From 45fce56984af3dfe7eb8265c42d4853af9dd6c72 Mon Sep 17 00:00:00 2001 From: Adam Coffman Date: Wed, 4 Oct 2023 12:44:07 -0500 Subject: [PATCH 1/9] do not force variant aliases to be all caps --- server/app/models/variant_alias.rb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/server/app/models/variant_alias.rb b/server/app/models/variant_alias.rb index 498a29fd1..088254c8b 100644 --- a/server/app/models/variant_alias.rb +++ b/server/app/models/variant_alias.rb @@ -10,7 +10,7 @@ def self.get_or_create_by_name(name) if found = self.where('lower(name) = ?', name.downcase).first found else - self.create!(name: name.upcase) + self.create!(name: name) end end end From 4ff020ddb62040d5fab4a4f5fbdb1ce0f631fa6f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Oct 2023 15:41:28 +0000 Subject: [PATCH 2/9] Bump undici from 5.22.0 to 5.26.3 in /client Bumps [undici](https://github.com/nodejs/undici) from 5.22.0 to 5.26.3. - [Release notes](https://github.com/nodejs/undici/releases) - [Commits](https://github.com/nodejs/undici/compare/v5.22.0...v5.26.3) --- updated-dependencies: - dependency-name: undici dependency-type: indirect ... Signed-off-by: dependabot[bot] --- client/yarn.lock | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/client/yarn.lock b/client/yarn.lock index ff4a5b3e7..bbad87cd7 100644 --- a/client/yarn.lock +++ b/client/yarn.lock @@ -1934,6 +1934,11 @@ dependencies: eslint-visitor-keys "^3.3.0" +"@fastify/busboy@^2.0.0": + version "2.0.0" + resolved "https://registry.yarnpkg.com/@fastify/busboy/-/busboy-2.0.0.tgz#f22824caff3ae506b18207bad4126dbc6ccdb6b8" + integrity sha512-JUFJad5lv7jxj926GPgymrWQxxjPYuJNiNjNMzqT+HiuP6Vl3dk5xzG+8sTX96np0ZAluvaMzPsjhHZ5rNuNQQ== + "@gar/promisify@^1.1.3": version "1.1.3" resolved "https://registry.yarnpkg.com/@gar/promisify/-/promisify-1.1.3.tgz#555193ab2e3bb3b6adc3d551c9c030d9e860daf6" @@ -9123,11 +9128,11 @@ unc-path-regex@^0.1.2: integrity sha512-eXL4nmJT7oCpkZsHZUOJo8hcX3GbsiDOa0Qu9F646fi8dT3XuSVopVqAcEiVzSKKH7UoDti23wNX3qGFxcW5Qg== undici@^5.12.0: - version "5.22.0" - resolved "https://registry.yarnpkg.com/undici/-/undici-5.22.0.tgz#5e205d82a5aecc003fc4388ccd3d2c6e8674a0ad" - integrity sha512-fR9RXCc+6Dxav4P9VV/sp5w3eFiSdOjJYsbtWfd4s5L5C4ogyuVpdKIVHeW0vV1MloM65/f7W45nR9ZxwVdyiA== + version "5.26.3" + resolved "https://registry.yarnpkg.com/undici/-/undici-5.26.3.tgz#ab3527b3d5bb25b12f898dfd22165d472dd71b79" + integrity sha512-H7n2zmKEWgOllKkIUkLvFmsJQj062lSm3uA4EYApG8gLuiOM0/go9bIoC3HVaSnfg4xunowDE2i9p8drkXuvDw== dependencies: - busboy "^1.6.0" + "@fastify/busboy" "^2.0.0" unicode-canonical-property-names-ecmascript@^2.0.0: version "2.0.0" From 3eea1cdb91796498a2742ca537eacee727e3e10a Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Mon, 16 Oct 2023 13:11:29 -0500 Subject: [PATCH 3/9] Set allele_registry_id to None if the coordinates no longer resolve --- .../jobs/set_allele_registry_id_single_variant.rb | 13 +++++++++++-- server/app/jobs/update_allele_registry_ids.rb | 3 +++ 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/server/app/jobs/set_allele_registry_id_single_variant.rb b/server/app/jobs/set_allele_registry_id_single_variant.rb index fe7063491..7aefeba9a 100644 --- a/server/app/jobs/set_allele_registry_id_single_variant.rb +++ b/server/app/jobs/set_allele_registry_id_single_variant.rb @@ -3,14 +3,23 @@ class SetAlleleRegistryIdSingleVariant < AlleleRegistryIds def perform(variant) + old_allele_registry_id = variant.allele_registry_id allele_registry_id = get_allele_registry_id(variant) - if allele_registry_id == '_:CA' && variant.allele_registry_id != 'unregistered' + if allele_registry_id == '_:CA' && old_allele_registry_id != 'unregistered' variant.allele_registry_id = 'unregistered' variant.save - elsif allele_registry_id.present? && allele_registry_id != '_:CA' && allele_registry_id != variant.allele_registry_id + elsif allele_registry_id.present? && allele_registry_id != '_:CA' && allele_registry_id != old_allele_registry_id variant.allele_registry_id = allele_registry_id variant.save add_allele_registry_link(allele_registry_id) + elsif old_allele_registry_id.present? && allele_registry_id.nil? + variant.allele_registry_id = None + variant.save + end + unless Variant.where(allele_registry_id: old_allele_registry_id).exists? + if old_allele_registry_id != '_:CA' and old_allele_registry_id != 'undefined' + delete_allele_registry_link(old_allele_registry_id) + end end end end diff --git a/server/app/jobs/update_allele_registry_ids.rb b/server/app/jobs/update_allele_registry_ids.rb index 33f1a4179..c6fa32334 100644 --- a/server/app/jobs/update_allele_registry_ids.rb +++ b/server/app/jobs/update_allele_registry_ids.rb @@ -14,6 +14,9 @@ def perform v.allele_registry_id = allele_registry_id v.save add_allele_registry_link(allele_registry_id) + elsif old_allele_registry_id.present? && allele_registry_id.nil? + v.allele_registry_id = None + v.save end #delete the linkout if no other variant has this allele registry ID unless Variant.where(allele_registry_id: old_allele_registry_id).exists? From 8d67ae79a91243c687ebf76e3bc9adb782446700 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:12:34 +0000 Subject: [PATCH 4/9] Bump @babel/traverse from 7.16.5 to 7.23.2 in /server Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.16.5 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] --- server/yarn.lock | 143 +++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 131 insertions(+), 12 deletions(-) diff --git a/server/yarn.lock b/server/yarn.lock index 85e9c6a4e..c2412a776 100644 --- a/server/yarn.lock +++ b/server/yarn.lock @@ -9,6 +9,14 @@ dependencies: "@babel/highlight" "^7.16.0" +"@babel/code-frame@^7.22.13": + version "7.22.13" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.22.13.tgz#e3c1c099402598483b7a8c46a721d1038803755e" + integrity sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w== + dependencies: + "@babel/highlight" "^7.22.13" + chalk "^2.4.2" + "@babel/compat-data@^7.13.11", "@babel/compat-data@^7.16.0", "@babel/compat-data@^7.16.4": version "7.16.4" resolved "https://registry.yarnpkg.com/@babel/compat-data/-/compat-data-7.16.4.tgz#081d6bbc336ec5c2435c6346b2ae1fb98b5ac68e" @@ -44,6 +52,16 @@ jsesc "^2.5.1" source-map "^0.5.0" +"@babel/generator@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.23.0.tgz#df5c386e2218be505b34837acbcb874d7a983420" + integrity