Merge pull request #15 from ncbo/master

Sync: ncbo v5.33.0 release
ontoportal · Oct 8, 2024 · 23c63a2 · 23c63a2
2 parents 4dc3b11 + 9ab4be4
commit 23c63a2
Show file tree

Hide file tree

Showing 52 changed files with 384,344 additions and 1,990 deletions.
diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
@@ -17,14 +17,14 @@ jobs:
       run: ./test/solr/generate_ncbo_configsets.sh
     - name: create config.rb file
       run: cp config/config.test.rb config/config.rb
-    - name: Build docker-compose
-      run: docker-compose --profile 4store build #profile flag is set in order to build all containers in this step
+    - name: Build docker compose
+      run: docker compose --profile 4store build #profile flag is set in order to build all containers in this step
     - 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 ${{ matrix.backend }} 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@v4
       with:

diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+.bundle/
 *.swp
 *.gemtags
 .bundle

diff --git a/Dockerfile b/Dockerfile
@@ -14,10 +14,6 @@ COPY Gemfile* /srv/ontoportal/ontologies_linked_data/
 
 WORKDIR /srv/ontoportal/ontologies_linked_data
 
-# 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

diff --git a/Gemfile b/Gemfile
@@ -16,6 +16,8 @@ gem 'rest-client'
 gem 'rsolr'
 gem 'rubyzip', '~> 1.0'
 gem 'thin'
+gem 'request_store'
+
 
 # Testing
 group :test do
@@ -31,7 +33,6 @@ end
 group :development do
   gem 'rubocop', require: false
 end
-
 # NCBO gems (can be from a local dev path or from rubygems/git)
 gem 'goo', github: 'ncbo/goo', branch: 'master'
 gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,21 +1,22 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
+  revision: f943ac33e87c55c88131c32d826ed5d39c89302c
   branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
       pry
       rdf (= 1.0.8)
       redis
+      request_store
       rest-client
       rsolr
       sparql-client
       uuid
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
+  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
   branch: master
   specs:
     sparql-client (1.0.1)
@@ -32,58 +33,64 @@ GEM
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     ansi (1.5.0)
     ast (2.4.2)
-    base64 (0.2.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.6)
-    builder (3.2.4)
+    bigdecimal (3.1.8)
+    builder (3.3.0)
+    childprocess (5.1.0)
+      logger (~> 1.5)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.4)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
     date (3.3.4)
-    docile (1.4.0)
+    docile (1.4.1)
     domain_name (0.6.20240107)
-    email_spec (2.2.2)
+    email_spec (2.3.0)
       htmlentities (~> 4.3.3)
-      launchy (~> 2.1)
+      launchy (>= 2.1, < 4.0)
       mail (~> 2.7)
     eventmachine (1.2.7)
-    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)
+    ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
     hashie (5.0.0)
     htmlentities (4.3.4)
     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 (2.7.1)
-    json_pure (2.7.1)
+    json (2.7.2)
+    json_pure (2.7.2)
     language_server-protocol (3.17.0.3)
-    launchy (2.5.2)
+    launchy (3.0.1)
       addressable (~> 2.8)
+      childprocess (~> 5.0)
     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)
       mini_mime (>= 0.1.1)
       net-imap
       net-pop
       net-smtp
-    method_source (1.0.0)
-    mime-types (3.5.2)
+    method_source (1.1.0)
+    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)
     minitest-reporters (0.14.24)
@@ -92,23 +99,27 @@ GEM
       minitest (>= 2.12, < 5.0)
       powerbar
     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)
       net-protocol
     net-protocol (0.2.2)
       timeout
-    net-smtp (0.4.0.1)
+    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
-    parallel (1.24.0)
-    parser (3.3.0.5)
+    ostruct (0.6.0)
+    parallel (1.26.3)
+    parser (3.3.5.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -118,44 +129,44 @@ GEM
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.4)
-    racc (1.7.3)
-    rack (2.2.8.1)
+    public_suffix (6.0.1)
+    racc (1.8.1)
+    rack (2.2.9)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rainbow (3.1.1)
     rake (10.5.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.1.0)
-      redis-client (>= 0.17.0)
-    redis-client (0.21.0)
+    redis (5.3.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.2)
       connection_pool
-    regexp_parser (2.9.0)
+    regexp_parser (2.9.2)
+    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)
-    rsolr (2.5.0)
+    rexml (3.3.8)
+    rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.62.1)
+    rubocop (1.66.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
       parser (>= 3.3.0.2)
       rainbow (>= 2.2.2, < 4.0)
-      regexp_parser (>= 1.8, < 3.0)
-      rexml (>= 3.2.5, < 4.0)
-      rubocop-ast (>= 1.31.1, < 2.0)
+      regexp_parser (>= 2.4, < 3.0)
+      rubocop-ast (>= 1.32.2, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.31.2)
-      parser (>= 3.3.0.4)
+    rubocop-ast (1.32.3)
+      parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
-    ruby2_keywords (0.0.5)
     rubyzip (1.3.0)
     simplecov (0.22.0)
       docile (~> 1.1)
@@ -164,7 +175,7 @@ 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)
     thin (1.8.2)
@@ -174,14 +185,14 @@ GEM
     thread_safe (0.3.6)
     timeout (0.4.1)
     tzinfo (0.3.62)
-    unicode-display_width (2.5.0)
+    unicode-display_width (2.6.0)
+    uri (0.13.1)
     uuid (2.3.9)
       macaddr (~> 1.0)
 
 PLATFORMS
   aarch64-linux
   arm64-darwin-22
-  x86_64-darwin-21
   x86_64-linux
 
 DEPENDENCIES
@@ -203,6 +214,7 @@ DEPENDENCIES
   rack
   rack-test (~> 0.6)
   rake (~> 10.0)
+  request_store
   rest-client
   rsolr
   rubocop