Merge pull request #1 from seek4science/master

Merge 1.11 changes to local fork

Author: abecam

.github/workflows/tests.yml

@@ -28,6 +28,15 @@ jobs:
         ports:
           - 33306:3306
         options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
+      virtuoso:
+        image: tenforce/virtuoso
+        env:
+          DBA_PASSWORD: tester
+          SPARQL_UPDATE: true
+          DEFAULT_GRAPH: http://www.example.com/my-graph
+        ports:
+          - 8890:8890
+          - 1111:1111
     strategy:
       fail-fast: false
       matrix:
@@ -38,9 +47,11 @@ jobs:
           - rails test test/functional
           - rails test test/integration
           - rspec spec
-          - rake teaspoon
+          # - rake teaspoon
           - rake assets:precompile
           - rake db:setup
+          - rake db:migrate
+          - rake seek:upgrade
         include:
           - database: postgres
             suite: rails test test/unit
@@ -85,7 +96,18 @@ jobs:
       - name: Set MySQL char set and collation
         if: matrix.database == 'mysql'
         run: echo -e "ALTER DATABASE seek_test CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci;\n" | bundle exec rails dbconsole -p
+      - name: Checkout previous schema
+        if: github.event_name == 'push' && matrix.suite == 'rake db:migrate' && github.event.before != '0000000000000000000000000000000000000000'
+        run: |
+          git fetch origin ${{ github.event.before }}
+          git checkout ${{ github.event.before }} -- db/schema.rb
       - name: Load test database schema
         run: bundle exec rake db:schema:load
+      - name: Seed database
+        if: matrix.suite == 'rake seek:upgrade'
+        run: bundle exec rake db:seed
+      - name: Virtuoso config
+        if: matrix.suite == 'rails test test/integration'
+        run: cp test/config/virtuoso_test_settings.yml config/virtuoso_settings.yml
       - name: Run tests
         run: bundle exec ${{ matrix.suite }}

.gitignore

@@ -82,3 +82,5 @@ coverage/
 Test\ Results*.html
 
 docker-compose.override.yml
+
+.vscode/

.rubocop.yml

@@ -1,10 +1,11 @@
 AllCops:
+  SuggestExtensions: false
   Exclude:
     - test/unit/assay_test.rb
 
-Metrics/LineLength:
+Layout/LineLength:
   Max: 120
 
 # Don't enforce frozen string literals
 Style/FrozenStringLiteralComment:
-  Enabled: false
+  Enabled: false

.travis.yml

@@ -13,8 +13,7 @@ addons:
       - python3-pip
       - python3-setuptools
 
-services:
-  - docker
+services:  
   - mysql
   - postgresql
   - xvfb
@@ -28,14 +27,12 @@ env:
   - SUITE="rails test test/functional" DB_TYPE=mysql
   - SUITE="rails test test/integration" DB_TYPE=mysql
   - SUITE="rspec spec" DB_TYPE=mysql
-  - SUITE="rake teaspoon" RAILS_ENV=test DB_TYPE=mysql
+  # - SUITE="rake teaspoon" RAILS_ENV=test DB_TYPE=mysql
   - SUITE="rake assets:precompile RAILS_ENV=production" DB_TYPE=mysql
   - SUITE="rake db:setup RAILS_ENV=production" DB_TYPE=mysql
 
 before_install:
   - pip3 install -r requirements.txt
-  # starts up a virtuoso docker repository and sets up the config to use it, for the rdf repository related integration tests
-  - sh -c "if [ '$SUITE' = 'rails test test/integration' ]; then sh -e script/virtuoso-docker-for-travis.sh; fi"
 
 before_script:
   - sh -c "if [ '$DB_TYPE' = 'pgsql' ]; then psql -c 'create database travis_ci_test; create database travis_ci_dev; create database travis_ci_prod;' -U postgres; fi"

Dockerfile

@@ -60,6 +60,17 @@ RUN bundle exec rake assets:precompile && \
 #root access needed for next couple of steps
 USER root
 