sha512-lN85QRR+5IbYrMWM6Y4pE/noaQtg4pNiqeNGX60eqOfo6gtEj6uw/JagelB8vVztSd7R6M5n1+PQkDbHbBRU4g== + dependencies: + "@babel/types" "^7.23.0" + "@jridgewell/gen-mapping" "^0.3.2" + "@jridgewell/trace-mapping" "^0.3.17" + jsesc "^2.5.1" + "@babel/helper-annotate-as-pure@^7.16.0": version "7.16.0" resolved "https://registry.yarnpkg.com/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.16.0.tgz#9a1f0ebcda53d9a2d00108c4ceace6a5d5f1f08d" @@ -111,6 +129,11 @@ dependencies: "@babel/types" "^7.16.0" +"@babel/helper-environment-visitor@^7.22.20": + version "7.22.20" + resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz#96159db61d34a29dba454c959f5ae4a649ba9167" + integrity sha512-zfedSIzFhat/gFhWfHtgWvlec0nqB9YEIVrpuwjruLlXfUSnA8cJB0miHKwqDnQ7d32aKo2xt88/xZptwxbfhA== + "@babel/helper-explode-assignable-expression@^7.16.0": version "7.16.0" resolved "https://registry.yarnpkg.com/@babel/helper-explode-assignable-expression/-/helper-explode-assignable-expression-7.16.0.tgz#753017337a15f46f9c09f674cff10cee9b9d7778" @@ -127,6 +150,14 @@ "@babel/template" "^7.16.0" "@babel/types" "^7.16.0" +"@babel/helper-function-name@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.23.0.tgz#1f9a3cdbd5b2698a670c30d2735f9af95ed52759" + integrity sha512-OErEqsrxjZTJciZ4Oo+eoZqeW9UIiOcuYKRJA4ZAgV9myA+pOXhhmpfNCKjEH/auVfEYVFJ6y1Tc4r0eIApqiw== + dependencies: + "@babel/template" "^7.22.15" + "@babel/types" "^7.23.0" + "@babel/helper-get-function-arity@^7.16.0": version "7.16.0" resolved "https://registry.yarnpkg.com/@babel/helper-get-function-arity/-/helper-get-function-arity-7.16.0.tgz#0088c7486b29a9cb5d948b1a1de46db66e089cfa" @@ -141,6 +172,13 @@ dependencies: "@babel/types" "^7.16.0" +"@babel/helper-hoist-variables@^7.22.5": + version "7.22.5" + resolved "https://registry.yarnpkg.com/@babel/helper-hoist-variables/-/helper-hoist-variables-7.22.5.tgz#c01a007dac05c085914e8fb652b339db50d823bb" + integrity sha512-wGjk9QZVzvknA6yKIUURb8zY3grXCcOZt+/7Wcy8O2uctxhplmUPkOdlgoNhmdVee2c92JXbf1xpMtVNbfoxRw== + dependencies: + "@babel/types" "^7.22.5" + "@babel/helper-member-expression-to-functions@^7.16.5": version "7.16.5" resolved "https://registry.yarnpkg.com/@babel/helper-member-expression-to-functions/-/helper-member-expression-to-functions-7.16.5.tgz#1bc9f7e87354e86f8879c67b316cb03d3dc2caab" @@ -222,11 +260,28 @@ dependencies: "@babel/types" "^7.16.0" +"@babel/helper-split-export-declaration@^7.22.6": + version "7.22.6" + resolved "https://registry.yarnpkg.com/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.22.6.tgz#322c61b7310c0997fe4c323955667f18fcefb91c" + integrity sha512-AsUnxuLhRYsisFiaJwvp1QF+I3KjD5FOxut14q/GzovUe6orHLesW2C7d754kRm53h5gqrz6sFl6sxc4BVtE/g== + dependencies: + "@babel/types" "^7.22.5" + +"@babel/helper-string-parser@^7.22.5": + version "7.22.5" + resolved "https://registry.yarnpkg.com/@babel/helper-string-parser/-/helper-string-parser-7.22.5.tgz#533f36457a25814cf1df6488523ad547d784a99f" + integrity sha512-mM4COjgZox8U+JcXQwPijIZLElkgEpO5rsERVDJTc2qfCDfERyob6k5WegS14SX18IIjv+XD+GrqNumY5JRCDw== + "@babel/helper-validator-identifier@^7.15.7": version "7.15.7" resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.15.7.tgz#220df993bfe904a4a6b02ab4f3385a5ebf6e2389" integrity