From a1cecde0b46b145bd2667ad4d39a824d01ed5c2d Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 9 Feb 2024 23:58:05 -0800 Subject: [PATCH 1/9] unpin mail gem --- Gemfile | 2 +- Gemfile.lock | 30 ++++++++++++++++++++---------- 2 files changed, 21 insertions(+), 11 deletions(-) diff --git a/Gemfile b/Gemfile index ea60eb54..8b180c6e 100644 --- a/Gemfile +++ b/Gemfile @@ -10,7 +10,6 @@ gem 'ffi' gem "google-apis-analytics_v3" gem 'google-analytics-data' -gem 'mail', '2.6.6' gem 'multi_json' gem 'oj', '~> 3.0' gem 'parseconfig' @@ -36,4 +35,5 @@ group :test do gem 'simplecov' gem 'simplecov-cobertura' # for codecov.io gem 'test-unit-minitest' + gem 'webrick' end diff --git a/Gemfile.lock b/Gemfile.lock index 99ebaaa5..f5495129 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -85,13 +85,14 @@ GEM 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) domain_name (0.6.20240107) - email_spec (2.1.1) + email_spec (2.2.2) htmlentities (~> 4.3.3) launchy (~> 2.1) - mail (~> 2.6) + mail (~> 2.7) faraday (2.8.1) base64 faraday-net_http (>= 2.0, < 3.1) @@ -131,7 +132,6 @@ GEM faraday (>= 1.0, < 3.a) google-cloud-errors (1.3.1) google-protobuf (3.25.2) - google-protobuf (3.25.2-x86_64-darwin) google-protobuf (3.25.2-x86_64-linux) googleapis-common-protos (1.4.0) google-protobuf (~> 3.14) @@ -149,9 +149,6 @@ GEM grpc (1.61.0) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) - grpc (1.61.0-x86_64-darwin) - google-protobuf (~> 3.25) - googleapis-common-protos-types (~> 1.0) grpc (1.61.0-x86_64-linux) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) @@ -171,8 +168,11 @@ GEM logger (1.6.0) macaddr (1.7.2) systemu (~> 2.6.5) - mail (2.6.6) - mime-types (>= 1.16, < 4) + mail (2.8.1) + mini_mime (>= 0.1.1) + net-imap + net-pop + net-smtp method_source (1.0.0) mime-types (3.5.2) mime-types-data (~> 3.2015) @@ -183,6 +183,15 @@ GEM redis multi_json (1.15.0) net-http-persistent (2.9.4) + net-imap (0.4.10) + date + net-protocol + net-pop (0.1.2) + net-protocol + net-protocol (0.2.2) + timeout + net-smtp (0.4.0.1) + net-protocol netrc (0.11.0) oj (3.16.3) bigdecimal (>= 3.0) @@ -244,16 +253,17 @@ GEM systemu (2.6.5) test-unit-minitest (0.9.1) minitest (~> 4.7) + timeout (0.4.1) trailblazer-option (0.1.2) tzinfo (2.0.6) concurrent-ruby (~> 1.0) uber (0.1.0) uuid (2.3.9) macaddr (~> 1.0) + webrick (1.8.1) PLATFORMS ruby - x86_64-darwin-21 x86_64-linux DEPENDENCIES @@ -263,7 +273,6 @@ DEPENDENCIES goo! google-analytics-data google-apis-analytics_v3 - mail (= 2.6.6) minitest (< 5.0) multi_json ncbo_annotator! @@ -281,6 +290,7 @@ DEPENDENCIES sparql-client! sys-proctable test-unit-minitest + webrick BUNDLED WITH 2.4.22 From 0aa17c3e85c82aa1e200290faca690e1806e496b Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Sat, 10 Feb 2024 00:07:48 -0800 Subject: [PATCH 2/9] rename AG repo to 'ontoportal_test' --- docker-compose.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index af25ac24..fb747a66 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -63,9 +63,9 @@ services: GOO_BACKEND_NAME: ag GOO_PORT: 10035 GOO_HOST: agraph-ut - GOO_PATH_QUERY: /repositories/bioportal_test - GOO_PATH_DATA: /repositories/bioportal_test/statements - GOO_PATH_UPDATE: /repositories/bioportal_test/statements + GOO_PATH_QUERY: /repositories/ontoportal_test + GOO_PATH_DATA: /repositories/ontoportal_test/statements + GOO_PATH_UPDATE: /repositories/ontoportal_test/statements profiles: - agraph depends_on: @@ -122,12 +122,12 @@ services: # - 10035:10035 command: > bash -c "/agraph/bin/agraph-control --config /agraph/etc/agraph.cfg start - ; agtool repos create bioportal_test + ; agtool repos create --supersede ontoportal_test ; agtool users add anonymous - ; agtool users grant anonymous root:bioportal_test:rw + ; agtool users grant anonymous root:ontoportal_test:rw ; tail -f /agraph/data/agraph.log" healthcheck: - test: ["CMD-SHELL", "agtool storage-report bioportal_test || exit 1"] + test: ["CMD-SHELL", "agtool storage-report ontoportal_test || exit 1"] start_period: 30s #AllegroGraph can take a loooooong time to start interval: 20s timeout: 10s From c8c86b99d5d480e5063adbff860e7f5c3c75530e Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 14 Feb 2024 10:45:29 -0800 Subject: [PATCH 3/9] Gemfile.lock update --- Gemfile.