From 0c0aeac66313faf586eefd52de6474531de849ce Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 7 Sep 2023 22:55:03 +0200 Subject: [PATCH 01/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 44537959..0293f031 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: 1d78bde5a711d05475da0459308c7db074af5e21 + revision: ddb95e427950fde3ac715aec340394208c8166fe branch: development specs: goo (0.0.2) @@ -248,7 +248,7 @@ GEM rack (>= 0.4) rack-attack (6.6.1) rack (>= 1.0, < 3) - rack-cache (1.14.0) + rack-cache (1.13.0) rack (>= 0.4) rack-cors (1.0.6) rack (>= 1.6.0) @@ -294,7 +294,7 @@ GEM rubyzip (2.3.2) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) - signet (0.17.0) + signet (0.18.0) addressable (~> 2.8) faraday (>= 0.17.5, < 3.a) jwt (>= 1.5, < 3.0) @@ -350,7 +350,6 @@ GEM webrick (1.8.1) PLATFORMS - x86_64-darwin-21 x86_64-linux DEPENDENCIES @@ -407,4 +406,4 @@ DEPENDENCIES webmock BUNDLED WITH - 2.3.23 + 2.3.15 From dd212da6aad11c7b6b38f3730c8082b6116b3df8 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Fri, 8 Sep 2023 02:29:22 +0200 Subject: [PATCH 02/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 0293f031..ef17cd24 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: 83e835de368bc9f19da800a477982e0ad770900d + revision: f440ae855a217807fead1d20629a0f187997b973 branch: master specs: ncbo_ontology_recommender (0.0.1) @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: ddb95e427950fde3ac715aec340394208c8166fe + revision: 0c0dba92e28fd8c8261db1b3183946e0cf183b53 branch: development specs: goo (0.0.2) @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: 4c89c8346766d23e09b24c8e29750bf3a91e6b53 + revision: 1204ede68ed0a5af5e3fb355172496d5e0134544 branch: development specs: ontologies_linked_data (0.0.1) From c9f51c3db254a0dae05affa30aecec1f93c4a897 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 21 Sep 2023 21:27:20 +0200 Subject: [PATCH 03/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index ef17cd24..1e48fcef 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: 0c0dba92e28fd8c8261db1b3183946e0cf183b53 + revision: 0019b4b7b6e18be15fe068084510c03b674d23d8 branch: development specs: goo (0.0.2) @@ -173,10 +173,9 @@ GEM retriable (>= 2.0, < 4.a) rexml webrick - googleauth (1.7.0) + googleauth (1.8.1) faraday (>= 0.17.3, < 3.a) jwt (>= 1.4, < 3.0) - memoist (~> 0.16) multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) @@ -205,7 +204,6 @@ GEM net-imap net-pop net-smtp - memoist (0.16.2) method_source (1.0.0) mime-types (3.5.1) mime-types-data (~> 3.2015) @@ -227,11 +225,11 @@ GEM timeout net-scp (4.0.0) net-ssh (>= 2.6.5, < 8.0.0) - net-smtp (0.3.3) + net-smtp (0.4.0) net-protocol net-ssh (7.2.0) netrc (0.11.0) - newrelic_rpm (9.4.2) + newrelic_rpm (9.5.0) oj (2.18.5) omni_logger (0.1.4) logger @@ -326,7 +324,7 @@ GEM net-ssh (>= 2.8.0) systemu (2.6.5) temple (0.10.2) - tilt (2.2.0) + tilt (2.3.0) timeout (0.4.0) trailblazer-option (0.1.2) tzinfo (2.0.6) From b60eb5c8830a91a0eff243a8a23854a5134a77fc Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 21 Sep 2023 21:40:53 +0200 Subject: [PATCH 04/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 01ff5a99..1e48fcef 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -110,7 +110,6 @@ GEM backports (3.24.1) bcrypt (3.1.19) bcrypt_pbkdf (1.1.0) - benchmark-ips (2.12.0) bigdecimal (1.4.2) builder (3.2.4) capistrano (3.17.3) @@ -354,7 +353,6 @@ PLATFORMS DEPENDENCIES activesupport (~> 3.1) bcrypt_pbkdf (>= 1.0, < 2.0) - benchmark-ips (~> 2.12) bigdecimal (= 1.4.2) capistrano (~> 3) capistrano-bundler @@ -406,4 +404,4 @@ DEPENDENCIES webmock BUNDLED WITH - 2.4.12 + 2.3.15 From 295fa2fb485e385280615f723375c79091e43207 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Fri, 