From 3c1c4287469049802f611226ea0fa786693825aa Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 17:04:59 -0700 Subject: [PATCH 1/4] comply with Minitest Style Guide --- test/test_scheduler.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_scheduler.rb b/test/test_scheduler.rb index 58808ea5..d3d0ac04 100644 --- a/test/test_scheduler.rb +++ b/test/test_scheduler.rb @@ -104,8 +104,8 @@ def test_scheduler_locking assert job1_thread.alive? assert job2_thread.alive? - assert listen_string.include?("JOB1") - refute listen_string.include?("JOB2") + assert_includes listen_string, "JOB1" + refute_includes listen_string, "JOB2" job1_thread.kill job1_thread.join refute job1_thread.alive? From 8701996034a3134ba8a81e07e0be8896adfd1ef2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 17:05:25 -0700 Subject: [PATCH 2/4] ruby v3.0 upgrade --- Dockerfile | 5 ---- Gemfile.lock | 72 +++++++++++++++++++++++++--------------------- docker-compose.yml | 4 +-- 3 files changed, 41 insertions(+), 40 deletions(-) diff --git a/Dockerfile b/Dockerfile index 73e1379c..34a38160 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,11 +14,6 @@ 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 diff --git a/Gemfile.lock b/Gemfile.lock index ec8cbc58..eb43927b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 70007faf43d0d96292809f89f15a27a757ccaa25 + revision: aaa3941b48edbc317ec42ba4ecb44c0defeccef6 branch: develop specs: goo (0.0.2) @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 2fb892f92f66b876b9793944124f72821f3b3eb8 + 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: 30a367b22becf1bb8300666b16ad08ff016d10c9 + revision: a22fae3150d8e84e3b6fd19223a5ce2111e8ce94 branch: develop specs: ontologies_linked_data (0.0.1) @@ -98,29 +98,30 @@ GEM htmlentities (~> 4.3.3) launchy (>= 2.1, < 4.0) mail (~> 2.7) - faraday (2.8.1) - base64 - faraday-net_http (>= 2.0, < 3.1) - ruby2_keywords (>= 0.0.4) + faraday (2.12.0) + faraday-net_http (>= 2.0, < 3.4) + json + logger faraday-follow_redirects (0.3.0) faraday (>= 1, < 3) - faraday-net_http (3.0.2) + faraday-net_http (3.3.0) + net-http faraday-retry (2.2.1) faraday (~> 2.0) ffi (1.17.0) ffi (1.17.0-x86_64-linux-gnu) - gapic-common (0.21.1) + gapic-common (0.22.0) 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-protobuf (>= 3.25, < 5.a) + googleapis-common-protos (~> 1.6) + googleapis-common-protos-types (~> 1.15) + googleauth (~> 1.11) + grpc (~> 1.65) google-analytics-data (0.6.1) google-analytics-data-v1beta (>= 0.11, < 2.a) google-cloud-core (~> 1.6) - google-analytics-data-v1beta (0.13.0) + google-analytics-data-v1beta (0.13.1) gapic-common (>= 0.21.1, < 2.a) google-cloud-errors (~> 1.0) google-apis-analytics_v3 (0.16.0) @@ -136,15 +137,20 @@ GEM google-cloud-core (1.7.1) google-cloud-env (>= 1.0, < 3.a) google-cloud-errors (~> 1.0) - google-cloud-env (2.1.1) + google-cloud-env (2.2.0) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) - google-protobuf (3.25.4) + google-protobuf (4.28.2) + bigdecimal + rake (>= 13) + google-protobuf (4.28.2-x86_64-linux) + bigdecimal + rake (>= 13) googleapis-common-protos (1.6.0) google-protobuf (>= 3.18, < 5.a) googleapis-common-protos-types (~> 1.7) grpc (~> 1.41) - googleapis-common-protos-types (1.15.0) + googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) googleauth (1.11.0) faraday (>= 1.0, < 3.a) @@ -153,10 +159,10 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.65.2) + grpc (1.66.0) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.65.2-x86_64-linux) + grpc (1.66.0-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) htmlentities (4.3.4) @@ -168,13 +174,13 @@ GEM concurrent-ruby (~> 1.0) json (2.7.2) json_pure (2.7.2) - jwt (2.8.2) + jwt (2.9.1) base64 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) @@ -185,15 +191,17 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0820) + mime-types-data (3.2024.0903) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) mutex_m (0.2.0) + net-http (0.4.1) + uri net-http-persistent (2.9.4) - net-imap (0.4.14) + net-imap (0.4.16) date net-protocol net-pop (0.1.2) @@ -203,7 +211,7 @@ GEM net-smtp (0.5.0) net-protocol netrc (0.11.0) - oj (3.16.5) + oj (3.16.6) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) @@ -216,7 +224,7 @@ GEM pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) - public_suffix (5.1.1) + public_suffix (6.0.1) rack (3.1.7) rack-test (2.1.0) rack (>= 1.3) @@ -239,13 +247,11 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.6) - strscan + rexml (3.3.7) 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) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) @@ -261,9 +267,8 @@ 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) sys-proctable (1.3.0) ffi (~> 1.1) systemu (2.6.5) @@ -274,9 +279,10 @@ GEM tzinfo (2.0.6) concurrent-ruby (~> 1.0) uber (0.1.0) + uri (0.13.1) uuid (2.3.9) macaddr (~> 1.0) - webrick (1.8.1) + webrick (1.8.2) PLATFORMS ruby @@ -309,4 +315,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.4.22 + 2.5.7 diff --git a/docker-compose.yml b/docker-compose.yml index 50e83dcf..066debce 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -2,9 +2,9 @@ x-app: &app build: context: . args: - RUBY_VERSION: '2.7' + RUBY_VERSION: '3.0' # Increase the version number in the image tag every time Dockerfile or its arguments is changed - image: ncbo_cron:0.0.2 + image: ncbo_cron:0.0.3 environment: &env BUNDLE_PATH: /srv/ontoportal/bundle # default bundle config resolves to /usr/local/bundle/config inside of the container From b457f327ef315f6b7bff4f7b7c97e0f75ab53241 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 20:01:21 -0700 Subject: [PATCH 3/4] add rugygem update --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 34a38160..dfc03492 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,6 +14,7 @@ COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_cron/ WORKDIR /srv/ontoportal/ncbo_cron +RUN gem update --system RUN gem install bundler ENV BUNDLE_PATH=/srv/ontoportal/bundle RUN bundle install From 64621dd37d2598dc6ca1bc665c0d9cb2c55a35f2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 1 Oct 2024 11:20:58 -0700 Subject: [PATCH 4/4] Gemfile.lock update --- Gemfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 496c2aa9..b5b9590e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: aaa3941b48edbc317ec42ba4ecb44c0defeccef6 + revision: 74a012eebb9433d031eb00df5abbe488cb8b4512 branch: develop specs: goo (0.0.2) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a22fae3150d8e84e3b6fd19223a5ce2111e8ce94 + revision: 8572cd25722cab2fbb73813d0fe011b5647d5067 branch: develop specs: ontologies_linked_data (0.0.1) @@ -246,7 +246,7 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.7) + rexml (3.3.8) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0)