mirror of
https://github.com/scinote-eln/scinote-web.git
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Upgrade Rails to 6.0 [SCI-3745]
This commit is contained in:
Oleksii Kriuchykhin
parent
9512b448e6
commit
c068901b00
70 changed files with 467 additions and 381 deletions
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@ -1,4 +1,4 @@
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FROM ruby:2.6.3-buster
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FROM ruby:2.6.4-buster
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MAINTAINER BioSistemika <info@biosistemika.com>
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# additional dependecies
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@ -13,11 +13,14 @@ RUN apt-get update -qq && \
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postgresql-client \
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default-jre-headless \
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poppler-utils \
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librsvg2-2 \
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libvips42 \
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sudo graphviz --no-install-recommends \
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libreoffice \
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libfile-mimeinfo-perl \
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chromium-driver && \
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npm install -g yarn && \
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ln -s /usr/lib/x86_64-linux-gnu/libvips.so.42 /usr/lib/x86_64-linux-gnu/libvips.so && \
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rm -rf /var/lib/apt/lists/*
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# heroku tools
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@ -1,4 +1,4 @@
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FROM ruby:2.6.3-buster
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FROM ruby:2.6.4-buster
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MAINTAINER BioSistemika <info@biosistemika.com>
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# additional dependecies
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@ -16,10 +16,13 @@ RUN apt-get update -qq && \
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netcat \
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default-jre-headless \
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poppler-utils \
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librsvg2-2 \
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libvips42 \
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sudo graphviz --no-install-recommends \
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libreoffice \
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libfile-mimeinfo-perl && \
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npm install -g yarn && \
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ln -s /usr/lib/x86_64-linux-gnu/libvips.so.42 /usr/lib/x86_64-linux-gnu/libvips.so && \
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rm -rf /var/lib/apt/lists/*
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ENV RAILS_ENV production
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16
Gemfile
16
Gemfile
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@ -2,21 +2,21 @@
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source 'http://rubygems.org'
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ruby '2.6.3'
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ruby '2.6.4'
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gem 'bootsnap', require: false
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gem 'bootstrap-sass', '~> 3.3.7'
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gem 'bootstrap_form', '~> 2.7.0'
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gem 'devise', '~> 4.6.2'
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gem 'devise', '~> 4.7.1'
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gem 'devise_invitable'
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gem 'figaro'
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gem 'pg', '~> 1.1'
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gem 'pg_search' # PostgreSQL full text search
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gem 'rails', '~> 5.2.3'
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gem 'rails', '~> 6.0.0'
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gem 'recaptcha', require: 'recaptcha/rails'
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gem 'sanitize', '~> 5.0'
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gem 'sassc-rails'
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gem 'simple_token_authentication', '~> 1.15.1' # Token authentication for Devise
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gem 'simple_token_authentication', '~> 1.16.0' # Token authentication for Devise
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gem 'webpacker', '~> 4.0.0'
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gem 'yomu'
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@ -32,7 +32,7 @@ gem 'omniauth-rails_csrf_protection', '~> 0.1'
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# Gems for API implementation
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gem 'active_model_serializers', '~> 0.10.7'
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gem 'json-jwt'
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gem 'jsonapi-renderer', '= 0.2.0'
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gem 'jsonapi-renderer', '~> 0.2.2'
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gem 'jwt', '~> 1.5'
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gem 'kaminari'
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gem 'rack-attack'
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@ -92,7 +92,7 @@ gem 'delayed_job_active_record'
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gem 'devise-async',
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git: 'https://github.com/mhfs/devise-async.git',
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branch: 'devise-4.x'
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gem 'mini_magick'
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gem 'image_processing', '~> 1.2'
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gem 'paperclip', '~> 6.1' # File attachment, image attachment library
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gem 'rufus-scheduler', '~> 3.5'
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@ -108,7 +108,7 @@ gem 'base62' # Used for smart annotations
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gem 'newrelic_rpm'
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# Permission helper Gem
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gem 'canaid', git: 'https://github.com/biosistemika/canaid', branch: 'master'
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gem 'canaid', git: 'https://github.com/biosistemika/canaid', branch: 'rails_6'
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group :development, :test do
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gem 'awesome_print'
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@ -123,7 +123,7 @@ group :development, :test do
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gem 'pry-byebug'
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gem 'pry-rails'
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gem 'rails-controller-testing'
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gem 'rspec-rails'
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gem 'rspec-rails', '>= 4.0.0.beta2'
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gem 'rubocop', '>= 0.59.0', require: false
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gem 'rubocop-performance'
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gem 'timecop'
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236
Gemfile.lock
236
Gemfile.lock
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@ -1,19 +1,19 @@
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GIT
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remote: https://github.com/biosistemika/canaid
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revision: c65ea0a2fae1edb368aa561e35a153c2cd3bccdd
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branch: master
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revision: 8c87ae49648f4ca2c37313b0d9b9c561a10a71a2
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branch: rails_6
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specs:
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canaid (1.0.4)
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devise (~> 4.6.2)
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canaid (1.0.3)
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devise (>= 3.4.1)
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docile (>= 1.1.0)
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rails (~> 5.2.3)
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rails (>= 4)
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GIT
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remote: https://github.com/biosistemika/jquery-scrollto-rails
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revision: d1d40d5334e0bccfc64208ba81b9a7792f6cb591
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revision: 7b09a7bd9dbf0bbee420c92be32d7ce2f75d0766
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specs:
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jquery-scrollto-rails (1.4.3)
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railties (> 3.1, < 6.0)
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railties (> 3.1, < 7.0)
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GIT
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remote: https://github.com/einzige/sneaky-save
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@ -42,72 +42,85 @@ GIT
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GEM
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remote: http://rubygems.org/
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specs:
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actioncable (5.2.3)
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actionpack (= 5.2.3)
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actioncable (6.0.0)
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actionpack (= 6.0.0)
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nio4r (~> 2.0)
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websocket-driver (>= 0.6.1)
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actionmailer (5.2.3)
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actionpack (= 5.2.3)
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actionview (= 5.2.3)
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activejob (= 5.2.3)
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actionmailbox (6.0.0)
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actionpack (= 6.0.0)
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activejob (= 6.0.0)
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activerecord (= 6.0.0)
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activestorage (= 6.0.0)
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activesupport (= 6.0.0)
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mail (>= 2.7.1)
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actionmailer (6.0.0)
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actionpack (= 6.0.0)
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actionview (= 6.0.0)
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activejob (= 6.0.0)
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mail (~> 2.5, >= 2.5.4)
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rails-dom-testing (~> 2.0)
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actionpack (5.2.3)
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actionview (= 5.2.3)
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activesupport (= 5.2.3)
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actionpack (6.0.0)
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actionview (= 6.0.0)
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activesupport (= 6.0.0)
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rack (~> 2.0)
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rack-test (>= 0.6.3)
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rails-dom-testing (~> 2.0)
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rails-html-sanitizer (~> 1.0, >= 1.0.2)
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actionview (5.2.3)
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activesupport (= 5.2.3)
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rails-html-sanitizer (~> 1.0, >= 1.2.0)
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actiontext (6.0.0)
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actionpack (= 6.0.0)
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activerecord (= 6.0.0)
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activestorage (= 6.0.0)
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activesupport (= 6.0.0)
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nokogiri (>= 1.8.5)
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actionview (6.0.0)
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activesupport (= 6.0.0)
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builder (~> 3.1)
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erubi (~> 1.4)
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rails-dom-testing (~> 2.0)
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rails-html-sanitizer (~> 1.0, >= 1.0.3)
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rails-html-sanitizer (~> 1.1, >= 1.2.0)
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active_model_serializers (0.10.10)
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actionpack (>= 4.1, < 6.1)
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activemodel (>= 4.1, < 6.1)
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case_transform (>= 0.2)
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jsonapi-renderer (>= 0.1.1.beta1, < 0.3)
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activejob (5.2.3)
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activesupport (= 5.2.3)
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activejob (6.0.0)
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activesupport (= 6.0.0)
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globalid (>= 0.3.6)
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activemodel (5.2.3)
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activesupport (= 5.2.3)
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activerecord (5.2.3)
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activemodel (= 5.2.3)
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activesupport (= 5.2.3)
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arel (>= 9.0)
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activemodel (6.0.0)
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activesupport (= 6.0.0)
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activerecord (6.0.0)
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activemodel (= 6.0.0)
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activesupport (= 6.0.0)
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activerecord-import (1.0.2)
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activerecord (>= 3.2)
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activestorage (5.2.3)
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actionpack (= 5.2.3)
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activerecord (= 5.2.3)
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activestorage (6.0.0)
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actionpack (= 6.0.0)
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activejob (= 6.0.0)
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activerecord (= 6.0.0)
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marcel (~> 0.3.1)