22 Sep 2023 03:35:21 +0200 Subject: [PATCH 05/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 1e48fcef..be074377 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: 0019b4b7b6e18be15fe068084510c03b674d23d8 + revision: 69466682c1e9cb2c338539195013dbec9714ca7d branch: development specs: goo (0.0.2) From ad9413f8cf872a83f36584a616ae61b2af418e32 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Mon, 9 Oct 2023 10:55:19 +0200 Subject: [PATCH 06/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index be074377..d04a6edb 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -105,7 +105,7 @@ GEM multi_json (~> 1.0) addressable (2.8.5) public_suffix (>= 2.0.2, < 6.0) - airbrussh (1.4.2) + airbrussh (1.5.0) sshkit (>= 1.6.1, != 1.7.0) backports (3.24.1) bcrypt (3.1.19) @@ -159,7 +159,7 @@ GEM faraday-patron (1.0.0) faraday-rack (1.0.0) faraday-retry (1.0.3) - ffi (1.15.5) + ffi (1.16.3) get_process_mem (0.2.7) ffi (~> 1.0) google-apis-analytics_v3 (0.13.0) @@ -207,7 +207,7 @@ GEM method_source (1.0.0) mime-types (3.5.1) mime-types-data (~> 3.2015) - mime-types-data (3.2023.0808) + mime-types-data (3.2023.1003) mini_mime (1.1.5) minitest (4.7.5) minitest-stub_any_instance (1.0.3) @@ -216,7 +216,7 @@ GEM multi_json (1.15.0) multipart-post (2.3.0) net-http-persistent (2.9.4) - net-imap (0.3.7) + net-imap (0.4.0) date net-protocol net-pop (0.1.2) @@ -323,7 +323,7 @@ GEM net-scp (>= 1.1.2) net-ssh (>= 2.8.0) systemu (2.6.5) - temple (0.10.2) + temple (0.10.3) tilt (2.3.0) timeout (0.4.0) trailblazer-option (0.1.2) From 999423402a20f7db3c85900353f8f9ed81299e06 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 12 Oct 2023 18:47:12 +0200 Subject: [PATCH 07/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index d04a6edb..9dca2612 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: 1204ede68ed0a5af5e3fb355172496d5e0134544 + revision: 03710bf41b091732b93f85f7a6b8dc06de321542 branch: development specs: ontologies_linked_data (0.0.1) @@ -216,7 +216,7 @@ GEM multi_json (1.15.0) multipart-post (2.3.0) net-http-persistent (2.9.4) - net-imap (0.4.0) + net-imap (0.4.1) date net-protocol net-pop (0.1.2) From f07830c47768855a8bbcf52e58591c3584731488 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 12 Oct 2023 21:15:12 +0200 Subject: [PATCH 08/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 9dca2612..b4891f00 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: 03710bf41b091732b93f85f7a6b8dc06de321542 + revision: 087c28b92527a1df1665d25c38277456e9acf06e branch: development specs: ontologies_linked_data (0.0.1) From f92c3f7f25f50544f67803d4880305818943eeaf Mon Sep 17 00:00:00 2001 From: Syphax bouazzouni Date: Fri, 13 Oct 2023 00:10:18 +0200 Subject: [PATCH 09/18] add ontology submissions filter by status test --- helpers/request_params_helper.rb | 2 +- .../test_ontology_submissions_controller.rb | 14 ++++++++++++++ 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/helpers/request_params_helper.rb b/helpers/request_params_helper.rb index 842ee0a7..f1b8268c 100644 --- a/helpers/request_params_helper.rb +++ b/helpers/request_params_helper.rb @@ -45,9 +45,9 @@ def apply_submission_filters(query) isOfType: params[:isOfType]&.split(','), #["http://omv.ontoware.org/2005/05/ontology#Vocabulary"], hasFormalityLevel: params[:hasFormalityLevel]&.split(','), #["http://w3id.org/nkos/nkostype#thesaurus"], ontology_viewingRestriction: params[:viewingRestriction]&.split(','), #["private"] + status: params[:status]&.split(','), #"retired", } inverse_filters = { - status: params[:status], #"retired", submissionStatus: params[:submissionStatus] #"RDF", } diff --git a/test/controllers/test_ontology_submissions_controller.rb