+# Install supercronic - a cron alternative
+ENV SUPERCRONIC_URL=https://github.com/aptible/supercronic/releases/download/v0.1.12/supercronic-linux-amd64 \
+    SUPERCRONIC=supercronic-linux-amd64 \
+    SUPERCRONIC_SHA1SUM=048b95b48b708983effb2e5c935a1ef8483d9e3e
+
+RUN curl -fsSLO "$SUPERCRONIC_URL" \
+ && echo "${SUPERCRONIC_SHA1SUM}  ${SUPERCRONIC}" | sha1sum -c - \
+ && chmod +x "$SUPERCRONIC" \
+ && mv "$SUPERCRONIC" "/usr/local/bin/${SUPERCRONIC}" \
+ && ln -s "/usr/local/bin/${SUPERCRONIC}" /usr/local/bin/supercronic
+
 # NGINX config
 COPY docker/nginx.conf /etc/nginx/nginx.conf
 

Gemfile

@@ -54,8 +54,8 @@ gem 'will_paginate', '~> 3.1'
 gem 'yaml_db'
 gem 'rails_autolink'
 gem 'rfc-822'
-gem 'nokogiri', '>= 1.10.4'
-gem 'rdf-virtuoso', git: 'https://github.com/ruby-rdf/rdf-virtuoso', branch: 'develop'
+gem 'nokogiri', '~> 1.11.2'
+gem 'rdf-virtuoso', '>= 0.2.0'
 gem 'terrapin'
 gem 'lograge'
 gem 'psych'
@@ -77,21 +77,21 @@ gem 'jquery-ui-rails'
 gem 'recaptcha', '~> 4.1.0'
 gem 'metainspector'
 gem 'mechanize'
-gem 'mimemagic','0.3.2'
+gem 'mimemagic','~> 0.3.7'
 gem 'auto_strip_attributes'
 gem 'coffee-rails', '~> 4.2'
 gem 'bootstrap-sass', '>=3.4.1'
 gem 'sass-rails', '~> 5.0'
 gem 'sprockets-rails'
 
-gem 'ro-bundle', '~> 0.2.4'
+gem 'ro-bundle', '~> 0.2.5'
 gem 'handlebars_assets'
 gem 'zenodo-client', git: 'https://github.com/seek4science/zenodo-client.git'
 
 gem 'unicorn-rails'
 gem 'seedbank'
 
-gem 'rspec-rails'
+gem 'rspec-rails','~> 3.6'
 
 gem 'citeproc-ruby', '~> 1.1.4'
 gem 'citeproc', '~> 1.0.4'
@@ -134,13 +134,12 @@ gem 'request_store'
 # javascript assets from https://rails-assets.org
 gem 'bundler', '>= 1.8.4'
 
-gem 'ro-crate-ruby', git: 'https://github.com/fbacall/ro-crate-ruby.git'
+gem 'ro-crate-ruby', git: 'https://github.com/ResearchObject/ro-crate-ruby.git', ref: '70804d34264481e70d0fe83ecc6ad76eda164e74'
 
 gem 'git'
-
 gem 'redcarpet'
-
 gem 'i18n-js'
+gem 'whenever', '~> 1.0.0', require: false
 
 source 'https://rails-assets.org' do
   gem 'rails-assets-bootstrap-multiselect', '~> 0.9.13'
@@ -174,13 +173,14 @@ group :test do
   gem 'ruby-prof'
   gem 'test-prof'
   gem 'rails-perftest'
-  gem 'minitest', '5.10.3'
+  gem 'minitest', '~> 5.14'
   gem 'minitest-reporters'
   gem 'sunspot_matchers'
   gem 'database_cleaner', '~> 1.7.0'
   gem 'vcr', '~> 2.9'
   gem 'rails-controller-testing'
   gem 'simplecov'
+  gem 'whenever-test'
 end
 
 group :test, :development do