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activesupport (5.2.3)
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activesupport (6.0.0)
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concurrent-ruby (~> 1.0, >= 1.0.2)
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i18n (>= 0.7, < 2)
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minitest (~> 5.1)
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tzinfo (~> 1.1)
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addressable (2.6.0)
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public_suffix (>= 2.0.2, < 4.0)
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zeitwerk (~> 2.1, >= 2.1.8)
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addressable (2.7.0)
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public_suffix (>= 2.0.2, < 5.0)
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aes_key_wrap (1.0.1)
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ajax-datatables-rails (0.3.1)
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railties (>= 3.1)
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arel (9.0.0)
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aspector (0.14.0)
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ast (2.4.0)
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auto_strip_attributes (2.5.0)
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activerecord (>= 4.0)
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autoprefixer-rails (9.6.1)
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autoprefixer-rails (9.6.1.1)
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execjs
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autosize-rails (1.18.17)
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rails (>= 3.1)
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awesome_print (1.8.0)
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aws-eventstream (1.0.3)
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aws-partitions (1.197.0)
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aws-sdk-core (3.62.0)
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aws-partitions (1.211.0)
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aws-sdk-core (3.67.0)
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aws-eventstream (~> 1.0, >= 1.0.2)
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aws-partitions (~> 1.0)
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aws-sigv4 (~> 1.1)
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@ -118,7 +131,7 @@ GEM
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aws-sdk-rails (2.1.0)
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aws-sdk-ses (~> 1)
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railties (>= 3)
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aws-sdk-s3 (1.46.0)
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aws-sdk-s3 (1.48.0)
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aws-sdk-core (~> 3, >= 3.61.1)
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aws-sdk-kms (~> 1)
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aws-sigv4 (~> 1.1)
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@ -137,7 +150,7 @@ GEM
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bindata (2.4.4)
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binding_of_caller (0.8.0)
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debug_inspector (>= 0.0.1)
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bootsnap (1.4.4)
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bootsnap (1.4.5)
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msgpack (~> 1.0)
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bootstrap-sass (3.3.7)
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autoprefixer-rails (>= 5.2.1)
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@ -147,11 +160,11 @@ GEM
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momentjs-rails (>= 2.8.1)
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bootstrap_form (2.7.0)
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builder (3.2.3)
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bullet (6.0.1)
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bullet (6.0.2)
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activesupport (>= 3.0.0)
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uniform_notifier (~> 1.11)
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byebug (11.0.1)
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capybara (3.28.0)
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capybara (3.29.0)
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addressable
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mini_mime (>= 0.1.3)
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nokogiri (~> 1.8)
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@ -201,30 +214,30 @@ GEM
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cucumber-tag_expressions (~> 1.1.0)
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gherkin (~> 5.0)
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cucumber-expressions (6.0.1)
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cucumber-rails (1.7.0)
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capybara (>= 2.3.0, < 4)
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cucumber-rails (1.8.0)
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capybara (>= 2.12, < 4)
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cucumber (>= 3.0.2, < 4)
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mime-types (>= 1.17, < 4)
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mime-types (>= 2.0, < 4)
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nokogiri (~> 1.8)
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railties (>= 4.2, < 7)
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cucumber-tag_expressions (1.1.1)
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cucumber-wire (0.0.1)
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database_cleaner (1.7.0)
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debug_inspector (0.0.3)
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deface (1.5.0)
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deface (1.5.1)
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nokogiri (>= 1.6)
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polyglot
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rails (>= 4.1)
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rainbow (>= 2.1.0)
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delayed_job (4.1.7)
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activesupport (>= 3.0, < 5.3)
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delayed_job_active_record (4.1.3)
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activerecord (>= 3.0, < 5.3)
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delayed_job (4.1.8)
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activesupport (>= 3.0, < 6.1)
|
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delayed_job_active_record (4.1.4)
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activerecord (>= 3.0, < 6.1)
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delayed_job (>= 3.0, < 5)
|
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devise (4.6.2)
|
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devise (4.7.1)
|
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bcrypt (~> 3.0)
|
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orm_adapter (~> 0.1)
|
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railties (>= 4.1.0, < 6.0)
|
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railties (>= 4.1.0)
|
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responders
|
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warden (~> 1.2.3)
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devise_invitable (2.0.1)
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|
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@ -237,7 +250,7 @@ GEM
|
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doorkeeper (5.1.0)
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railties (>= 5)
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erubi (1.8.0)
|
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et-orbi (1.2.1)
|
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et-orbi (1.2.2)
|
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tzinfo
|
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execjs (2.7.0)
|
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factory_bot (5.0.2)
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|
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@ -245,15 +258,15 @@ GEM
|
|||
factory_bot_rails (5.0.2)
|
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factory_bot (~> 5.0.2)
|
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railties (>= 4.2.0)
|
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faker (1.9.3)
|
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i18n (>= 0.7)
|
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faker (2.2.2)
|
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i18n (~> 1.6.0)
|
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faraday (0.15.4)
|
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multipart-post (>= 1.2, < 3)
|
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fastimage (2.1.5)
|
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fastimage (2.1.7)
|
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ffi (1.11.1)
|
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figaro (1.1.1)
|
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thor (~> 0.14)
|
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fugit (1.3.1)
|
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fugit (1.3.3)
|
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et-orbi (~> 1.1, >= 1.1.8)
|
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raabro (~> 1.1)
|
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gherkin (5.1.0)
|
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|
|
@ -269,6 +282,9 @@ GEM
|
|||
concurrent-ruby (~> 1.0)
|
||||
i18n-js (3.3.0)
|
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i18n (>= 0.6.6)
|
||||
image_processing (1.9.3)
|
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mini_magick (>= 4.9.5, < 5)
|
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ruby-vips (>= 2.0.13, < 3)
|
||||
iniparse (1.4.4)
|
||||
jaro_winkler (1.5.3)
|
||||
jbuilder (2.9.1)
|
||||
|
|
@ -290,7 +306,7 @@ GEM
|
|||
json_matchers (0.11.1)
|
||||
json_schema
|
||||
json_schema (0.20.7)
|
||||
jsonapi-renderer (0.2.0)
|
||||
jsonapi-renderer (0.2.2)
|
||||
jwt (1.5.6)
|
||||
kaminari (1.1.1)
|
||||
activesupport (>= 4.1.0)
|
||||
|
|
@ -321,7 +337,9 @@ GEM
|
|||
marcel (0.3.3)
|
||||
mimemagic (~> 0.3.2)
|
||||
method_source (0.9.2)
|
||||
mime-types (1.25.1)
|
||||
mime-types (3.3)
|
||||
mime-types-data (~> 3.2015)
|
||||
mime-types-data (3.2019.0904)
|
||||
mimemagic (0.3.3)
|
||||
mini_magick (4.9.5)
|
||||
mini_mime (1.0.2)
|
||||
|
|
@ -338,8 +356,8 @@ GEM
|
|||
coffee-rails (>= 3.2.1)
|
||||
jquery-rails
|
||||
rails (>= 3.2.0)
|
||||
newrelic_rpm (6.5.0.357)
|
||||
nio4r (2.4.0)
|
||||
newrelic_rpm (6.6.0.358)
|
||||
nio4r (2.5.1)
|
||||
nokogiri (1.10.4)
|
||||
mini_portile2 (~> 2.4.0)
|
||||
nokogumbo (2.0.1)
|
||||
|
|
@ -362,7 +380,7 @@ GEM
|
|||
actionpack (>= 4.2)
|
||||
omniauth (>= 1.3.1)
|
||||
orm_adapter (0.5.0)
|
||||
overcommit (0.49.0)
|
||||
overcommit (0.49.1)
|
||||
childprocess (>= 0.6.3, < 2.0)
|
||||
iniparse (~> 1.4)
|
||||
paperclip (6.1.0)
|
||||
|
|
@ -372,7 +390,7 @@ GEM
|
|||
mimemagic (~> 0.3.0)
|
||||
terrapin (~> 0.6.0)
|
||||
parallel (1.17.0)
|
||||
parser (2.6.3.0)
|
||||
parser (2.6.4.0)
|
||||
ast (~> 2.4.0)
|
||||
pg (1.1.4)
|
||||
pg_search (2.3.0)
|
||||
|
|
@ -387,8 +405,8 @@ GEM
|
|||
pry (~> 0.10)
|
||||
pry-rails (0.3.9)
|
||||
pry (>= 0.10.4)
|
||||
public_suffix (3.1.1)
|
||||
puma (4.0.1)
|
||||
public_suffix (4.0.1)
|
||||
puma (4.1.1)
|
||||
nio4r (~> 2.0)
|
||||
raabro (1.1.6)
|
||||
rack (2.0.7)
|
||||
|
|
@ -398,18 +416,20 @@ GEM
|
|||
rack
|
||||
rack-test (1.1.0)
|
||||
rack (>= 1.0, < 3)
|
||||
rails (5.2.3)
|
||||
actioncable (= 5.2.3)
|
||||
actionmailer (= 5.2.3)
|
||||
actionpack (= 5.2.3)
|
||||
actionview (= 5.2.3)
|
||||
activejob (= 5.2.3)
|
||||
activemodel (= 5.2.3)
|
||||
activerecord (= 5.2.3)
|
||||
activestorage (= 5.2.3)
|
||||
activesupport (= 5.2.3)
|
||||
rails (6.0.0)
|
||||
actioncable (= 6.0.0)
|
||||
actionmailbox (= 6.0.0)
|
||||
actionmailer (= 6.0.0)
|
||||
actionpack (= 6.0.0)
|
||||
actiontext (= 6.0.0)
|
||||
actionview (= 6.0.0)
|
||||
activejob (= 6.0.0)
|
||||
activemodel (= 6.0.0)
|
||||
activerecord (= 6.0.0)
|
||||
activestorage (= 6.0.0)
|
||||
activesupport (= 6.0.0)
|
||||
bundler (>= 1.3.0)
|
||||
railties (= 5.2.3)
|
||||
railties (= 6.0.0)
|
||||
sprockets-rails (>= 2.0.0)
|
||||
rails-controller-testing (1.0.4)
|
||||
actionpack (>= 5.0.1.x)
|
||||
|
|
@ -427,25 +447,25 @@ GEM
|
|||
rails (> 3.1)
|
||||
rails_serve_static_assets (0.0.5)
|
||||
rails_stdout_logging (0.0.5)
|
||||
railties (5.2.3)
|
||||
actionpack (= 5.2.3)
|
||||
activesupport (= 5.2.3)
|
||||
railties (6.0.0)
|
||||
actionpack (= 6.0.0)
|
||||
activesupport (= 6.0.0)
|
||||
method_source
|
||||
rake (>= 0.8.7)
|
||||
thor (>= 0.19.0, < 2.0)
|
||||
thor (>= 0.20.3, < 2.0)
|
||||
rainbow (3.0.0)
|
||||
rake (12.3.3)
|
||||
rb-fsevent (0.10.3)
|
||||
rb-inotify (0.10.0)
|
||||
ffi (~> 1.0)
|
||||
rdoc (6.1.1)
|
||||
rdoc (6.2.0)
|
||||
recaptcha (5.1.0)
|
||||
json
|
||||
regexp_parser (1.6.0)
|
||||
responders (3.0.0)
|
||||
actionpack (>= 5.0)
|
||||
railties (>= 5.0)
|
||||
rgl (0.5.4)
|
||||
rgl (0.5.6)
|
||||
lazy_priority_queue (~> 0.1.0)
|
||||
stream (~> 0.5.2)
|
||||
roo (2.8.2)
|
||||
|
|
@ -459,14 +479,14 @@ GEM
|
|||
rspec-mocks (3.8.1)
|
||||
diff-lcs (>= 1.2.0, < 2.0)
|
||||
rspec-support (~> 3.8.0)
|
||||
rspec-rails (3.8.2)
|
||||
actionpack (>= 3.0)
|
||||
activesupport (>= 3.0)
|
||||
railties (>= 3.0)
|
||||
rspec-core (~> 3.8.0)
|
||||
rspec-expectations (~> 3.8.0)
|
||||
rspec-mocks (~> 3.8.0)
|
||||
rspec-support (~> 3.8.0)
|
||||
rspec-rails (4.0.0.beta2)
|
||||
actionpack (>= 4.2)
|
||||
activesupport (>= 4.2)
|
||||
railties (>= 4.2)
|
||||
rspec-core (~> 3.8)
|
||||
rspec-expectations (~> 3.8)
|
||||
rspec-mocks (~> 3.8)
|
||||
rspec-support (~> 3.8)
|
||||
rspec-support (3.8.2)
|
||||
rubocop (0.74.0)
|
||||
jaro_winkler (~> 1.5.1)
|
||||
|
|
@ -479,12 +499,14 @@ GEM
|
|||
rubocop (>= 0.71.0)
|
||||
ruby-graphviz (1.2.4)
|
||||
ruby-progressbar (1.10.1)
|
||||
ruby-vips (2.0.15)
|
||||
ffi (~> 1.9)
|
||||
ruby_dep (1.5.0)
|
||||
rubyzip (1.2.3)
|
||||
rubyzip (1.2.4)
|
||||
rufus-scheduler (3.6.0)
|
||||
fugit (~> 1.1, >= 1.1.6)
|
||||
safe_yaml (1.0.5)
|
||||
sanitize (5.0.0)
|
||||
sanitize (5.1.0)
|
||||
crass (~> 1.0.2)
|
||||
nokogiri (>= 1.8.0)
|
||||
nokogumbo (~> 2.0)
|
||||
|
|
@ -493,9 +515,8 @@ GEM
|
|||
sass-listen (4.0.0)
|
||||
rb-fsevent (~> 0.9, >= 0.9.4)
|
||||
rb-inotify (~> 0.9, >= 0.9.7)
|
||||
sassc (2.0.1)
|
||||
sassc (2.2.0)
|
||||
ffi (~> 1.9)
|
||||
rake
|
||||
sassc-rails (2.1.2)
|
||||
railties (>= 4.0.0)
|
||||
sassc (>= 2.0)
|
||||
|
|
@ -513,9 +534,9 @@ GEM
|
|||
shoulda-matchers (4.1.2)
|
||||
activesupport (>= 4.2.0)
|
||||
silencer (1.0.1)
|
||||
simple_token_authentication (1.15.1)
|
||||
actionmailer (>= 3.2.6, < 6)
|
||||
actionpack (>= 3.2.6, < 6)
|
||||
simple_token_authentication (1.16.0)
|
||||
actionmailer (>= 3.2.6, < 7)
|
||||
actionpack (>= 3.2.6, < 7)
|
||||
devise (>= 3.2, < 6)
|
||||
simplecov (0.17.0)
|
||||
docile (~> 1.1)
|
||||
|
|
@ -552,7 +573,7 @@ GEM
|
|||
uniform_notifier (1.12.1)
|
||||
warden (1.2.8)
|
||||
rack (>= 2.0.6)
|
||||
webmock (3.6.2)
|
||||
webmock (3.7.2)
|
||||
addressable (>= 2.3.6)
|
||||
crack (>= 0.3.2)
|
||||
hashdiff (>= 0.4.0, < 2.0.0)
|
||||
|
|
@ -568,9 +589,8 @@ GEM
|
|||
wkhtmltopdf-heroku (2.12.4.0)
|
||||
xpath (3.2.0)
|
||||
nokogiri (~> 1.8)
|
||||
yomu (0.2.4)
|
||||
json (~> 1.8)
|
||||
mime-types (~> 1.23)
|
||||
yomu (0.1.5)
|
||||
zeitwerk (2.1.10)
|
||||
|
||||
PLATFORMS
|
||||
ruby
|
||||
|
|
@ -606,7 +626,7 @@ DEPENDENCIES
|
|||
deface (~> 1.0)
|
||||
delayed_job_active_record
|
||||
delayed_paperclip!
