler --no-ri --no-rdoc
+    - gem install bundler
     - bundle install --path vendor --jobs $(nproc)  "${FLAGS[@]}"
     - bundle exec rubocop
 
 brakeman:
   stage: test
   script:
     - ruby -v
-    - gem install brakeman --no-ri --no-rdoc
+    - gem install brakeman
     - brakeman --exit-on-warn --quiet -f plain
 
 deploy_development:
@@ -82,6 +82,8 @@ deploy_production:
   - git push $PROD_GIT_REPO $CI_COMMIT_TAG
   only:
   - tags
+  except:
+  - /^process-.*$/
   environment:
     name: production
     url: https://valve.cyfronet.pl

.rubocop.yml

@@ -28,6 +28,10 @@ Metrics/BlockLength:
     - "**/factories/**"
     - "**/tasks/**"
 
+Lint/AmbiguousBlockAssociation:
+  Exclude:
+    - "spec/**/*"
+
 Layout/DotPosition:
   Description: Checks the position of the dot in multi-line method calls.
   StyleGuide: https://github.com/bbatsov/ruby-style-guide#consistent-multi-line-chains

.ruby-version

@@ -1 +1 @@
-2.4.1
+2.5.3

.tool-versions

@@ -1 +1 @@
-ruby 2.4.1
+ruby 2.5.3

CHANGELOG.md

@@ -8,19 +8,84 @@ Please view this file on the master branch, on stable branches it's out of date.
 
 ## Unreleased
 
+### Added
+- All active user computation are aborted when user is deleted (@mkasztelnik)
+- Pipelines API (@Nuanda)
+- New provenance data file type (@mkasztelnik)
+- Data file synchronization API (@mkasztelnik)
+- Description how to start https development server using puma (@mkasztelnik)
+- Data file type stored in DB (@mkasztelnik)
+- Start runnable computation after new file appears (@mkasztelnik)
+- First version of automatic patient synchronization machinery (@Nuanda)
+
+### Changed
+- Move application controller configurations to separate concerns (@mkasztelnik)
+
+### Deprecated
+
+### Removed
+- Remove `thin` from `Gemfile` since puma can be used to start https development server (@mkasztelnik)
+- Remove `Patient#procedure_status` not used anymore (@mkasztelnik)
+- Remove `guard` since no one from the team is using it right now (@mkasztelnik)
+
+### Fixed
+- Issue #361 regression when running a rimrock step without tag or branch (@Nuanda)
+
+### Security
+
+## 0.12.1
+
+### Fixed
+- Fix pipeline list: CRC model CFD/ROM pipelines (@mkasztelnik)
+
+## 0.12.0
+
+### Added
+- Pipelines API (@Nuanda)
+- New provenance data file type (@mkasztelnik)
+- Add FileStore IP to rake attack safelist (@mkasztelnik)
+
+### Changed
+- `pressure_drops` file pattern extension changed to `dat` (@mkasztelnik)
+- JWT expiration time is now the same as for other envs (@mkasztelnik)
+- JWT expiration time can be configured using ENV variable (@mkasztelnik)
+- `stage_in` adds commented line when file cannot be found (@mkasztelnik)
+- Update to ruby 2.5.3 (@mkasztelnik)
+- Update to rails 5.2.1 (@mkasztelnik)
+- Replaced ERB-based templating with a Liquid-based system (@Nuanda, @mkasztelnik)
+
+### Deprecated
+
+### Removed
+
+### Fixed
+- Seg output shortening rule fix to deal with both success and failure outputs (@Nuanda)
+- ExclusivelyOwnedGroups incorrect positive removed (@Nuanda)
+- Updated truncated_off_mesh regular expression to recognize new segmentation output (@Nuanda)
+- STDOUT and STDERR files reset to nil for a re-run computation (@Nuanda)
+- Uploading input files via WebDAV triggers computation run (@Nuanda)
+- `Pipelines::StartRunnable` starts only configured computations (@mkasztelnik)
+
+### Security
+
+## 0.11.0
+
 ### Added
 - Patients API (@mkasztelnik)
 - Accepting `file.zip` as a correct input for segmentation (@Nuanda)
-- First version of automatic patient synchronization machinery (@Nuanda)
+- Extended clinical details section with a multi-entry widget (@Nuanda)
 
 ### Changed
+- Exclude process-\* tags from the EurValve CI (@jmeizner)
+- Segmentation output files have shorter names (@Nuanda)
 
 ### Deprecated
 
 ### Removed
 
 ### Fixed
 - Fixed GitLab integration spec (@Nuanda)
+- Missing clinical data for some patients (@Nuanda)
 
 ### Security
 

Gemfile

@@ -1,13 +1,17 @@
 # frozen_string_literal: true
 
 source 'https://rubygems.org'
+git_source(:github) { |repo| "https://github.com/#{repo}.git" }
 
-gem 'rails', '~> 5.1.0'
+gem 'rails', '~> 5.2.0'
 
-gem 'pg', '~> 0.15'
+gem 'pg', '>= 0.18', '< 2.0'
 gem 'sass-rails', '~> 5.0'
 gem 'uglifier', '>= 1.3.0'
 
+# Reduces boot times through caching; required in config/boot.rb
+gem 'bootsnap', '>= 1.1.0', require: false
+
 # javascript
 gem 'animate-rails', '1.0.10'
 gem 'clipboard-rails' # copy text to clipboard
@@ -36,7 +40,9 @@ gem 'json-schema'
 gem 'github-markup'
 gem 'redcarpet'
 
-gem 'devise', '~> 4.3.0'
+gem 'liquid'
+
+gem 'devise', '~> 4.5.0'
 gem 'jwt'
 gem 'omniauth-openid'
 gem 'pundit'
@@ -60,15 +66,14 @@ gem 'addressable', '~> 2.5'
 # Gitlab integration
 gem 'gitlab'
 
-gem 'puma', '~> 3.7'
-gem 'redis', '~> 3.0'
+gem 'puma', '~> 3.11'
+gem 'redis', '~> 4.0'
 
 group :development, :test do
   gem 'bullet'
   gem 'byebug', platform: [:mri, :mingw, :x64_mingw]
   gem 'dotenv-rails'
   gem 'factory_bot_rails'
-  gem 'guard-rspec', require: false
   gem 'rspec-rails', '~> 3.0'
 end
 
@@ -78,11 +83,7 @@ group :development do
   gem 'spring-watcher-listen', '~> 2.0.0'
   gem 'web-console', '>= 3.3.0'
 
-  # PLG OpenId requires ssh even for development
-  # start app using `thin start --ssl
-  gem 'thin'
-
-  gem 'rubocop', '0.51.0', require: false
+  gem 'rubocop', '~> 0.59', require: false
 end
 
 group :test do