From 2f8b1c1cff9a00da06ff68c1449f049e3f59c5ce Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Tue, 19 Mar 2024 11:37:21 -0700 Subject: [PATCH 01/32] Reset branch specifier to develop --- Gemfile | 8 ++++---- Gemfile.lock | 16 ++++++++-------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/Gemfile b/Gemfile index f136281f..8b180c6e 100644 --- a/Gemfile +++ b/Gemfile @@ -24,10 +24,10 @@ 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 4dfe242e..b4cefd61 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 75436fe8e387febc53e34ee31ff0e6dd837a9d3f - branch: master + revision: 87e991b0e720c580a71e2c2c10f9ab44183db322 + 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: fe0783c542479ed0a12da5663ef28e1673e80eba + 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: b6df920d03af15ee35a3a7c31078c6ea263ba41d - branch: master + revision: a466d530877cb48cdfb811d0b61ecaabd2b835eb + 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) From 2af844a10a31ae808e85821bc00e8d30e0504d20 Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 24 Apr 2024 12:39:36 -0700 Subject: [PATCH 02/32] Gemfile.lock update --- Gemfile.lock | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index b4cefd61..38c52dd4 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 87e991b0e720c580a71e2c2c10f9ab44183db322 + revision: c7ee4a6a44cdf69c8186decc5da0c80887af1b11 branch: develop specs: goo (0.0.2) @@ -26,7 +26,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a466d530877cb48cdfb811d0b61ecaabd2b835eb + revision: d885010c4dcb79a71fd161988a8feceb77331b58 branch: develop specs: ontologies_linked_data (0.0.1) @@ -46,7 +46,7 @@ GIT GIT remote: https://github.com/ncbo/sparql-client.git - revision: 55e7dbf858eb571c767bc67868f9af61663859cb + revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc branch: develop specs: sparql-client (1.0.1) @@ -78,7 +78,7 @@ GEM public_suffix (>= 2.0.2, < 6.0) base64 (0.2.0) bcrypt (3.1.20) - bigdecimal (3.1.6) + bigdecimal (3.1.7) builder (3.2.4) coderay (1.1.3) concurrent-ruby (1.2.3) @@ -98,7 +98,7 @@ GEM faraday-net_http (>= 2.0, < 3.1) ruby2_keywords (>= 0.0.4) faraday-net_http (3.0.2) - faraday-retry (2.2.0) + faraday-retry (2.2.1) faraday (~> 2.0) ffi (1.16.3) gapic-common (0.21.1) @@ -137,7 +137,7 @@ GEM google-protobuf (~> 3.18) googleapis-common-protos-types (~> 1.7) grpc (~> 1.41) - googleapis-common-protos-types (1.13.0) + googleapis-common-protos-types (1.14.0) google-protobuf (~> 3.18) googleauth (1.11.0) faraday (>= 1.0, < 3.a) @@ -159,8 +159,8 @@ GEM httpclient (2.8.3) i18n (0.9.5) concurrent-ruby (~> 1.0) - json (2.7.1) - json_pure (2.7.1) + json (2.7.2) + json_pure (2.7.2) jwt (2.8.1) base64 launchy (2.5.2) @@ -174,7 +174,7 @@ GEM net-imap net-pop net-smtp - method_source (1.0.0) + method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) mime-types-data (3.2024.0305) @@ -184,14 +184,14 @@ 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) net-protocol net-protocol (0.2.2) timeout - net-smtp (0.4.0.1) + net-smtp (0.5.0) net-protocol netrc (0.11.0) oj (3.16.3) @@ -205,16 +205,16 @@ GEM pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) - public_suffix (5.0.4) - rack (3.0.9.1) + public_suffix (5.0.5) + rack (3.0.10) rack-test (2.1.0) rack (>= 1.3) - rake (13.1.0) + rake (13.2.1) rdf (1.0.8) addressable (>= 2.2) - redis (5.1.0) - redis-client (>= 0.17.0) - redis-client (0.21.0) + redis (5.2.0) + redis-client (>= 0.22.0) + redis-client (0.22.1) connection_pool representable (3.2.0) declarative (< 0.1.0) @@ -227,7 +227,7 @@ GEM netrc (~> 0.8) retriable (3.1.2) rexml (3.2.6) - rsolr (2.5.0) + rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) ruby-xxHash (0.4.0.2) @@ -294,4 +294,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.4.22 + 2.3.15 From ec8f5367b090e851ff199e869432efd89f3d14bc Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 24 Apr 2024 14:19:04 -0700 Subject: [PATCH 03/32] Gemfile.lock update after merging pull request #150 --- Gemfile.lock | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 38c52dd4..b7cf36af 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: c7ee4a6a44cdf69c8186decc5da0c80887af1b11 + revision: 563a47fa4329ffb8a774731be210f44a054726c0 branch: develop specs: goo (0.0.2) @@ -8,6 +8,7 @@ GIT pry rdf (= 1.0.8) redis + request_store rest-client rsolr sparql-client @@ -15,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: fe0783c542479ed0a12da5663ef28e1673e80eba + revision: a427ff3719f88f887e04ac695a002ef24ce3afb8 branch: develop specs: ncbo_annotator (0.0.1) @@ -26,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: d885010c4dcb79a71fd161988a8feceb77331b58 + revision: ab7b2f0eb6c4256ff1a01ace55b5a966c040e1ca branch: develop specs: ontologies_linked_data (0.0.1) @@ -184,7 +185,7 @@ 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) @@ -220,6 +221,8 @@ GEM declarative (< 0.1.0) trailblazer-option (>= 0.1.1, < 0.2.0) uber (< 0.2.0) + request_store (1.6.0) + rack (>= 1.4) rest-client (2.1.0) http-accept (>= 1.7.0, < 2.0) http-cookie (>= 1.0.2, < 2.0) @@ -294,4 +297,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.3.15 + 2.4.22 From c47a445eba2aef58efe68a36e800f649b8c76cfa Mon Sep 17 00:00:00 2001 From: mdorf Date: Wed, 24 Apr 2024 14:32:04 -0700 Subject: [PATCH 04/32] Gemfile.lock update --- Gemfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index b7cf36af..190f2b40 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 563a47fa4329ffb8a774731be210f44a054726c0 + revision: 5d911f587f22059581ae3e713e5fe9bde9de82e7 branch: develop specs: goo (0.0.2) @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: a427ff3719f88f887e04ac695a002ef24ce3afb8 + revision: 36125bdaafd36f394263b9495af96d21a81b1217 