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index f5495129..2ee23820 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: c77d0b390e19c394989e9467e447fcc653b53fa5 + revision: f0d101bfa888c714b71062e68862c722f82a5072 branch: develop specs: ontologies_linked_data (0.0.1) @@ -137,7 +137,7 @@ GEM google-protobuf (~> 3.14) googleapis-common-protos-types (~> 1.2) grpc (~> 1.27) - googleapis-common-protos-types (1.11.0) + googleapis-common-protos-types (1.12.0) google-protobuf (~> 3.18) googleauth (1.10.0) faraday (>= 1.0, < 3.a) @@ -213,7 +213,7 @@ GEM addressable (>= 2.2) redis (5.1.0) redis-client (>= 0.17.0) - redis-client (0.19.1) + redis-client (0.20.0) connection_pool representable (3.2.0) declarative (< 0.1.0) @@ -234,7 +234,7 @@ GEM rubyzip (2.3.2) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) - signet (0.18.0) + signet (0.19.0) addressable (~> 2.8) faraday (>= 0.17.5, < 3.a) jwt (>= 1.5, < 3.0) From e4495072f3fd6214db1a571ca3f1eefc358ea62a Mon Sep 17 00:00:00 2001 From: mdorf Date: Tue, 27 Feb 2024 16:09:40 -0800 Subject: [PATCH 4/9] Gemfile.lock update --- Gemfile.lock | 43 ++++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 2ee23820..5e33f516 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 7a897a8e9c01d3a412d9011df8e26d770d58cd7d + revision: 4ad4db41216ab9a0e328d4c08cd4a27c82e9b917 branch: develop specs: goo (0.0.2) @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: f0d101bfa888c714b71062e68862c722f82a5072 + revision: 4cdcf8d96d9e525aecb8110f02656bd45520b133 branch: develop specs: ontologies_linked_data (0.0.1) @@ -109,15 +109,15 @@ GEM googleapis-common-protos-types (>= 1.11.0, < 2.a) googleauth (~> 1.9) grpc (~> 1.59) - google-analytics-data (0.5.0) + google-analytics-data (0.6.0) google-analytics-data-v1beta (>= 0.11, < 2.a) google-cloud-core (~> 1.6) - google-analytics-data-v1beta (0.11.2) + google-analytics-data-v1beta (0.12.0) gapic-common (>= 0.21.1, < 2.a) google-cloud-errors (~> 1.0) - google-apis-analytics_v3 (0.14.0) - google-apis-core (>= 0.12.0, < 2.a) - google-apis-core (0.13.0) + google-apis-analytics_v3 (0.15.0) + google-apis-core (>= 0.14.0, < 2.a) + google-apis-core (0.14.0) addressable (~> 2.5, >= 2.5.1) googleauth (~> 1.9) httpclient (>= 2.8.1, < 3.a) @@ -131,25 +131,25 @@ GEM google-cloud-env (2.1.1) faraday (>= 1.0, < 3.a) google-cloud-errors (1.3.1) - google-protobuf (3.25.2) - google-protobuf (3.25.2-x86_64-linux) - googleapis-common-protos (1.4.0) - google-protobuf (~> 3.14) - googleapis-common-protos-types (~> 1.2) - grpc (~> 1.27) - googleapis-common-protos-types (1.12.0) + google-protobuf (3.25.3) + google-protobuf (3.25.3-x86_64-linux) + googleapis-common-protos (1.5.0) google-protobuf (~> 3.18) - googleauth (1.10.0) + googleapis-common-protos-types (~> 1.7) + grpc (~> 1.41) + googleapis-common-protos-types (1.13.0) + google-protobuf (~> 3.18) + googleauth (1.11.0) 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 (1.61.0) + grpc (1.62.0) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) - grpc (1.61.0-x86_64-linux) + grpc (1.62.0-x86_64-linux) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) htmlentities (4.3.4) @@ -161,7 +161,8 @@ GEM concurrent-ruby (~> 1.0) json (2.7.1) json_pure (2.7.1) - jwt (2.7.1) + jwt (2.8.0) + base64 launchy (2.5.2) addressable (~> 2.8) libxml-ruby (5.0.2) @@ -183,7 +184,7 @@ GEM redis multi_json (1.15.0) net-http-persistent (2.9.4) - net-imap (0.4.10) + net-imap (0.3.7) date net-protocol net-pop (0.1.2) @@ -205,7 +206,7 @@ GEM coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.0.4) - rack (3.0.9) + rack (3.0.9.1) rack-test (2.1.0) rack (>= 1.3) rake (13.1.0) @@ -293,4 +294,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.4.22 + 2.3.15 From a9559a678730f4bae6f582b6ba25772be6620560 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 28 Feb 2024 16:36:03 -0800 Subject: [PATCH 5/9] Gemfile.lock update --- Gemfile.