Merge Develop to Master, release v5.28.0

.github/workflows/ruby-unit-tests.yml

@@ -22,8 +22,9 @@ jobs:
         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'
     - name: Upload coverage reports to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
+        token: ${{ secrets.CODECOV_TOKEN }}
         flags: unittests
         verbose: true
         fail_ci_if_error: false # optional (default = false)

Gemfile

@@ -25,10 +25,10 @@ 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: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f
-  branch: master
+  revision: 7a897a8e9c01d3a412d9011df8e26d770d58cd7d
+  branch: develop
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -15,8 +15,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ncbo_annotator.git
-  revision: 63c986880aa88c9384043e6611a682434a14aba7
-  branch: master
+  revision: f60341e8426adcad447a6fc3adb5b80207c5987a
+  branch: develop
   specs:
     ncbo_annotator (0.0.1)
       goo
@@ -26,8 +26,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/ontologies_linked_data.git
-  revision: 8319482644c5ea81604968fdf6680b4b4154213f
-  branch: master
+  revision: c77d0b390e19c394989e9467e447fcc653b53fa5
+  branch: develop
   specs:
     ontologies_linked_data (0.0.1)
       activesupport
@@ -46,8 +46,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: d418d56a6c9ff5692f925b45739a2a1c66bca851
-  branch: master
+  revision: 55e7dbf858eb571c767bc67868f9af61663859cb
+  branch: develop
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -111,7 +111,7 @@ GEM
     google-analytics-data (0.5.0)
       google-analytics-data-v1beta (>= 0.11, < 2.a)
       google-cloud-core (~> 1.6)
-    google-analytics-data-v1beta (0.11.1)
+    google-analytics-data-v1beta (0.11.2)
       gapic-common (>= 0.21.1, < 2.a)
       google-cloud-errors (~> 1.0)
     google-apis-analytics_v3 (0.14.0)
@@ -127,7 +127,7 @@ GEM
     google-cloud-core (1.6.1)
       google-cloud-env (>= 1.0, < 3.a)
       google-cloud-errors (~> 1.0)
-    google-cloud-env (2.1.0)
+    google-cloud-env (2.1.1)
       faraday (>= 1.0, < 3.a)
     google-cloud-errors (1.3.1)
     google-protobuf (3.25.2)
@@ -139,20 +139,20 @@ GEM
       grpc (~> 1.27)
     googleapis-common-protos-types (1.11.0)
       google-protobuf (~> 3.18)
-    googleauth (1.9.2)
+    googleauth (1.10.0)
       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 (1.60.0)
+    grpc (1.61.0)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.60.0-x86_64-darwin)
+    grpc (1.61.0-x86_64-darwin)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
-    grpc (1.60.0-x86_64-linux)
+    grpc (1.61.0-x86_64-linux)
       google-protobuf (~> 3.25)
       googleapis-common-protos-types (~> 1.0)
     htmlentities (4.3.4)
@@ -176,7 +176,7 @@ GEM
     method_source (1.0.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2023.1205)
+    mime-types-data (3.2024.0206)
     mini_mime (1.1.5)
     minitest (4.7.5)
     mlanett-redis-lock (0.2.7)
@@ -202,7 +202,7 @@ GEM
     rake (13.1.0)
     rdf (1.0.8)
       addressable (>= 2.2)
-    redis (5.0.8)
+    redis (5.1.0)
       redis-client (>= 0.17.0)
     redis-client (0.19.1)
       connection_pool

docker-compose.yml

@@ -112,7 +112,7 @@ services:
       retries: 5
 
   agraph-ut:
-    image: franzinc/agraph:v8.0.0
+    image: franzinc/agraph:v8.0.1
     platform: linux/amd64
     environment:
       - AGRAPH_SUPER_USER=test
@@ -128,10 +128,10 @@ services:
        ; tail -f /agraph/data/agraph.log"
     healthcheck:
       test: ["CMD-SHELL", "agtool storage-report bioportal_test || exit 1"]
-      start_period: 20s
-      interval: 60s
-      timeout: 5s
-      retries: 3
+      start_period: 30s #AllegroGraph can take a loooooong time to start
+      interval: 20s
+      timeout: 10s
+      retries: 10
     profiles:
       - agraph
 

test/test_ontology_pull.rb

@@ -156,7 +156,7 @@ def test_pull_error_notification
       pull = NcboCron::Models::OntologyPull.new
       pull.do_remote_ontology_pull
 
-      assert last_email_sent.subject.include? "[BioPortal] Load from URL failure for #{ont.name}"
+      assert_match "] Load from URL failure for #{ont.name}", last_email_sent.subject
       user = ont.administeredBy[0]
       user.bring(:email)
       assert (last_email_sent.to.first.include? user.email) || (last_email_sent.header['Overridden-Sender'].value.include? user.email)