|
||||
devise (~> 4.6.2)
|
||||
devise (~> 4.7.1)
|
||||
devise-async!
|
||||
devise_invitable
|
||||
discard (~> 1.0)
|
||||
|
|
@ -618,6 +638,7 @@ DEPENDENCIES
|
|||
hammerjs-rails
|
||||
httparty (~> 0.13.1)
|
||||
i18n-js (~> 3.0)
|
||||
image_processing (~> 1.2)
|
||||
jbuilder
|
||||
jquery-rails
|
||||
jquery-scrollto-rails!
|
||||
|
|
@ -625,12 +646,11 @@ DEPENDENCIES
|
|||
js_cookie_rails
|
||||
json-jwt
|
||||
json_matchers
|
||||
jsonapi-renderer (= 0.2.0)
|
||||
jsonapi-renderer (~> 0.2.2)
|
||||
jwt (~> 1.5)
|
||||
kaminari
|
||||
listen (~> 3.0)
|
||||
logging (~> 2.0.0)
|
||||
mini_magick
|
||||
momentjs-rails (~> 2.17.1)
|
||||
nested_form_fields
|
||||
newrelic_rpm
|
||||
|
|
@ -647,14 +667,14 @@ DEPENDENCIES
|
|||
pry-rails
|
||||
puma
|
||||
rack-attack
|
||||
rails (~> 5.2.3)
|
||||
rails (~> 6.0.0)
|
||||
rails-controller-testing
|
||||
rails_12factor
|
||||
rails_autolink (~> 1.1, >= 1.1.6)
|
||||
recaptcha
|
||||
rgl
|
||||
roo (~> 2.8.2)
|
||||
rspec-rails
|
||||
rspec-rails (>= 4.0.0.beta2)
|
||||
rubocop (>= 0.59.0)
|
||||
rubocop-performance
|
||||
ruby-graphviz (~> 1.2)
|
||||
|
|
@ -667,7 +687,7 @@ DEPENDENCIES
|
|||
selenium-webdriver
|
||||
shoulda-matchers
|
||||
silencer
|
||||
simple_token_authentication (~> 1.15.1)
|
||||
simple_token_authentication (~> 1.16.0)
|
||||
simplecov
|
||||
sneaky-save!
|
||||
spinjs-rails
|
||||
|
|
@ -685,7 +705,7 @@ DEPENDENCIES
|
|||
yomu
|
||||
|
||||
RUBY VERSION
|
||||
ruby 2.6.3p62
|
||||
ruby 2.6.4p104
|
||||
|
||||
BUNDLED WITH
|
||||
1.17.3
|
||||
|
|
|
|||
|
|
@ -3,6 +3,8 @@
|
|||
# The base controller for all ActiveStorage controllers.
|
||||
module ActiveStorage
|
||||
class BaseController < ApplicationController
|
||||
include ActiveStorage::SetCurrent
|
||||
|
||||
before_action do
|
||||
ActiveStorage::Current.host = request.base_url
|
||||
end
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ module ActiveStorage
|
|||
include ActiveStorage::CheckBlobPermissions
|
||||
|
||||
def show
|
||||
expires_in ActiveStorage::Blob.service.url_expires_in
|
||||
expires_in ActiveStorage.service_urls_expire_in
|
||||
redirect_to @blob.service_url(disposition: params[:disposition])
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ module ActiveStorage
|
|||
include ActiveStorage::CheckBlobPermissions
|
||||
|
||||
def show
|
||||
expires_in ActiveStorage::Blob.service.url_expires_in
|
||||
expires_in ActiveStorage.service_urls_expire_in
|
||||
redirect_to @blob.representation(params[:variation_key]).processed.service_url(disposition: params[:disposition])
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -91,7 +91,7 @@ class ExperimentsController < ApplicationController
|
|||
end
|
||||
|
||||
old_text = @experiment.description
|
||||
@experiment.update_attributes(experiment_params)
|
||||
@experiment.update(experiment_params)
|
||||
@experiment.last_modified_by = current_user
|
||||
|
||||
if @experiment.save
|
||||
|
|
|
|||
|
|
@ -97,7 +97,7 @@ class RepositoriesController < ApplicationController
|
|||
|
||||
def update
|
||||
old_name = @repository.name
|
||||
@repository.update_attributes(repository_params)
|
||||
@repository.update(repository_params)
|
||||
|
||||
respond_to do |format|
|
||||
format.json do
|
||||
|
|
|
|||
|
|
@ -87,7 +87,7 @@ class RepositoryColumnsController < ApplicationController
|
|||
def update
|
||||
respond_to do |format|
|
||||
format.json do
|
||||
@repository_column.update_attributes(repository_column_params)
|
||||
@repository_column.update(repository_column_params)
|
||||
if @repository_column.save
|
||||
log_activity(:edit_column_inventory)
|
||||
|
||||
|
|
|
|||
|
|
@ -492,7 +492,7 @@ class StepsController < ApplicationController
|
|||
update_params = {}
|
||||
delete_step_tables(params)
|
||||
extract_destroy_params(params, update_params)
|
||||
@step.update_attributes(update_params) unless update_params.empty?
|
||||
@step.update(update_params) unless update_params.empty?
|
||||
end
|
||||
|
||||
# Delete the step table
|
||||
|
|
|
|||
|
|
@ -73,7 +73,7 @@ class TagsController < ApplicationController
|
|||
|
||||
def update
|
||||
@tag.last_modified_by = current_user
|
||||
if @tag.update_attributes(tag_params)
|
||||
if @tag.update(tag_params)
|
||||
log_activity(:edit_tag, @tag.project, tag: @tag.id, project: @tag.project.id)
|
||||
respond_to do |format|
|
||||
format.html
|
||||
|
|
|
|||
|
|
@ -1,7 +1,6 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
class Asset < ApplicationRecord
|
||||
include ActiveStorage::Downloading
|
||||
include SearchableModel
|
||||
include DatabaseHelper
|
||||
include Encryptor
|
||||
|
|
@ -199,15 +198,15 @@ class Asset < ApplicationRecord
|
|||
end
|
||||
|
||||
def medium_preview
|
||||
return file.variant(resize: Constants::MEDIUM_PIC_FORMAT) if previewable_image?
|
||||
return file.variant(resize_to_limit: Constants::MEDIUM_PIC_FORMAT) if previewable_image?
|
||||
|
||||
file.preview(resize: Constants::MEDIUM_PIC_FORMAT)
|
||||
file.preview(resize_to_limit: Constants::MEDIUM_PIC_FORMAT)
|
||||
end
|
||||
|
||||
def large_preview
|
||||
return file.variant(resize: Constants::LARGE_PIC_FORMAT) if previewable_image?
|
||||
return file.variant(resize_to_limit: Constants::LARGE_PIC_FORMAT) if previewable_image?