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 5e33f516..73b37219 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 4ad4db41216ab9a0e328d4c08cd4a27c82e9b917 + revision: 4ea0e70a4361fc694700e11f1012129452278c7d branch: develop specs: goo (0.0.2) @@ -15,7 +15,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: f60341e8426adcad447a6fc3adb5b80207c5987a + revision: b111a1d5b61d112ad6752f17d3ad94c9c3cf69db branch: develop specs: ncbo_annotator (0.0.1) @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 4cdcf8d96d9e525aecb8110f02656bd45520b133 + revision: 68296aa27bfe5991f1eef871cecd8d5bb4960c01 branch: develop specs: ontologies_linked_data (0.0.1) @@ -184,7 +184,7 @@ GEM redis multi_json (1.15.0) net-http-persistent (2.9.4) - net-imap (0.3.7) + net-imap (0.4.10) date net-protocol net-pop (0.1.2) From 556d711e0f538f7cd0bde04f4f9dd434b5674a21 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 28 Feb 2024 17:21:09 -0800 Subject: [PATCH 6/9] solr schema.xml update --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index fb747a66..13faa35b 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -93,7 +93,7 @@ services: - 4store solr-ut: - image: ontoportal/solr-ut:0.0.2 + image: ontoportal/solr-ut:0.1.0 healthcheck: test: ["CMD-SHELL", "curl -sf http://localhost:8983/solr/term_search_core1/admin/ping?wt=json | grep -iq '\"status\":\"OK\"}' || exit 1"] start_period: 3s From 52c43bdd8592dcdca4edd28d0fdba406f0ca87f7 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Fri, 1 Mar 2024 23:11:33 -0800 Subject: [PATCH 7/9] fixed bug in ontology analytics population process --- lib/ncbo_cron/ontology_analytics.rb | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/lib/ncbo_cron/ontology_analytics.rb b/lib/ncbo_cron/ontology_analytics.rb index c5a4de00..3a0f25ee 100644 --- a/lib/ncbo_cron/ontology_analytics.rb +++ b/lib/ncbo_cron/ontology_analytics.rb @@ -158,15 +158,15 @@ def merge_and_fill_missing_data(ga4_data) ua_ga4_intersecting_month = Date.parse(GA4_START_DATE).month.to_s # add up hits for June of 2023 (the only intersecting month between UA and GA4) - ua_data.each do |acronym, _| - if ga4_data.has_key?(acronym) - if ga4_data[acronym][ua_ga4_intersecting_year].has_key?(ua_ga4_intersecting_month) - ua_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month] += - ga4_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month] - # delete data for June of 2023 from ga4_data to avoid overwriting when merging - ga4_data[acronym][ua_ga4_intersecting_year].delete(ua_ga4_intersecting_month) - end - end + ua_data.each do |acronym| + next unless ga4_data.key?(acronym) + next unless ga4_data[acronym].key?(ua_ga4_intersecting_year) + next unless ga4_data[acronym][ua_ga4_intersecting_year].key?(ua_ga4_intersecting_month) + + ua_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month] += + ga4_data[acronym][ua_ga4_intersecting_year][ua_ga4_intersecting_month] + # delete data for June of 2023 from ga4_data to avoid overwriting when merging + ga4_data[acronym][ua_ga4_intersecting_year].delete(ua_ga4_intersecting_month) end end From b5bc460250aa8a61e5825615e1337fb1dc46f335 Mon Sep 17 00:00:00 2001 From: mdorf Date: Sat, 2 Mar 2024 11:54:50 -0800 Subject: [PATCH 8/9] Gemfile.lock update --- Gemfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 73b37219..6f491218 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 68296aa27bfe5991f1eef871cecd8d5bb4960c01 + revision: 2575a6ecf62f6f1161f103429fc278939630ad87 branch: develop specs: ontologies_linked_data (0.0.1) @@ -161,7 +161,7 @@ GEM concurrent-ruby (~> 1.0) json (2.7.1) json_pure (2.7.1) - jwt (2.8.0) + jwt (2.8.1) base64 launchy (2.5.2) addressable (~> 2.8) @@ -184,7 +184,7 @@ GEM redis multi_json (1.15.0) net-http-persistent (2.9.4) - net-imap (0.4.10) + net-imap (0.3.7) date net-protocol net-pop (0.1.2) From 4bab0051ab9169ea61720d4a64e1aa525119be09 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 13 Mar 2024 17:05:54 -0700 Subject: [PATCH 9/9] AG version v8.0.1 to v8.1.0 upgrade --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 13faa35b..44c9fda4 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -112,7 +112,7 @@ services: retries: 5 agraph-ut: - image: franzinc/agraph:v8.0.1 + image: franzinc/agraph:v8.1.0 platform: linux/amd64 environment: - AGRAPH_SUPER_USER=test