Merge pull request #22 from ncbo/ruby-v3

Ruby v3

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

@@ -6,22 +6,25 @@ on:
 
 jobs:
   test:
+    strategy:
+      fail-fast: false
+      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@v3
-    - name: copy config file
-      run: cp config/config.test.rb config/config.rb
+    - uses: actions/checkout@v4
+    - name: copy config.rb file from template
+      run:  cp config/config.test.rb config/config.rb
     - name: Build docker compose
       run: docker compose build
     - name: Run unit tests
-      # unit tests are run inside a container
-      # http://docs.codecov.io/docs/testing-with-docker
       run: |
         ci_env=`bash <(curl -s https://codecov.io/env)`
-        docker compose run $ci_env -e CI --rm ruby bundle exec rake test TESTOPTS='-v'
+        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
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         flags: unittests
         verbose: true
         fail_ci_if_error: false # optional (default = false)

.ruby-version

@@ -0,0 +1 @@
+3.0.6

Dockerfile

@@ -1,4 +1,4 @@
-ARG RUBY_VERSION
+ARG RUBY_VERSION=3.0
 ARG DISTRO_NAME=bullseye
 
 FROM ruby:$RUBY_VERSION-$DISTRO_NAME
@@ -8,14 +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_ontology_recommender
-COPY *.gemspec Gemfile* /srv/ontoportal/ncbo_ontology_recommender/
+ENV BUNDLE_PATH=/usr/local/bundle \
+    BUNDLE_BIN=/usr/local/bundle/bin \
+    BUNDLE_APP_CONFIG=/usr/local/bundle/config
 
-WORKDIR /srv/ontoportal/ncbo_ontology_recommender
+WORKDIR /usr/src/app
 
-RUN gem install bundler
-ENV BUNDLE_PATH /bundle
+COPY Gemfile* *.gemspec ./
+
+RUN gem update --system
 RUN bundle install
-COPY . /srv/ontoportal/ncbo_ontology_recommender
-CMD ["/bin/bash"]
+
+COPY . .
+CMD ["irb"]

Gemfile

@@ -1,7 +1,7 @@
 source 'https://rubygems.org'
 
 gem 'cube-ruby'
-gem 'faraday', '~> 2.0'
+gem 'faraday'
 gem 'ffi'
 gem 'oj', '~> 3.0'
 gem 'rake', '~> 10.0'

Gemfile.lock

@@ -1,6 +1,6 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 33583fd1c1d72b449cd6bb91815e3422b8448983
+  revision: 74a012eebb9433d031eb00df5abbe488cb8b4512
   branch: develop
   specs:
     goo (0.0.2)
@@ -16,7 +16,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: f9a1be204e81d72f408927b8f60c0be208611929
+  revision: b2731c98bfef0958fecb440c8648b7755a670895
   branch: develop
   specs:
     ncbo_annotator (0.0.1)
@@ -27,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: da1642ed8f9f04db2e427e35d88f235a55138d03
+  revision: 812dd78f02b77c9c6d579b0febf1c2a42d513022
   branch: develop
   specs:
     ontologies_linked_data (0.0.1)
@@ -64,34 +64,34 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
-    base64 (0.2.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.7)
-    builder (3.2.4)
+    bigdecimal (3.1.8)
+    builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    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 (1.16.3)
+    faraday (2.12.0)
+      faraday-net_http (>= 2.0, < 3.4)
+      json
+      logger
+    faraday-net_http (3.3.0)
+      net-http
+    ffi (1.17.0-aarch64-linux-gnu)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    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)
@@ -100,14 +100,17 @@ GEM
       net-pop
       net-smtp
     method_source (1.1.0)
-    mime-types (3.5.2)
+    mime-types (3.6.0)
+      logger
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0305)
+    mime-types-data (3.2024.1001)
     mini_mime (1.1.5)
     minitest (4.7.5)
     multi_json (1.15.0)
+    net-http (0.4.1)
+      uri
     net-http-persistent (2.9.4)
-    net-imap (0.4.10)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -117,39 +120,40 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.3)
+    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 (5.0.5)
-    rack (3.0.10)
+    public_suffix (6.0.1)
+    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 (0.22.1)
+    redis-client (0.22.2)
       connection_pool
-    request_store (1.6.0)
+    request_store (1.7.0)
       rack (>= 1.4)
     rest-client (2.1.0)
       http-accept (>= 1.7.0, < 2.0)
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.6)
+    rexml (3.3.8)
     rsolr (2.6.0)
       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)
@@ -158,26 +162,22 @@ 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)
     systemu (2.6.5)
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
+    uri (0.13.1)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
   aarch64-linux
-  arm64-darwin-22
-  ruby
-  x86_64-darwin-18
-  x86_64-darwin-21
-  x86_64-linux
 
 DEPENDENCIES
   cube-ruby
-  faraday (~> 2.0)
+  faraday
   ffi
   goo!
   minitest (~> 4.0)
@@ -192,4 +192,4 @@ DEPENDENCIES
   sparql-client!
 
