From b5422b1a1ba3c394ddb341e07855c23f844ff739 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 15 Oct 2024 16:36:50 -0700 Subject: [PATCH 01/18] Gemfile.lock update --- Gemfile.lock | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index c21d2c66..26feb8ff 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 32a721543f518167385256fa4f0a08c8c6d987b7 + revision: 25d54ae938e63e9d1a6f4b8eb697e0ec2ff1ef87 branch: master specs: ncbo_cron (0.0.1) @@ -194,13 +194,13 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.66.0-aarch64-linux) + grpc (1.67.0-aarch64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.66.0-arm64-darwin) + grpc (1.67.0-arm64-darwin) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.66.0-x86_64-linux) + grpc (1.67.0-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) haml (5.2.2) @@ -245,7 +245,7 @@ GEM net-http (0.4.1) uri net-http-persistent (2.9.4) - net-imap (0.4.16) + net-imap (0.4.17) date net-protocol net-pop (0.1.2) @@ -323,7 +323,7 @@ GEM rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.66.1) + rubocop (1.67.0) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) @@ -367,7 +367,7 @@ GEM rack-test sinatra (~> 1.4.0) tilt (>= 1.3, < 3) - sshkit (1.23.1) + sshkit (1.23.2) base64 net-scp (>= 1.1.2) net-sftp (>= 2.1.2) From fd54ad2d6758564dc5ccbf0adaef0be1fe0aea61 Mon Sep 17 00:00:00 2001 From: mdorf Date: Sat, 19 Oct 2024 11:12:38 -0700 Subject: [PATCH 02/18] changes required to support ncbo/ontologies_linked_data#220 --- Gemfile | 4 +-- Gemfile.lock | 28 +++++++-------- test/controllers/test_classes_controller.rb | 39 ++++++++++++++------- 3 files changed, 42 insertions(+), 29 deletions(-) diff --git a/Gemfile b/Gemfile index c836033a..927a1291 100644 --- a/Gemfile +++ b/Gemfile @@ -47,8 +47,8 @@ gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop' gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' -gem 'goo', github: 'ncbo/goo', branch: 'develop' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' +gem 'goo', github: 'ncbo/goo', branch: 'multilingual_preflabels' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'multilingual_preflabels' group :development do diff --git a/Gemfile.lock b/Gemfile.lock index c12a226d..68121ef3 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 74a012eebb9433d031eb00df5abbe488cb8b4512 - branch: develop + revision: d6b84e12d61317dbddc1b86cb1451acb37915369 + branch: multilingual_preflabels specs: goo (0.0.2) addressable (~> 2.8) @@ -56,8 +56,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 812dd78f02b77c9c6d579b0febf1c2a42d513022 - branch: develop + revision: dec2e789e808e5edea18ca015ee487ddbe02f288 + branch: multilingual_preflabels specs: ontologies_linked_data (0.0.1) activesupport @@ -176,7 +176,7 @@ GEM google-cloud-core (1.7.1) google-cloud-env (>= 1.0, < 3.a) google-cloud-errors (~> 1.0) - google-cloud-env (2.2.0) + google-cloud-env (2.2.1) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) google-protobuf (3.25.5-aarch64-linux) @@ -189,23 +189,23 @@ GEM grpc (~> 1.41) googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) - googleauth (1.11.0) + 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 (1.66.0-aarch64-linux) + grpc (1.67.0-aarch64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.66.0-arm64-darwin) + grpc (1.67.0-arm64-darwin) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.66.0-x86_64-darwin) + grpc (1.67.0-x86_64-darwin) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.66.0-x86_64-linux) + grpc (1.67.0-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) haml (5.2.2) @@ -221,7 +221,7 @@ GEM json-schema (2.8.1) addressable (>= 2.4) json_pure (2.7.2) - jwt (2.9.1) + jwt (2.9.3) base64 kgio (2.11.4) language_server-protocol (3.17.0.3) @@ -250,7 +250,7 @@ GEM net-http (0.4.1) uri net-http-persistent (2.9.4) - net-imap (0.4.16) + net-imap (0.4.17) date net-protocol net-pop (0.1.2) @@ -328,7 +328,7 @@ GEM rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.66.1) + rubocop (1.67.0) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) @@ -372,7 +372,7 @@ GEM rack-test sinatra (~> 1.4.0) tilt (>= 1.3, < 3) - sshkit (1.23.1) + sshkit (1.23.2) base64 net-scp (>= 1.1.2) net-sftp (>= 2.1.2) diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb index ab8ff63e..69ae98a0 100644 --- a/test/controllers/test_classes_controller.rb +++ b/test/controllers/test_classes_controller.rb @@ -82,7 +82,6 @@ def test_notation_lookup assert response["@id"] == "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Ontology_Development_and_Management" end - def test_all_class_pages ont = Ontology.find("TEST-ONT-0").include(:acronym).first @@ -99,7 +98,7 @@ def test_all_class_pages assert last_response.ok? page_response = MultiJson.load(last_response.body) page_response["collection"].each do |item| - assert_instance_of String, item["prefLabel"] + assert_instance_of String, item["prefLabel"], item["@id"] assert_instance_of String, item["@id"] assert_instance_of Hash, item["@context"] assert_instance_of Hash, item["links"] @@ -131,6 +130,7 @@ def test_single_cls_all ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] + clss_ids.each do |cls_id| escaped_cls= CGI.escape(cls_id) call = "/ontologies/#{ont.acronym}/classes/#{escaped_cls}?include=all" @@ -149,6 +149,7 @@ def test_single_cls_properties ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] + clss_ids.each do |cls_id| escaped_cls= CGI.escape(cls_id) call = "/ontologies/#{ont.acronym}/classes/#{escaped_cls}?include=properties" @@ -163,7 +164,6 @@ def test_single_cls_properties def test_single_cls ont = Ontology.find("TEST-ONT-0").include(:acronym).first - clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] @@ -208,7 +208,7 @@ def test_roots_for_cls roots = MultiJson.load(last_response.body) assert_equal 9, roots.length roots.each do |r| - assert_instance_of String, r["prefLabel"] + assert_instance_of String, r["prefLabel"], r["@id"] assert_instance_of String, r["@id"] assert r.include?"hasChildren" #By definition roots have no parents @@ -221,7 +221,6 @@ def test_roots_for_cls end def test_classes_for_not_parsed_ontology - ont = Ontology.find("TEST-ONT-0").include(:acronym).first #first submission was not parsed @@ -232,7 +231,6 @@ def test_classes_for_not_parsed_ontology end def test_tree - ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', @@ -251,7 +249,6 @@ def test_tree end def test_path_to_root_for_cls - ont = Ontology.find("TEST-ONT-0").include(:acronym).first clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Electron_Microscope" ] @@ -264,7 +261,6 @@ def test_path_to_root_for_cls end def test_ancestors_for_cls - ont = Ontology.find("TEST-ONT-0").include(:acronym).first ancestors_data = {} ancestors_data['http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_Interaction'] =[ @@ -454,7 +450,6 @@ def test_calls_not_found end def test_children_for_cls_round_trip - clss_ids = [ 'http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Molecular_and_Cellular_Data', "http://bioontology.org/ontologies/BiomedicalResourceOntology.owl#Microscope" ] @@ -511,7 +506,7 @@ def test_class_page_with_metric_count assert last_response.ok? page_response = MultiJson.load(last_response.body) page_response["collection"].each do |item| - assert_instance_of String, item["prefLabel"] + assert_instance_of String, item["prefLabel"], item["@id"] assert_instance_of String, item["@id"] assert_instance_of Hash, item["@context"] assert_instance_of Hash, item["links"] @@ -536,22 +531,40 @@ def test_default_multilingual sub = ont.latest_submission sub.bring_remaining - get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}" + # rdfs:label is NOT present and the prefLabel is NOT defined for the ontology or portal language + sub.naturalLanguage = ['es'] + sub.save + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Community_Engagement')}" assert last_response.ok? page_response = MultiJson.load(last_response.body) + # does not contain a value in english show the generated one + assert_equal 'Community_Engagement', page_response["prefLabel"] + # rdfs:label is present but NOT for either the ontology or portal language + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}" + assert last_response.ok? + page_response = MultiJson.load(last_response.body) # does not contain a value in english show the generated one assert_equal 'Biospecimen_Management', page_response["prefLabel"] + # prefLabel NOT present, rdfs:label is present but NOT for either the ontology or portal language + get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Gene_Therapy')}" + assert last_response.ok? + page_response = MultiJson.load(last_response.body) + # does not contain a value in english show the generated one + assert_equal 'Gene_Therapy', page_response["prefLabel"] + # prefLabel is present in the ontology language sub.naturalLanguage = ['fr'] sub.save - get "/ontologies/#{ont.acronym}/classes/#{CGI.escape('http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management')}" assert last_response.ok? page_response = MultiJson.load(last_response.body) - # show french value as specified in submission naturalLanguage assert_equal 'Biospecimen Management', page_response["prefLabel"] + + sub.naturalLanguage = [] + sub.save end + end From d8d723360195840da69e532a4997f0835130c498 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 21 Oct 2024 15:24:38 -0700 Subject: [PATCH 03/18] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 68121ef3..1fadb9ff 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: dec2e789e808e5edea18ca015ee487ddbe02f288 + revision: 79eeef6b89726e8d9563fc93ce54a7d5fab9a0e1 branch: multilingual_preflabels specs: ontologies_linked_data (0.0.1) From 609f2afe1b59ffa26ede6039142fb31b87734400 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 21 Oct 2024 16:44:31 -0700 Subject: [PATCH 04/18] reset branch specifier to develop --- Gemfile | 2 +- Gemfile.lock | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile b/Gemfile index 927a1291..a2fb486d 100644 --- a/Gemfile +++ b/Gemfile @@ -48,7 +48,7 @@ gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' gem 'goo', github: 'ncbo/goo', branch: 'multilingual_preflabels' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'multilingual_preflabels' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' group :development do diff --git a/Gemfile.lock b/Gemfile.lock index 63dcb72f..e0a074b9 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -56,8 +56,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: e7d2124381003283696ff863de5ed0dc4c18ecda - branch: multilingual_preflabels + revision: 02ffe85324271f7cdf3601d57315ebb54d716309 + branch: develop specs: ontologies_linked_data (0.0.1) activesupport From 37deda26a17a813016d25f42c20c7025fe618ac1 