|
||||
|
||||
file.preview(resize: Constants::LARGE_PIC_FORMAT)
|
||||
file.preview(resize_to_limit: Constants::LARGE_PIC_FORMAT)
|
||||
end
|
||||
|
||||
def file_name
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
class SystemNotification < ApplicationRecord
|
||||
include PgSearch
|
||||
include PgSearch::Model
|
||||
|
||||
scope :modals, -> { select(:modal_title, :modal_body, :id) }
|
||||
# Full text postgreSQL search configuration
|
||||
|
|
|
|||
|
|
@ -1,11 +1,10 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
class TinyMceAsset < ApplicationRecord
|
||||
include ActiveStorage::Downloading
|
||||
extend ProtocolsExporter
|
||||
extend MarvinJsActions
|
||||
attr_accessor :reference
|
||||
before_create :set_reference, optional: true
|
||||
before_create :set_reference
|
||||
after_create :calculate_estimated_size, :self_destruct
|
||||
after_destroy :release_team_space
|
||||
|
||||
|
|
@ -98,7 +97,7 @@ class TinyMceAsset < ApplicationRecord
|
|||
end
|
||||
|
||||
def preview
|
||||
image.variant(resize: Constants::LARGE_PIC_FORMAT)
|
||||
image.variant(resize_to_limit: Constants::LARGE_PIC_FORMAT)
|
||||
end
|
||||
|
||||
def self.delete_unsaved_image(id)
|
||||
|
|
|
|||
|
|
@ -8,7 +8,6 @@ class User < ApplicationRecord
|
|||
include User::ProjectRoles
|
||||
include TeamBySubjectModel
|
||||
include InputSanitizeHelper
|
||||
include ActiveStorage::Downloading
|
||||
include ImageVariantProcessing
|
||||
|
||||
acts_as_token_authenticatable
|
||||
|
|
@ -264,7 +263,7 @@ class User < ApplicationRecord
|
|||
else
|
||||
Constants::ICON_SMALL_PIC_FORMAT
|
||||
end
|
||||
avatar.variant(resize: format)
|
||||
avatar.variant(resize_to_limit: format)
|
||||
end
|
||||
|
||||
def avatar_url(style)
|
||||
|
|
|
|||
|
|
@ -2,9 +2,11 @@
|
|||
# archived (for restore permissions) or active (for all other permissions) -
|
||||
# now we mostly do the check only for the permission level for which the
|
||||
# permission was made
|
||||
Canaid::Permissions.register_generic do
|
||||
# organization: create team
|
||||
can :create_teams do |_|
|
||||
true
|
||||
module Organization
|
||||
Canaid::Permissions.register_generic do
|
||||
# organization: create team
|
||||
can :create_teams do |_|
|
||||
true
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -28,8 +28,7 @@ module ActiveStorage
|
|||
# Wraps the Amazon Simple Storage Service (S3) as an Active Storage service.
|
||||
# See ActiveStorage::Service for the generic API documentation that applies to all services.
|
||||
class Service::CustomS3Service < Service
|
||||
attr_reader :client, :bucket
|
||||
attr_reader :multipart_upload_threshold, :upload_options
|
||||
attr_reader :client, :bucket, :upload_options
|
||||
attr_reader :subfolder
|
||||
|
||||
def initialize(bucket:, upload: {}, **options)
|
||||
|
|
@ -38,17 +37,14 @@ module ActiveStorage
|
|||
@client = Aws::S3::Resource.new(**options)
|
||||
@bucket = @client.bucket(bucket)
|
||||
|
||||
@multipart_upload_threshold = upload.fetch(:multipart_threshold, 100.megabytes)
|
||||
@upload_options = upload
|
||||
end
|
||||
|
||||
def upload(key, io, checksum: nil, content_type: nil, **)
|
||||
instrument :upload, key: key, checksum: checksum do
|
||||
if io.size < multipart_upload_threshold
|
||||
upload_with_single_part key, io, checksum: checksum, content_type: content_type
|
||||
else
|
||||
upload_with_multipart key, io, content_type: content_type
|
||||
end
|
||||
object_for(key).put(upload_options.merge(body: io, content_md5: checksum, content_type: content_type))
|
||||
rescue Aws::S3::Errors::BadDigest
|
||||
raise ActiveStorage::IntegrityError
|
||||
end
|
||||
end
|
||||
|
||||
|
|
@ -60,6 +56,8 @@ module ActiveStorage
|
|||
else
|
||||
instrument :download, key: key do
|
||||
object_for(key).get.body.string.force_encoding(Encoding::BINARY)
|
||||
rescue Aws::S3::Errors::NoSuchKey
|
||||
raise ActiveStorage::FileNotFoundError
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -68,8 +66,10 @@ module ActiveStorage
|
|||
instrument :download_chunk, key: key, range: range do
|
||||
object_for(key).get(range: "bytes=#{range.begin}-#{range.exclude_end? ? range.end - 1 : range.end}")
|
||||
.body
|
||||
.string
|
||||
.read
|
||||
.force_encoding(Encoding::BINARY)
|
||||
rescue Aws::S3::Errors::NoSuchKey
|
||||
raise ActiveStorage::FileNotFoundError
|
||||
end
|
||||
end
|
||||
|
||||
|
|
@ -81,7 +81,6 @@ module ActiveStorage
|
|||
|
||||
def delete_prefixed(prefix)
|
||||
instrument :delete_prefixed, prefix: prefix do
|
||||
prefix = subfolder.present? ? File.join(subfolder, prefix) : prefix
|
||||
bucket.objects(prefix: prefix).batch_delete!
|
||||
end
|
||||
end
|
||||
|
|
@ -107,11 +106,10 @@ module ActiveStorage
|
|||
end
|
||||
|
||||
def url_for_direct_upload(key, expires_in:, content_type:, content_length:, checksum:)
|
||||
raise ActiveStorage::IntegrityError if content_length > Rails.configuration.x.file_max_size_mb.megabytes
|
||||
|
||||
instrument :url, key: key do |payload|
|
||||
generated_url = object_for(key).presigned_url :put, expires_in: expires_in.to_i,
|
||||
content_type: content_type, content_length: content_length, content_md5: checksum
|
||||
content_type: content_type, content_length: content_length, content_md5: checksum,
|
||||
whitelist_headers: ['content-length']
|
||||
|
||||
payload[:url] = generated_url
|
||||
|
||||
|
|
@ -119,7 +117,7 @@ module ActiveStorage
|
|||
end
|
||||
end
|
||||
|
||||
def headers_for_direct_upload(_key, content_type:, checksum:, **)
|
||||
def headers_for_direct_upload(_, content_type:, checksum:, **)
|
||||
{ 'Content-Type' => content_type, 'Content-MD5' => checksum }
|
||||
end
|
||||
|
||||
|
|
@ -129,23 +127,6 @@ module ActiveStorage
|
|||
|
||||
private
|
||||
|
||||
MAXIMUM_UPLOAD_PARTS_COUNT = 10000
|
||||
MINIMUM_UPLOAD_PART_SIZE = 5.megabytes
|
||||
|
||||
def upload_with_single_part(key, io, checksum: nil, content_type: nil)
|
||||
object_for(key).put(body: io, content_md5: checksum, content_type: content_type, **upload_options)
|
||||
rescue Aws::S3::Errors::BadDigest
|
||||
raise ActiveStorage::IntegrityError
|
||||
end
|
||||
|
||||
def upload_with_multipart(key, io, content_type: nil)
|
||||
part_size = [io.size.fdiv(MAXIMUM_UPLOAD_PARTS_COUNT).ceil, MINIMUM_UPLOAD_PART_SIZE].max
|
||||
|
||||
object_for(key).upload_stream(content_type: content_type, part_size: part_size, **upload_options) do |out|
|
||||
IO.copy_stream(io, out)
|
||||
end
|
||||
end
|
||||
|
||||
def object_for(key)
|
||||
key = subfolder.present? ? File.join(subfolder, key) : key
|
||||
bucket.object(key)
|
||||
|
|
@ -158,25 +139,12 @@ module ActiveStorage
|
|||
chunk_size = 5.megabytes
|
||||
offset = 0
|
||||
|
||||
raise ActiveStorage::FileNotFoundError unless object.exists?
|
||||
|
||||
while offset < object.content_length
|
||||
yield object.get(range: "bytes=#{offset}-#{offset + chunk_size - 1}")
|
||||
.body
|
||||
.string
|
||||
.force_encoding(Encoding::BINARY)
|
||||
yield object.get(range: "bytes=#{offset}-#{offset + chunk_size - 1}").body.read.force_encoding(Encoding::BINARY)
|
||||
offset += chunk_size
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
module S3SignerModifier
|
||||
def build_signer(cfg)
|
||||
signer = super(cfg)
|
||||
signer.unsigned_headers.delete('content-length')
|
||||
signer
|
||||
end
|
||||
end
|
||||
|
||||
Aws::S3::Presigner.class_eval do
|
||||
prepend S3SignerModifier
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ module ClientApi
|
|||
|
||||
def update_team!
|
||||
raise ClientApi::CustomTeamError unless @params
|
||||
return if @team.update_attributes(@params)
|
||||
return if @team.update(@params)
|
||||
raise ClientApi::CustomTeamError, @team.errors.full_messages
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -91,7 +91,7 @@ module Notifications
|
|||
if n.new_record?
|
||||
save_notification n
|
||||
elsif n.last_time_changed_at < attrs[:last_time_changed_at]
|
||||
n.update_attributes!(attrs)
|
||||
n.update!(attrs)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
|
||||
module ProtocolImporters
|
||||
class BuildProtocolFromClientService
|
||||
require 'protocol_importers/protocols_io/v3/errors'
|
||||
extend Service
|
||||
|
||||
attr_reader :errors, :built_protocol, :steps_assets
|
||||
|
|
|
|||
|
|
@ -3,7 +3,6 @@
|
|||
module ProtocolImporters
|
||||
class SearchProtocolsService
|
||||
extend Service
|
||||
require 'protocol_importers/protocols_io/v3/errors'
|
||||
|
||||
attr_reader :errors, :protocols_list
|
||||
|
||||
|
|
|
|||
|
|
@ -3,13 +3,8 @@
|
|||
class SpreadsheetParser
|
||||
# Based on file's extension opens file (used for importing)
|
||||
def self.open_spreadsheet(file)
|
||||
if file.class == ActionDispatch::Http::UploadedFile
|
||||
filename = file.original_filename
|
||||
file_path = file.path
|
||||
else
|
||||
filename = file.filename.to_s
|
||||
file_path = file.service_url
|
||||
end
|
||||
filename = file.original_filename
|
||||
file_path = file.path
|
||||
|
||||
case File.extname(filename)
|
||||
when '.csv'
|
||||
|
|
|
|||
|
|
@ -335,33 +335,32 @@ class TeamImporter
|
|||
tiny_mce_asset = TinyMceAsset.new(tiny_mce_asset_json['tiny_mce_asset'])
|
||||
tiny_mce_asset_blob = tiny_mce_asset_json['tiny_mce_asset_blob']
|
||||
# Try to find and load file
|
||||
File.open(
|
||||
File.join(@import_dir, 'tiny_mce_assets', tiny_mce_asset.id.to_s,
|
||||
tiny_mce_asset_blob['filename'])
|
||||
) do |tiny_mce_file|
|
||||
orig_tmce_id = tiny_mce_asset.id
|
||||
tiny_mce_asset.id = nil
|
||||
if tiny_mce_asset.object_id.present?
|
||||
mappings = instance_variable_get("@#{tiny_mce_asset.object_type.underscore}_mappings")
|
||||
tiny_mce_asset.object_id = mappings[tiny_mce_asset.object_id]
|
||||
end
|
||||
tiny_mce_asset.team = team
|
||||
tiny_mce_asset.save!
|
||||
tiny_mce_asset.image.attach(io: tiny_mce_file, filename: File.basename(tiny_mce_file))
|
||||
@mce_asset_counter += 1
|
||||
if tiny_mce_asset.object_id.present?
|
||||
object = tiny_mce_asset.object
|
||||
object_field = Extends::RICH_TEXT_FIELD_MAPPINGS[object.class.name]
|
||||
encoded_id = Base62.encode(tiny_mce_asset.id)
|
||||
object.public_send(object_field).sub!("data-mce-token=\"#{Base62.encode(orig_tmce_id)}\"",
|
||||
"data-mce-token=\"#{encoded_id}\"")
|
||||
# Check for old fields
|
||||
new_asset_format = "<img src=\"\" class=\"img-responsive\" data-mce-token=\"#{encoded_id}\"/>"
|
||||
object.public_send(object_field).sub!("[~tiny_mce_id:#{orig_tmce_id}]",
|
||||
new_asset_format)
|
||||
object.save!
