From 701091b6f8d6c30624200b71b438efc362441db1 Mon Sep 17 00:00:00 2001 From: Michael Dorf Date: Mon, 27 Jul 2026 21:32:22 -0700 Subject: [PATCH] chore: drop sparql-client fork pin; use vanilla 3.2.2 via goo Part of the sparql-client de-fork (ncbo/goo#194). Lock: goo -> 78ff860, ontologies_linked_data -> 29e9fa7, ncbo_annotator -> c572808, ncbo_cron -> 4368911, ncbo_ontology_recommender -> b3215d9, sparql-client 3.2.2 (rubygems), fork GIT source removed. --- Gemfile | 1 - Gemfile.lock | 67 +++++++++++++++++++++++----------------------------- 2 files changed, 30 insertions(+), 38 deletions(-) diff --git a/Gemfile b/Gemfile index 9867a4b00..b688240de 100644 --- a/Gemfile +++ b/Gemfile @@ -51,7 +51,6 @@ gem 'kramdown' # NCBO gems (can be from a local dev path or from rubygems/git) gem 'goo', github: 'ncbo/goo', branch: 'development' -gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'development' gem 'ncbo_annotator', github: 'ncbo/ncbo_annotator', branch: 'develop' gem 'ncbo_cron', github: 'ncbo/ncbo_cron', branch: 'develop' gem 'ncbo_ontology_recommender', github: 'ncbo/ncbo_ontology_recommender', branch: 'develop' diff --git a/Gemfile.lock b/Gemfile.lock index 6872e6a74..e6f2fa1f0 100644 --- a/Gemfile.lock +++ b/Gemfile.lock @@ -8,7 +8,7 @@ GIT GIT remote: https://github.com/ncbo/goo.git - revision: 752fb6b3fe2ec0ba9417397f3283baeac7a9abfc + revision: 78ff8608a1d1350de134ce524ccc31befa172abf branch: development specs: goo (0.0.2) @@ -21,12 +21,12 @@ GIT redis rest-client rsolr - sparql-client + sparql-client (= 3.2.2) uuid GIT remote: https://github.com/ncbo/ncbo_annotator.git - revision: 6c53ee737ca1e2562cc75df61158c9b15ccfa43b + revision: c5728085cf50589637bc66f88eeda0ebba7d2d3c branch: develop specs: ncbo_annotator (0.0.1) @@ -37,7 +37,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_cron.git - revision: 414ea23eab9a801ad80becaa9e46c6933f4cba8c + revision: 4368911185dd74fd3a9396b15368590d411ac918 branch: develop specs: ncbo_cron (0.0.1) @@ -55,7 +55,7 @@ GIT GIT remote: https://github.com/ncbo/ncbo_ontology_recommender.git - revision: d036131b473a52b88fcc7ad5eb69f5d4d181995e + revision: b3215d9ba146adcfa2492d43804891074a7eb063 branch: develop specs: ncbo_ontology_recommender (0.0.1) @@ -66,7 +66,7 @@ GIT GIT remote: https://github.com/ncbo/ontologies_linked_data.git - revision: 6409971110e728b00ec69d43e3f40c9a6f3eb4f1 + revision: 29e9fa79e2a14e3d974f3d17cd1fffc33560fca8 branch: develop specs: ontologies_linked_data (0.0.1) @@ -84,15 +84,6 @@ GIT rsolr rubyzip (~> 3.0) -GIT - remote: https://github.com/ncbo/sparql-client.git - revision: 2ac20b217bb7ad2b11305befe0ee77d75e44eac5 - branch: development - specs: - sparql-client (3.2.2) - net-http-persistent (~> 4.0, >= 4.0.2) - rdf (~> 3.2, >= 3.2.11) - GIT remote: https://github.com/palexander/rack-post-body-to-params.git revision: 0fd30e710386d0cb8a3a6833d9549d7b655d5398 @@ -163,7 +154,7 @@ GEM capistrano (~> 3.1) sshkit (~> 1.3) coderay (1.1.3) - concurrent-ruby (1.3.7) + concurrent-ruby (1.3.8) connection_pool (3.0.2) crack (0.4.5) rexml @@ -199,7 +190,7 @@ GEM ffi (1.17.4-x86_64-darwin) ffi (1.17.4-x86_64-linux-gnu) ffi (1.17.4-x86_64-linux-musl) - fugit (1.12.3) + fugit (1.13.0) et-orbi (~> 1.4) raabro (~> 1.4) gapic-common (1.1.0) @@ -223,10 +214,10 @@ GEM google-cloud-core (1.9.0) google-cloud-env (>= 1.0, < 3.a) google-cloud-errors (~> 1.0) - google-cloud-env (2.3.1) + google-cloud-env (2.4.0) base64 (~> 0.2) faraday (>= 1.0, < 3.a) - google-cloud-errors (1.6.0) + google-cloud-errors (1.7.0) google-logging-utils (0.2.0) google-protobuf (3.25.3) google-protobuf (3.25.3-aarch64-linux) @@ -240,7 +231,7 @@ GEM grpc (~> 1.41) googleapis-common-protos-types (1.20.0) google-protobuf (>= 3.18, < 5.a) - googleauth (1.17.1) + googleauth (1.17.3) faraday (>= 1.0, < 3.a) google-cloud-env (~> 2.2) google-logging-utils (~> 0.1) @@ -277,7 +268,7 @@ GEM i18n (1.15.2) concurrent-ruby (~> 1.0) io-console (0.8.2) - json (2.20.0) + json (2.21.1) json-canonicalization (0.4.0) json-ld (3.2.5) htmlentities (~> 4.3) @@ -335,7 +326,7 @@ GEM uri (>= 0.11.1) net-http-persistent (4.0.8) connection_pool (>= 2.2.4, < 4) - net-imap (0.6.4.1) + net-imap (0.6.6) date net-protocol net-pop (0.1.2) @@ -352,7 +343,7 @@ GEM netrc (0.11.0) newrelic_rpm (10.5.0) logger - oj (3.17.3) + oj (3.17.4) bigdecimal (>= 3.0) ostruct (>= 0.2) omni_logger (0.1.4) @@ -373,7 +364,7 @@ GEM reline (>= 0.6.0) pstore (0.2.1) public_suffix (7.0.5) - raabro (1.4.0) + raabro (1.5.0) racc (1.8.1) rack (3.2.6) rack-accept (0.4.5) @@ -419,7 +410,7 @@ GEM rexml (~> 3.2) redis (5.4.1) redis-client (>= 0.22.0) - redis-client (0.30.0) + redis-client (0.30.1) connection_pool redis-rack-cache (2.2.1) rack-cache (>= 1.10, < 2) @@ -486,6 +477,9 @@ GEM rack-protection (= 4.2.1) sinatra (= 4.2.1) tilt (~> 2.0) + sparql-client (3.2.2) + net-http-persistent (~> 4.0, >= 4.0.2) + rdf (~> 3.2, >= 3.2.11) sshkit (1.25.0) base64 logger @@ -593,7 +587,6 @@ DEPENDENCIES simplecov-cobertura sinatra sinatra-contrib - sparql-client! unicorn unicorn-worker-killer webmock @@ -619,7 +612,7 @@ CHECKSUMS capistrano-locally (0.3.0) sha256=ad44252f19641e8dd980f7cb0241e9ac11919b1f4cbdb642d272a6d0edcb84eb capistrano-rbenv (2.2.0) sha256=3c8f39b7c624f3806630dcb475484bb3579aef07a40efe85089d83f64b0c35f5 coderay (1.1.3) sha256=dc530018a4684512f8f38143cd2a096c9f02a1fc2459edcfe534787a7fc77d4b - concurrent-ruby (1.3.7) sha256=4412caec3a5ea2e5fdc52076724c071a81f2c0593d83b2ac8cbb8ca63b3151b0 + concurrent-ruby (1.3.8) sha256=b2f1be836e968ccc78ccfce277ea79c72a88633f22306782c16ff23fb415d1e1 connection_pool (3.0.2) sha256=33fff5ba71a12d2aa26cb72b1db8bba2a1a01823559fb01d29eb74c286e62e0a crack (0.4.5) sha256=798416fb29b8c9f655d139d5559169b39c4a0a3b8f8f39b7f670eec1af9b21b3 dante (0.2.0) sha256=939776f04b4d253ffbbcf53341631aa2ee6e6cf314dedade2e60ac43b40a6fe6 @@ -645,15 +638,15 @@ CHECKSUMS ffi (1.17.4-x86_64-darwin) sha256=aa70390523cf3235096cf64962b709b4cfbd5c082a2cb2ae714eb0fe2ccda496 ffi (1.17.4-x86_64-linux-gnu) sha256=9d3db14c2eae074b382fa9c083fe95aec6e0a1451da249eab096c34002bc752d ffi (1.17.4-x86_64-linux-musl) sha256=3fdf9888483de005f8ef8d1cf2d3b20d86626af206cbf780f6a6a12439a9c49e - fugit (1.12.3) sha256=826d77739086482a6ac2805bc32693845395da688f637890cb4ca457dede2ec2 + fugit (1.13.0) sha256=a4f093fce740da52f216740a5041e2a594ea763cdb89e8b2754ca4399634ab18 gapic-common (1.1.0) sha256=3270ab3c5135012a4ab4d8848f945cf35014192f24504cdb40c66fc67f1beaa3 get_process_mem (0.2.7) sha256=4afd3c3641dd6a817c09806c7d6d509d8a9984512ac38dea8b917426bbf77eba goo (0.0.2) google-analytics-data (0.9.0) sha256=26d46b66bfecf8be325a09b91eaac0a095401af66842a83b957c36afa269e1ce google-analytics-data-v1beta (0.17.0) sha256=1145d30d794bcf6bf8b723140a0ee2c445e740b82cf4051a31d992e7393168a6 google-cloud-core (1.9.0) sha256=ab55409f51488e8deefb6edcc1ce4771dfb5da2fe7b3bc075709a030c2b682a4 - google-cloud-env (2.3.1) sha256=0faac01eb27be78c2591d64433663b1a114f8f7af55a4f819755426cac9178e7 - google-cloud-errors (1.6.0) sha256=1da8476dd706ad04b9d32e3c4b90d07d3463b37d6407cb56d41342ea7647d0a1 + google-cloud-env (2.4.0) sha256=01cb35ecee5d1c4d1cd4deaed8bb5bddc838e296bcc2a35c5d1ddd07ce40d28d + google-cloud-errors (1.7.0) sha256=6e682f42d89aae08689f36f28495de629d756da076bafff0003bac7f8042ebb3 google-logging-utils (0.2.0) sha256=675462b4ea5affa825a3442694ca2d75d0069455a1d0956127207498fca3df7b google-protobuf (3.25.3) sha256=39bd97cbc7631905e76cdf8f1bf3dda1c3d05200d7e23f575aced78930fbddd6 google-protobuf (3.25.3-aarch64-linux) sha256=5ea9d20d60e5d3bef8d881b426946345e5ac6cf4779ac81cd900e45f40567243 @@ -663,7 +656,7 @@ CHECKSUMS google-protobuf (3.25.3-x86_64-linux) sha256=ceeba879d9313a2bd0600a97d6fe3cf529a9b37d12ca026f891996c118b7ffb2 googleapis-common-protos (1.8.0) sha256=bfe89cb75d1a8f13e4591d262a20333e145481d803adb74dd13ac0517decdffe googleapis-common-protos-types (1.20.0) sha256=5e374b06bcfc7e13556e7c0d87b99f1fa3d42de6396a1de3d8fc13aefb4dd07f - googleauth (1.17.1) sha256=0f7e6fc70e204cee1b2d71f1e1de2d3b349d432404197fe68ebf7fa23d0821b9 + googleauth (1.17.3) sha256=9a655455885c0c17a8b70537acd2a992a7c7842c43c06c6612dfb0d93e755d58 grpc (1.70.1) sha256=174594605c96df3caed44a83221665aa6e11f554e56028f89bef82c07ffb83cb grpc (1.70.1-aarch64-linux) sha256=48e0b22b8b96e61ca7054a7fea894a4845498e6bf366b50eff03e588f714ed96 grpc (1.70.1-arm64-darwin) sha256=eeb6758dd58135e4e5fcd78726b9a18d34d7313e41bc81528ff4b3dce65cf525 @@ -677,7 +670,7 @@ CHECKSUMS http-cookie (1.1.6) sha256=ba4b82be64de61dc281243dac70e3c382c45142f20268ed9276a3670c93feaa9 i18n (1.15.2) sha256=00f9eb62412fe593b2a65a97daa75300d37abb8f7202ec748e94b6d46a9dd1b5 io-console (0.8.2) sha256=d6e3ae7a7cc7574f4b8893b4fca2162e57a825b223a177b7afa236c5ef9814cc - json (2.20.0) sha256=9362bc6e55a952b056abf9167cf053358181c904cb70cd6eee0808ea830fc32b + json (2.21.1) sha256=13a43df75d95641443f5702dff350f237164a9d811ff0f2c2800d4d980220583 json-canonicalization (0.4.0) sha256=73ea88b68f210d1a09c2116d4cd1ff5a39684c6a409f7ccac70d5b1a426a8bef json-ld (3.2.5) sha256=98b96f1831b0fe9c7d2568a7d43b64f6b8c3f5892d55ccf91640e32a99c273fc json-schema (6.2.0) sha256=e8bff46ed845a22c1ab2bd0d7eccf831c01fe23bb3920caa4c74db4306813666 @@ -708,7 +701,7 @@ CHECKSUMS net-ftp (0.3.9) sha256=307817ccf7f428f79d083f7e36dbb46a9d1d375e0d23027824de1866f0b13b65 net-http (0.9.1) sha256=25ba0b67c63e89df626ed8fac771d0ad24ad151a858af2cc8e6a716ca4336996 net-http-persistent (4.0.8) sha256=ef3de8319d691537b329053fae3a33195f8b070bbbfae8bf1a58c796081960e6 - net-imap (0.6.4.1) sha256=29f0360d75a7efd3539f16ac1957dea5c0a51ddeceb348db4553c3120914ea0d + net-imap (0.6.6) sha256=96aa4ee50df3060203e649efc341f53480b791d49e150f2fdebf68beb141a8df net-pop (0.1.2) sha256=848b4e982013c15b2f0382792268763b748cce91c9e91e36b0f27ed26420dff3 net-protocol (0.2.2) sha256=aa73e0cba6a125369de9837b8d8ef82a61849360eba0521900e2c3713aa162a8 net-scp (4.1.0) sha256=a99b0b92a1e5d360b0de4ffbf2dc0c91531502d3d4f56c28b0139a7c093d1a5d @@ -717,7 +710,7 @@ CHECKSUMS net-ssh (7.3.2) sha256=65029e213c380e20e5fd92ece663934ab0a0fe888e0cd7cc6a5b664074362dd4 netrc (0.11.0) sha256=de1ce33da8c99ab1d97871726cba75151113f117146becbe45aa85cb3dabee3f newrelic_rpm (10.5.0) sha256=93c3d34813a1145705002283d7c32fa9a6b0b8e4fabe2cfbcfc791ee4c2ccd6d - oj (3.17.3) sha256=ebe3967b0bb7ac4f206561d0d9ac8875b9973f778600d7b61b5c355662a707ed + oj (3.17.4) sha256=733fe3bcb7a5d985bd2e943620b7bea1bffb2809318af7021c841b833a6858e1 omni_logger (0.1.4) sha256=b61596f7d96aa8426929e46c3500558d33e838e1afd7f4735244feb4d082bb3e ontologies_linked_data (0.0.1) ontoportal_testkit (0.1.0) @@ -731,7 +724,7 @@ CHECKSUMS pry (0.16.0) sha256=d76c69065698ed1f85e717bd33d7942c38a50868f6b0673c636192b3d1b6054e pstore (0.2.1) sha256=03904d0f2c66579e96d1e6704cdabc0c88df7ea8ed8782d9f3569f6f6c702c1a public_suffix (7.0.5) sha256=1a8bb08f1bbea19228d3bed6e5ed908d1cb4f7c2726d18bd9cadf60bc676f623 - raabro (1.4.0) sha256=d4fa9ff5172391edb92b242eed8be802d1934b1464061ae5e70d80962c5da882 + raabro (1.5.0) sha256=3f998a7bc84f9c84df3ab580634d2e0a5bda4f0841168d56035f529c9877440a racc (1.8.1) sha256=4a7f6929691dbec8b5209a0b373bc2614882b55fc5d2e447a21aaa691303d62f rack (3.2.6) sha256=5ed78e1f73b2e25679bec7d45ee2d4483cc4146eb1be0264fc4d94cb5ef212c2 rack-accept (0.4.5) sha256=66247b5449db64ebb93ae2ec4af4764b87d1ae8a7463c7c68893ac13fa8d4da2 @@ -755,7 +748,7 @@ CHECKSUMS rdf-vocab (3.3.3) sha256=d3b642edb37be7b37b73cafa9e01d55762f99292838e7b0868a3575bd297bf8b rdf-xsd (3.3.0) sha256=fab51d27b20344237d9b622ef32e83e4c44940840bfc76a245ce6b6abba44772 redis (5.4.1) sha256=b5e675b57ad22b15c9bcc765d5ac26f60b675408af916d31527af9bd5a81faae - redis-client (0.30.0) sha256=743f11ed42f0a41a0341554087b077479fec7e2d47a7c123fd90a12c0db5e477 + redis-client (0.30.1) sha256=5151bc5c7bbfe48623732cdae3b900d8a22dc691cc7cdfacfb351ac55116522d redis-rack-cache (2.2.1) sha256=9c72978a6354e02efeb2f933dd32c94a4a13f1137dac492442126bf25cc19970 redis-store (1.11.0) sha256=edc4f3e239dcd1fdd9905584e6b1e623a84618e14436e6e8a07c70891008eda4 regexp_parser (2.12.0) sha256=35a916a1d63190ab5c9009457136ae5f3c0c7512d60291d0d1378ba18ce08ebb @@ -779,7 +772,7 @@ CHECKSUMS simplecov_json_formatter (0.1.4) sha256=529418fbe8de1713ac2b2d612aa3daa56d316975d307244399fa4838c601b428 sinatra (4.2.1) sha256=b7aeb9b11d046b552972ade834f1f9be98b185fa8444480688e3627625377080 sinatra-contrib (4.2.1) sha256=10d091c944d268aa910c618ea40a3c3ebe0533e6e32990d84af92235a3d26b4a - sparql-client (3.2.2) + sparql-client (3.2.2) sha256=d3bac6bea08598dad617c0cdc6d380f9d416ef4ab91ca28309fdf40b93f5a571 sshkit (1.25.0) sha256=c8c6543cdb60f91f1d277306d585dd11b6a064cb44eab0972827e4311ff96744 systemu (2.6.5) sha256=01f7d014b1453b28e5781e15c4d7d63fc9221c29b174b7aae5253207a75ab33e temple (0.10.4) sha256=b7a1e94b6f09038ab0b6e4fe0126996055da2c38bec53a8a336f075748fff72c