Merge pull request #11 from ontoportal-lirmm/development

Merge development and upstream
ontoportal-lirmm · Dec 24, 2022 · 3296b76 · 3296b76
2 parents d099991 + b2521da
commit 3296b76
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diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
@@ -6,15 +6,26 @@ on:
 
 jobs:
   test:
+    strategy:
+      matrix:
+        backend: ['ruby', 'ruby-agraph'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: copy config.rb file from template
       run:  cp config/config.test.rb config/config.rb
     - name: Build docker-compose
       working-directory: ./test
       run: docker-compose build
     - name: Run unit tests
       working-directory: ./test
-      run: docker-compose run unit-test wait-for-it solr-ut:8983 -- rake test TESTOPTS='-v'
+      run: |
+        ci_env=`bash <(curl -s https://codecov.io/env)`
+        docker-compose run $ci_env -e CI --rm ${{ matrix.backend }} bundle exec rake test TESTOPTS='-v'
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        flags: unittests
+        verbose: true
+        fail_ci_if_error: false # optional (default = false)
 
diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,9 @@ repo*
 .DS_Store
 tmp
 
+# Code coverage reports
+coverage*
+
 # Ignore eclipse .project
 .project
 .pmd

diff --git a/Dockerfile b/Dockerfile
@@ -1,14 +1,23 @@
-FROM ruby:2.6
+ARG RUBY_VERSION
+ARG DISTRO_NAME=bullseye
 
-RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends openjdk-11-jre-headless raptor2-utils wait-for-it
+FROM ruby:$RUBY_VERSION-$DISTRO_NAME
+
+RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
+  openjdk-11-jre-headless \
+  raptor2-utils \
+  && rm -rf /var/lib/apt/lists/*
 
-# The Gemfile Caching Trick
-# we install gems before copying the code in its own layer so that gems would not have to get
-# installed every single time code is updated
 RUN mkdir -p /srv/ontoportal/ncbo_cron
+RUN mkdir -p /srv/ontoportal/bundle
 COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_cron/
+
 WORKDIR /srv/ontoportal/ncbo_cron
-RUN gem install bundler -v "$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1)"
+
+RUN gem update --system
+RUN gem install bundler
+ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install
+
 COPY . /srv/ontoportal/ncbo_cron
-#CMD ["bundle","exec","rackup","-p","9393","--host","0.0.0.0"]
+CMD ["/bin/bash"]
diff --git a/Gemfile b/Gemfile
@@ -4,7 +4,7 @@ gemspec
 
 gem 'faraday', '~> 1.9'
 gem 'ffi'
-gem 'google-api-client', '~> 0.10'
+gem "google-apis-analytics_v3"
 gem 'mail', '2.6.6'
 gem 'minitest', '< 5.0'
 gem 'multi_json'
@@ -20,17 +20,15 @@ gem 'sys-proctable'
 # Monitoring
 gem 'cube-ruby', require: 'cube'
 
-# NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ontoportal-lirmm/goo', branch: 'master'
 gem 'sparql-client', github: 'ontoportal-lirmm/sparql-client', branch: 'master'
 gem 'ontologies_linked_data', github: 'ontoportal-lirmm/ontologies_linked_data', branch: 'master'
 gem 'ncbo_annotator', github: 'ontoportal-lirmm/ncbo_annotator', branch: 'master'
-gem 'ncbo_resource_index', github: 'ncbo/resource_index'
-
-
 # Testing
 group :test do
   gem 'email_spec'
+  gem 'simplecov'
+  gem 'simplecov-cobertura' # for codecov.io
   gem 'test-unit-minitest'
 end
 
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,30 +1,16 @@
-GIT
-  remote: https://github.com/ncbo/resource_index.git
-  revision: 24a7f14a6da4f4a0eaba1016ca5a378dfccd7441
-  specs:
-    ncbo_resource_index (0.0.1)
-      elasticsearch (= 2.0.0)
-      mysql2 (= 0.5.2)
-      pony
-      ref
-      ruby-xxHash
-      sequel
-      typhoeus
-
 GIT
   remote: https://github.com/ontoportal-lirmm/goo.git
-  revision: 199f12edacb7efba7f192cd24149e3dc656fb5de
+  revision: 92968978e5d2436c648bf7956e25aff05440b59d
   branch: master
   specs:
     goo (0.0.2)
-      addressable (= 2.3.5)
+      addressable (~> 2.8)
       pry
       rdf (= 1.0.8)
       redis
       rest-client
       rsolr
       sparql-client
-      systemu
       uuid
 