branch: develop specs: ncbo_annotator (0.0.1) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: ab7b2f0eb6c4256ff1a01ace55b5a966c040e1ca + revision: cf8100e47090be1bfb79e7ea642eb6a528013efa branch: develop specs: ontologies_linked_data (0.0.1) From 252edb210cde06bdeed6404eb2d78f3204a1b10d Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Thu, 25 Apr 2024 14:44:54 -0700 Subject: [PATCH 05/32] Gemfile Update --- Gemfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 190f2b40..72b41e55 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 5d911f587f22059581ae3e713e5fe9bde9de82e7 + revision: 33583fd1c1d72b449cd6bb91815e3422b8448983 branch: develop specs: goo (0.0.2) @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 36125bdaafd36f394263b9495af96d21a81b1217 + revision: f9a1be204e81d72f408927b8f60c0be208611929 branch: develop specs: ncbo_annotator (0.0.1) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: cf8100e47090be1bfb79e7ea642eb6a528013efa + revision: da1642ed8f9f04db2e427e35d88f235a55138d03 branch: develop specs: ontologies_linked_data (0.0.1) From 56de5c91e3b8b7c17bafcc2bec7f439fd9629c0e Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 26 Apr 2024 16:07:32 -0700 Subject: [PATCH 06/32] Update .gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index ccf97ea0..0cd105fc 100644 --- a/.gitignore +++ b/.gitignore @@ -6,6 +6,7 @@ config/*.p12 config/*.json data/ projectFilesBackup/ +.bundle .ruby-version repo* *.turtle From afbb335a5fc562d33ce01fdc4f31e0e52294c6c3 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 26 Apr 2024 16:07:56 -0700 Subject: [PATCH 07/32] Add faraday and follow redirects gems --- Gemfile | 2 ++ Gemfile.lock | 4 ++++ 2 files changed, 6 insertions(+) diff --git a/Gemfile b/Gemfile index 8b180c6e..1a60adbd 100644 --- a/Gemfile +++ b/Gemfile @@ -2,6 +2,8 @@ source 'https://rubygems.org' gemspec +gem 'faraday', '~> 2' +gem 'faraday-follow_redirects', '~> 0' gem 'ffi' # This is needed temporarily to pull the Google Universal Analytics (UA) diff --git a/Gemfile.lock b/Gemfile.lock index 72b41e55..2db69597 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -98,6 +98,8 @@ GEM base64 faraday-net_http (>= 2.0, < 3.1) ruby2_keywords (>= 0.0.4) + faraday-follow_redirects (0.3.0) + faraday (>= 1, < 3) faraday-net_http (3.0.2) faraday-retry (2.2.1) faraday (~> 2.0) @@ -273,6 +275,8 @@ PLATFORMS DEPENDENCIES cube-ruby email_spec + faraday (~> 2) + faraday-follow_redirects (~> 0) ffi goo! google-analytics-data From ab20f8a9a1ba11415716ee15f88955eea7ac741b Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 26 Apr 2024 16:11:12 -0700 Subject: [PATCH 08/32] Replace GraphQL queries with HTTP --- lib/ncbo_cron/obofoundry_sync.rb | 71 +++++++++----------------------- 1 file changed, 19 insertions(+), 52 deletions(-) diff --git a/lib/ncbo_cron/obofoundry_sync.rb b/lib/ncbo_cron/obofoundry_sync.rb index 2437a9f3..23dd6e8d 100644 --- a/lib/ncbo_cron/obofoundry_sync.rb +++ b/lib/ncbo_cron/obofoundry_sync.rb @@ -1,7 +1,6 @@ -require 'base64' -require 'json' -require 'net/http' -require 'uri' +require 'faraday' +require 'faraday/follow_redirects' +require 'multi_json' module NcboCron module Models @@ -9,9 +8,6 @@ class OBOFoundrySync def initialize @logger = Logger.new(STDOUT) - @oauth_token = Base64.decode64(NcboCron.settings.git_repo_access_token) - @graphql_uri = URI.parse("https://api.github.com/graphql") - @request_options = { use_ssl: @graphql_uri.scheme == "https" } end def run @@ -19,24 +15,25 @@ def run map = get_ids_to_acronyms_map onts = get_obofoundry_ontologies - @logger.info("Found #{onts.size} OBO Library ontologies") + @logger.info("Found #{onts.size} OBO Foundry ontologies") - # Are any OBO Library ontologies missing from BioPortal? + # Are any OBO Foundry ontologies missing from BioPortal? missing_onts = [] - active_onts = onts.reject { |ont| ont.key?("is_obsolete") } + active_onts = onts.reject { |ont| ont.key?('is_obsolete') } + @logger.info("#{active_onts.size} OBO Foundry ontologies are currently active") active_onts.each do |ont| - if not map.key?(ont["id"]) + if not map.key?(ont['id']) missing_onts << ont - @logger.info("Missing OBO Library ontology: #{ont['title']} (#{ont['id']})") + @logger.info("Missing OBO Foundry ontology: #{ont['title']} (#{ont['id']})") end end - # Have any of the OBO Library ontologies that BioPortal hosts become obsolete? + # Have any of the OBO Foundry ontologies that BioPortal hosts become obsolete? obsolete_onts = [] - ids = active_onts.map{ |ont| ont["id"] } + ids = active_onts.map{ |ont| ont['id'] } obsolete_ids = map.keys - ids obsolete_ids.each do |id| - ont = onts.find{ |ont| ont["id"] == id } + ont = onts.find{ |ont| ont['id'] == id } @logger.info("Deprecated OBO Library ontology: #{ont['title']} (#{ont['id']})") obsolete_onts << ont end @@ -45,49 +42,19 @@ def run end def get_ids_to_acronyms_map - query = "query { - repository(name: \"ncbo.github.io\", owner: \"ncbo\") { - object(expression: \"master:oboids_to_bpacronyms.json\") { - ... on Blob { - text - } - } - } - }" - - response = issue_request(query) - JSON.parse(response) + response = Faraday.get('https://ncbo.github.io/oboids_to_bpacronyms.json') + MultiJson.load(response.body) end def get_obofoundry_ontologies - query = "query { - repository(name: \"OBOFoundry.github.io\", owner: \"OBOFoundry\") { - object(expression: \"master:registry/ontologies.jsonld\") { - ... on Blob { - text - } - } - } - }" - - response = issue_request(query) - ont_registry = JSON.parse(response) - ont_registry["ontologies"].to_a - end - - def issue_request(query) - request = Net::HTTP::Post.new(@graphql_uri) - request["Authorization"] = "bearer #{@oauth_token}" - request.body = JSON.dump({"query" => query}) - - response = Net::HTTP.start(@graphql_uri.hostname, @graphql_uri.port, @request_options) do |http| - http.request(request) + conn = Faraday.new do |faraday| + faraday.response :follow_redirects + faraday.adapter Faraday.default_adapter end + response = conn.get('http://purl.obolibrary.org/meta/ontologies.jsonld') - parsed = JSON.parse(response.body) - parsed.dig("data", "repository", "object", "text") + MultiJson.load(response.body)['ontologies'] end - end end end From fcd37b869308bebf4535d4eedf2d194c841fd313 Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 26 Apr 2024 16:15:33 -0700 Subject: [PATCH 09/32] Update Gemfile.lock --- Gemfile.lock | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 2db69597..fa2be763 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -94,13 +94,12 @@ GEM htmlentities (~> 4.3.3) launchy (~> 2.1) mail (~> 2.7) - faraday (2.8.1) - base64 - faraday-net_http (>= 2.0, < 3.1) - ruby2_keywords (>= 0.0.4) + faraday (2.9.0) + faraday-net_http (>= 2.0, < 3.2) faraday-follow_redirects (0.3.0) faraday (>= 1, < 3) - faraday-net_http (3.0.2) + faraday-net_http (3.1.0) + net-http faraday-retry (2.2.1) faraday (~> 2.0) ffi (1.16.3) @@ -186,6 +185,8 @@ GEM mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) + net-http (0.4.1) + uri net-http-persistent (2.9.4) net-imap (0.4.10) date @@ -236,7 +237,6 @@ GEM builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) ruby-xxHash (0.4.0.2) - ruby2_keywords (0.0.5) rubyzip (2.3.2) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) @@ -264,6 +264,7 @@ GEM tzinfo (2.0.6) concurrent-ruby (~> 1.0) uber (0.1.0) + uri (0.13.0) uuid (2.3.9) macaddr (~> 1.0) webrick (1.8.1) From 290c86de0ec957d73a2187b012a1fdf7ac5afabf Mon Sep 17 00:00:00 2001 From: Jennifer Vendetti Date: Fri, 26 Apr 2024 17:14:07 -0700 Subject: [PATCH 10/32] Move faraday gems to the gemspec --- Gemfile | 2 -- Gemfile.lock | 17 ++++++++--------- ncbo_cron.gemspec | 2 ++ 3 files changed, 10 insertions(+), 11 deletions(-) diff --git a/Gemfile b/Gemfile index 1a60adbd..8b180c6e 100644 --- a/Gemfile +++ b/Gemfile @@ -2,8 +2,6 @@ source 'https://rubygems.org' gemspec -gem 'faraday', '~> 2' -gem 'faraday-follow_redirects', '~> 0' gem 'ffi' # This is needed temporarily to pull the Google Universal Analytics (UA) diff --git a/Gemfile.lock b/Gemfile.lock index fa2be763..c4298f48 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -60,6 +60,8 @@ PATH specs: ncbo_cron (0.0.1) dante + faraday (~> 2) + faraday-follow_redirects (~> 0) goo google-analytics-data mlanett-redis-lock @@ -94,12 +96,13 @@ GEM htmlentities (~> 4.3.3) launchy (~> 2.1) mail (~> 2.7) - faraday (2.9.0) - faraday-net_http (>= 2.0, < 3.2) + faraday (2.8.1) + base64 + faraday-net_http (>= 2.0, < 3.1) + ruby2_keywords (>= 0.0.4) faraday-follow_redirects (0.3.0) faraday (>= 1, < 3) - faraday-net_http (3.1.0) - net-http + faraday-net_http (3.0.2) faraday-retry (2.2.1) faraday (~> 2.0) ffi (1.16.3) @@ -185,8 +188,6 @@ GEM mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) - net-http (0.4.1) - uri net-http-persistent (2.9.4) net-imap (0.4.10) date @@ -237,6 +238,7 @@ GEM builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) ruby-xxHash (0.4.0.2) + ruby2_keywords (0.0.5) rubyzip (2.3.2) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) @@ -264,7 +266,6 @@ GEM tzinfo (2.0.6) concurrent-ruby (~> 1.0) uber (0.1.0) - uri (0.13.0) uuid (2.3.9) macaddr (~> 1.0) webrick (1.8.1) @@ -276,8 +277,6 @@ PLATFORMS DEPENDENCIES cube-ruby email_spec - faraday (~> 2) - faraday-follow_redirects (~> 0) ffi goo! google-analytics-data diff --git a/ncbo_cron.gemspec b/ncbo_cron.gemspec index c8faa03d..e48d7e7f 100644 --- a/ncbo_cron.gemspec +++ b/ncbo_cron.gemspec @@ -15,6 +15,8 @@ Gem::Specification.new do |gem| gem.require_paths = ["lib"] gem.add_dependency("dante") + gem.add_dependency('faraday', '~> 2') + gem.add_dependency('faraday-follow_redirects', '~> 0') gem.add_dependency("goo") gem.add_dependency("google-analytics-data") gem.add_dependency("mlanett-redis-lock") From da577f143e5ace303116a682f31c775514be4aaf Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 6 May 2024 11:35:22 -0700 Subject: [PATCH 11/32] Gemfile update --- Gemfile.lock | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index c4298f48..4e13127e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: f9a1be204e81d72f408927b8f60c0be208611929 + revision: 7531e10ad55ac66e925c099d7fc05a5a3ceae67e branch: develop specs: ncbo_annotator (0.0.1) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: da1642ed8f9f04db2e427e35d88f235a55138d03 + revision: a3f6cf0493bb595011f98acf95efda33111c537b branch: develop specs: ontologies_linked_data (0.0.1) @@ -151,10 +151,10 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.62.0) + grpc (1.63.0) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) - grpc (1.62.0-x86_64-linux) + grpc (1.63.0-x86_64-linux) google-protobuf (~> 3.25) googleapis-common-protos-types (~> 1.0) htmlentities (4.3.4) @@ -225,7 +225,7 @@ GEM declarative (< 0.1.0) trailblazer-option (>= 0.1.1, < 0.2.0) uber (< 0.2.0) - request_store (1.6.0) + request_store (1.7.0) rack (>= 1.4) rest-client (2.1.0) http-accept (>= 1.7.0, < 2.0) From 67810ddd2e14876d789c63c427b08af6919f661e Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 6 May 2024 12:11:28 -0700 Subject: [PATCH 12/32] 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 89b68775fca3ab7d6451171bc3fee7679a82a1d5 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 21 May 2024 18:01:40 -0700 Subject: [PATCH 13/32] Gemfile update --- Gemfile.lock | 22 ++++++++++++---------- docker-compose.yml | 4 ++-- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 4e13127e..ec317ca3 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 33583fd1c1d72b449cd6bb91815e3422b8448983 + revision: 70007faf43d0d96292809f89f15a27a757ccaa25 branch: develop specs: goo (0.0.2) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a3f6cf0493bb595011f98acf95efda33111c537b + revision: 048087406b7e7ea6530ed3e02254544f3ca74c0f branch: develop specs: ontologies_linked_data (0.0.1) @@ -81,7 +81,7 @@ GEM public_suffix (>= 2.0.2, < 6.0) base64 (0.2.0) bcrypt (3.1.20) - bigdecimal (3.1.7) + bigdecimal (3.1.8) builder (3.2.4) coderay (1.1.3) concurrent-ruby (1.2.3) @@ -120,9 +120,9 @@ 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) @@ -182,14 +182,14 @@ 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 (3.2024.0507) 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 (0.4.11) date net-protocol net-pop (0.1.2) @@ -211,7 +211,7 @@ GEM coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.0.5) - rack (3.0.10) + rack (3.0.11) rack-test (2.1.0) rack (>= 1.3) rake (13.2.1) @@ -233,7 +233,8 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.2.6) + rexml (3.2.8) + strscan (>= 3.0.9) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) @@ -256,6 +257,7 @@ 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) diff --git a/docker-compose.yml b/docker-compose.yml index 44c9fda4..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 @@ -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 1ee0c07e0c286fe11d9c45e6de773138a49d6ced Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 11 Jun 2024 23:22:02 -0700 Subject: [PATCH 14/32] 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 15/32] 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 16/32] 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 8333a71b0291c719680bdae2a40cb1b1f831c596 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 1 Jul 2024 11:53:26 -0700 Subject: [PATCH 17/32] fixed #81 - ncbo_ontology_pull script throws undefined method error --- Gemfile.lock | 36 ++++++++++++++++++------------------ bin/ncbo_ontology_pull | 3 +-- 2 files changed, 19 insertions(+), 20 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index ec317ca3..17b34f38 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 048087406b7e7ea6530ed3e02254544f3ca74c0f + revision: 013a322440b4cfd899908d15ff605799acf8e6ef branch: develop specs: ontologies_linked_data (0.0.1) @@ -82,9 +82,9 @@ GEM base64 (0.2.0) bcrypt (3.1.20) bigdecimal (3.1.8) - builder (3.2.4) + 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 +105,7 @@ GEM faraday-net_http (3.0.2) faraday-retry (2.2.1) faraday (~> 2.0) - ffi (1.16.3) + ffi (1.17.0) gapic-common (0.21.1) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) @@ -138,12 +138,12 @@ 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 +151,15 @@ 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 +182,14 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0507) + 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 (0.4.11) + net-imap (0.4.12) date net-protocol net-pop (0.1.2) @@ -199,7 +199,7 @@ 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 +211,7 @@ GEM coderay (~> 1.1) method_source (~> 1.0) public_suffix (5.0.5) - rack (3.0.11) + rack (3.1.3) rack-test (2.1.0) rack (>= 1.3) rake (13.2.1) @@ -219,7 +219,7 @@ 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) @@ -233,8 +233,8 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.2.8) - strscan (>= 3.0.9) + rexml (3.3.0) + strscan rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) diff --git a/bin/ncbo_ontology_pull b/bin/ncbo_ontology_pull index be3e08de..5cbe4359 100755 --- a/bin/ncbo_ontology_pull +++ b/bin/ncbo_ontology_pull @@ -30,9 +30,8 @@ opt_parser.parse! logger = Logger.new($stdout) logger.info "Starting ncbo pull"; logger.flush -puller = NcboCron::Models::OntologyPull.new begin - puller.do_ontology_pull(ontology_acronym, logger: logger, enable_pull_umls: true) + NcboCron::Helpers::OntologyHelper.do_ontology_pull(ontology_acronym, logger: logger, enable_pull_umls: true) rescue StandardError => e logger.error e.message logger.flush From 1fbfc8f7f3ca62de35912ec09f23cac72fea1550 Mon Sep 17 00:00:00 2001 From: mdorf Date: Mon, 1 Jul 2024 11:54:06 -0700 Subject: [PATCH 18/32] Gemfile.lock update --- Gemfile.lock | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 17b34f38..8749905e 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) @@ -166,7 +166,7 @@ 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) @@ -189,7 +189,7 @@ GEM 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) @@ -210,8 +210,8 @@ GEM pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) - public_suffix (5.0.5) - rack (3.1.3) + public_suffix (5.1.1) + rack (3.1.4) rack-test (2.1.0) rack (>= 1.3) rake (13.2.1) @@ -233,7 +233,7 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.0) + rexml (3.3.1) strscan rsolr (2.6.0) builder (>= 2.1.2) From 83ad2b9cdbe8eb8859150ef627dbecbdf95a22b9 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 16 Jul 2024 12:45:02 -0700 Subject: [PATCH 19/32] 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) From e03c48179968b20a54693f876433514b8a60ff6f Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 16 Jul 2024 17:54:18 -0700 Subject: [PATCH 20/32] do not send notifications to ontology owners when running admin scripts fix https://github.com/ncbo/ncbo_cron/issues/77 --- bin/ncbo_ontology_delete | 3 +++ bin/ncbo_ontology_index | 3 +++ bin/ncbo_ontology_metrics | 4 ++++ bin/ncbo_ontology_process | 3 +++ bin/ncbo_ontology_property_index | 3 +++ bin/ncbo_ontology_pull | 3 +++ 6 files changed, 19 insertions(+) diff --git a/bin/ncbo_ontology_delete b/bin/ncbo_ontology_delete index ff36e6d6..f3bdbc16 100755 --- a/bin/ncbo_ontology_delete +++ b/bin/ncbo_ontology_delete @@ -12,6 +12,9 @@ config_exists = File.exist?