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 21 Oct 2024 16:56:34 -0700 Subject: [PATCH 05/18] add x86_64-linux platform --- Gemfile.lock | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index e0a074b9..ce262da4 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -155,6 +155,7 @@ GEM faraday (~> 2.0) 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) @@ -179,6 +180,7 @@ GEM google-cloud-errors (1.4.0) google-protobuf (3.25.5-aarch64-linux) google-protobuf (3.25.5-arm64-darwin) + google-protobuf (3.25.5-x86_64-linux) googleapis-common-protos (1.6.0) google-protobuf (>= 3.18, < 5.a) googleapis-common-protos-types (~> 1.7) @@ -198,6 +200,9 @@ GEM grpc (1.67.0-arm64-darwin) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) + grpc (1.67.0-x86_64-linux) + google-protobuf (>= 3.25, < 5.0) + googleapis-common-protos-types (~> 1.0) haml (5.2.2) temple (>= 0.8.0) tilt @@ -394,6 +399,7 @@ GEM PLATFORMS aarch64-linux arm64-darwin-22 + x86_64-linux DEPENDENCIES activesupport (~> 5) @@ -450,4 +456,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.5.7 + 2.5.20 From 8fee0e2d73ba9ad82ddfad4955b20de402bc4b98 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 21 Oct 2024 20:53:12 -0700 Subject: [PATCH 06/18] reset branch specifier to master --- Gemfile | 12 ++++++------ Gemfile.lock | 24 ++++++++++++------------ 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/Gemfile b/Gemfile index 8832064f..ee7b592a 100644 --- a/Gemfile +++ b/Gemfile @@ -42,12 +42,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107 gem 'redcarpet' # NCBO gems (can be from a local dev path or from rubygems/git) -gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop' -gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' -gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' -gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' -gem 'goo', github: 'ncbo/goo', branch: 'multilingual_preflabels' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' +gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master' +gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master' +gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master' +gem 'goo', github: 'ncbo/goo', branch: 'master' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master' group :development do diff --git a/Gemfile.lock b/Gemfile.lock index 15327a67..a03cb89f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: a27d6ca79d47eb045b1bdfe311531827428aa504 - branch: multilingual_preflabels + revision: 3c3ab5ae2824e9a1149b907b01a6c0c461a347e3 + branch: master specs: goo (0.0.2) addressable (~> 2.8) @@ -16,8 +16,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: b2731c98bfef0958fecb440c8648b7755a670895 - branch: develop + revision: d46d667ec1b2343fbcdab587f1a70e763b894133 + branch: master specs: ncbo_annotator (0.0.1) goo @@ -27,8 +27,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 4255106846207d79a41716615bc57a379256212b - branch: develop + revision: 25d54ae938e63e9d1a6f4b8eb697e0ec2ff1ef87 + branch: master specs: ncbo_cron (0.0.1) dante @@ -45,8 +45,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: 084cfc74a78b1c6334f3b74e228ddbf80d36e30a - branch: develop + revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3 + branch: master specs: ncbo_ontology_recommender (0.0.1) goo @@ -56,8 +56,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a65341b714f2734c6ad5fd1999c9e1bf03a17585 - branch: develop + revision: 883344784ef9d9be80e3809ea154f67dc9975590 + branch: master specs: ontologies_linked_data (0.0.1) activesupport @@ -76,8 +76,8 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc - branch: develop + revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc + branch: master specs: sparql-client (1.0.1) json_pure (>= 1.4) From db7b02022d2d57901657d8e3e6d55ee1728afed9 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 13 Nov 2024 23:50:46 -0800 Subject: [PATCH 07/18] Gemfile.lock update --- Gemfile.lock | 46 +++++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 15327a67..d27a4fbb 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 4255106846207d79a41716615bc57a379256212b + revision: a9e8bf81b314b0a5f8a32ed814f1b6943496c1ee branch: develop specs: ncbo_cron (0.0.1) @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a65341b714f2734c6ad5fd1999c9e1bf03a17585 + revision: db05a3b22c4187fb73dd83312a038fb7f7741271 branch: develop specs: ontologies_linked_data (0.0.1) @@ -120,7 +120,7 @@ GEM bcrypt_pbkdf (1.1.1-arm64-darwin) bigdecimal (3.1.8) builder (3.3.0) - capistrano (3.19.1) + capistrano (3.19.2) airbrussh (>= 1.0.0) i18n rake (>= 10.0.0) @@ -139,7 +139,7 @@ GEM rexml cube-ruby (0.0.3) dante (0.2.0) - date (3.3.4) + date (3.4.0) docile (1.4.1) domain_name (0.6.20240107) ed25519 (1.3.0) @@ -156,7 +156,7 @@ GEM 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) + gapic-common (0.23.0) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) google-protobuf (>= 3.25, < 5.a) @@ -187,7 +187,7 @@ GEM grpc (~> 1.41) googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) - googleauth (1.11.1) + googleauth (1.11.2) faraday (>= 1.0, < 3.a) google-cloud-env (~> 2.1) jwt (>= 1.4, < 3.0) @@ -206,16 +206,16 @@ GEM haml (5.2.2) temple (>= 0.8.0) tilt - hashdiff (1.1.1) + hashdiff (1.1.2) http-accept (1.7.0) http-cookie (1.0.7) domain_name (~> 0.5) i18n (1.14.6) concurrent-ruby (~> 1.0) - json (2.7.2) + json (2.8.1) json-schema (2.8.1) addressable (>= 2.4) - json_pure (2.7.2) + json_pure (2.8.1) jwt (2.9.3) base64 kgio (2.11.4) @@ -233,7 +233,7 @@ GEM mime-types (3.6.0) logger mime-types-data (~> 3.2015) - mime-types-data (3.2024.1001) + mime-types-data (3.2024.1105) mini_mime (1.1.5) minitest (5.25.1) minitest-hooks (1.5.2) @@ -242,10 +242,10 @@ GEM mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) - net-http (0.4.1) + net-http (0.5.0) uri net-http-persistent (2.9.4) - net-imap (0.4.17) + net-imap (0.4.18) date net-protocol net-pop (0.1.2) @@ -260,17 +260,17 @@ GEM net-protocol net-ssh (7.3.0) netrc (0.11.0) - newrelic_rpm (9.14.0) - oj (3.16.6) + newrelic_rpm (9.15.0) + oj (3.16.7) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) logger os (1.1.4) - ostruct (0.6.0) + ostruct (0.6.1) parallel (1.26.3) parseconfig (1.1.2) - parser (3.3.5.0) + parser (3.3.6.0) ast (~> 2.4.1) racc pony (1.13.1) @@ -319,11 +319,11 @@ GEM http-cookie (>= 1.0.2, < 2.0) mime-types (>= 1.16, < 4.0) netrc (~> 0.8) - rexml (3.3.8) + rexml (3.3.9) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.67.0) + rubocop (1.68.0) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) @@ -333,7 +333,7 @@ GEM rubocop-ast (>= 1.32.2, < 2.0) ruby-progressbar (~> 1.7) unicode-display_width (>= 2.4.0, < 3.0) - rubocop-ast (1.32.3) + rubocop-ast (1.36.1) parser (>= 3.3.1.0) ruby-progressbar (1.13.0) ruby-xxHash (0.4.0.2) @@ -377,7 +377,7 @@ GEM temple (0.10.3) thread_safe (0.3.6) tilt (2.4.0) - timeout (0.4.1) + timeout (0.4.2) tzinfo (1.2.11) thread_safe (~> 0.1) unicode-display_width (2.6.0) @@ -387,14 +387,14 @@ GEM unicorn-worker-killer (0.4.5) get_process_mem (~> 0) unicorn (>= 4, < 7) - uri (0.13.1) + uri (1.0.2) uuid (2.3.9) macaddr (~> 1.0) webmock (3.19.1) addressable (>= 2.8.0) crack (>= 0.3.2) hashdiff (>= 0.4.0, < 2.0.0) - webrick (1.8.2) + webrick (1.9.0) PLATFORMS aarch64-linux @@ -456,4 +456,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.5.20 + 2.5.7 From 792e257f054d9474f32960311fc25285958a59cb Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 18 Nov 2024 21:07:21 -0800 Subject: [PATCH 08/18] Gemfile.lock update --- Gemfile.lock | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index d27a4fbb..524508ed 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: b2731c98bfef0958fecb440c8648b7755a670895 + revision: 2abcd54c148d0983570d681506002d9d3782d2eb branch: develop specs: ncbo_annotator (0.0.1) @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: db05a3b22c4187fb73dd83312a038fb7f7741271 + revision: 3aadf69fa004886b8e08830003788d09e9d550d5 branch: develop specs: ontologies_linked_data (0.0.1) @@ -143,14 +143,14 @@ GEM docile (1.4.1) domain_name (0.6.20240107) ed25519 (1.3.0) - faraday (2.12.0) - faraday-net_http (>= 2.0, < 3.4) + faraday (2.12.1) + faraday-net_http (>= 2.0, < 3.5) json logger faraday-follow_redirects (0.3.0) faraday (>= 1, < 3) - faraday-net_http (3.3.0) - net-http + faraday-net_http (3.4.0) + net-http (>= 0.5.0) faraday-retry (2.2.1) faraday (~> 2.0) ffi (1.17.0-aarch64-linux-gnu) @@ -212,7 +212,7 @@ GEM domain_name (~> 0.5) i18n (1.14.6) concurrent-ruby (~> 1.0) - json (2.8.1) + json (2.8.2) json-schema (2.8.1) addressable (>= 2.4) json_pure (2.8.1) @@ -275,7 +275,7 @@ GEM racc pony (1.13.1) mail (>= 2.0) - pry (0.14.2) + pry (0.15.0) coderay (~> 1.1) method_source (~> 1.0) public_suffix (6.0.1) From c1c0494a226140954a6af265f6d9f38742628075 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 18 Nov 2024 21:19:38 -0800 Subject: [PATCH 09/18] Gemfile.lock update --- Gemfile.lock | 60 ++++++++++++++++++++++++++-------------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index a03cb89f..8c28aa1d 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 3c3ab5ae2824e9a1149b907b01a6c0c461a347e3 + revision: 39f67ab7fae7675b6ff417ace0ab923e40ffcbcd branch: master specs: goo (0.0.2) @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: d46d667ec1b2343fbcdab587f1a70e763b894133 + revision: b6d50ebb79f114bf81a1cd89d0f8b4d4cbcddda2 branch: master specs: ncbo_annotator (0.0.1) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 25d54ae938e63e9d1a6f4b8eb697e0ec2ff1ef87 + revision: 095ee0fab70b0fe0f2486655811cc8347b6a63ff branch: master specs: ncbo_cron (0.0.1) @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 883344784ef9d9be80e3809ea154f67dc9975590 + revision: 0ce77f2781ac3353716407c22d8fc16d9bfd2c8f branch: master specs: ontologies_linked_data (0.0.1) @@ -120,7 +120,7 @@ GEM bcrypt_pbkdf (1.1.1-arm64-darwin) bigdecimal (3.1.8) builder (3.3.0) - capistrano (3.19.1) + capistrano (3.19.2) airbrussh (>= 1.0.0) i18n rake (>= 10.0.0) @@ -139,24 +139,24 @@ GEM rexml cube-ruby (0.0.3) dante (0.2.0) - date (3.3.4) + date (3.4.0) docile (1.4.1) domain_name (0.6.20240107) ed25519 (1.3.0) - faraday (2.12.0) - faraday-net_http (>= 2.0, < 3.4) + faraday (2.12.1) + faraday-net_http (>= 2.0, < 3.5) json logger faraday-follow_redirects (0.3.0) faraday (>= 1, < 3) - faraday-net_http (3.3.0) - net-http + faraday-net_http (3.4.0) + net-http (>= 0.5.0) faraday-retry (2.2.1) faraday (~> 2.0) 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) + gapic-common (0.23.0) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) google-protobuf (>= 3.25, < 5.a) @@ -187,7 +187,7 @@ GEM grpc (~> 1.41) googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) - googleauth (1.11.1) + googleauth (1.11.2) faraday (>= 1.0, < 3.a) google-cloud-env (~> 2.1) jwt (>= 1.4, < 3.0) @@ -206,16 +206,16 @@ GEM haml (5.2.2) temple (>= 0.8.0) tilt - hashdiff (1.1.1) + hashdiff (1.1.2) http-accept (1.7.0) http-cookie (1.0.7) domain_name (~> 0.5) i18n (1.14.6) concurrent-ruby (~> 1.0) - json (2.7.2) + json (2.8.2) json-schema (2.8.1) addressable (>= 2.4) - json_pure (2.7.2) + json_pure (2.8.1) jwt (2.9.3) base64 kgio (2.11.4) @@ -233,7 +233,7 @@ GEM mime-types (3.6.0) logger mime-types-data (~> 3.2015) - mime-types-data (3.2024.1001) + mime-types-data (3.2024.1105) mini_mime (1.1.5) minitest (5.25.1) minitest-hooks (1.5.2) @@ -242,10 +242,10 @@ GEM mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) - net-http (0.4.1) + net-http (0.5.0) uri net-http-persistent (2.9.4) - net-imap (0.4.17) + net-imap (0.4.18) date net-protocol net-pop (0.1.2) @@ -260,22 +260,22 @@ GEM net-protocol net-ssh (7.3.0) netrc (0.11.0) - newrelic_rpm (9.14.0) - oj (3.16.6) + newrelic_rpm (9.15.0) + oj (3.16.7) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) logger os (1.1.4) - ostruct (0.6.0) + ostruct (0.6.1) parallel (1.26.3) parseconfig (1.1.2) - parser (3.3.5.0) + parser (3.3.6.0) ast (~> 2.4.1) racc pony (1.13.1) mail (>= 2.0) - pry (0.14.2) + pry (0.15.0) coderay (~> 1.1) method_source (~> 1.0) public_suffix (6.0.1) @@ -319,11 +319,11 @@ GEM http-cookie (>= 1.0.2, < 2.0) mime-types (>= 1.16, < 4.0) netrc (~> 0.8) - rexml (3.3.8) + rexml (3.3.9) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.67.0) + rubocop (1.68.0) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) @@ -333,7 +333,7 @@ GEM rubocop-ast (>= 1.32.2, < 2.0) ruby-progressbar (~> 1.7) unicode-display_width (>= 2.4.0, < 3.0) - rubocop-ast (1.32.3) + rubocop-ast (1.36.1) parser (>= 3.3.1.0) ruby-progressbar (1.13.0) ruby-xxHash (0.4.0.2) @@ -377,7 +377,7 @@ GEM temple (0.10.3) thread_safe (0.3.6) tilt (2.4.0) - timeout (0.4.1) + timeout (0.4.2) tzinfo (1.2.11) thread_safe (~> 0.1) unicode-display_width (2.6.0) @@ -387,14 +387,14 @@ GEM unicorn-worker-killer (0.4.5) get_process_mem (~> 0) unicorn (>= 4, < 7) - uri (0.13.1) + uri (1.0.2) uuid (2.3.9) macaddr (~> 1.0) webmock (3.19.1) addressable (>= 2.8.0) crack (>= 0.3.2) hashdiff (>= 0.4.0, < 2.0.0) - webrick (1.8.2) + webrick (1.9.0) PLATFORMS aarch64-linux @@ -456,4 +456,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.5.20 + 2.5.7 From 7640adeab7e3b705af64aa763935bbd419b89488 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 20 Nov 2024 12:18:22 -0800 Subject: [PATCH 10/18] Gemfile.lock --- Gemfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile b/Gemfile index 927a1291..82a20aa9 100644 --- a/Gemfile +++ b/Gemfile @@ -47,7 +47,7 @@ gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop' gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' -gem 'goo', github: 'ncbo/goo', branch: 'multilingual_preflabels' +gem 'goo', github: 'ncbo/goo', branch: 'develop' gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'multilingual_preflabels' From 6e2e4f0c275ba361f1ee95ad3851f52a66d42959 Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 21 Nov 2024 14:01:54 -0800 Subject: [PATCH 11/18] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index be642f4a..ebd691ab 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 3aadf69fa004886b8e08830003788d09e9d550d5 + revision: cbada0066156727195b350ca365de480e5fdde7a branch: multilingual_preflabels specs: ontologies_linked_data (0.0.1) @@ -234,7 +234,7 @@ GEM mime-types-data (~> 3.2015) mime-types-data (3.2024.1105) mini_mime (1.1.5) - minitest (5.25.1) + minitest (5.25.2) minitest-hooks (1.5.2) minitest (> 5.3) minitest-stub_any_instance (1.0.3) From 9f9b8f1d694b6a20e0bcad58a3b1260dc5959f13 Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 21 Nov 2024 15:30:00 -0800 Subject: [PATCH 12/18] fixed failing unit tests as a result of modifying the test ontologies --- Gemfile.lock | 2 +- test/controllers/test_classes_controller.rb | 67 +++++++++++---------- test/controllers/test_metrics_controller.rb | 28 ++++----- 3 files changed, 49 insertions(+), 48 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index ebd691ab..26e296d3 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -56,7 +56,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: cbada0066156727195b350ca365de480e5fdde7a + revision: 0598b9f6e8a37a42938f1db8648ff1b3355be519 branch: multilingual_preflabels specs: ontologies_linked_data (0.0.1) diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb index 9e1f9609..1811062d 100644 --- a/test/controllers/test_classes_controller.rb +++ b/test/controllers/test_classes_controller.rb @@ -295,42 +295,43 @@ def test_descendants_for_cls descendants_data = {} descendants_data['http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research'] =[ "http://bioontology.org/ontologies/ResearchArea.owl#Behavioral_Science", - "http://bioontology.org/ontologies/ResearchArea.owl#Bioinformatics", - "http://bioontology.org/ontologies/ResearchArea.owl#Biostatistics", - "http://bioontology.org/ontologies/ResearchArea.owl#Clinical_Studies", - "http://bioontology.org/ontologies/ResearchArea.owl#Computational_Biology", - "http://bioontology.org/ontologies/ResearchArea.owl#Epidemiology", - "http://bioontology.org/ontologies/ResearchArea.owl#Genomics", - "http://bioontology.org/ontologies/ResearchArea.owl#Metabolomics", - "http://bioontology.org/ontologies/ResearchArea.owl#Nursing", - "http://bioontology.org/ontologies/ResearchArea.owl#Outcomes_Research", - "http://bioontology.org/ontologies/ResearchArea.owl#Pathology", - "http://bioontology.org/ontologies/ResearchArea.owl#Pediatrics", - "http://bioontology.org/ontologies/ResearchArea.owl#Pharmacokinetics_Pharmacodynamics", - "http://bioontology.org/ontologies/ResearchArea.owl#Physiology", - "http://bioontology.org/ontologies/ResearchArea.owl#Preclinical", - "http://bioontology.org/ontologies/ResearchArea.owl#Proteomics", - "http://bioontology.org/ontologies/ResearchArea.owl#Psychometrics", - "http://bioontology.org/ontologies/ResearchArea.owl#Research_IT", - "http://bioontology.org/ontologies/ResearchArea.owl#Toxicology"] + "http://bioontology.org/ontologies/ResearchArea.owl#Bioinformatics", + "http://bioontology.org/ontologies/ResearchArea.owl#Biostatistics", + "http://bioontology.org/ontologies/ResearchArea.owl#Clinical_Studies", + "http://bioontology.org/ontologies/ResearchArea.owl#Computational_Biology", + "http://bioontology.org/ontologies/ResearchArea.owl#Epidemiology", + "http://bioontology.org/ontologies/ResearchArea.owl#Genomics", + "http://bioontology.org/ontologies/ResearchArea.owl#Metabolomics", + "http://bioontology.org/ontologies/ResearchArea.owl#Nursing", + "http://bioontology.org/ontologies/ResearchArea.owl#Outcomes_Research", + "http://bioontology.org/ontologies/ResearchArea.owl#Pathology", + "http://bioontology.org/ontologies/ResearchArea.owl#Pediatrics", + "http://bioontology.org/ontologies/ResearchArea.owl#Pharmacokinetics_Pharmacodynamics", + "http://bioontology.org/ontologies/ResearchArea.owl#Physiology", + "http://bioontology.org/ontologies/ResearchArea.owl#Preclinical", + "http://bioontology.org/ontologies/ResearchArea.owl#Proteomics", + "http://bioontology.org/ontologies/ResearchArea.owl#Psychometrics", + "http://bioontology.org/ontologies/ResearchArea.owl#Research_IT", + "http://bioontology.org/ontologies/ResearchArea.owl#Toxicology"] descendants_data['http://bioontology.org/ontologies/Activity.owl#Activity'] = ["http://bioontology.org/ontologies/Activity.owl#Biospecimen_Management", - "http://bioontology.org/ontologies/Activity.owl#Community_Engagement", - "http://bioontology.org/ontologies/Activity.owl#Gene_Therapy", - "http://bioontology.org/ontologies/Activity.owl#Health_Services", - "http://bioontology.org/ontologies/Activity.owl#IRB", - "http://bioontology.org/ontologies/Activity.owl#Medical_Device_Development", - "http://bioontology.org/ontologies/Activity.owl#Regulatory_Compliance", - "http://bioontology.org/ontologies/Activity.owl#Research_Funding", - "http://bioontology.org/ontologies/Activity.owl#Research_Lab_Management", - "http://bioontology.org/ontologies/Activity.owl#Resource_Inventory", - "http://bioontology.org/ontologies/Activity.owl#Small_Molecule", - "http://bioontology.org/ontologies/Activity.owl#Social_Networking", - "http://bioontology.org/ontologies/Activity.owl#Software_Development", - "http://bioontology.org/ontologies/Activity.owl#Surgical_Procedure", - "http://bioontology.org/ontologies/Activity.owl#Therapeutics", - "http://bioontology.org/ontologies/Activity.owl#Training"] + "http://bioontology.org/ontologies/Activity.owl#Catalog", + "http://bioontology.org/ontologies/Activity.owl#Community_Engagement", + "http://bioontology.org/ontologies/Activity.owl#Gene_Therapy", + "http://bioontology.org/ontologies/Activity.owl#Health_Services", + "http://bioontology.org/ontologies/Activity.owl#IRB", + "http://bioontology.org/ontologies/Activity.owl#Medical_Device_Development", + "http://bioontology.org/ontologies/Activity.owl#Regulatory_Compliance", + "http://bioontology.org/ontologies/Activity.owl#Research_Funding", + "http://bioontology.org/ontologies/Activity.owl#Research_Lab_Management", + "http://bioontology.org/ontologies/Activity.owl#Resource_Inventory", + "http://bioontology.org/ontologies/Activity.owl#Small_Molecule", + "http://bioontology.org/ontologies/Activity.owl#Social_Networking", + "http://bioontology.org/ontologies/Activity.owl#Software_Development", + "http://bioontology.org/ontologies/Activity.owl#Surgical_Procedure", + "http://bioontology.org/ontologies/Activity.owl#Therapeutics", + "http://bioontology.org/ontologies/Activity.owl#Training"] clss_ids = [ 'http://bioontology.org/ontologies/Activity.owl#Activity', "http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research" ] diff --git a/test/controllers/test_metrics_controller.rb b/test/controllers/test_metrics_controller.rb index 0d8b547d..eb06c3f8 100644 --- a/test/controllers/test_metrics_controller.rb +++ b/test/controllers/test_metrics_controller.rb @@ -9,15 +9,15 @@ def before_suite end OntologySubmission.all.each {|s| s.delete } Ontology.all.each {|o| o.delete } - @@data = {"classes"=>486, - "averageChildCount"=>5, - "maxChildCount"=>65, - "classesWithOneChild"=>14, - "classesWithMoreThan25Children"=>2, - "classesWithNoDefinition"=>11, - "individuals"=>124, - "properties"=>63, - "maxDepth"=> 7 } + @@data = {"classes" => 487, + "averageChildCount" => 5, + "maxChildCount" => 65, + "classesWithOneChild" => 14, + "classesWithMoreThan25Children" => 2, + "classesWithNoDefinition" => 11, + "individuals" => 124, + "properties" => 63, + "maxDepth" => 7 } @@options = { ont_count: 2, submission_count: 3, submissions_to_process: [1, 2], @@ -35,8 +35,8 @@ def