From c8ad1608e9873b561326179a61112b702db6ece4 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 6 Feb 2024 12:52:25 -0800 Subject: [PATCH 1/7] Gemfile.lock update --- Gemfile.lock | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 9a3aedd3..808dffb6 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 13f2d6e065d2380fc6f16d9fc4148741f4c1f83d + revision: 602a44cbe83ff13d304650f3c4352497d0071a8a branch: develop specs: ontologies_linked_data (0.0.1) @@ -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) @@ -146,13 +146,13 @@ GEM 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) @@ -196,7 +196,7 @@ GEM coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.0.4) - rack (3.0.8) + rack (3.0.9) rack-test (2.1.0) rack (>= 1.3) rake (13.1.0) @@ -284,4 +284,4 @@ DEPENDENCIES test-unit-minitest BUNDLED WITH - 2.3.22 + 2.4.22 From 577ff7fad09529e733796fda4d19667cfa7ede51 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 6 Feb 2024 13:27:12 -0800 Subject: [PATCH 2/7] fix unit test for email notification change is due to the refactor of notifications in ontologies_linked_data --- test/test_ontology_pull.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_ontology_pull.rb b/test/test_ontology_pull.rb index ca3c6130..8ac6dce6 100644 --- a/test/test_ontology_pull.rb +++ b/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) From c69a330746ae0ef3d9228cf10b4da5013dd51367 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 6 Feb 2024 13:36:37 -0800 Subject: [PATCH 3/7] codecov GH action version update --- .github/workflows/ruby-unit-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml index 8b493c41..cb67aac7 100644 --- a/.github/workflows/ruby-unit-tests.yml +++ b/.github/workflows/ruby-unit-tests.yml @@ -22,7 +22,7 @@ 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: flags: unittests verbose: true From b1fad77dc2d7acc6e3be228c91a6d4fae806017b Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 9 Feb 2024 00:01:02 -0800 Subject: [PATCH 4/7] Update ruby-unit-tests.yml add codecov token --- .github/workflows/ruby-unit-tests.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml index cb67aac7..df4372fa 100644 --- a/.github/workflows/ruby-unit-tests.yml +++ b/.github/workflows/ruby-unit-tests.yml @@ -24,6 +24,7 @@ jobs: - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v4 with: + token: ${{ secrets.CODECOV_TOKEN }} flags: unittests verbose: true fail_ci_if_error: false # optional (default = false) From 0bc44c025ea4186f15f3de8d1015309fb775ba5d Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 9 Feb 2024 00:11:28 -0800 Subject: [PATCH 5/7] Update docker-compose.yml AllegroAgraph v8.0.0 -> v8.0.1 upgrade --- docker-compose.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 5f4e9307..af25ac24 100644 --- a/docker-compose.yml +++ b/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 From b928033b102fe1b57d43fff555468c6c25b53657 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 9 Feb 2024 13:52:01 -0800 Subject: [PATCH 6/7] Gemfile.lock update --- Gemfile.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 808dffb6..91b04ff9 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 602a44cbe83ff13d304650f3c4352497d0071a8a + revision: c77d0b390e19c394989e9467e447fcc653b53fa5 branch: develop specs: ontologies_linked_data (0.0.1) @@ -139,7 +139,7 @@ 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) @@ -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 From 6185e9f59f35fe131bf53624ef82dd8e399e5448 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 9 Feb 2024 14:36:58 -0800 Subject: [PATCH 7/7] reset branch specifier to develop --- Gemfile | 8 ++++---- Gemfile.lock | 16 ++++++++-------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/Gemfile b/Gemfile index bcf5f137..ea60eb54 100644 --- a/Gemfile +++ b/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' diff --git a/Gemfile.lock b/Gemfile.lock index b2682918..99ebaaa5 100644 --- a/Gemfile.lock +++ b/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: ec3236a71ff172579923245646d0ea058844794e - 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)