(File.expand_path('../../config/config.rb', __FILE__) abort("Please create a config/config.rb file using the config/config.rb.sample as a template") unless config_exists require_relative '../config/config' +# do not send notifications to ontology owners when running this script +LinkedData.settings.enable_notifications = false + require 'optparse' options = {} opt_parser = OptionParser.new do |opts| diff --git a/bin/ncbo_ontology_index b/bin/ncbo_ontology_index index 746d8d95..706b0741 100755 --- a/bin/ncbo_ontology_index +++ b/bin/ncbo_ontology_index @@ -12,6 +12,9 @@ config_exists = File.exist?(File.expand_path('../../config/config.rb', __FILE__) abort("Please create a config/config.rb file using the config/config.rb.sample as a template") unless config_exists require_relative '../config/config' +# do not send notifications to ontology owners when running this script +LinkedData.settings.enable_notifications = false + platform = "local" if LinkedData.settings.goo_host.include? "stage" platform = "stage" diff --git a/bin/ncbo_ontology_metrics b/bin/ncbo_ontology_metrics index 6497314b..ca714ba5 100755 --- a/bin/ncbo_ontology_metrics +++ b/bin/ncbo_ontology_metrics @@ -12,6 +12,10 @@ config_exists = File.exist?(File.expand_path('../../config/config.rb', __FILE__) abort("Please create a config/config.rb file using the config/config.rb.sample as a template") unless config_exists require_relative '../config/config' +# do not send notifications to ontology owners when running this script +LinkedData.settings.enable_notifications = false + + platform = "local" if LinkedData.settings.goo_host.include? "stage" platform = "stage" diff --git a/bin/ncbo_ontology_process b/bin/ncbo_ontology_process index 879e749d..4c0a8957 100755 --- a/bin/ncbo_ontology_process +++ b/bin/ncbo_ontology_process @@ -13,6 +13,9 @@ abort("Please create a config/config.rb file using the config/config.rb.sample a require_relative '../config/config' require 'optparse' +# do not send notifications to ontology owners when running this script +LinkedData.settings.enable_notifications = false + options = {all: false} opt_parser = OptionParser.new do |opts| # Set a banner, displayed at the top of the help screen. diff --git a/bin/ncbo_ontology_property_index b/bin/ncbo_ontology_property_index index 0d908777..12eb05e1 100755 --- a/bin/ncbo_ontology_property_index +++ b/bin/ncbo_ontology_property_index @@ -12,6 +12,9 @@ config_exists = File.exist?(File.expand_path('../../config/config.rb', __FILE__) abort("Please create a config/config.rb file using the config/config.rb.sample as a template") unless config_exists require_relative '../config/config' +# do not send notifications to ontology owners when running this script +LinkedData.settings.enable_notifications = false + platform = "local" if LinkedData.settings.goo_host.include? "stage" platform = "stage" diff --git a/bin/ncbo_ontology_pull b/bin/ncbo_ontology_pull index 5cbe4359..45720492 100755 --- a/bin/ncbo_ontology_pull +++ b/bin/ncbo_ontology_pull @@ -14,6 +14,9 @@ require_relative '../lib/ncbo_cron' require_relative '../config/config' require 'optparse' +# do not send notifications to ontology owners when running this script +LinkedData.settings.enable_notifications = false + ontology_acronym = '' opt_parser = OptionParser.new do |opts| opts.on('-o', '--ontology ACRONYM', 'Ontology acronym to pull if new version exist') do |acronym| From f403169603ada9e22cbdd5d5086c3e003564d95d Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 26 Aug 2024 16:46:20 -0700 Subject: [PATCH 21/32] use docker compose instead of docker-compose --- .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 df4372fa..8b75e9ce 100644 --- a/.github/workflows/ruby-unit-tests.yml +++ b/.github/workflows/ruby-unit-tests.yml @@ -20,7 +20,7 @@ jobs: - name: Run unit tests run: | 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' + 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@v4 with: From 3bb491139267efc37d3b752888824ca3dd976e85 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 26 Aug 2024 16:48:47 -0700 Subject: [PATCH 22/32] use docker compose instead of docker-compose --- .github/workflows/ruby-unit-tests.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ruby-unit-tests.yml b/.github/workflows/ruby-unit-tests.yml index 8b75e9ce..ba9979f8 100644 --- a/.github/workflows/ruby-unit-tests.yml +++ b/.github/workflows/ruby-unit-tests.yml @@ -15,8 +15,8 @@ jobs: - uses: actions/checkout@v4 - name: copy config.rb file from template run: cp config/config.test.rb config/config.rb - - name: Build docker-compose - run: docker-compose build + - name: Build docker compose + run: docker compose build - name: Run unit tests run: | ci_env=`bash <(curl -s https://codecov.io/env)` From 058fff47f0be38dde31f639c98d2b793e352693f Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 26 Aug 2024 17:07:29 -0700 Subject: [PATCH 23/32] bundle update --- 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 ec8cbc58..5d6366e2 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 70007faf43d0d96292809f89f15a27a757ccaa25 - branch: develop + revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2 + 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: 2fb892f92f66b876b9793944124f72821f3b3eb8 - 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: 30a367b22becf1bb8300666b16ad08ff016d10c9 - branch: develop + revision: 70fc2c8b377b9deabc838ecd56d3bc75ec764cc2 + 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 