Merge pull request #83 from ncbo/develop

Develop to master merge, release v5.30.1

.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:

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: 70007faf43d0d96292809f89f15a27a757ccaa25
+  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: 2fb892f92f66b876b9793944124f72821f3b3eb8
+  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: 70fc2c8b377b9deabc838ecd56d3bc75ec764cc2
-  branch: master
+  revision: 30a367b22becf1bb8300666b16ad08ff016d10c9
+  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)
@@ -83,18 +83,20 @@ GEM
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
     builder (3.3.0)
+    childprocess (5.1.0)
+      logger (~> 1.5)
     coderay (1.1.3)
-    concurrent-ruby (1.3.3)
+    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
@@ -115,30 +117,29 @@ GEM
       googleapis-common-protos-types (>= 1.11.0, < 2.a)
       googleauth (~> 1.9)
       grpc (~> 1.59)
-    google-analytics-data (0.6.0)
+    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 (0.13.0)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.16.0)
       google-apis-core (>= 0.15.0, < 2.a)
-    google-apis-core (0.15.0)
+    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)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.4.0)
-    google-protobuf (3.25.3)
-    google-protobuf (3.25.3-x86_64-linux)
+    google-protobuf (3.25.4)
     googleapis-common-protos (1.6.0)
       google-protobuf (>= 3.18, < 5.a)
       googleapis-common-protos-types (~> 1.7)
@@ -152,15 +153,15 @@ GEM
       multi_json (~> 1.11)
       os (>= 0.9, < 2.0)
       signet (>= 0.16, < 2.a)
-    grpc (1.65.0)
+    grpc (1.65.2)
       google-protobuf (>= 3.25, < 5.0)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.65.0-x86_64-linux)
+    grpc (1.65.2-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 (1.0.6)
+    http-cookie (1.0.7)
       domain_name (~> 0.5)
     httpclient (2.8.3)
     i18n (0.9.5)
@@ -169,8 +170,9 @@ GEM
     json_pure (2.7.2)
     jwt (2.8.2)
       base64
-    launchy (2.5.2)
+    launchy (3.0.1)
       addressable (~> 2.8)
+      childprocess (~> 5.0)
     libxml-ruby (5.0.3)
     logger (1.6.0)
     macaddr (1.7.2)
@@ -183,12 +185,13 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0702)
+    mime-types-data (3.2024.0820)
     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-persistent (2.9.4)
     net-imap (0.4.14)
       date
@@ -200,11 +203,13 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.4)
+    oj (3.16.5)
       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)
@@ -218,7 +223,7 @@ GEM
     rake (13.2.1)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.2.0)
+    redis (5.3.0)
       redis-client (>= 0.22.0)
     redis-client (0.22.2)
       connection_pool
@@ -234,7 +239,7 @@ GEM
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
     retriable (3.1.2)
-    rexml (3.3.2)
+    rexml (3.3.6)
       strscan
     rsolr (2.6.0)
       builder (>= 2.1.2)

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|

bin/ncbo_ontology_index

@@ -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
+
 platform = "local"
 if LinkedData.settings.goo_host.include? "stage"
   platform = "stage"

bin/ncbo_ontology_metrics

@@ -12,6 +12,10 @@ 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
+
+
 platform = "local"
 if LinkedData.settings.goo_host.include? "stage"
   platform = "stage"

bin/ncbo_ontology_process

@@ -13,6 +13,9 @@ abort("Please create a config/config.rb file using the config/config.rb.sample a
 require_relative '../config/config'
 require 'optparse'
 
+# do not send notifications to ontology owners when running this script
+LinkedData.settings.enable_notifications = false
+
 options = {all: false}
 opt_parser = OptionParser.new do |opts|
   # Set a banner, displayed at the top of the help screen.

bin/ncbo_ontology_property_index

@@ -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
+
 platform = "local"
 if LinkedData.settings.goo_host.include? "stage"
   platform = "stage"

bin/ncbo_ontology_pull

@@ -14,6 +14,9 @@ require_relative '../lib/ncbo_cron'
 require_relative '../config/config'
 require 'optparse'
 
+# do not send notifications to ontology owners when running this script
+LinkedData.settings.enable_notifications = false
+
 ontology_acronym = ''
 opt_parser = OptionParser.new do |opts|
   opts.on('-o', '--ontology ACRONYM', 'Ontology acronym to pull if new version exist') do |acronym|
@@ -30,9 +33,8 @@ opt_parser.parse!
 
 logger = Logger.new($stdout)
 logger.info "Starting ncbo pull"; logger.flush
-puller = NcboCron::Models::OntologyPull.new
 begin
-  puller.do_ontology_pull(ontology_acronym, logger: logger, enable_pull_umls: true)
+  NcboCron::Helpers::OntologyHelper.do_ontology_pull(ontology_acronym, logger: logger, enable_pull_umls: true)
 rescue StandardError => e
   logger.error e.message
   logger.flush