diff --git a/Dockerfile b/Dockerfile index 73e1379c..dfc03492 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,10 +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 diff --git a/Gemfile b/Gemfile index f136281f..8b180c6e 100644 --- a/Gemfile +++ b/Gemfile @@ -24,10 +24,10 @@ gem 'sys-proctable' gem 'cube-ruby', require: 'cube' # NCBO -gem 'goo', github: 'ncbo/goo', branch: 'master' -gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master' -gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master' +gem 'goo', github: 'ncbo/goo', branch: 'develop' +gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' group :test do gem 'email_spec' diff --git a/Gemfile.lock b/Gemfile.lock index 816109f8..b5b9590e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2 - branch: master + revision: 74a012eebb9433d031eb00df5abbe488cb8b4512 + branch: develop specs: goo (0.0.2) addressable (~> 2.8) @@ -16,8 +16,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 63c986880aa88c9384043e6611a682434a14aba7 - branch: master + revision: b2731c98bfef0958fecb440c8648b7755a670895 + branch: develop specs: ncbo_annotator (0.0.1) goo @@ -27,8 +27,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: f32bc171e487b7c87fee28b80d9a411a7d45aa79 - branch: master + revision: 8572cd25722cab2fbb73813d0fe011b5647d5067 + branch: develop specs: ontologies_linked_data (0.0.1) activesupport @@ -47,8 +47,8 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc - branch: master + revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc + branch: develop specs: sparql-client (1.0.1) json_pure (>= 1.4) @@ -98,25 +98,25 @@ 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) @@ -136,11 +136,15 @@ 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 (3.25.5) - google-protobuf (3.25.5-x86_64-linux) + 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) @@ -154,10 +158,10 @@ 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) @@ -193,6 +197,8 @@ GEM 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 (0.4.16) date @@ -217,7 +223,7 @@ 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) @@ -240,12 +246,11 @@ 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) ruby-xxHash (0.4.0.2) - ruby2_keywords (0.0.5) rubyzip (2.3.2) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) @@ -273,6 +278,7 @@ 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 (1.8.2) @@ -308,4 +314,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.4.22 + 2.5.20 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 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?