test_all_metrics #TODO: improve this test and test for two different ontologies #though this is tested in LD metrics.each do |m| - @@data.each do |k,v| - assert_equal(m[k], v) + @@data.each do |k, v| + assert_equal(v, m[k]) end assert m["@id"] == m["submission"].first + "/metrics" end @@ -49,7 +49,7 @@ def test_single_metrics metrics = MultiJson.load(last_response.body) @@data.each do |k,v| - assert_equal(metrics[k], v) + assert_equal(v, metrics[k]) end end @@ -59,7 +59,7 @@ def test_metrics_with_submission_id assert last_response.ok? metrics = MultiJson.load(last_response.body) @@data.each do |k,v| - assert_equal(metrics[k], v) + assert_equal(v, metrics[k]) end end @@ -69,7 +69,7 @@ def test_metrics_with_submission_id_as_param assert last_response.ok? metrics = MultiJson.load(last_response.body) @@data.each do |k,v| - assert_equal(metrics[k], v) + assert_equal(v, metrics[k]) end end From 637eed0db6c4f0fea09ef9ca4556fd5e138c0166 Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 21 Nov 2024 21:25:39 -0800 Subject: [PATCH 13/18] another fix to the metrics unit tests that were faling --- test/controllers/test_metrics_controller.rb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/controllers/test_metrics_controller.rb b/test/controllers/test_metrics_controller.rb index eb06c3f8..8031d967 100644 --- a/test/controllers/test_metrics_controller.rb +++ b/test/controllers/test_metrics_controller.rb @@ -55,9 +55,10 @@ def test_single_metrics def test_metrics_with_submission_id ontology = 'TEST-ONT-0' - get "/ontologies/#{ontology}/submissions/1/metrics" + get "/ontologies/#{ontology}/submissions/2/metrics" assert last_response.ok? metrics = MultiJson.load(last_response.body) + @@data.each do |k,v| assert_equal(v, metrics[k]) end @@ -65,9 +66,10 @@ def test_metrics_with_submission_id def test_metrics_with_submission_id_as_param ontology = 'TEST-ONT-0' - get "/ontologies/#{ontology}/metrics?submissionId=1" + get "/ontologies/#{ontology}/metrics?ontology_submission_id=2" assert last_response.ok? metrics = MultiJson.load(last_response.body) + @@data.each do |k,v| assert_equal(v, metrics[k]) end From e0e4ab903ccdee211de1faa37f501ddebc821e5a Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 21 Nov 2024 21:25:39 -0800 Subject: [PATCH 14/18] another fix to the metrics unit tests that were failing --- test/controllers/test_metrics_controller.rb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/controllers/test_metrics_controller.rb b/test/controllers/test_metrics_controller.rb index eb06c3f8..8031d967 100644 --- a/test/controllers/test_metrics_controller.rb +++ b/test/controllers/test_metrics_controller.rb @@ -55,9 +55,10 @@ def test_single_metrics def test_metrics_with_submission_id ontology = 'TEST-ONT-0' - get "/ontologies/#{ontology}/submissions/1/metrics" + get "/ontologies/#{ontology}/submissions/2/metrics" assert last_response.ok? metrics = MultiJson.load(last_response.body) + @@data.each do |k,v| assert_equal(v, metrics[k]) end @@ -65,9 +66,10 @@ def test_metrics_with_submission_id def test_metrics_with_submission_id_as_param ontology = 'TEST-ONT-0' - get "/ontologies/#{ontology}/metrics?submissionId=1" + get "/ontologies/#{ontology}/metrics?ontology_submission_id=2" assert last_response.ok? metrics = MultiJson.load(last_response.body) + @@data.each do |k,v| assert_equal(v, metrics[k]) end From f765dbd98fe0f120f4a958abfd97dfa6de9b2d6e Mon Sep 17 00:00:00 2001 From: mdorf Date: Thu, 21 Nov 2024 22:29:24 -0800 Subject: [PATCH 15/18] some tests still failed due to the changes to the test ontology --- test/controllers/test_classes_controller.rb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/test/controllers/test_classes_controller.rb b/test/controllers/test_classes_controller.rb index 1811062d..838385d7 100644 --- a/test/controllers/test_classes_controller.rb +++ b/test/controllers/test_classes_controller.rb @@ -106,8 +106,7 @@ def test_all_class_pages assert last_response.ok? count_terms = count_terms + page_response["collection"].length end while page_response["nextPage"] - #bnodes thing got fixed. changed to 486. - assert_equal 486, count_terms + assert_equal 487, count_terms #one more page should bring no results call = "/ontologies/#{ont.acronym}/classes" @@ -515,8 +514,7 @@ def test_class_page_with_metric_count assert last_response.ok? count_terms = count_terms + page_response["collection"].length end while page_response["nextPage"] - #bnodes thing got fixed. changed to 486. - assert_equal 486, count_terms + assert_equal 487, count_terms #one more page should bring no results call = "/ontologies/#{ont.acronym}/classes" From 0488f52dbd9e1fb68cb25718eb65a20b2474bbc9 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 22 Nov 2024 10:16:44 -0800 Subject: [PATCH 16/18] Gemfile.lock update --- Gemfile | 2 +- Gemfile.lock | 13 +++++++------ 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/Gemfile b/Gemfile index 393bb442..12273e84 100644 --- a/Gemfile +++ b/Gemfile @@ -47,7 +47,7 @@ gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' gem 'goo', github: 'ncbo/goo', branch: 'develop' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'multilingual_preflabels' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' group :development do # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42 diff --git a/Gemfile.lock b/Gemfile.lock index 26e296d3..d9d400d4 