|
||||
end
|
||||
tiny_mce_file = File.open(File.join(@import_dir,
|
||||
'tiny_mce_assets',
|
||||
tiny_mce_asset.id.to_s,
|
||||
tiny_mce_asset_blob['filename']))
|
||||
orig_tmce_id = tiny_mce_asset.id
|
||||
tiny_mce_asset.id = nil
|
||||
if tiny_mce_asset.object_id.present?
|
||||
mappings = instance_variable_get("@#{tiny_mce_asset.object_type.underscore}_mappings")
|
||||
tiny_mce_asset.object_id = mappings[tiny_mce_asset.object_id]
|
||||
end
|
||||
tiny_mce_asset.team = team
|
||||
tiny_mce_asset.save!
|
||||
tiny_mce_asset.image.attach(io: tiny_mce_file, filename: File.basename(tiny_mce_file))
|
||||
@mce_asset_counter += 1
|
||||
next unless tiny_mce_asset.object_id.present?
|
||||
|
||||
object = tiny_mce_asset.object
|
||||
object_field = Extends::RICH_TEXT_FIELD_MAPPINGS[object.class.name]
|
||||
encoded_id = Base62.encode(tiny_mce_asset.id)
|
||||
object.public_send(object_field).sub!("data-mce-token=\"#{Base62.encode(orig_tmce_id)}\"",
|
||||
"data-mce-token=\"#{encoded_id}\"")
|
||||
# Check for old fields
|
||||
new_asset_format = "<img src=\"\" class=\"img-responsive\" data-mce-token=\"#{encoded_id}\"/>"
|
||||
object.public_send(object_field).sub!("[~tiny_mce_id:#{orig_tmce_id}]",
|
||||
new_asset_format)
|
||||
object.save!
|
||||
end
|
||||
end
|
||||
|
||||
|
|
@ -806,22 +805,19 @@ class TeamImporter
|
|||
else
|
||||
asset_json['file_file_name']
|
||||
end
|
||||
File.open(
|
||||
"#{@import_dir}/assets/#{asset.id}/#{asset_file_name}"
|
||||
) do |file|
|
||||
orig_asset_id = asset.id
|
||||
asset.id = nil
|
||||
asset.created_by_id = user_id || find_user(asset.created_by_id)
|
||||
asset.last_modified_by_id =
|
||||
user_id || find_user(asset.last_modified_by_id)
|
||||
asset.team = team
|
||||
asset.in_template = true if @is_template
|
||||
asset.save!
|
||||
asset.file.attach(io: file, filename: File.basename(file))
|
||||
asset.post_process_file(team)
|
||||
@asset_mappings[orig_asset_id] = asset.id
|
||||
@asset_counter += 1
|
||||
end
|
||||
file = File.open("#{@import_dir}/assets/#{asset.id}/#{asset_file_name}")
|
||||
orig_asset_id = asset.id
|
||||
asset.id = nil
|
||||
asset.created_by_id = user_id || find_user(asset.created_by_id)
|
||||
asset.last_modified_by_id =
|
||||
user_id || find_user(asset.last_modified_by_id)
|
||||
asset.team = team
|
||||
asset.in_template = true if @is_template
|
||||
asset.save!
|
||||
asset.file.attach(io: file, filename: File.basename(file))
|
||||
asset.post_process_file(team)
|
||||
@asset_mappings[orig_asset_id] = asset.id
|
||||
@asset_counter += 1
|
||||
asset
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@ class UserDataDeletion
|
|||
my_module.user_my_modules.destroy_all
|
||||
my_module.report_elements.destroy_all
|
||||
my_module.sample_my_modules.destroy_all
|
||||
my_module.protocols.each { |p| p.update_attributes(parent_id: nil) }
|
||||
my_module.protocols.each { |p| p.update(parent_id: nil) }
|
||||
my_module.protocols.each do |protocol|
|
||||
destroy_protocol(protocol)
|
||||
end
|
||||
|
|
@ -65,7 +65,7 @@ class UserDataDeletion
|
|||
|
||||
project.delete
|
||||
end
|
||||
team.protocols.each { |p| p.update_attributes(parent_id: nil) }
|
||||
team.protocols.each { |p| p.update(parent_id: nil) }
|
||||
team.protocols.where(my_module: nil).each do |protocol|
|
||||
destroy_protocol(protocol)
|
||||
end
|
||||
|
|
|
|||
|
|
@ -6,11 +6,9 @@ module ProtocolImporters
|
|||
return [] unless step_json[:attachments]&.any?
|
||||
|
||||
step_json[:attachments].map do |f|
|
||||
Asset.new(file: URI.parse(f[:url]),
|
||||
created_by: user,
|
||||
last_modified_by: user,
|
||||
team: team,
|
||||
file_file_name: f[:name])
|
||||
asset = Asset.new(created_by: user, last_modified_by: user, team: team)
|
||||
asset.file.attach(io: URI.open(f[:url]), filename: f[:name])
|
||||
asset
|
||||
end
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -1,11 +1,10 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIO
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
class ApiClient
|
||||
include HTTParty
|
||||
require 'protocol_importers/protocols_io/v3/errors'
|
||||
|
||||
CONSTANTS = Constants::PROTOCOLS_IO_V3_API
|
||||
|
||||
|
|
@ -89,7 +88,7 @@ module ProtocolImporters
|
|||
rescue StandardError => e
|
||||
Rails.logger.error "Error: #{e.class}, message: #{e.message}"
|
||||
|
||||
raise ProtocolImporters::ProtocolsIO::V3::NetworkError.new(e.class),
|
||||
raise ProtocolImporters::ProtocolsIo::V3::NetworkError.new(e.class),
|
||||
I18n.t('protocol_importers.errors.cannot_import_protocol')
|
||||
end
|
||||
|
||||
|
|
@ -100,13 +99,13 @@ module ProtocolImporters
|
|||
when 0
|
||||
return response
|
||||
when 1
|
||||
raise ProtocolImporters::ProtocolsIO::V3::ArgumentError.new(:missing_or_empty_parameters), error_message
|
||||
raise ProtocolImporters::ProtocolsIo::V3::ArgumentError.new(:missing_or_empty_parameters), error_message
|
||||
when 1218
|
||||
raise ProtocolImporters::ProtocolsIO::V3::UnauthorizedError.new(:invalid_token), error_message
|
||||
raise ProtocolImporters::ProtocolsIo::V3::UnauthorizedError.new(:invalid_token), error_message
|
||||
when 1219
|
||||
raise ProtocolImporters::ProtocolsIO::V3::UnauthorizedError.new(:token_expires), error_message
|
||||
raise ProtocolImporters::ProtocolsIo::V3::UnauthorizedError.new(:token_expires), error_message
|
||||
else
|
||||
raise ProtocolImporters::ProtocolsIO::V3::Error.new(:api_response_error), response.parsed_response
|
||||
raise ProtocolImporters::ProtocolsIo::V3::Error.new(:api_response_error), response.parsed_response
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -0,0 +1,10 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
# MissingOrEmptyParameters
|
||||
class ArgumentError < Error; end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -1,7 +1,7 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIO
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
class Error < StandardError
|
||||
attr_reader :error_type
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
# SocketError, HTTPParty::Error
|
||||
class NetworkError < Error; end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
# General NormalizerError
|
||||
class NormalizerError < Error; end
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -1,11 +1,9 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIO
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
class ProtocolNormalizer < ProtocolImporters::ProtocolNormalizer
|
||||
require 'protocol_importers/protocols_io/v3/errors'
|
||||
|
||||
def normalize_protocol(client_data)
|
||||
# client_data is HttpParty ApiReponse object
|
||||
protocol_hash = client_data.parsed_response.with_indifferent_access[:protocol]
|
||||
|
|
@ -67,7 +65,7 @@ module ProtocolImporters
|
|||
|
||||
{ protocol: normalized_data }
|
||||
rescue StandardError => e
|
||||
raise ProtocolImporters::ProtocolsIO::V3::NormalizerError.new(e.class.to_s.downcase.to_sym), e.message
|
||||
raise ProtocolImporters::ProtocolsIo::V3::NormalizerError.new(e.class.to_s.downcase.to_sym), e.message
|
||||
end
|
||||
|
||||
def normalize_list(client_data)
|
||||
|
|
@ -108,7 +106,7 @@ module ProtocolImporters
|
|||
|
||||
normalized_data
|
||||
rescue StandardError => e
|
||||
raise ProtocolImporters::ProtocolsIO::V3::NormalizerError.new(e.class.to_s.downcase.to_sym), e.message
|
||||
raise ProtocolImporters::ProtocolsIo::V3::NormalizerError.new(e.class.to_s.downcase.to_sym), e.message
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIO
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
class StepComponents
|
||||
AVAILABLE_COMPONENTS = {
|
||||
|
|
|
|||
|
|
@ -0,0 +1,10 @@
|
|||
# frozen_string_literal: true
|
||||
|
||||
module ProtocolImporters
|
||||
module ProtocolsIo
|
||||
module V3
|
||||
# InvalidToken, ExpiredToken
|
||||
class UnauthorizedError < Error; end
|
||||
end
|
||||
end
|
||||
end
|
||||
10
app/utilities/user_subdomain.rb
Normal file
10
app/utilities/user_subdomain.rb
Normal file
|
|
@ -0,0 +1,10 @@
|
|||
class UserSubdomain
|
||||
def self.matches?(request)
|
||||
if ENV['USER_SUBDOMAIN']
|
||||
return (request.subdomain.present? &&
|
||||
request.subdomain == ENV['USER_SUBDOMAIN'])
|
||||
else
|
||||
return true
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -1,14 +1,3 @@
|
|||
class UserSubdomain
|
||||
def self.matches?(request)
|
||||
if ENV['USER_SUBDOMAIN']
|
||||
return (request.subdomain.present? &&
|
||||
request.subdomain == ENV['USER_SUBDOMAIN'])
|
||||
else
|
||||
return true
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
class WopiSubdomain
|
||||
def self.matches?(request)
|
||||
if ENV['WOPI_ENABLED'] == 'true'
|
||||
12
bin/setup
12
bin/setup
|
|
@ -1,6 +1,5 @@
|
|||
#!/usr/bin/env ruby
|
||||
require 'fileutils'
|
||||
include FileUtils
|
||||
|
||||
# path to your application root.
|
||||
APP_ROOT = File.expand_path('..', __dir__)
|
||||
|
|
@ -9,24 +8,25 @@ def system!(*args)
|
|||
system(*args) || abort("\n== Command #{args} failed ==")
