Merge to master: Release v2.2.1

.dockerignore

@@ -1,5 +1,6 @@
 # Git
-#.git
+.git
+.github
 .gitignore
 # Logs
 log/*
@@ -8,3 +9,9 @@ tmp/*
 # Editor temp files
 *.swp
 *.swo
+coverage
+create_permissions.log
+# Ignore generated test data
+test/data/dictionary.txt
+test/data/ontology_files/repo/**/*
+test/data/tmp/*

.github/workflows/docker-image.yml

@@ -0,0 +1,42 @@
+name: Docker Image CI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: bioportal/ncbo_cron
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          build-args: |
+            RUBY_VERSION=2.7
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/ruby-unit-tests.yml

@@ -7,18 +7,17 @@ on:
 jobs:
   test:
     strategy:
+      fail-fast: false
       matrix:
-        backend: ['ruby'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
+        backend: ['ncbo_cron'] # ruby runs tests with 4store backend and ruby-agraph runs with AllegroGraph backend
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
     - name: copy config.rb file from template
       run:  cp config/config.rb.sample config/config.rb
     - name: Build docker-compose
-      working-directory: ./test
       run: docker-compose build
     - name: Run unit tests
-      working-directory: ./test
       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'

.gitignore

@@ -5,6 +5,8 @@ config/config.rb
 config/appliance.rb
 config/config_*.rb
 config/*.p12
+config/*.json
+data/
 projectFilesBackup/
 .ruby-version
 repo*

Dockerfile

@@ -14,10 +14,16 @@ COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_cron/
 
 WORKDIR /srv/ontoportal/ncbo_cron
 
+# set rubygem and bundler to the last version supported by ruby 2.7
+# remove version after ruby v3 upgrade
+RUN gem update --system '3.4.22'
+RUN gem install bundler -v '2.4.22'
 RUN gem update --system
 RUN gem install bundler
 ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install
 
 COPY . /srv/ontoportal/ncbo_cron
+RUN cp /srv/ontoportal/ncbo_cron/config/config.rb.sample /srv/ontoportal/ncbo_cron/config/config.rb
+
 CMD ["/bin/bash"]

Gemfile

@@ -2,13 +2,17 @@ source 'https://rubygems.org'
 
 gemspec
 
-gem 'faraday', '~> 1.9'
 gem 'ffi'
+
+# This is needed temporarily to pull the Google Universal Analytics (UA)
+# data and store it in a file. See (bin/import_google_ua_analytics_data)
+# The ability to pull this data from Google will cease on July 1, 2024
 gem "google-apis-analytics_v3"
+
+gem 'google-analytics-data'
 gem 'mail', '2.6.6'
-gem 'minitest', '< 5.0'
 gem 'multi_json'
-gem 'oj', '~> 2.0'
+gem 'oj', '~> 3.0'
 gem 'parseconfig'
 gem 'pony'
 gem 'pry'
@@ -28,6 +32,7 @@ gem 'ncbo_annotator', github: 'ontoportal-lirmm/ncbo_annotator', branch: 'master
 # Testing
 group :test do
   gem 'email_spec'
+  gem 'minitest', '< 5.0'
   gem 'simplecov'
   gem 'simplecov-cobertura' # for codecov.io
   gem 'test-unit-minitest'

