update ruby v3.0

Dockerfile

@@ -8,15 +8,16 @@ RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \
   raptor2-utils \
   && rm -rf /var/lib/apt/lists/*
 
-# The Gemfile Caching Trick
 RUN mkdir -p /srv/ontoportal/ncbo_annotator
-COPY *.gemspec Gemfile* /srv/ontoportal/ncbo_annotator/
+RUN mkdir -p /srv/ontoportal/bundle
+COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_annotator/
 
 WORKDIR /srv/ontoportal/ncbo_annotator
 
-# set bundler to v2.4.22 which is the last version supported by ruby 2.7
-RUN gem install bundler -v 2.4.22
-ENV BUNDLE_PATH /bundle
+RUN gem update --system
+RUN gem install bundler
+ENV BUNDLE_PATH=/srv/ontoportal/bundle
 RUN bundle install
+
 COPY . /srv/ontoportal/ncbo_annotator
 CMD ["/bin/bash"]

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 
 gem 'cube-ruby'
-gem 'faraday', '~> 1.9'
+gem 'faraday'
 gem 'ffi'
 gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'

Gemfile.lock

@@ -15,7 +15,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 2575a6ecf62f6f1161f103429fc278939630ad87
+  revision: b78284bac1a2d9c7b04245e55f3708de5dfe591e
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -64,29 +64,10 @@ GEM
     date (3.3.4)
     docile (1.4.0)
     domain_name (0.6.20240107)
-    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)
-      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 (2.9.0)
+      faraday-net_http (>= 2.0, < 3.2)
+    faraday-net_http (3.1.0)
+      net-http
     ffi (1.16.3)
     http-accept (1.7.0)
     http-cookie (1.0.5)
@@ -111,9 +92,10 @@ GEM
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
-    multipart-post (2.4.0)
+    net-http (0.4.1)
+      uri
     net-http-persistent (2.9.4)
-    net-imap (0.3.7)
+    net-imap (0.4.10)
       date
       net-protocol
     net-pop (0.1.2)
@@ -141,7 +123,7 @@ GEM
       addressable (>= 2.2)
     redis (5.1.0)
       redis-client (>= 0.17.0)
-    redis-client (0.20.0)
+    redis-client (0.21.0)
       connection_pool
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
@@ -153,7 +135,6 @@ GEM
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
     ruby-xxHash (0.4.0.2)
-    ruby2_keywords (0.0.5)
     rubyzip (2.3.2)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -168,6 +149,7 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
+    uri (0.13.0)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
@@ -177,7 +159,7 @@ PLATFORMS
 
 DEPENDENCIES
   cube-ruby
-  faraday (~> 1.9)
+  faraday
   ffi
   goo!
   minitest (~> 4.0)
@@ -192,4 +174,4 @@ DEPENDENCIES
   sparql-client!
 
 BUNDLED WITH
-   2.3.15
+   2.4.22

dip.yml

@@ -0,0 +1,56 @@
+version: '7.1'
+
+# Define default environment variables to pass
+# to Docker Compose
+#environment:
+#  RAILS_ENV: development
+
+compose:
+  files:
+    - docker-compose.yml
+      #  project_name: ncbo_annotator
+
+interaction:
+  # This command spins up a ontologies_api container with the required dependencies (solr, 4store, etc),
+  # and opens a terminal within it.
+  runner:
+    description: Open a Bash shell within a ontologies_api container (with dependencies up)
+    service: ruby
+    command: /bin/bash
+
+  # Run a Rails container without any dependent services (useful for non-Rails scripts)
+  bash:
+    description: Run an arbitrary script within a container (or open a shell without deps)
+    service: ruby
+    command: /bin/bash
+    compose_run_options: [ no-deps ]
+
+  # A shortcut to run Bundler commands
+  bundle:
+    description: Run Bundler commands
+    service: ruby
+    command: bundle
+    compose_run_options: [ no-deps ]
+
+  # A shortcut to run unit tests
+  test:
+    description: Run minitest unit tests
+    service: ruby
+    command: bundle exec rake test
+
+  test-ag:
+    description: Run minitest unit tests
+    service: ruby-ag
+    command: bundle exec rake test
+
+
+  'redis-cli':
+    description: Run Redis console
+    service: redis-ut
+    command: redis-cli -h redis-ut
+
+#provision:
+  #- dip compose down --volumes
+  #- dip compose up -d solr 4store
+  #- dip bundle install
+  #- dip bash -c bin/setup

docker-compose.yml

@@ -1,30 +1,35 @@
 version: '3.8'
 
 x-app: &app
-    build:
-      context: .
-      args:
-        RUBY_VERSION: '2.7'
-    environment: &env
-      COVERAGE: 'true' # enable simplecov code coverage
-      REDIS_HOST: redis-ut
-      REDIS_PORT: 6379
-      MGREP_HOST: mgrep-ut
-      MGREP_PORT: 55556
-      SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr/term_search_core1
-      SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr/prop_search_core1
-    volumes:
-      - .:/srv/ontoportal/ncbo_annotator
-    stdin_open: true
-    tty: true
-    command: "bundle exec rake test TESTOPTS='-v'"
-    depends_on: &depends_on
-      solr-ut:
-        condition: service_healthy
-      redis-ut:
-        condition: service_healthy
-      mgrep-ut:
-        condition: service_healthy
+  image: ncbo_annotator:0.0.1
+  build:
+    context: .
+    args:
+      RUBY_VERSION: '3.0'
+  environment: &env
+    BUNDLE_PATH: /srv/ontoportal/bundle
+    # default bundle config resolves to /usr/local/bundle/config inside of the container
+    # we are setting it to local app directory if we need to use 'bundle config local'
+    BUNDLE_APP_CONFIG: /srv/ontoportal/ncbo_annotator/.bundle
+    COVERAGE: 'true' # enable simplecov code coverage
+    REDIS_HOST: redis-ut
+    REDIS_PORT: 6379
+    MGREP_HOST: mgrep-ut
+    MGREP_PORT: 55556
+    SOLR_TERM_SEARCH_URL: http://solr-ut:8983/solr/term_search_core1
+    SOLR_PROP_SEARCH_URL: http://solr-ut:8983/solr/prop_search_core1
+  volumes:
+    - .:/srv/ontoportal/ncbo_annotator
+  stdin_open: true
+  tty: true
+  command: "bundle exec rake test TESTOPTS='-v'"
+  depends_on: &depends_on
+    solr-ut:
+      condition: service_healthy
+    redis-ut:
+      condition: service_healthy
+    mgrep-ut:
+      condition: service_healthy
 
 services:
   ruby:
@@ -59,7 +64,7 @@ services:
       - agraph
 
   solr-ut:
-    image: ontoportal/solr-ut:0.0.2
+    image: ontoportal/solr-ut:0.1.0
     healthcheck:
       test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"]
       start_period: 3s
@@ -96,7 +101,7 @@ services:
       - 4store
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.0
+    image: franzinc/agraph:v8.1.0
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test

run-unit-tests.sh

@@ -5,6 +5,6 @@
 [ -f config/config.rb ] || cp config/config.test.rb config/config.rb
 docker-compose build
 
-docker-compose run --rm ruby bundle exec rake test TESTOPTS='-v'
-#docker-compose run --rm ruby-agraph bundle exec rake test TESTOPTS='-v'
-docker-compose --profile agraph --profile 4store kill
+docker compose run --rm ruby bundle exec rake test TESTOPTS='-v'
+#docker compose run --rm ruby-agraph bundle exec rake test TESTOPTS='-v'
+docker compose --profile agraph --profile 4store stop