15ccdaa2835be9f35f9c3afdcc4ed5bf5d130999 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 11:44:35 -0700 Subject: [PATCH 24/32] Gemfile.lock update --- Gemfile.lock | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 5d6366e2..816109f8 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 70fc2c8b377b9deabc838ecd56d3bc75ec764cc2 + revision: f32bc171e487b7c87fee28b80d9a411a7d45aa79 branch: master specs: ontologies_linked_data (0.0.1) @@ -120,7 +120,7 @@ GEM google-analytics-data (0.6.1) google-analytics-data-v1beta (>= 0.11, < 2.a) google-cloud-core (~> 1.6) - google-analytics-data-v1beta (0.13.0) + google-analytics-data-v1beta (0.13.1) gapic-common (>= 0.21.1, < 2.a) google-cloud-errors (~> 1.0) google-apis-analytics_v3 (0.16.0) @@ -139,12 +139,13 @@ GEM google-cloud-env (2.1.1) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) - google-protobuf (3.25.4) + google-protobuf (3.25.5) + 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) grpc (~> 1.41) - googleapis-common-protos-types (1.15.0) + googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) googleauth (1.11.0) faraday (>= 1.0, < 3.a) @@ -168,13 +169,13 @@ GEM concurrent-ruby (~> 1.0) json (2.7.2) json_pure (2.7.2) - jwt (2.8.2) + jwt (2.9.1) base64 launchy (3.0.1) addressable (~> 2.8) childprocess (~> 5.0) libxml-ruby (5.0.3) - logger (1.6.0) + logger (1.6.1) macaddr (1.7.2) systemu (~> 2.6.5) mail (2.8.1) @@ -185,7 +186,7 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0820) + mime-types-data (3.2024.0903) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) @@ -193,7 +194,7 @@ GEM multi_json (1.15.0) mutex_m (0.2.0) net-http-persistent (2.9.4) - net-imap (0.4.14) + net-imap (0.4.16) date net-protocol net-pop (0.1.2) @@ -203,7 +204,7 @@ GEM net-smtp (0.5.0) net-protocol netrc (0.11.0) - oj (3.16.5) + oj (3.16.6) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) @@ -239,8 +240,7 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.6) - strscan + rexml (3.3.7) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) @@ -261,9 +261,8 @@ GEM simplecov-cobertura (2.1.0) rexml simplecov (~> 0.19) - simplecov-html (0.12.3) + simplecov-html (0.13.1) simplecov_json_formatter (0.1.4) - strscan (3.1.0) sys-proctable (1.3.0) ffi (~> 1.1) systemu (2.6.5) @@ -276,7 +275,7 @@ GEM uber (0.1.0) uuid (2.3.9) macaddr (~> 1.0) - webrick (1.8.1) + webrick (1.8.2) PLATFORMS ruby From 3c1c4287469049802f611226ea0fa786693825aa Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 17:04:59 -0700 Subject: [PATCH 25/32] comply with Minitest Style Guide --- test/test_scheduler.rb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/test_scheduler.rb b/test/test_scheduler.rb index 58808ea5..d3d0ac04 100644 --- a/test/test_scheduler.rb +++ b/test/test_scheduler.rb @@ -104,8 +104,8 @@ def test_scheduler_locking assert job1_thread.alive? assert job2_thread.alive? - assert listen_string.include?("JOB1") - refute listen_string.include?("JOB2") + assert_includes listen_string, "JOB1" + refute_includes listen_string, "JOB2" job1_thread.kill job1_thread.join refute job1_thread.alive? From 8701996034a3134ba8a81e07e0be8896adfd1ef2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 17:05:25 -0700 Subject: [PATCH 26/32] ruby v3.0 upgrade --- Dockerfile | 5 ---- Gemfile.lock | 72 +++++++++++++++++++++++++--------------------- docker-compose.yml | 4 +-- 3 files changed, 41 insertions(+), 40 deletions(-) diff --git a/Dockerfile b/Dockerfile index 73e1379c..34a38160 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,11 +14,6 @@ COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_cron/ WORKDIR /srv/ontoportal/ncbo_cron -# set rubygem and bundler to the last version supported by ruby 2.7 -# remove version after ruby v3 upgrade -RUN gem update --system '3.4.22' -RUN gem install bundler -v '2.4.22' -RUN gem update --system RUN gem install bundler ENV BUNDLE_PATH=/srv/ontoportal/bundle RUN bundle install diff --git a/Gemfile.lock b/Gemfile.lock index ec8cbc58..eb43927b 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 70007faf43d0d96292809f89f15a27a757ccaa25 + revision: aaa3941b48edbc317ec42ba4ecb44c0defeccef6 branch: develop specs: goo (0.0.2) @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 2fb892f92f66b876b9793944124f72821f3b3eb8 + revision: b2731c98bfef0958fecb440c8648b7755a670895 branch: develop specs: ncbo_annotator (0.0.1) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 30a367b22becf1bb8300666b16ad08ff016d10c9 + revision: a22fae3150d8e84e3b6fd19223a5ce2111e8ce94 branch: develop specs: ontologies_linked_data (0.0.1) @@ -98,29 +98,30 @@ GEM htmlentities (~> 4.3.3) launchy (>= 2.1, < 4.0) mail (~> 2.7) - faraday (2.8.1) - base64 - faraday-net_http (>= 2.0, < 3.1) - ruby2_keywords (>= 0.0.4) + faraday (2.12.0) + faraday-net_http (>= 2.0, < 3.4) + json + logger faraday-follow_redirects (0.3.0) faraday (>= 1, < 3) - faraday-net_http (3.0.2) + faraday-net_http (3.3.0) + net-http faraday-retry (2.2.1) faraday (~> 2.0) ffi (1.17.0) ffi (1.17.0-x86_64-linux-gnu) - gapic-common (0.21.1) + gapic-common (0.22.0) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) - google-protobuf (~> 3.18) - googleapis-common-protos (>= 1.4.0, < 2.a) - googleapis-common-protos-types (>= 1.11.0, < 2.a) - googleauth (~> 1.9) - grpc (~> 1.59) + google-protobuf (>= 3.25, < 5.a) + googleapis-common-protos (~> 1.6) + googleapis-common-protos-types (~> 1.15) + googleauth (~> 1.11) + grpc (~> 1.65) google-analytics-data (0.6.1) google-analytics-data-v1beta (>= 0.11, < 2.a) google-cloud-core (~> 1.6) - google-analytics-data-v1beta (0.13.0) + google-analytics-data-v1beta (0.13.1) gapic-common (>= 0.21.1, < 2.a) google-cloud-errors (~> 1.0) google-apis-analytics_v3 (0.16.0) @@ -136,15 +137,20 @@ GEM google-cloud-core (1.7.1) google-cloud-env (>= 1.0, < 3.a) google-cloud-errors (~> 1.0) - google-cloud-env (2.1.1) + google-cloud-env (2.2.0) faraday (>= 1.0, < 3.a) google-cloud-errors (1.4.0) - google-protobuf (3.25.4) + google-protobuf (4.28.2) + bigdecimal + rake (>= 13) + google-protobuf (4.28.2-x86_64-linux) + bigdecimal + rake (>= 13) 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 (1.15.0) + googleapis-common-protos-types (1.16.0) google-protobuf (>= 3.18, < 5.a) googleauth (1.11.0) faraday (>= 1.0, < 3.a) @@ -153,10 +159,10 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (>= 0.16, < 2.a) - grpc (1.65.2) + grpc (1.66.0) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) - grpc (1.65.2-x86_64-linux) + grpc (1.66.0-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) htmlentities (4.3.4) @@ -168,13 +174,13 @@ GEM concurrent-ruby (~> 1.0) json (2.7.2) json_pure (2.7.2) - jwt (2.8.2) + jwt (2.9.1) base64 launchy (3.0.1) addressable (~> 2.8) childprocess (~> 5.0) libxml-ruby (5.0.3) - logger (1.6.0) + logger (1.6.1) macaddr (1.7.2) systemu (~> 2.6.5) mail (2.8.1) @@ -185,15 +191,17 @@ GEM method_source (1.1.0) mime-types (3.5.2) mime-types-data (~> 3.2015) - mime-types-data (3.2024.0820) + mime-types-data (3.2024.0903) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) redis multi_json (1.15.0) mutex_m (0.2.0) + net-http (0.4.1) + uri net-http-persistent (2.9.4) - net-imap (0.4.14) + net-imap (0.4.16) date net-protocol net-pop (0.1.2) @@ -203,7 +211,7 @@ GEM net-smtp (0.5.0) net-protocol netrc (0.11.0) - oj (3.16.5) + oj (3.16.6) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) @@ -216,7 +224,7 @@ GEM pry (0.14.2) coderay (~> 1.1) method_source (~> 1.0) - public_suffix (5.1.1) + public_suffix (6.0.1) rack (3.1.7) rack-test (2.1.0) rack (>= 1.3) @@ -239,13 +247,11 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.6) - strscan + rexml (3.3.7) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) ruby-xxHash (0.4.0.2) - ruby2_keywords (0.0.5) rubyzip (2.3.2) rufus-scheduler (2.0.24) tzinfo (>= 0.3.22) @@ -261,9 +267,8 @@ GEM simplecov-cobertura (2.1.0) rexml simplecov (~> 0.19) - simplecov-html (0.12.3) + simplecov-html (0.13.1) simplecov_json_formatter (0.1.4) - strscan (3.1.0) sys-proctable (1.3.0) ffi (~> 1.1) systemu (2.6.5) @@ -274,9 +279,10 @@ GEM tzinfo (2.0.6) concurrent-ruby (~> 1.0) uber (0.1.0) + uri (0.13.1) uuid (2.3.9) macaddr (~> 1.0) - webrick (1.8.1) + webrick (1.8.2) PLATFORMS ruby @@ -309,4 +315,4 @@ DEPENDENCIES webrick BUNDLED WITH - 2.4.22 + 2.5.7 diff --git a/docker-compose.yml b/docker-compose.yml index 50e83dcf..066debce 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -2,9 +2,9 @@ x-app: &app build: context: . args: - RUBY_VERSION: '2.7' + RUBY_VERSION: '3.0' # Increase the version number in the image tag every time Dockerfile or its arguments is changed - image: ncbo_cron:0.0.2 + image: ncbo_cron:0.0.3 environment: &env BUNDLE_PATH: /srv/ontoportal/bundle # default bundle config resolves to /usr/local/bundle/config inside of the container From b457f327ef315f6b7bff4f7b7c97e0f75ab53241 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 25 Sep 2024 20:01:21 -0700 Subject: [PATCH 27/32] add rugygem update --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 34a38160..dfc03492 100644 --- a/Dockerfile +++ b/Dockerfile @@ -14,6 +14,7 @@ COPY Gemfile* *.gemspec /srv/ontoportal/ncbo_cron/ WORKDIR /srv/ontoportal/ncbo_cron +RUN gem update --system RUN gem install bundler ENV BUNDLE_PATH=/srv/ontoportal/bundle RUN bundle install From 64621dd37d2598dc6ca1bc665c0d9cb2c55a35f2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 1 Oct 2024 11:20:58 -0700 Subject: [PATCH 28/32] Gemfile.lock update --- Gemfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 496c2aa9..b5b9590e 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: aaa3941b48edbc317ec42ba4ecb44c0defeccef6 + revision: 74a012eebb9433d031eb00df5abbe488cb8b4512 branch: develop specs: goo (0.0.2) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a22fae3150d8e84e3b6fd19223a5ce2111e8ce94 + revision: 8572cd25722cab2fbb73813d0fe011b5647d5067 branch: develop specs: ontologies_linked_data (0.0.1) @@ -246,7 +246,7 @@ GEM mime-types (>= 1.16, < 4.0) netrc (~> 0.8) retriable (3.1.2) - rexml (3.3.7) + rexml (3.3.8) rsolr (2.6.0) builder (>= 2.1.2) faraday (>= 0.9, < 3, != 2.0.0) From 9d1b6ba54019cac2eeeb5c173e452b4eebbeaa3a Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 1 Oct 2024 13:56:53 -0700 Subject: [PATCH 29/32] set default ruby version for image builds in Dockerfile follow up to PR #84 --- .github/workflows/docker-image.yml | 4 ++-- Dockerfile | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/docker-image.yml b/.github/workflows/docker-image.yml index 824a2753..70e9cfe2 100644 --- a/.github/workflows/docker-image.yml +++ b/.github/workflows/docker-image.yml @@ -35,8 +35,8 @@ jobs: with: context: . platforms: linux/amd64,linux/arm64 - build-args: | - RUBY_VERSION=2.7 + # build-args: | + # RUBY_VERSION=2.7 push: true tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} diff --git a/Dockerfile b/Dockerfile index dfc03492..6ac0eecf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -ARG RUBY_VERSION +ARG RUBY_VERSION=3.0 ARG DISTRO_NAME=bullseye FROM ruby:$RUBY_VERSION-$DISTRO_NAME From 5322a2310326c171f9e096b65b31cecae17bc818 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Tue, 1 Oct 2024 14:43:34 -0700 Subject: [PATCH 30/32] 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 b5b9590e..464a20b0 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,7 +1,7 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 