 BUNDLED WITH
-   2.4.22
+   2.5.21

config/config.test.rb

@@ -1,27 +1,40 @@
 # frozen_string_literal: true
 
-#
 # This file is designed for used for unit testing
 #
 # All the defaults are set in
 # https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/config/config.rb
 ###
-GOO_HOST   = ENV.include?('GOO_HOST')   ? ENV['GOO_HOST']   : 'localhost'
-GOO_PORT   = ENV.include?('GOO_PORT')   ? ENV['GOO_PORT']   : 9000
-REDIS_HOST = ENV.include?('REDIS_HOST') ? ENV['REDIS_HOST'] : 'localhost'
-REDIS_PORT = ENV.include?('REDIS_PORT') ? ENV['REDIS_PORT'] : 6379
-SOLR_HOST  = ENV.include?('SOLR_HOST')  ? ENV['SOLR_HOST']  : 'localhost'
-MGREP_HOST = ENV.include?('MGREP_HOST') ? ENV['MGREP_HOST'] : 'localhost'
-MGREP_PORT = ENV.include?('MGREP_PORT') ? ENV['MGREP_PORT'] : 55555
+GOO_BACKEND_NAME = ENV.include?("GOO_BACKEND_NAME") ? ENV["GOO_BACKEND_NAME"] : "4store"
+GOO_PATH_QUERY   = ENV.include?("GOO_PATH_QUERY")   ? ENV["GOO_PATH_QUERY"]   : "/sparql/"
+GOO_PATH_DATA    = ENV.include?("GOO_PATH_DATA")    ? ENV["GOO_PATH_DATA"]    : "/data/"
+GOO_PATH_UPDATE  = ENV.include?("GOO_PATH_UPDATE")  ? ENV["GOO_PATH_UPDATE"]  : "/update/"
+GOO_PORT         = ENV.include?("GOO_PORT")         ? ENV["GOO_PORT"]         : 9000
+GOO_HOST         = ENV.include?("GOO_HOST")         ? ENV["GOO_HOST"]         : "localhost"
+REDIS_HOST       = ENV.include?("REDIS_HOST")       ? ENV["REDIS_HOST"]       : "localhost"
+REDIS_PORT       = ENV.include?("REDIS_PORT")       ? ENV["REDIS_PORT"]       : 6379
+MGREP_HOST       = ENV.include?('MGREP_HOST')       ? ENV['MGREP_HOST']       : 'localhost'
+MGREP_PORT       = ENV.include?('MGREP_PORT')       ? ENV['MGREP_PORT']       : 55556
+SOLR_TERM_SEARCH_URL = ENV.include?("SOLR_TERM_SEARCH_URL") ? ENV["SOLR_TERM_SEARCH_URL"] : "http://localhost:8983/solr/term_search_core1"
+SOLR_PROP_SEARCH_URL = ENV.include?("SOLR_PROP_SEARCH_URL") ? ENV["SOLR_PROP_SEARCH_URL"] : "http://localhost:8983/solr/prop_search_core1"
 
 LinkedData.config do |config|
-  config.goo_host                   = GOO_HOST.to_s
-  config.goo_port                   = GOO_PORT.to_i
+  config.goo_backend_name              = GOO_BACKEND_NAME.to_s
+  config.goo_host                      = GOO_HOST.to_s
+  config.goo_port                      = GOO_PORT.to_i
+  config.goo_path_query                = GOO_PATH_QUERY.to_s
+  config.goo_path_data                 = GOO_PATH_DATA.to_s
+  config.goo_path_update               = GOO_PATH_UPDATE.to_s
+  config.goo_redis_host                = REDIS_HOST.to_s
+  config.goo_redis_port                = REDIS_PORT.to_i
+  config.http_redis_host               = REDIS_HOST.to_s
+  config.http_redis_port               = REDIS_PORT.to_i
   config.ontology_analytics_redis_host = REDIS_HOST.to_s
   config.ontology_analytics_redis_port = REDIS_PORT.to_i
-  config.search_server_url          = "http://#{SOLR_HOST}:8983/solr/term_search_core1".to_s
-  config.property_search_server_url = "http://#{SOLR_HOST}:8983/solr/prop_search_core1".to_s
+  config.search_server_url             = SOLR_TERM_SEARCH_URL.to_s
+  config.property_search_server_url    = SOLR_PROP_SEARCH_URL.to_s
 end
+
 Annotator.config do |config|
   config.mgrep_host            = MGREP_HOST.to_s
   config.mgrep_port            = MGREP_PORT.to_i

dip.yml

@@ -0,0 +1,55 @@
+version: '7.1'
+
+# Define default environment variables to pass
+# to Docker Compose
+#environment:
+#  RAILS_ENV: development
+
+compose:
+  files:
+    - docker-compose.yml
+
+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