|
||||
end
|
||||
|
||||
chdir APP_ROOT do
|
||||
# This script is a starting point to setup your application.
|
||||
FileUtils.chdir APP_ROOT do
|
||||
# This script is a way to setup or update your development environment automatically.
|
||||
# This script is idempotent, so that you can run it at anytime and get an expectable outcome.
|
||||
# Add necessary setup steps to this file.
|
||||
|
||||
puts '== Installing dependencies =='
|
||||
system! 'gem install bundler --conservative'
|
||||
system('bundle check') || system!('bundle install')
|
||||
|
||||
# Install JavaScript dependencies if using Yarn
|
||||
# Install JavaScript dependencies
|
||||
# system('bin/yarn')
|
||||
|
||||
# puts "\n== Copying sample files =="
|
||||
# unless File.exist?('config/database.yml')
|
||||
# cp 'config/database.yml.sample', 'config/database.yml'
|
||||
# FileUtils.cp 'config/database.yml.sample', 'config/database.yml'
|
||||
# end
|
||||
|
||||
puts "\n== Preparing database =="
|
||||
system! 'bin/rails db:setup'
|
||||
system! 'bin/rails db:prepare'
|
||||
|
||||
puts "\n== Removing old logs and tempfiles =="
|
||||
system! 'bin/rails log:clear tmp:clear'
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ Bundler.require(*Rails.groups)
|
|||
module Scinote
|
||||
class Application < Rails::Application
|
||||
# Initialize configuration defaults for originally generated Rails version.
|
||||
config.load_defaults 5.2
|
||||
config.load_defaults '6.0'
|
||||
|
||||
# Settings in config/environments/* take precedence over those specified here.
|
||||
# Application configuration should go into files in config/initializers
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@ development:
|
|||
adapter: async
|
||||
|
||||
test:
|
||||
adapter: async
|
||||
adapter: test
|
||||
|
||||
production:
|
||||
adapter: redis
|
||||
|
|
|
|||
|
|
@ -2,3 +2,7 @@
|
|||
|
||||
Rails.application.config.active_storage.previewers = [ActiveStorage::Previewer::PopplerPDFPreviewer,
|
||||
ActiveStorage::Previewer::LibreofficePreviewer]
|
||||
|
||||
Rails.application.config.active_storage.variable_content_types << 'image/svg+xml'
|
||||
|
||||
Rails.application.config.active_storage.variant_processor = :vips
|
||||
|
|
|
|||
|
|
@ -91,11 +91,11 @@ class Constants
|
|||
#=============================================================================
|
||||
|
||||
# Picture size formats
|
||||
LARGE_PIC_FORMAT = '800x600>'.freeze
|
||||
MEDIUM_PIC_FORMAT = '300x300>'.freeze
|
||||
THUMB_PIC_FORMAT = '100x100'.freeze
|
||||
ICON_PIC_FORMAT = '40x40'.freeze
|
||||
ICON_SMALL_PIC_FORMAT = '30x30'.freeze
|
||||
LARGE_PIC_FORMAT = [800, 600].freeze
|
||||
MEDIUM_PIC_FORMAT = [300, 300].freeze
|
||||
THUMB_PIC_FORMAT = [100, 100].freeze
|
||||
ICON_PIC_FORMAT = [40, 40].freeze
|
||||
ICON_SMALL_PIC_FORMAT = [30, 30].freeze
|
||||
|
||||
# Hands-on-table number of starting columns and rows
|
||||
HANDSONTABLE_INIT_COLS_CNT = 5
|
||||
|
|
@ -217,7 +217,7 @@ class Constants
|
|||
|
||||
PROTOCOLS_ENDPOINTS = {
|
||||
protocolsio: {
|
||||
v3: 'ProtocolsIO::V3'
|
||||
v3: 'ProtocolsIo::V3'
|
||||
}
|
||||
}.freeze
|
||||
|
||||
|
|
|
|||
|
|
@ -11,6 +11,8 @@
|
|||
# policy.object_src :none
|
||||
# policy.script_src :self, :https
|
||||
# policy.style_src :self, :https
|
||||
# # If you are using webpack-dev-server then specify webpack-dev-server host
|
||||
# policy.connect_src :self, :https, "http://localhost:3035", "ws://localhost:3035" if Rails.env.development?
|
||||
|
||||
# # Specify URI for violation reports
|
||||
# # policy.report_uri "/csp-violation-report-endpoint"
|
||||
|
|
@ -19,6 +21,9 @@
|
|||
# If you are using UJS then enable automatic nonce generation
|
||||
# Rails.application.config.content_security_policy_nonce_generator = -> request { SecureRandom.base64(16) }
|
||||
|
||||
# Set the nonce only to specific directives
|
||||
# Rails.application.config.content_security_policy_nonce_directives = %w(script-src)
|
||||
|
||||
# Report CSP violations to a specified URI
|
||||
# For further information see the following documentation:
|
||||
# https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Content-Security-Policy-Report-Only
|
||||
|
|
|
|||
16
config/initializers/cors.rb
Normal file
16
config/initializers/cors.rb
Normal file
|
|
@ -0,0 +1,16 @@
|
|||
# Be sure to restart your server when you modify this file.
|
||||
|
||||
# Avoid CORS issues when API is called from the frontend app.
|
||||
# Handle Cross-Origin Resource Sharing (CORS) in order to accept cross-origin AJAX requests.
|
||||
|
||||
# Read more: https://github.com/cyu/rack-cors
|
||||
|
||||
# Rails.application.config.middleware.insert_before 0, Rack::Cors do
|
||||
# allow do
|
||||
# origins 'example.com'
|
||||
#
|
||||
# resource '*',
|
||||
# headers: :any,
|
||||
# methods: [:get, :post, :put, :patch, :delete, :options, :head]
|
||||
# end
|
||||
# end
|
||||
45
config/initializers/new_framework_defaults_6_0.rb
Normal file
45
config/initializers/new_framework_defaults_6_0.rb
Normal file
|
|
@ -0,0 +1,45 @@
|
|||
# Be sure to restart your server when you modify this file.
|
||||
#
|
||||
# This file contains migration options to ease your Rails 6.0 upgrade.
|
||||
#
|
||||
# Once upgraded flip defaults one by one to migrate to the new default.
|
||||
#
|
||||
# Read the Guide for Upgrading Ruby on Rails for more info on each option.
|
||||
|
||||
# Don't force requests from old versions of IE to be UTF-8 encoded.
|
||||
# Rails.application.config.action_view.default_enforce_utf8 = false
|
||||
|
||||
# Embed purpose and expiry metadata inside signed and encrypted
|
||||
# cookies for increased security.
|
||||
#
|
||||
# This option is not backwards compatible with earlier Rails versions.
|
||||
# It's best enabled when your entire app is migrated and stable on 6.0.
|
||||
# Rails.application.config.action_dispatch.use_cookies_with_metadata = true
|
||||
|
||||
# Change the return value of `ActionDispatch::Response#content_type` to Content-Type header without modification.
|
||||
# Rails.application.config.action_dispatch.return_only_media_type_on_content_type = false
|
||||
|
||||
# Return false instead of self when enqueuing is aborted from a callback.
|
||||
# Rails.application.config.active_job.return_false_on_aborted_enqueue = true
|
||||
|
||||
# Send Active Storage analysis and purge jobs to dedicated queues.
|
||||
# Rails.application.config.active_storage.queues.analysis = :active_storage_analysis
|
||||
# Rails.application.config.active_storage.queues.purge = :active_storage_purge
|
||||
|
||||
# When assigning to a collection of attachments declared via `has_many_attached`, replace existing
|
||||
# attachments instead of appending. Use #attach to add new attachments without replacing existing ones.
|
||||
# Rails.application.config.active_storage.replace_on_assign_to_many = true
|
||||
|
||||
# Use ActionMailer::MailDeliveryJob for sending parameterized and normal mail.
|
||||
#
|
||||
# The default delivery jobs (ActionMailer::Parameterized::DeliveryJob, ActionMailer::DeliveryJob),
|
||||
# will be removed in Rails 6.1. This setting is not backwards compatible with earlier Rails versions.
|
||||
# If you send mail in the background, job workers need to have a copy of
|
||||
# MailDeliveryJob to ensure all delivery jobs are processed properly.
|
||||
# Make sure your entire app is migrated and stable on 6.0 before using this setting.
|
||||
# Rails.application.config.action_mailer.delivery_job = "ActionMailer::MailDeliveryJob"
|
||||
|
||||
# Enable the same cache key to be reused when the object being cached of type
|
||||
# `ActiveRecord::Relation` changes by moving the volatile information (max updated at and count)
|
||||
# of the relation's cache key into the cache version to support recycling cache key.
|
||||
# Rails.application.config.active_record.collection_cache_versioning = true
|
||||
|
|
@ -2188,4 +2188,4 @@ en:
|
|||
new_button: "Create Chemical Drawing"
|
||||
structure_placeholder: "Click here to enter Chemical Drawing name"
|
||||
modal_name_title: "Chemical Drawing name:"
|
||||
checmical_drawing: "Chemical drawings"
|
||||
checmical_drawing: "Chemical drawings"
|
||||
|
|
|
|||
|
|
@ -2,29 +2,19 @@ Rails.application.routes.draw do
|
|||
use_doorkeeper do
|
||||
skip_controllers :applications, :authorized_applications, :token_info
|
||||
end
|
||||
require 'subdomain'
|
||||
|
||||
def draw(routes_name)
|
||||
instance_eval(File.read(Rails.root.join("config/routes/#{routes_name}.rb")))
|
||||
end
|
||||
|
||||
constraints UserSubdomain do
|
||||
devise_for :users,
|
||||
controllers: { registrations: 'users/registrations',
|
||||
sessions: 'users/sessions',
|
||||
invitations: 'users/invitations',
|
||||
confirmations: 'users/confirmations',
|
||||
omniauth_callbacks: 'users/omniauth_callbacks' }
|
||||
devise_for :users, controllers: { registrations: 'users/registrations',
|
||||
sessions: 'users/sessions',
|
||||
invitations: 'users/invitations',
|
||||
confirmations: 'users/confirmations',
|
||||
omniauth_callbacks: 'users/omniauth_callbacks' }
|
||||
|
||||
devise_scope :user do
|
||||
authenticated :user do
|
||||
root 'projects#index'
|
||||
end
|
||||
|
||||
unauthenticated do
|
||||
root 'users/sessions#new'
|
||||
end
|
||||
end
|
||||
root 'projects#index'
|
||||
|
||||
# # Client APP endpoints
|
||||
# get '/settings', to: 'client_api/settings#index'
|
||||
|
|
|
|||
|
|
@ -0,0 +1,10 @@
|
|||
# This migration comes from active_storage (originally 20180723000244)
|
||||
class AddForeignKeyConstraintToActiveStorageAttachmentsForBlobId < ActiveRecord::Migration[6.0]
|
||||
def up
|
||||
return if foreign_key_exists?(:active_storage_attachments, column: :blob_id)
|
||||
|
||||
if table_exists?(:active_storage_blobs)
|
||||
add_foreign_key :active_storage_attachments, :active_storage_blobs, column: :blob_id
