Merge pull request #3 from ncbo/master

Sync: ncbo v5.33.0 release
ontoportal · Oct 8, 2024 · 91cd15e · 91cd15e
2 parents f239b34 + 25d54ae
commit 91cd15e
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diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml
@@ -35,8 +35,8 @@ jobs:
         with:
           context: .
           platforms: linux/amd64,linux/arm64
-          build-args: |
-            RUBY_VERSION=2.7
+          # build-args: |
+          # RUBY_VERSION=2.7
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml
@@ -15,12 +15,12 @@ jobs:
     - 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: Build docker compose
+      run: docker compose build
     - name: Run unit tests
       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
@@ -6,6 +6,7 @@ config/*.p12
 config/*.json
 data/
 projectFilesBackup/
+.bundle
 .ruby-version
 repo*
 *.turtle

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-ARG RUBY_VERSION
+ARG RUBY_VERSION=3.0
 ARG DISTRO_NAME=bullseye
 
 FROM ruby:$RUBY_VERSION-$DISTRO_NAME
@@ -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.lock b/Gemfile.lock
@@ -1,21 +1,22 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: f01386fe55ffba39cbf5e0bf95c8e2dc18767711
+  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/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
+  revision: d46d667ec1b2343fbcdab587f1a70e763b894133
   branch: master
   specs:
     ncbo_annotator (0.0.1)
@@ -26,7 +27,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 4dc3b1123e871b53ba9eb51983ff69c5d2c75c18
+  revision: 9ab4be437ed84f5a480e7f0d8799824fcea310ae
   branch: master
   specs:
     ontologies_linked_data (0.0.1)
@@ -46,7 +47,7 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
+  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
   branch: master
   specs:
     sparql-client (1.0.1)
@@ -59,6 +60,8 @@ PATH
   specs:
     ncbo_cron (0.0.1)
       dante
+      faraday (~> 2)
+      faraday-follow_redirects (~> 0)
       goo
       google-analytics-data
       mlanett-redis-lock
@@ -74,117 +77,146 @@ GEM
     activesupport (3.2.22.5)
       i18n (~> 0.6, >= 0.6.4)
       multi_json (~> 1.0)
-    addressable (2.8.6)
-      public_suffix (>= 2.0.2, < 6.0)
+    addressable (2.8.7)
+      public_suffix (>= 2.0.2, < 7.0)
     base64 (0.2.0)
     bcrypt (3.1.20)
-    bigdecimal (3.1.7)
-    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)
     dante (0.2.0)
     date (3.3.4)
     declarative (0.0.20)
-    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)
-    faraday (2.8.1)
-      base64
-      faraday-net_http (>= 2.0, < 3.1)
-      ruby2_keywords (>= 0.0.4)
-    faraday-net_http (3.0.2)
-    faraday-retry (2.2.0)
+    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 (3.3.0)
+      net-http
+    faraday-retry (2.2.1)
       faraday (~> 2.0)
-    ffi (1.16.3)
-    gapic-common (0.21.1)
+    ffi (1.17.0)
+    ffi (1.17.0-aarch64-linux-gnu)
+    ffi (1.17.0-arm64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
+    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-analytics-data (0.6.0)
+      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 (0.12.0)
+    google-analytics-data-v1beta (0.13.1)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
-    google-apis-analytics_v3 (0.15.0)
-      google-apis-core (>= 0.14.0, < 2.a)
-    google-apis-core (0.14.1)
+    google-apis-analytics_v3 (0.16.0)
+      google-apis-core (>= 0.15.0, < 2.a)
+    google-apis-core (0.15.1)
       addressable (~> 2.5, >= 2.5.1)
       googleauth (~> 1.9)
-      httpclient (>= 2.8.1, < 3.a)
+      httpclient (>= 2.8.3, < 3.a)
       mini_mime (~> 1.0)
+      mutex_m
       representable (~> 3.0)
       retriable (>= 2.0, < 4.a)
-      rexml
-    google-cloud-core (1.7.0)
+    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 (2.2.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.3)
-    google-protobuf (3.25.3-x86_64-linux)
-    googleapis-common-protos (1.5.0)
-      google-protobuf (~> 3.18)
+    google-protobuf (4.28.2)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.28.2-aarch64-linux)
+      bigdecimal
+      rake (>= 13)
+    google-protobuf (4.28.2-arm64-darwin)
+      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 (1.14.0)
-      google-protobuf (~> 3.18)
-    googleauth (1.11.0)
+    googleapis-common-protos-types (1.16.0)
+      google-protobuf (>= 3.18, < 5.a)
+    googleauth (1.11.1)
       faraday (>= 1.0, < 3.a)
       google-cloud-env (~> 2.1)
       jwt (>= 1.4, < 3.0)
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.62.0)
-      google-protobuf (~> 3.25)
+    grpc (1.66.0)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.66.0-aarch64-linux)
+      google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.62.0-x86_64-linux)
-      google-protobuf (~> 3.25)
+    grpc (1.66.0-arm64-darwin)
+      google-protobuf (>= 3.25, < 5.0)
+      googleapis-common-protos-types (~> 1.0)
+    grpc (1.66.0-x86_64-linux)
+      google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
-    json (2.7.1)
-    json_pure (2.7.1)
-    jwt (2.8.1)
+    json (2.7.2)
+    json_pure (2.7.2)
+    jwt (2.9.3)
       base64
-    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)
     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 (0.4.10)
+    net-imap (0.4.16)
       date
       net-protocol
     net-pop (0.1.2)
@@ -194,44 +226,47 @@ 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
     os (1.1.4)
+    ostruct (0.6.0)
     parseconfig (1.1.2)
     pony (1.13.1)
       mail (>= 2.0)
     pry (0.14.2)
       coderay (~> 1.1)
       method_source (~> 1.0)
-    public_suffix (5.0.4)
-    rack (3.0.10)
+    public_suffix (6.0.1)
+    rack (3.1.7)
     rack-test (2.1.0)
       rack (>= 1.3)
-    rake (13.1.0)
+    rake (13.2.1)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.1.0)
-      redis-client (>= 0.17.0)
-    redis-client (0.21.1)
+    redis (5.3.0)
+      redis-client (>= 0.22.0)
+    redis-client (0.22.2)
       connection_pool
     representable (3.2.0)
       declarative (< 0.1.0)
       trailblazer-option (>= 0.1.1, < 0.2.0)
       uber (< 0.2.0)
+    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)
     retriable (3.1.2)
-    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)
     rufus-scheduler (2.0.24)
       tzinfo (>= 0.3.22)
@@ -247,7 +282,7 @@ 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)
     sys-proctable (1.3.0)
       ffi (~> 1.1)
@@ -259,11 +294,14 @@ 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
+  aarch64-linux
+  arm64-darwin-22
   ruby
   x86_64-linux
 
@@ -294,4 +332,4 @@ DEPENDENCIES
   webrick
 
 BUNDLED WITH
-   2.4.22
+   2.5.20
diff --git a/bin/ncbo_ontology_delete b/bin/ncbo_ontology_delete
@@ -12,6 +12,9 @@ config_exists = File.exist?(File.expand_path('../../config/config.rb', __FILE__)
 abort("Please create a config/config.rb file using the config/config.rb.sample as a template") unless config_exists
 require_relative '../config/config'
 
+# do not send notifications to ontology owners when running this script
+LinkedData.settings.enable_notifications = false
+
 require 'optparse'
 options = {}
 opt_parser = OptionParser.new do |opts|