Gemfile.lock

@@ -60,7 +60,7 @@ PATH
     ncbo_cron (0.0.1)
       dante
       goo
-      google-apis-analytics_v3
+      google-analytics-data
       mlanett-redis-lock
       multi_json
       ncbo_annotator
@@ -76,7 +76,9 @@ GEM
       multi_json (~> 1.0)
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
+    base64 (0.2.0)
     bcrypt (3.1.20)
+    bigdecimal (3.1.5)
     binding_of_caller (1.0.0)
       debug_inspector (>= 0.0.1)
     builder (3.2.4)
@@ -93,30 +95,28 @@ GEM
       htmlentities (~> 4.3.3)
       launchy (~> 2.1)
       mail (~> 2.6)
-    faraday (1.10.3)
-      faraday-em_http (~> 1.0)
-      faraday-em_synchrony (~> 1.0)
-      faraday-excon (~> 1.1)
-      faraday-httpclient (~> 1.0)
-      faraday-multipart (~> 1.0)
-      faraday-net_http (~> 1.0)
-      faraday-net_http_persistent (~> 1.0)
-      faraday-patron (~> 1.0)
-      faraday-rack (~> 1.0)
-      faraday-retry (~> 1.0)
+    faraday (2.8.1)
+      base64
+      faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
-    faraday-em_http (1.0.0)
-    faraday-em_synchrony (1.0.0)
-    faraday-excon (1.1.0)
-    faraday-httpclient (1.0.1)
-    faraday-multipart (1.0.4)
-      multipart-post (~> 2)
-    faraday-net_http (1.0.1)
-    faraday-net_http_persistent (1.2.0)
-    faraday-patron (1.0.0)
-    faraday-rack (1.0.0)
-    faraday-retry (1.0.3)
+    faraday-net_http (3.0.2)
+    faraday-retry (2.2.0)
+      faraday (~> 2.0)
     ffi (1.16.3)
+    gapic-common (0.21.1)
+      faraday (>= 1.9, < 3.a)
+      faraday-retry (>= 1.0, < 3.a)
+      google-protobuf (~> 3.18)
+      googleapis-common-protos (>= 1.4.0, < 2.a)
+      googleapis-common-protos-types (>= 1.11.0, < 2.a)
+      googleauth (~> 1.9)
+      grpc (~> 1.59)
+    google-analytics-data (0.4.0)
+      google-analytics-data-v1beta (>= 0.7, < 2.a)
+      google-cloud-core (~> 1.6)
+    google-analytics-data-v1beta (0.10.0)
+      gapic-common (>= 0.20.0, < 2.a)
+      google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.13.0)
       google-apis-core (>= 0.11.0, < 2.a)
     google-apis-core (0.11.2)
@@ -128,15 +128,29 @@ GEM
       retriable (>= 2.0, < 4.a)
       rexml
       webrick
+    google-cloud-core (1.6.1)
+      google-cloud-env (>= 1.0, < 3.a)
+      google-cloud-errors (~> 1.0)
     google-cloud-env (2.1.0)
       faraday (>= 1.0, < 3.a)
+    google-cloud-errors (1.3.1)
+    google-protobuf (3.25.1-x86_64-linux)
+    googleapis-common-protos (1.4.0)
+      google-protobuf (~> 3.14)
+      googleapis-common-protos-types (~> 1.2)
+      grpc (~> 1.27)
+    googleapis-common-protos-types (1.11.0)
+      google-protobuf (~> 3.18)
     googleauth (1.9.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
+    grpc (1.60.0-x86_64-linux)
+      google-protobuf (~> 3.25)
+      googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
     http-cookie (1.0.5)
@@ -164,10 +178,10 @@ GEM
     mlanett-redis-lock (0.2.7)
       redis
     multi_json (1.15.0)
-    multipart-post (2.3.0)
     net-http-persistent (2.9.4)
     netrc (0.11.0)
-    oj (2.18.5)
+    oj (3.16.3)
+      bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
     os (1.1.4)
@@ -186,7 +200,7 @@ GEM
       addressable (>= 2.2)
     redis (5.0.8)
       redis-client (>= 0.17.0)
-    redis-client (0.19.0)
+    redis-client (0.19.1)
       connection_pool
     representable (3.2.0)
       declarative (< 0.1.0)
@@ -243,16 +257,16 @@ DEPENDENCIES
   binding_of_caller (~> 1.0)
   cube-ruby
   email_spec
-  faraday (~> 1.9)
   ffi
   goo!
+  google-analytics-data
   google-apis-analytics_v3
   mail (= 2.6.6)
   minitest (< 5.0)
   multi_json
   ncbo_annotator!
   ncbo_cron!
-  oj (~> 2.0)
+  oj (~> 3.0)
   ontologies_linked_data!
   parseconfig
   pony