|
||||
end
|
||||
end
|
||||
end
|
||||
12
db/schema.rb
12
db/schema.rb
|
|
@ -2,15 +2,15 @@
|
|||
# of editing this file, please use the migrations feature of Active Record to
|
||||
# incrementally modify your database, and then regenerate this schema definition.
|
||||
#
|
||||
# Note that this schema.rb definition is the authoritative source for your
|
||||
# database schema. If you need to create the application database on another
|
||||
# system, you should be using db:schema:load, not running all the migrations
|
||||
# from scratch. The latter is a flawed and unsustainable approach (the more migrations
|
||||
# you'll amass, the slower it'll run and the greater likelihood for issues).
|
||||
# This file is the source Rails uses to define your schema when running `rails
|
||||
# db:schema:load`. When creating a new database, `rails db:schema:load` tends to
|
||||
# be faster and is potentially less error prone than running all of your
|
||||
# migrations from scratch. Old migrations may fail to apply correctly if those
|
||||
# migrations use external dependencies or application code.
|
||||
#
|
||||
# It's strongly recommended that you check this file into your version control system.
|
||||
|
||||
ActiveRecord::Schema.define(version: 2019_06_13_134100) do
|
||||
ActiveRecord::Schema.define(version: 2019_09_10_125740) do
|
||||
|
||||
# These are extensions that must be enabled in order to support this database
|
||||
enable_extension "btree_gist"
|
||||
|
|
|
|||
|
|
@ -108,7 +108,7 @@ namespace :samples_to_repository_migration do
|
|||
# Update report elements
|
||||
team.reports.each do |r|
|
||||
r.report_elements.where(type_of: 7).each do |e|
|
||||
e.update_attributes(type_of: 17, repository_id: repository.id)
|
||||
e.update(type_of: 17, repository_id: repository.id)
|
||||
end
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,6 @@ describe Api::ApiController, type: :controller do
|
|||
end
|
||||
|
||||
it 'Returns HTTP success' do
|
||||
expect(response).to be_success
|
||||
expect(response).to have_http_status(200)
|
||||
end
|
||||
|
||||
|
|
@ -36,7 +35,6 @@ describe Api::ApiController, type: :controller do
|
|||
end
|
||||
|
||||
it 'Returns HTTP success' do
|
||||
expect(response).to be_success
|
||||
expect(response).to have_http_status(200)
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -34,7 +34,7 @@ describe ClientApi::Users::InvitationsController, type: :controller, broken: tru
|
|||
format: :json
|
||||
expect(response).to_not be_success
|
||||
expect(response).to have_http_status(:unprocessable_entity)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ describe ExternalProtocolsController, type: :controller do
|
|||
it 'returns JSON, 200 response when protocol parsing was valid' do
|
||||
action
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
|
||||
it 'contains html key in the response' do
|
||||
|
|
@ -79,17 +79,17 @@ describe ExternalProtocolsController, type: :controller do
|
|||
end
|
||||
|
||||
it 'returns JSON, 200 response when preview was successfully returned' do
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:protocol_html_preview)).and_return(html_preview)
|
||||
|
||||
# Call action
|
||||
action
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
|
||||
it 'should return html preview in the JSON' do
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:protocol_html_preview)).and_return(html_preview)
|
||||
|
||||
# Call action
|
||||
|
|
@ -98,7 +98,7 @@ describe ExternalProtocolsController, type: :controller do
|
|||
end
|
||||
|
||||
it 'returns error JSON and 400 response when something went wrong' do
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:protocol_html_preview)).and_raise(StandardError)
|
||||
|
||||
# Call action
|
||||
|
|
@ -139,7 +139,7 @@ describe ExternalProtocolsController, type: :controller do
|
|||
it 'returns JSON, 200 response when protocol parsing was valid' do
|
||||
action
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
|
||||
it 'should return html form in the JSON' do
|
||||
|
|
@ -160,7 +160,7 @@ describe ExternalProtocolsController, type: :controller do
|
|||
# Call action
|
||||
action
|
||||
expect(response).to have_http_status(:bad_request)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
|
||||
|
|
@ -189,7 +189,7 @@ describe ExternalProtocolsController, type: :controller do
|
|||
# Call action
|
||||
action
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
|
||||
it 'returns JSON, 400 response when protocol parsing was invalid' do
|
||||
|
|
@ -203,7 +203,7 @@ describe ExternalProtocolsController, type: :controller do
|
|||
# Call action
|
||||
action
|
||||
expect(response).to have_http_status(:bad_request)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -71,7 +71,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :index, params: params, format: :json
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -85,7 +85,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :index_dt, params: params, format: :json
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -97,7 +97,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :archive, params: params, format: :json
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -113,10 +113,10 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response, then unprocessable_entity on second run' do
|
||||
get :create, params: params, format: :json
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
get :create, params: params, format: :json
|
||||
expect(response).to have_http_status(:unprocessable_entity)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
|
||||
it 'calls create activity for creating project' do
|
||||
|
|
@ -141,7 +141,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :edit, params: params, format: :json
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -158,7 +158,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns redirect response' do
|
||||
action
|
||||
expect(response).to have_http_status(:redirect)
|
||||
expect(response.content_type).to eq 'text/html'
|
||||
expect(response.media_type).to eq 'text/html'
|
||||
end
|
||||
|
||||
it 'calls create activity service (change_project_visibility)' do
|
||||
|
|
@ -209,7 +209,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :show, params: params
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'text/html'
|
||||
expect(response.media_type).to eq 'text/html'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -225,7 +225,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :notifications, format: :json, params: params
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'application/json'
|
||||
expect(response.media_type).to eq 'application/json'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -241,7 +241,7 @@ describe ProjectsController, type: :controller do
|
|||
it 'returns success response' do
|
||||
get :experiment_archive, params: params
|
||||
expect(response).to have_http_status(:success)
|
||||
expect(response.content_type).to eq 'text/html'
|
||||
expect(response.media_type).to eq 'text/html'
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
FactoryBot.define do
|
||||
factory :activity do
|
||||
type_of { :create_project }
|
||||
message { Faker::Lorem.sentence(10) }
|
||||
message { Faker::Lorem.sentence(word_count: 10) }
|
||||
subject { create :project }
|
||||
owner { create :user }
|
||||
team
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
FactoryBot.define do
|
||||
factory :checklist_item do
|
||||
text { Faker::Lorem.sentence(10) }
|
||||
text { Faker::Lorem.sentence(word_count: 10) }
|
||||
checklist
|
||||
checked { false }
|
||||
end
|
||||
|
|
|
|||
|
|
@ -3,8 +3,8 @@
|
|||
FactoryBot.define do
|
||||
factory :my_module do
|
||||
sequence(:name) { |n| "Task-#{n}" }
|
||||
x { Faker::Number.between(1, 100) }
|
||||
y { Faker::Number.between(1, 100) }
|
||||
x { Faker::Number.between(from: 1, to: 100) }
|
||||
y { Faker::Number.between(from: 1, to: 100) }
|
||||
workflow_order { MyModule.where(experiment_id: experiment.id).count + 1 }
|
||||
experiment
|
||||
my_module_group { create :my_module_group, experiment: experiment }
|
||||
|
|
@ -12,7 +12,7 @@ FactoryBot.define do
|
|||
tags { create_list :tag, 3, project: experiment.project }
|
||||
end
|
||||
trait :with_due_date do
|
||||
due_date { Faker::Time.between(Date.today, Date.today + 10.days) }
|
||||
due_date { Faker::Time.between(from: Date.today, to: Date.today + 10.days) }
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -3,7 +3,7 @@
|
|||
FactoryBot.define do
|
||||
factory :step do
|
||||
name { Faker::Name.unique.name }
|
||||
position { Faker::Number.between(1, 10) }
|
||||
position { Faker::Number.between(from: 1, to: 10) }
|
||||
completed { true }
|
||||
user
|
||||
protocol
|
||||
|
|
|
|||
|
|
@ -5,8 +5,8 @@ FactoryBot.define do
|
|||
sequence(:title) { |n| "System notification #{n}" }
|
||||
description { Faker::ChuckNorris.fact[0..255] }
|
||||
modal_title { Faker::Name.first_name }
|
||||
modal_body { Faker::Lorem.paragraphs(4).map { |pr| "<p>#{pr}</p>" }.join }
|
||||
source_created_at { Faker::Time.between(3.days.ago, Date.today) }
|
||||
modal_body { Faker::Lorem.paragraphs(number: 4).map { |pr| "<p>#{pr}</p>" }.join }
|
||||
source_created_at { Faker::Time.between(from: 3.days.ago, to: Date.today) }
|
||||
source_id { SystemNotification.order(source_id: :desc).first&.source_id.to_i + 1 }
|
||||
last_time_changed_at { Time.now }
|
||||
trait :show_on_login do
|
||||
|
|
|
|||
|
|
@ -2,6 +2,6 @@
|
|||
|
||||
FactoryBot.define do
|
||||
factory :temp_file do
|
||||
session_id { Faker::Lorem.characters(20) }
|
||||
session_id { Faker::Lorem.characters(number: 20) }
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
FactoryBot.define do
|
||||
factory :token do
|
||||
token { Faker::Lorem.characters(100) }
|
||||
token { Faker::Lorem.characters(number: 100) }
|
||||
ttl { 60 }
|
||||
user
|
||||
end
|
||||
|
|
|
|||
|
|
@ -5,14 +5,14 @@ FactoryBot.define do
|
|||
user
|
||||
system_notification
|
||||
trait :seen do
|
||||
seen_at { Faker::Time.between(3.days.ago, Date.today) }
|
||||
seen_at { Faker::Time.between(from: 3.days.ago, to: Date.today) }
|
||||
end
|
||||
trait :read do
|
||||
read_at { Faker::Time.between(3.days.ago, Date.today) }
|
||||
read_at { Faker::Time.between(from: 3.days.ago, to: Date.today) }
|
||||
end
|
||||
trait :seen_and_read do
|
||||
seen_at { Faker::Time.between(3.days.ago, Date.today) }
|
||||
read_at { Faker::Time.between(seen_at, Date.today) }
|
||||
seen_at { Faker::Time.between(from: 3.days.ago, to: Date.today) }
|
||||
read_at { Faker::Time.between(from: seen_at, to: Date.today) }
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -2,10 +2,10 @@
|
|||
|
||||
FactoryBot.define do
|
||||
factory :wopi_discovery do
|
||||
proof_key_mod { Faker::Lorem.characters(20) }
|
||||
