From 67810ddd2e14876d789c63c427b08af6919f661e Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 6 May 2024 12:11:28 -0700 Subject: [PATCH 1/5] reset branch specifier to master --- Gemfile | 8 ++++---- Gemfile.lock | 16 ++++++++-------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/Gemfile b/Gemfile index 8b180c6e..f136281f 100644 --- a/Gemfile +++ b/Gemfile @@ -24,10 +24,10 @@ gem 'sys-proctable' gem 'cube-ruby', require: 'cube' # NCBO -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' +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' group :test do gem 'email_spec' diff --git a/Gemfile.lock b/Gemfile.lock index 4e13127e..1aa9740f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 33583fd1c1d72b449cd6bb91815e3422b8448983 - branch: develop + revision: ef2d816df2d263c905bd034efd449a964fa4890f + 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: 7531e10ad55ac66e925c099d7fc05a5a3ceae67e - branch: develop + revision: 63c986880aa88c9384043e6611a682434a14aba7 + branch: master specs: ncbo_annotator (0.0.1) goo @@ -27,8 +27,8 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a3f6cf0493bb595011f98acf95efda33111c537b - branch: develop + revision: 02986ff6db698cd56fdc062fed21b65d706a9598 + branch: master specs: ontologies_linked_data (0.0.1) activesupport @@ -47,8 +47,8 @@ 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 1ee0c07e0c286fe11d9c45e6de773138a49d6ced Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 11 Jun 2024 23:22:02 -0700 Subject: [PATCH 2/5] Gemfile update --- Gemfile.lock | 47 +++++++++++++++++++++++++---------------------- 1 file changed, 25 insertions(+), 22 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 1aa9740f..80aedbd8 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: ef2d816df2d263c905bd034efd449a964fa4890f + revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2 branch: master specs: goo (0.0.2) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 02986ff6db698cd56fdc062fed21b65d706a9598 + revision: 70fc2c8b377b9deabc838ecd56d3bc75ec764cc2 branch: master specs: ontologies_linked_data (0.0.1) @@ -81,10 +81,10 @@ GEM public_suffix (>= 2.0.2, < 6.0) base64 (0.2.0) bcrypt (3.1.20) - bigdecimal (3.1.7) - builder (3.2.4) + bigdecimal (3.1.8) + builder (3.3.0) coderay (1.1.3) - concurrent-ruby (1.2.3) + concurrent-ruby (1.3.3) connection_pool (2.4.1) cube-ruby (0.0.3) dante (0.2.0) @@ -105,7 +105,8 @@ GEM faraday-net_http (3.0.2) faraday-retry (2.2.1) faraday (~> 2.0) - ffi (1.16.3) + ffi (1.17.0) + ffi (1.17.0-x86_64-linux-gnu) gapic-common (0.21.1) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) @@ -120,9 +121,9 @@ GEM google-analytics-data-v1beta (0.12.0) gapic-common (>= 0.21.1, < 2.a) google-cloud-errors (~> 1.0) - google-apis-analytics_v3 (0.15.0) - google-apis-core (>= 0.14.0, < 2.a) - google-apis-core (0.14.1) + google-apis-analytics_v3 (0.16.0) + google-apis-core (>= 0.15.0, < 2.a) + google-apis-core (0.15.0) addressable (~> 2.5, >= 2.5.1) googleauth (~> 1.9) httpclient (>= 2.8.1, < 3.a) @@ -138,12 +139,12 @@ GEM google-cloud-errors (1.4.0) google-protobuf (3.25.3) google-protobuf (3.25.3-x86_64-linux) - googleapis-common-protos (1.5.0) - google-protobuf (~> 3.18) + googleapis-common-protos (1.6.0) + google-protobuf (>= 3.18, < 5.a) googleapis-common-protos-types (~> 1.7) grpc (~> 1.41) - googleapis-common-protos-types (1.14.0) - google-protobuf (~> 3.18) + googleapis-common-protos-types (1.15.0) + google-protobuf (>= 3.18, < 5.a) googleauth (1.11.0) faraday (>= 1.0, < 3.a) google-cloud-env (~> 2.1) @@ -151,15 +152,15 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.63.0) + grpc (1.64.0) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) - grpc (1.63.0-x86_64-linux) + grpc (1.64.0-x86_64-linux) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) htmlentities (4.3.4) http-accept (1.7.0) - http-cookie (1.0.5) + http-cookie (1.0.6) domain_name (~> 0.5) httpclient (2.8.3) i18n (0.9.5) @@ -182,14 +183,14 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0305) + mime-types-data (3.2024.0604) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) net-http-persistent (2.9.4) - net-imap (0.4.10) + net-imap (0.4.12) date net-protocol net-pop (0.1.2) @@ -199,7 +200,7 @@ GEM net-smtp (0.5.0) net-protocol netrc (0.11.0) - oj (3.16.3) + oj (3.16.4) bigdecimal (>= 3.0) omni_logger (0.1.4) logger @@ -211,7 +212,7 @@ GEM coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.0.5) - rack (3.0.10) + rack (3.1.2) rack-test (2.1.0) rack (>= 1.3) rake (13.2.1) @@ -219,7 +220,7 @@ GEM addressable (>= 2.2) redis (5.2.0) redis-client (>= 0.22.0) - redis-client (0.22.1) + redis-client (0.22.2) connection_pool representable (3.2.0) declarative (< 0.1.0) @@ -233,7 +234,8 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.2.6) + rexml (3.3.0) + strscan rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) @@ -256,6 +258,7 @@ GEM simplecov (~> 0.19) simplecov-html (0.12.3) simplecov_json_formatter (0.1.4) + strscan (3.1.0) sys-proctable (1.3.0) ffi (~> 1.1) systemu (2.6.5) From f6c4ca0e014a1744d5a6460b9bf72784cb8428c8 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 11 Jun 2024 23:23:35 -0700 Subject: [PATCH 3/5] use 127.0.0.1 for better compatibility --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 44c9fda4..e66bb56d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -105,7 +105,7 @@ services: image: ontoportal/mgrep:0.0.2 platform: linux/amd64 healthcheck: - test: ["CMD", "nc", "-z", "-v", "localhost", "55556"] + test: ["CMD", "nc", "-z", "-v", "127.0.0.1", "55556"] start_period: 3s interval: 10s timeout: 5s From 04a90017f9cd819f62e115e55c3d8bd6c8019c90 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 12 Jun 2024 00:13:09 -0700 Subject: [PATCH 4/5] use updated solr schema --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index e66bb56d..50e83dcf 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -93,7 +93,7 @@ services: - 4store solr-ut: - image: ontoportal/solr-ut:0.1.0 + image: ontoportal/solr-ut:0.2.0 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 83ad2b9cdbe8eb8859150ef627dbecbdf95a22b9 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 16 Jul 2024 12:45:02 -0700 Subject: [PATCH 5/5] Gemfile.lock update --- Gemfile.lock | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 80aedbd8..5115c2d3 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -77,8 +77,8 @@ GEM activesupport (3.2.22.5) i18n (~> 0.6, >= 0.6.4) multi_json (~> 1.0) - addressable (2.8.6) - public_suffix (>= 2.0.2, < 6.0) + addressable (2.8.7) + public_suffix (>= 2.0.2, < 7.0) base64 (0.2.0) bcrypt (3.1.20) bigdecimal (3.1.8) @@ -152,11 +152,11 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.64.0) - google-protobuf (~> 3.25) + grpc (1.65.0) + google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.64.0-x86_64-linux) - google-protobuf (~> 3.25) + grpc (1.65.0-x86_64-linux) + google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) htmlentities (4.3.4) http-accept (1.7.0) @@ -167,7 +167,7 @@ GEM concurrent-ruby (~> 1.0) json (2.7.2) json_pure (2.7.2) - jwt (2.8.1) + jwt (2.8.2) base64 launchy (2.5.2) addressable (~> 2.8) @@ -183,14 +183,14 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0604) + mime-types-data (3.2024.0702) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) net-http-persistent (2.9.4) - net-imap (0.4.12) + net-imap (0.4.14) date net-protocol net-pop (0.1.2) @@ -211,8 +211,8 @@ GEM pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) - public_suffix (5.0.5) - rack (3.1.2) + public_suffix (5.1.1) + rack (3.1.7) rack-test (2.1.0) rack (>= 1.3) rake (13.2.1) @@ -234,7 +234,7 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.0) + rexml (3.3.2) strscan rsolr (2.6.0) builder (>= 2.1.2)