Merge pull request #84 from ncbo/develop

Develop to master merge, release v5.32.0

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

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'

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

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

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?