proof_key_exp { Faker::Lorem.characters(20) }
|
||||
proof_key_old_mod { Faker::Lorem.characters(20) }
|
||||
proof_key_old_exp { Faker::Lorem.characters(20) }
|
||||
proof_key_mod { Faker::Lorem.characters(number: 20) }
|
||||
proof_key_exp { Faker::Lorem.characters(number: 20) }
|
||||
proof_key_old_mod { Faker::Lorem.characters(number: 20) }
|
||||
proof_key_old_exp { Faker::Lorem.characters(number: 20) }
|
||||
expires { 60 }
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -201,7 +201,7 @@ RSpec.describe 'Api::V1::InventoriesController', type: :request do
|
|||
updated_inventory[:data][:attributes][:name] =
|
||||
Faker::Name.unique.name
|
||||
patch api_v1_team_inventory_path(
|
||||
id: @teams.first.repositories.first.id,
|
||||
id: updated_inventory[:data][:id],
|
||||
team_id: @teams.first.id
|
||||
), params: updated_inventory.to_json,
|
||||
headers: @valid_headers
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ RSpec.describe 'Api::V1::ResultsController', type: :request do
|
|||
included: [
|
||||
{ type: 'result_texts',
|
||||
attributes: {
|
||||
text: Faker::Lorem.sentence(25)
|
||||
text: Faker::Lorem.sentence(word_count: 25)
|
||||
} }
|
||||
] }
|
||||
|
||||
|
|
|
|||
|
|
@ -32,9 +32,9 @@ describe ProtocolImporters::BuildProtocolFromClientService do
|
|||
|
||||
context 'when raise api client error' do
|
||||
it 'return api errors' do
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:single_protocol)
|
||||
.and_raise(ProtocolImporters::ProtocolsIO::V3::ArgumentError
|
||||
.and_raise(ProtocolImporters::ProtocolsIo::V3::ArgumentError
|
||||
.new(:missing_or_empty_parameters), 'Missing Or Empty Parameters Error'))
|
||||
|
||||
expect(service_call.errors).to have_key(:missing_or_empty_parameters)
|
||||
|
|
@ -45,13 +45,13 @@ describe ProtocolImporters::BuildProtocolFromClientService do
|
|||
it 'return normalizer errors' do
|
||||
client_data = double('api_response')
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:single_protocol)
|
||||
.and_return(client_data))
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ProtocolNormalizer)
|
||||
.to(receive(:normalize_protocol).with(client_data)
|
||||
.and_raise(ProtocolImporters::ProtocolsIO::V3::NormalizerError.new(:nil_protocol), 'Nil Protocol'))
|
||||
.and_raise(ProtocolImporters::ProtocolsIo::V3::NormalizerError.new(:nil_protocol), 'Nil Protocol'))
|
||||
|
||||
expect(service_call.errors).to have_key(:nil_protocol)
|
||||
end
|
||||
|
|
@ -61,11 +61,11 @@ describe ProtocolImporters::BuildProtocolFromClientService do
|
|||
before do
|
||||
client_data = double('api_response')
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:single_protocol)
|
||||
.and_return(client_data))
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ProtocolNormalizer)
|
||||
.to(receive(:normalize_protocol).with(client_data)
|
||||
.and_return(normalized_response))
|
||||
|
||||
|
|
|
|||
|
|
@ -34,9 +34,9 @@ describe ProtocolImporters::SearchProtocolsService do
|
|||
|
||||
context 'when raise api client error' do
|
||||
it 'return api errors' do
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:protocol_list)
|
||||
.and_raise(ProtocolImporters::ProtocolsIO::V3::ArgumentError
|
||||
.and_raise(ProtocolImporters::ProtocolsIo::V3::ArgumentError
|
||||
.new(:missing_or_empty_parameters), 'Missing Or Empty Parameters Error'))
|
||||
|
||||
expect(service_call.errors).to have_key(:missing_or_empty_parameters)
|
||||
|
|
@ -47,13 +47,13 @@ describe ProtocolImporters::SearchProtocolsService do
|
|||
it 'return normalizer errors' do
|
||||
client_data = double('api_response')
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:protocol_list)
|
||||
.and_return(client_data))
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ProtocolNormalizer)
|
||||
.to(receive(:normalize_list).with(client_data)
|
||||
.and_raise(ProtocolImporters::ProtocolsIO::V3::NormalizerError.new(:nil_protocol), 'Nil Protocol'))
|
||||
.and_raise(ProtocolImporters::ProtocolsIo::V3::NormalizerError.new(:nil_protocol), 'Nil Protocol'))
|
||||
|
||||
expect(service_call.errors).to have_key(:nil_protocol)
|
||||
end
|
||||
|
|
@ -63,11 +63,11 @@ describe ProtocolImporters::SearchProtocolsService do
|
|||
before do
|
||||
client_data = double('api_response')
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ApiClient)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ApiClient)
|
||||
.to(receive(:protocol_list)
|
||||
.and_return(client_data))
|
||||
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer)
|
||||
allow_any_instance_of(ProtocolImporters::ProtocolsIo::V3::ProtocolNormalizer)
|
||||
.to(receive(:normalize_list).with(client_data)
|
||||
.and_return(normalized_list))
|
||||
end
|
||||
|
|
|
|||
|
|
@ -113,7 +113,7 @@ describe Tasks::SamplesToRepositoryMigrationService do
|
|||
end
|
||||
|
||||
it 'generates valid list_items' do
|
||||
generated_list_items = subject.second.repository_list_items
|
||||
generated_list_items = subject.second.repository_list_items.order(:id)
|
||||
expect(generated_list_items.count).to eq 10
|
||||
generated_list_items.each_with_index do |item, index|
|
||||
expect(item.data).to eq "Sample Type Item (#{index})"
|
||||
|
|
@ -168,7 +168,7 @@ describe Tasks::SamplesToRepositoryMigrationService do
|
|||
end
|
||||
|
||||
it 'generates valid list_items' do
|
||||
generated_list_items = subject.first.repository_list_items
|
||||
generated_list_items = subject.first.repository_list_items.order(:id)
|
||||
expect(generated_list_items.count).to eq 10
|
||||
generated_list_items.each_with_index do |item, index|
|
||||
expect(item.data).to eq "Sample Group Item (#{index})"
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
require 'rails_helper'
|
||||
|
||||
describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
||||
describe ProtocolImporters::ProtocolsIo::V3::ApiClient do
|
||||
CONSTANTS = Constants::PROTOCOLS_IO_V3_API
|
||||
TOKEN = 'test_token'
|
||||
|
||||
|
|
@ -60,7 +60,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
it 'raises NetworkError on timeout' do
|
||||
stub_protocols.to_timeout
|
||||
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIO::V3::NetworkError)
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIo::V3::NetworkError)
|
||||
end
|
||||
|
||||
it 'raises ArgumentError when status_code = 1' do
|
||||
|
|
@ -68,7 +68,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
body: JSON.generate(status_code: 1, error_message: 'Argument error'),
|
||||
headers: { 'Content-Type': 'application/json' })
|
||||
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIO::V3::ArgumentError)
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIo::V3::ArgumentError)
|
||||
end
|
||||
|
||||
it 'raises UnauthorizedError when status_code = 1218' do
|
||||
|
|
@ -76,7 +76,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
body: JSON.generate(status_code: 1218, error_message: 'Argument error'),
|
||||
headers: { 'Content-Type': 'application/json' })
|
||||
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIO::V3::UnauthorizedError)
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIo::V3::UnauthorizedError)
|
||||
end
|
||||
|
||||
it 'raises UnauthorizedError when status_code = 1219' do
|
||||
|
|
@ -84,7 +84,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
body: JSON.generate(status_code: 1219, error_message: 'Argument error'),
|
||||
headers: { 'Content-Type': 'application/json' })
|
||||
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIO::V3::UnauthorizedError)
|
||||
expect { protocol_list_call }.to raise_error(ProtocolImporters::ProtocolsIo::V3::UnauthorizedError)
|
||||
end
|
||||
|
||||
it 'requests server with default query parameters if none are given' do
|
||||
|
|
@ -122,7 +122,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
body: JSON.generate(status_code: 0),
|
||||
headers: { 'Content-Type': 'application/json' })
|
||||
|
||||
ProtocolImporters::ProtocolsIO::V3::ApiClient.new(TOKEN).protocol_list(key_query)
|
||||
ProtocolImporters::ProtocolsIo::V3::ApiClient.new(TOKEN).protocol_list(key_query)
|
||||
expect(WebMock).to have_requested(:get, URL).with(headers: headers, query: default_query_params_with_key)
|
||||
end
|
||||
end
|
||||
|
|
@ -150,14 +150,14 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
it 'raises NetworkError on timeout' do
|
||||
stub_request(:get, SINGLE_PROTOCOL_URL).to_timeout
|
||||
|
||||
expect { subject.single_protocol(PROTOCOL_ID) }.to raise_error(ProtocolImporters::ProtocolsIO::V3::NetworkError)
|
||||
expect { subject.single_protocol(PROTOCOL_ID) }.to raise_error(ProtocolImporters::ProtocolsIo::V3::NetworkError)
|
||||
end
|
||||
|
||||
it 'should send authorization token if provided on initialization' do
|
||||
headers = { 'Authorization': "Bearer #{TOKEN}" }
|
||||
stub_single_protocol.with(headers: headers)
|
||||
|
||||
ProtocolImporters::ProtocolsIO::V3::ApiClient.new(TOKEN).single_protocol(PROTOCOL_ID)
|
||||
ProtocolImporters::ProtocolsIo::V3::ApiClient.new(TOKEN).single_protocol(PROTOCOL_ID)
|
||||
expect(WebMock).to have_requested(:get, SINGLE_PROTOCOL_URL).with(headers: headers)
|
||||
end
|
||||
end
|
||||
|
|
@ -180,7 +180,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ApiClient do
|
|||
stub_html_preview.to_timeout
|
||||
|
||||
expect { subject.protocol_html_preview(PROTOCOL_URI) }
|
||||
.to raise_error(ProtocolImporters::ProtocolsIO::V3::NetworkError)
|
||||
.to raise_error(ProtocolImporters::ProtocolsIo::V3::NetworkError)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
require 'rails_helper'
|
||||
|
||||
describe ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer do
|
||||
describe ProtocolImporters::ProtocolsIo::V3::ProtocolNormalizer do
|
||||
let(:client_data) { double('api_response') }
|
||||
|
||||
let(:protocols_io_single_protocol) do
|
||||
|
|
@ -48,7 +48,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer do
|
|||
.and_return({})
|
||||
|
||||
expect { subject.normalize_protocol(client_data) }
|
||||
.to raise_error(ProtocolImporters::ProtocolsIO::V3::NormalizerError)
|
||||
.to raise_error(ProtocolImporters::ProtocolsIo::V3::NormalizerError)
|
||||
end
|
||||
|
||||
context 'when do not have name' do
|
||||
|
|
@ -73,7 +73,7 @@ describe ProtocolImporters::ProtocolsIO::V3::ProtocolNormalizer do
|
|||
.and_return({})
|
||||
|
||||
expect { subject.normalize_list(client_data) }
|
||||
.to raise_error(ProtocolImporters::ProtocolsIO::V3::NormalizerError)
|
||||
.to raise_error(ProtocolImporters::ProtocolsIo::V3::NormalizerError)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
|
||||
require 'rails_helper'
|
||||
|
||||
describe ProtocolImporters::ProtocolsIO::V3::StepComponents do
|
||||
describe ProtocolImporters::ProtocolsIo::V3::StepComponents do
|
||||
let(:components) do
|
||||
[
|
||||
{ type_id: 1, source: { description: 'Description' } },
|
||||
|
|
|
|||
Loading…
Reference in a new issue