Merge pull request #34 from ncbo/ruby-v3

Update Ruby: v2.7 → v3.0

Dockerfile

@@ -8,15 +8,12 @@ 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/
-
 WORKDIR /srv/ontoportal/ncbo_annotator
+COPY Gemfile* *.gemspec /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 install bundler
+ENV BUNDLE_PATH=/bundle
 RUN bundle install
+
 COPY . /srv/ontoportal/ncbo_annotator
 CMD ["/bin/bash"]

Gemfile

@@ -1,6 +1,9 @@
 source 'https://rubygems.org'
 
 gem 'cube-ruby'
+gem 'faraday'
+gem 'ffi'
+gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'
 gem 'ruby-xxHash'
 

Gemfile.lock

@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 013a322440b4cfd899908d15ff605799acf8e6ef
+  revision: c30887ee907acd39500cae6c12f45edb06fe0802
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -60,26 +60,27 @@ GEM
     bigdecimal (3.1.8)
     builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.3.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     date (3.3.4)
-    docile (1.4.0)
+    docile (1.4.1)
     domain_name (0.6.20240107)
     faraday (2.8.1)
       base64
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-net_http (3.0.2)
+    ffi (1.17.0)
     http-accept (1.7.0)
-    http-cookie (1.0.6)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
     json (2.7.2)
     json_pure (2.7.2)
     libxml-ruby (5.0.3)
-    logger (1.6.0)
+    logger (1.6.1)
     macaddr (1.7.2)
       systemu (~> 2.6.5)
     mail (2.8.1)
@@ -90,12 +91,12 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0702)
+    mime-types-data (3.2024.0903)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.14)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -105,23 +106,25 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.4)
+    oj (3.16.6)
       bigdecimal (>= 3.0)
+      ostruct (>= 0.2)
     omni_logger (0.1.4)
       logger
+    ostruct (0.6.0)
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
     public_suffix (5.1.1)
-    rack (3.1.6)
+    rack (3.1.7)
     rack-test (2.1.0)
       rack (>= 1.3)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.2.0)
+    redis (5.3.0)
       redis-client (>= 0.22.0)
     redis-client (0.22.2)
       connection_pool
@@ -132,8 +135,7 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.3.1)
-      strscan
+    rexml (3.3.7)
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
@@ -147,9 +149,8 @@ GEM
     simplecov-cobertura (2.1.0)
       rexml
       simplecov (~> 0.19)
-    simplecov-html (0.12.3)
+    simplecov-html (0.13.1)
     simplecov_json_formatter (0.1.4)
-    strscan (3.1.0)
     systemu (2.6.5)
     thread_safe (0.3.6)
     timeout (0.4.1)
@@ -159,12 +160,16 @@ GEM
 
 PLATFORMS
   aarch64-linux
+  arm64-darwin-22
   x86_64-linux
 
 DEPENDENCIES
   cube-ruby
+  faraday
+  ffi
   goo!
   minitest (~> 4.0)
+  oj (~> 3.0)
   ontologies_linked_data!
   pry
   rake (~> 10.0)

docker-compose.yml

@@ -1,29 +1,34 @@
 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
-      - bundle:/bundle
-    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
+    # 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
+    BUNDLE_PATH: /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
+    - bundle:/bundle
+  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:

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