74a012eebb9433d031eb00df5abbe488cb8b4512 - branch: develop + revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2 + 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: 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: 8572cd25722cab2fbb73813d0fe011b5647d5067 - branch: develop + revision: a9da0982eef16ea8272002d14d6b8851dc07fb0a + 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 b279f9caa9a6a169bad7350890d7015d56e9e9b2 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Wed, 2 Oct 2024 21:12:26 -0700 Subject: [PATCH 31/32] add new method of determining free port fixes intermittent unit test failures due to port being in use --- test/test_case.rb | 7 +++++++ test/test_ontology_pull.rb | 4 ++-- test/test_scheduler.rb | 13 ++++++------- 3 files changed, 15 insertions(+), 9 deletions(-) diff --git a/test/test_case.rb b/test/test_case.rb index 75bb0454..cae57cda 100644 --- a/test/test_case.rb +++ b/test/test_case.rb @@ -107,4 +107,11 @@ def _run_suite(suite, type) ## # Base test class. Put shared test methods or setup here. class TestCase < MiniTest::Unit::TestCase + # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports + def self.unused_port + server = TCPServer.new('127.0.0.1', 0) + port = server.addr[1] + server.close + port + end end diff --git a/test/test_ontology_pull.rb b/test/test_ontology_pull.rb index 8ac6dce6..112fd11b 100644 --- a/test/test_ontology_pull.rb +++ b/test/test_ontology_pull.rb @@ -9,7 +9,7 @@ class TestOntologyPull < TestCase def self.before_suite ont_path = File.expand_path("../data/ontology_files/BRO_v3.2.owl", __FILE__) file = File.new(ont_path) - @@port = Random.rand(55000..65535) # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports + @@port = TestCase.unused_port @@url = "http://localhost:#{@@port}/" @@thread = Thread.new do server = WEBrick::HTTPServer.new(Port: @@port) @@ -103,7 +103,7 @@ def test_remote_pull_parsing_action end def test_pull_error_notification - server_port = Random.rand(55000..65535) + server_port = TestCase.unused_port begin thread = Thread.new do diff --git a/test/test_scheduler.rb b/test/test_scheduler.rb index d3d0ac04..db28f26e 100644 --- a/test/test_scheduler.rb +++ b/test/test_scheduler.rb @@ -1,9 +1,7 @@ -require 'minitest/unit' -MiniTest::Unit.autorun +require_relative 'test_case' +# require_relative '../lib/ncbo_cron' -require_relative '../lib/ncbo_cron' - -class TestScheduler < MiniTest::Unit::TestCase +class TestScheduler < TestCase def test_scheduler begin logger = Logger.new($stdout) @@ -19,7 +17,8 @@ def test_scheduler # Create a simple TCPServer to listen from the fork require 'socket' listen_string = "" - port = Random.rand(55000..65535) # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports + port = TestCase.unused_port + socket_server = Thread.new do server = TCPServer.new(port) loop { @@ -69,7 +68,7 @@ def test_scheduler_locking # Create a simple TCPServer to listen from the fork require 'socket' listen_string = "" - port = Random.rand(55000..65535) # http://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers#Dynamic.2C_private_or_ephemeral_ports + port = TestCase.unused_port socket_server = Thread.new do server = TCPServer.new(port) loop { From 25d54ae938e63e9d1a6f4b8eb697e0ec2ff1ef87 Mon Sep 17 00:00:00 2001 From: Alex Skrenchuk Date: Mon, 7 Oct 2024 20:51:05 -0700 Subject: [PATCH 32/32] Gemfile.lock update --- Gemfile.lock | 34 ++++++++++++++++++++++++++-------- 1 file changed, 26 insertions(+), 8 deletions(-) diff --git a/Gemfile.lock b/Gemfile.lock index 464a20b0..6462aa9f 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -1,6 +1,6 @@ GIT remote: https://github.com/ncbo/goo.git - revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2 + revision: f943ac33e87c55c88131c32d826ed5d39c89302c branch: master specs: goo (0.0.2) @@ -16,7 +16,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 63c986880aa88c9384043e6611a682434a14aba7 + revision: d46d667ec1b2343fbcdab587f1a70e763b894133 branch: master specs: ncbo_annotator (0.0.1) @@ -27,7 +27,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: a9da0982eef16ea8272002d14d6b8851dc07fb0a + revision: 9ab4be437ed84f5a480e7f0d8799824fcea310ae branch: master specs: ontologies_linked_data (0.0.1) @@ -109,6 +109,9 @@ GEM 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 (0.22.0) faraday (>= 1.9, < 3.a) faraday-retry (>= 1.0, < 3.a) @@ -136,12 +139,18 @@ 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 (4.28.2) bigdecimal rake (>= 13) + google-protobuf (4.28.2-aarch64-linux) + bigdecimal + rake (>= 13) + google-protobuf (4.28.2-arm64-darwin) + bigdecimal + rake (>= 13) google-protobuf (4.28.2-x86_64-linux) bigdecimal rake (>= 13) @@ -151,7 +160,7 @@ 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) @@ -161,6 +170,12 @@ GEM grpc (1.66.0) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) + grpc (1.66.0-aarch64-linux) + google-protobuf (>= 3.25, < 5.0) + googleapis-common-protos-types (~> 1.0) + grpc (1.66.0-arm64-darwin) + google-protobuf (>= 3.25, < 5.0) + googleapis-common-protos-types (~> 1.0) grpc (1.66.0-x86_64-linux) google-protobuf (>= 3.25, < 5.0) googleapis-common-protos-types (~> 1.0) @@ -173,7 +188,7 @@ GEM concurrent-ruby (~> 1.0) json (2.7.2) json_pure (2.7.2) - jwt (2.9.1) + jwt (2.9.3) base64 launchy (3.0.1) addressable (~> 2.8) @@ -188,9 +203,10 @@ GEM net-pop net-smtp method_source (1.1.0) - mime-types (3.5.2) + mime-types (3.6.0) + logger mime-types-data (~> 3.2015) - mime-types-data (3.2024.0903) + mime-types-data (3.2024.1001) mini_mime (1.1.5) minitest (4.7.5) mlanett-redis-lock (0.2.7) @@ -284,6 +300,8 @@ GEM webrick (1.8.2) PLATFORMS + aarch64-linux + arm64-darwin-22 ruby x86_64-linux