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 9d1b6ba54019cac2eeeb5c173e452b4eebbeaa3a + revision: 8fa7a03a5a6ca63ebb3675fb9f7b2f1e1f408e2f branch: develop specs: ncbo_cron (0.0.1) @@ -45,7 +45,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: f92a42f660635522eb8709e618ff2e641aef0d17 + revision: 084cfc74a78b1c6334f3b74e228ddbf80d36e30a branch: develop specs: ncbo_ontology_recommender (0.0.1) @@ -56,8 +56,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 0598b9f6e8a37a42938f1db8648ff1b3355be519 - branch: multilingual_preflabels + revision: 6389fa2052e06ff8e21c64fd1be0030beca4c828 + branch: develop specs: ontologies_linked_data (0.0.1) activesupport @@ -153,8 +153,9 @@ GEM net-http (>= 0.5.0) faraday-retry (2.2.1) faraday (~> 2.0) - 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 (0.23.0) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) @@ -456,4 +457,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.5.11 + 2.5.7 From e50ca267b49124ca519df998117669921f936fa2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 26 Nov 2024 16:32:56 -0800 Subject: [PATCH 17/18] reset branch specifier to master --- Gemfile | 12 ++++++------ Gemfile.lock | 36 +++++++++++++++++++----------------- 2 files changed, 25 insertions(+), 23 deletions(-) diff --git a/Gemfile b/Gemfile index ea0ef4e3..26aa283e 100644 --- a/Gemfile +++ b/Gemfile @@ -42,12 +42,12 @@ gem 'haml', '~> 5.2.2' # pin see https://github.com/ncbo/ontologies_api/pull/107 gem 'redcarpet' # NCBO gems (can be from a local dev path or from rubygems/git) -gem 'goo', github: 'ncbo/goo', branch: 'develop' -gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop' -gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' -gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' -gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'develop' -gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop' +gem 'goo', github: 'ncbo/goo', branch: 'master' +gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'master' +gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'master' +gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'master' +gem 'ontologies_linked_data', github: 'ncbo/ontologies_linked_data', branch: 'master' +gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master' group :development do # bcrypt_pbkdf and ed35519 is required for capistrano deployments when using ed25519 keys; see https://github.com/miloserdow/capistrano-deploy/issues/42 diff --git a/Gemfile.lock b/Gemfile.lock index 45fd55d0..f64175f8 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 35721855ba808517698d8b94eb38d4553001c4b6 - branch: develop + revision: 39f67ab7fae7675b6ff417ace0ab923e40ffcbcd + branch: master specs: goo (0.0.2) addressable (~> 2.8) @@ -16,8 +16,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 2abcd54c148d0983570d681506002d9d3782d2eb - branch: develop + revision: b6d50ebb79f114bf81a1cd89d0f8b4d4cbcddda2 + branch: master specs: ncbo_annotator (0.0.1) goo @@ -27,8 +27,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 8fa7a03a5a6ca63ebb3675fb9f7b2f1e1f408e2f - branch: develop + revision: 1e0cb7f5e230e1d19c02f11f3fd76ed9831a3807 + branch: master specs: ncbo_cron (0.0.1) dante @@ -45,8 +45,8 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: 084cfc74a78b1c6334f3b74e228ddbf80d36e30a - branch: develop + revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3 + branch: master specs: ncbo_ontology_recommender (0.0.1) goo @@ -56,8 +56,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 6389fa2052e06ff8e21c64fd1be0030beca4c828 - branch: develop + revision: 536cbe5cef9e23abc299ed44942c0b3966f9c18d + branch: master specs: ontologies_linked_data (0.0.1) activesupport @@ -76,8 +76,8 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc - branch: develop + revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc + branch: master specs: sparql-client (1.0.1) json_pure (>= 1.4) @@ -323,16 +323,16 @@ GEM rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) - rubocop (1.68.0) + rubocop (1.69.0) json (~> 2.3) language_server-protocol (>= 3.17.0) parallel (~> 1.10) parser (>= 3.3.0.2) rainbow (>= 2.2.2, < 4.0) regexp_parser (>= 2.4, < 3.0) - rubocop-ast (>= 1.32.2, < 2.0) + rubocop-ast (>= 1.36.1, < 2.0) ruby-progressbar (~> 1.7) - unicode-display_width (>= 2.4.0, < 3.0) + unicode-display_width (>= 2.4.0, < 4.0) rubocop-ast (1.36.1) parser (>= 3.3.1.0) ruby-progressbar (1.13.0) @@ -380,7 +380,9 @@ GEM timeout (0.4.2) tzinfo (1.2.11) thread_safe (~> 0.1) - unicode-display_width (2.6.0) + unicode-display_width (3.1.2) + unicode-emoji (~> 4.0, >= 4.0.4) + unicode-emoji (4.0.4) unicorn (6.1.0) kgio (~> 2.6) raindrops (~> 0.7) @@ -456,4 +458,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.5.20 + 2.5.7 From 78e6e0da6f0f8203401de05eca2c9318f927ee35 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 26 Nov 2024 18:44:28 -0800 Subject: [PATCH 18/18] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index f64175f8..e7e28b9c 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: b6d50ebb79f114bf81a1cd89d0f8b4d4cbcddda2 + revision: 95da15aad0168200703c0306c6bd714dc06f4d3d branch: master specs: ncbo_annotator (0.0.1) @@ -45,7 +45,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: 9dbd4f179e42c52095129d353a5ac584e9bd47f3 + revision: f9ef23d95b02279d68b6dfb74b218a67ded395e4 branch: master specs: ncbo_ontology_recommender (0.0.1)