 GIT
@@ -40,7 +26,7 @@ GIT
 
 GIT
   remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git
-  revision: 23fe9b9eddfa5cdb6bad677d57e9a8f0c55e78e1
+  revision: c98145605413e459d3c09a41d3c28a5acd0c49e4
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -74,7 +60,7 @@ PATH
     ncbo_cron (0.0.1)
       dante
       goo
-      google-api-client
+      google-apis-analytics_v3
       mlanett-redis-lock
       multi_json
       ncbo_annotator
@@ -88,7 +74,8 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.3.5)
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
     bcrypt (3.1.18)
     builder (3.2.4)
     coderay (1.1.3)
@@ -97,22 +84,13 @@ GEM
     cube-ruby (0.0.3)
     dante (0.2.0)
     declarative (0.0.20)
+    docile (1.4.0)
     domain_name (0.5.20190701)
       unf (>= 0.0.5, < 1.0.0)
-    elasticsearch (2.0.0)
-      elasticsearch-api (= 2.0.0)
-      elasticsearch-transport (= 2.0.0)
-    elasticsearch-api (2.0.0)
-      multi_json
-    elasticsearch-transport (2.0.0)
-      faraday
-      multi_json
     email_spec (2.1.1)
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
       mail (~> 2.6)
-    ethon (0.15.0)
-      ffi (>= 1.15.0)
     faraday (1.10.2)
       faraday-em_http (~> 1.0)
       faraday-em_synchrony (~> 1.0)
@@ -137,37 +115,38 @@ GEM
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
     ffi (1.15.5)
-    google-api-client (0.10.3)
-      addressable (~> 2.3)
-      googleauth (~> 0.5)
-      httpclient (~> 2.7)
-      hurley (~> 0.1)
-      memoist (~> 0.11)
-      mime-types (>= 1.6)
+    google-apis-analytics_v3 (0.12.0)
+      google-apis-core (>= 0.9.1, < 2.a)
+    google-apis-core (0.9.2)
+      addressable (~> 2.5, >= 2.5.1)
+      googleauth (>= 0.16.2, < 2.a)
+      httpclient (>= 2.8.1, < 3.a)
+      mini_mime (~> 1.0)
       representable (~> 3.0)
-      retriable (>= 2.0, < 4.0)
-    googleauth (0.17.1)
-      faraday (>= 0.17.3, < 2.0)
+      retriable (>= 2.0, < 4.a)
+      rexml
+      webrick
+    googleauth (1.3.0)
+      faraday (>= 0.17.3, < 3.a)
       jwt (>= 1.4, < 3.0)
       memoist (~> 0.16)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
-      signet (~> 0.15)
+      signet (>= 0.16, < 2.a)
     htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.5)
       domain_name (~> 0.5)
     httpclient (2.8.3)
-    hurley (0.2)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.6.2)
-    json_pure (2.6.2)
-    jwt (2.5.0)
-    launchy (2.4.3)
-      addressable (~> 2.3)
-    libxml-ruby (3.2.3)
-    logger (1.5.1)
+    json (2.6.3)
+    json_pure (2.6.3)
+    jwt (2.6.0)
+    launchy (2.5.0)
+      addressable (~> 2.7)
+    libxml-ruby (3.2.4)
+    logger (1.5.3)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.6.6)
@@ -177,12 +156,12 @@ GEM
     mime-types (3.4.1)
       mime-types-data (~> 3.2015)
     mime-types-data (3.2022.0105)
+    mini_mime (1.1.2)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
     multipart-post (2.2.3)
-    mysql2 (0.5.2)
     net-http-persistent (2.9.4)
     netrc (0.11.0)
     oj (2.18.5)
@@ -195,17 +174,17 @@ GEM
     pry (0.14.1)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    rack (3.0.0)
+    public_suffix (5.0.1)
+    rack (3.0.2)
     rack-test (2.0.2)
       rack (>= 1.3)
     rake (13.0.6)
     rdf (1.0.8)
       addressable (>= 2.2)
     redis (5.0.5)
       redis-client (>= 0.9.0)
-    redis-client (0.10.0)
+    redis-client (0.11.2)
       connection_pool
-    ref (2.0.0)
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
@@ -216,6 +195,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
+    rexml (3.2.5)
     rsolr (2.5.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -224,20 +204,26 @@ GEM
     rubyzip (2.3.2)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
-    sequel (5.61.0)
-    signet (0.15.0)
-      addressable (~> 2.3)
-      faraday (>= 0.17.3, < 2.0)
+    signet (0.17.0)
+      addressable (~> 2.8)
+      faraday (>= 0.17.5, < 3.a)
       jwt (>= 1.5, < 3.0)
       multi_json (~> 1.10)
-    sys-proctable (1.2.6)
-      ffi
+    simplecov (0.22.0)
+      docile (~> 1.1)
+      simplecov-html (~> 0.11)
+      simplecov_json_formatter (~> 0.1)
+    simplecov-cobertura (2.1.0)
+      rexml
+      simplecov (~> 0.19)
+    simplecov-html (0.12.3)
+    simplecov_json_formatter (0.1.4)
+    sys-proctable (1.2.7)
+      ffi (~> 1.1)
     systemu (2.6.5)
     test-unit-minitest (0.9.1)
       minitest (~> 4.7)
     trailblazer-option (0.1.2)
-    typhoeus (1.4.0)
-      ethon (>= 0.9.0)
     tzinfo (2.0.5)
       concurrent-ruby (~> 1.0)
     uber (0.1.0)
@@ -246,8 +232,10 @@ GEM
     unf_ext (0.0.8.2)
     uuid (2.3.9)
       macaddr (~> 1.0)
+    webrick (1.7.0)
 
 PLATFORMS
+  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
@@ -256,13 +244,12 @@ DEPENDENCIES
   faraday (~> 1.9)
   ffi
   goo!
-  google-api-client (~> 0.10)
+  google-apis-analytics_v3
   mail (= 2.6.6)
   minitest (< 5.0)
   multi_json
   ncbo_annotator!
   ncbo_cron!
-  ncbo_resource_index!
   oj (~> 2.0)
   ontologies_linked_data!
   parseconfig
@@ -271,9 +258,11 @@ DEPENDENCIES
   rake
   redis
   rest-client
+  simplecov
+  simplecov-cobertura
   sparql-client!
   sys-proctable
   test-unit-minitest
 
 BUNDLED WITH
-   2.3.23
+   2.3.22