b/test/controllers/test_ontology_submissions_controller.rb index 58359451..147b9c12 100644 --- a/test/controllers/test_ontology_submissions_controller.rb +++ b/test/controllers/test_ontology_submissions_controller.rb @@ -313,6 +313,7 @@ def test_submissions_pagination_filter ontologies.first.name = "sort by test" ontologies.first.save sub = ontologies.first.latest_submission(status: :any).bring_remaining + sub.status = 'retired' sub.creationDate = DateTime.yesterday.to_datetime sub.hasOntologyLanguage = LinkedData::Models::OntologyFormat.find('SKOS').first sub.save @@ -349,6 +350,19 @@ def test_submissions_pagination_filter submissions = MultiJson.load(last_response.body) refute_empty submissions["collection"] assert_equal ontologies2.size + 1 , submissions["collection"].size + + # test ontology filter with status + get "/submissions?page=1&pagesize=100&status=retired" + assert last_response.ok? + submissions = MultiJson.load(last_response.body) + refute_empty submissions["collection"] + assert_equal 1 , submissions["collection"].size + + get "/submissions?page=1&pagesize=100&status=alpha,beta,production" + assert last_response.ok? + submissions = MultiJson.load(last_response.body) + refute_empty submissions["collection"] + assert_equal ontologies.size - 1 , submissions["collection"].size end def test_submissions_default_includes From 027fc2da42d9869d4e63aa1040f514d087c4db56 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 19 Oct 2023 17:49:07 +0200 Subject: [PATCH 10/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index b4891f00..ed9de62f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: 69466682c1e9cb2c338539195013dbec9714ca7d + revision: 4c46c8a8d90f8d08c91e27164d337a899f852980 branch: development specs: goo (0.0.2) @@ -112,7 +112,7 @@ GEM bcrypt_pbkdf (1.1.0) bigdecimal (1.4.2) builder (3.2.4) - capistrano (3.17.3) + capistrano (3.18.0) airbrussh (>= 1.0.0) i18n rake (>= 10.0.0) From 34529af6b2252c017c3bf92d0201466492517312 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 19 Oct 2023 18:26:58 +0200 Subject: [PATCH 11/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index ed9de62f..bb548c46 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: 087c28b92527a1df1665d25c38277456e9acf06e + revision: a6b008c1819dbc52c2df2f5f48929b79a725ef0a branch: development specs: ontologies_linked_data (0.0.1) From 51cc581058fa20755d14d20142aa4dc3739ec82d Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 19 Oct 2023 19:25:41 +0200 Subject: [PATCH 12/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index bb548c46..d1ab430f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: 4c46c8a8d90f8d08c91e27164d337a899f852980 + revision: c6291e6f220cd24e1c814a9398eb57e493c7682f branch: development specs: goo (0.0.2) From 259a72cbf9620d28f1fe8e2c44027b9238e66c41 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Thu, 19 Oct 2023 20:07:30 +0200 Subject: [PATCH 13/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index d1ab430f..b9981c9a 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: a6b008c1819dbc52c2df2f5f48929b79a725ef0a + revision: af3d12d68aac31d8a6c0c9ebbe6042de7304fe52 branch: development specs: ontologies_linked_data (0.0.1) From 7d3276f15651dadf38f91448990c27f265c35274 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Fri, 20 Oct 2023 06:46:29 +0200 Subject: [PATCH 14/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index b9981c9a..6e600a05 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -11,7 +11,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/goo.git - revision: c6291e6f220cd24e1c814a9398eb57e493c7682f + revision: 5979402d5138850fb9bdb34edfa350e9af1b5d22 branch: development specs: goo (0.0.2) @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: af3d12d68aac31d8a6c0c9ebbe6042de7304fe52 + revision: f61e8f2bd303d70e5de4fc2181c4bd8e9f74ccc9 branch: development specs: ontologies_linked_data (0.0.1) From f50fb3661c3f8179e7fd22fb011905cd9bf4fd12 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Fri, 20 Oct 2023 13:19:04 +0200 Subject: [PATCH 15/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Gemfile.lock b/Gemfile.lock index 6e600a05..35be4752 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: f61e8f2bd303d70e5de4fc2181c4bd8e9f74ccc9 + revision: 57599ca3ef2872e525a93e4c3b3a6a76bc51fe13 branch: development specs: ontologies_linked_data (0.0.1) From 3a93734c4de5c6858f2bc55fd9e2780a52a860f4 Mon Sep 17 00:00:00 2001 From: Syphax bouazzouni Date: Fri, 20 Oct 2023 14:56:41 +0200 Subject: [PATCH 16/18] include all metrics attribues in the submissions endpoints --- helpers/submission_helper.rb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/helpers/submission_helper.rb b/helpers/submission_helper.rb index 07f82138..c68e8567 100644 --- a/helpers/submission_helper.rb +++ b/helpers/submission_helper.rb @@ -13,6 +13,11 @@ def submission_include_params if includes.find{|v| v.is_a?(Hash) && v.keys.include?(:contact)} includes << {:contact=>[:name, :email]} end + + if includes.find{|v| v.is_a?(Hash) && v.keys.include?(:metrics)} + includes << LinkedData::Models::Metric.goo_attrs_to_load([:all]) + end + includes end From 6665fd7df24f5d187267da04ebb95f92b7ccf3bb Mon Sep 17 00:00:00 2001 From: Syphax bouazzouni Date: Fri, 20 Oct 2023 14:56:41 +0200 Subject: [PATCH 17/18] include all metrics attribues in the submissions endpoints --- helpers/submission_helper.rb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/helpers/submission_helper.rb b/helpers/submission_helper.rb index 07f82138..b79737d0 100644 --- a/helpers/submission_helper.rb +++ b/helpers/submission_helper.rb @@ -13,6 +13,14 @@ def submission_include_params if includes.find{|v| v.is_a?(Hash) && v.keys.include?(:contact)} includes << {:contact=>[:name, :email]} end + + if includes.find{|v| v.is_a?(Hash) && v.keys.include?(:metrics)} + includes << { metrics: [:maxChildCount, :properties, :classesWithMoreThan25Children, + :classesWithOneChild, :individuals, :maxDepth, :classes, + :classesWithNoDefinition, :averageChildCount, :numberOfAxioms, + :entities]} + end + includes end From 2220e72ab7be403245fa1048cdf06361b702dd54 Mon Sep 17 00:00:00 2001 From: OntoPortal Bot Date: Wed, 1 Nov 2023 02:47:41 +0100 Subject: [PATCH 18/18] [ontoportal-bot] Gemfile.lock update --- Gemfile.lock | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 35be4752..bec188d8 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -53,7 +53,7 @@ GIT GIT remote: https://github.com/ontoportal-lirmm/ontologies_linked_data.git - revision: 57599ca3ef2872e525a93e4c3b3a6a76bc51fe13 + revision: e9ff8c19c97d9bc401a0dea29ec0eba6aceed290 branch: development specs: ontologies_linked_data (0.0.1) @@ -108,6 +108,7 @@ GEM airbrussh (1.5.0) sshkit (>= 1.6.1, != 1.7.0) backports (3.24.1) + base64 (0.1.1) bcrypt (3.1.19) bcrypt_pbkdf (1.1.0) bigdecimal (1.4.2) @@ -164,7 +165,7 @@ GEM ffi (~> 1.0) google-apis-analytics_v3 (0.13.0) google-apis-core (>= 0.11.0, < 2.a) - google-apis-core (0.11.1) + google-apis-core (0.11.2) addressable (~> 2.5, >= 2.5.1) googleauth (>= 0.16.2, < 2.a) httpclient (>= 2.8.1, < 3.a) @@ -216,7 +217,7 @@ GEM multi_json (1.15.0) multipart-post (2.3.0) net-http-persistent (2.9.4) - net-imap (0.4.1) + net-imap (0.4.3) date net-protocol net-pop (0.1.2) @@ -229,7 +230,8 @@ GEM net-protocol net-ssh (7.2.0) netrc (0.11.0) - newrelic_rpm (9.5.0) + newrelic_rpm (9.6.0) + base64 oj (2.18.5) omni_logger (0.1.4) logger