sha512-K4JvCtQqad9OY2+yTU8w+E82ywk/fe+ELNlt1G8z3bVGlZfn/hOcQQsUhGhW/N+tb3fxK800wLtKOE/aM0m72w== +"@babel/helper-validator-identifier@^7.22.20": + version "7.22.20" + resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.20.tgz#c4ae002c61d2879e724581d96665583dbc1dc0e0" + integrity sha512-Y4OZ+ytlatR8AI+8KZfKuL5urKp7qey08ha31L8b3BwewJAoJamTzyvxPR/5D+KkdJCGPq/+8TukHBlY10FX9A== + "@babel/helper-validator-option@^7.14.5": version "7.14.5" resolved "https://registry.yarnpkg.com/@babel/helper-validator-option/-/helper-validator-option-7.14.5.tgz#6e72a1fff18d5dfcb878e1e62f1a021c4b72d5a3" @@ -260,11 +315,25 @@ chalk "^2.0.0" js-tokens "^4.0.0" +"@babel/highlight@^7.22.13": + version "7.22.20" + resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.22.20.tgz#4ca92b71d80554b01427815e06f2df965b9c1f54" + integrity sha512-dkdMCN3py0+ksCgYmGG8jKeGA/8Tk+gJwSYYlFGxG5lmhfKNoAy004YpLxpS1W2J8m/EK2Ew+yOs9pVRwO89mg== + dependencies: + "@babel/helper-validator-identifier" "^7.22.20" + chalk "^2.4.2" + js-tokens "^4.0.0" + "@babel/parser@^7.16.0", "@babel/parser@^7.16.5": version "7.16.6" resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.16.6.tgz#8f194828193e8fa79166f34a4b4e52f3e769a314" integrity sha512-Gr86ujcNuPDnNOY8mi383Hvi8IYrJVJYuf3XcuBM/Dgd+bINn/7tHqsj+tKkoreMbmGsFLsltI/JJd8fOFWGDQ== +"@babel/parser@^7.22.15", "@babel/parser@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.23.0.tgz#da950e622420bf96ca0d0f2909cdddac3acd8719" + integrity sha512-vvPKKdMemU85V9WE/l5wZEmImpCtLqbnTvqDS2U1fJ96KrxoW7KrXhNsNCblQlg8Ck4b85yxdTyelsMUgFUXiw== + "@babel/plugin-bugfix-safari-id-destructuring-collision-in-function-expression@^7.16.2": version "7.16.2" resolved "https://registry.yarnpkg.com/@babel/plugin-bugfix-safari-id-destructuring-collision-in-function-expression/-/plugin-bugfix-safari-id-destructuring-collision-in-function-expression-7.16.2.tgz#2977fca9b212db153c195674e57cfab807733183" @@ -875,19 +944,28 @@ "@babel/parser" "^7.16.0" "@babel/types" "^7.16.0" -"@babel/traverse@^7.13.0", "@babel/traverse@^7.16.5": - version "7.16.5" - resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.16.5.tgz#d7d400a8229c714a59b87624fc67b0f1fbd4b2b3" - integrity sha512-FOCODAzqUMROikDYLYxl4nmwiLlu85rNqBML/A5hKRVXG2LV8d0iMqgPzdYTcIpjZEBB7D6UDU9vxRZiriASdQ== +"@babel/template@^7.22.15": + version "7.22.15" + resolved "https://registry.yarnpkg.com/@babel/template/-/template-7.22.15.tgz#09576efc3830f0430f4548ef971dde1350ef2f38" + integrity sha512-QPErUVm4uyJa60rkI73qneDacvdvzxshT3kksGqlGWYdOTIUOwJ7RDUL8sGqslY1uXWSL6xMFKEXDS3ox2uF0w== dependencies: - "@babel/code-frame" "^7.16.0" - "@babel/generator" "^7.16.5" - "@babel/helper-environment-visitor" "^7.16.5" - "@babel/helper-function-name" "^7.16.0" - "@babel/helper-hoist-variables" "^7.16.0" - "@babel/helper-split-export-declaration" "^7.16.0" - "@babel/parser" "^7.16.5" - "@babel/types" "^7.16.0" + "@babel/code-frame" "^7.22.13" + "@babel/parser" "^7.22.15" + "@babel/types" "^7.22.15" + +"@babel/traverse@^7.13.0", "@babel/traverse@^7.16.5": + version "7.23.2" + resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.23.2.tgz#329c7a06735e144a506bdb2cad0268b7f46f4ad8" + integrity sha512-azpe59SQ48qG6nu2CzcMLbxUudtN+dOM9kDbUqGq3HXUJRlo7i8fvPoxQUzYgLZ4cMVmuZgm8vvBpNeRhd6XSw== + dependencies: + "@babel/code-frame" "^7.22.13" + "@babel/generator" "^7.23.0" + "@babel/helper-environment-visitor" "^7.22.20" + "@babel/helper-function-name" "^7.23.0" + "@babel/helper-hoist-variables" "^7.22.5" + "@babel/helper-split-export-declaration" "^7.22.6" + "@babel/parser" "^7.23.0" + "@babel/types" "^7.23.0" debug "^4.1.0" globals "^11.1.0" @@ -899,6 +977,15 @@ "@babel/helper-validator-identifier" "^7.15.7" to-fast-properties "^2.0.0" +"@babel/types@^7.22.15", "@babel/types@^7.22.5", "@babel/types@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.23.0.tgz#8c1f020c9df0e737e4e247c0619f58c68458aaeb" + integrity 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"^1.0.1" + "@jridgewell/sourcemap-codec" "^1.4.10" + "@jridgewell/trace-mapping" "^0.3.9" + +"@jridgewell/resolve-uri@^3.1.0": + version "3.1.1" + resolved "https://registry.yarnpkg.com/@jridgewell/resolve-uri/-/resolve-uri-3.1.1.tgz#c08679063f279615a3326583ba3a90d1d82cc721" + integrity sha512-dSYZh7HhCDtCKm4QakX0xFpsRDqjjtZf/kjI/v3T3Nwt5r8/qz/M19F9ySyOqU94SXBmeG9ttTul+YnR4LOxFA== + +"@jridgewell/set-array@^1.0.1": + version "1.1.2" + resolved "https://registry.yarnpkg.com/@jridgewell/set-array/-/set-array-1.1.2.tgz#7c6cf998d6d20b914c0a55a91ae928ff25965e72" + integrity sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw== + +"@jridgewell/sourcemap-codec@^1.4.10", "@jridgewell/sourcemap-codec@^1.4.14": + version "1.4.15" + resolved "https://registry.yarnpkg.com/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.4.15.tgz#d7c6e6755c78567a951e04ab52ef0fd26de59f32" + integrity sha512-eF2rxCRulEKXHTRiDrDy6erMYWqNw4LPdQ8UQA4huuxaQsVeRPFl2oM8oDGxMFhJUWZf9McpLtJasDDZb/Bpeg== + +"@jridgewell/trace-mapping@^0.3.17", "@jridgewell/trace-mapping@^0.3.9": + version "0.3.19" + resolved "https://registry.yarnpkg.com/@jridgewell/trace-mapping/-/trace-mapping-0.3.19.tgz#f8a3249862f91be48d3127c3cfe992f79b4b8811" + integrity sha512-kf37QtfW+Hwx/buWGMPcR60iF9ziHa6r/CZJIHbmcm4+0qrXiVdxegAH0F6yddEVQ7zdkjcGCgCzUu+BcbhQxw== + dependencies: + "@jridgewell/resolve-uri" "^3.1.0" + "@jridgewell/sourcemap-codec" "^1.4.14" + "@npmcli/fs@^1.0.0": version "1.1.0" resolved "https://registry.yarnpkg.com/@npmcli/fs/-/fs-1.1.0.tgz#bec1d1b89c170d40e1b73ad6c943b0b75e7d2951" From 33158011b04988c6b444e5f840c4cc21ba2d2ddd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 17 Oct 2023 13:50:13 +0000 Subject: [PATCH 5/9] Bump @babel/traverse from 7.20.12 to 7.23.2 in /client Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.20.12 to 7.23.2. - [Release notes](https://github.com/babel/babel/releases) - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md) - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse) --- updated-dependencies: - dependency-name: "@babel/traverse" dependency-type: indirect ... Signed-off-by: dependabot[bot] --- client/yarn.lock | 107 +++++++++++++++++++++++++++++++++-------------- 1 file changed, 76 insertions(+), 31 deletions(-) diff --git a/client/yarn.lock b/client/yarn.lock index ff4a5b3e7..ce674aad4 100644 --- a/client/yarn.lock +++ b/client/yarn.lock @@ -353,6 +353,14 @@ dependencies: "@babel/highlight" "^7.18.6" +"@babel/code-frame@^7.22.13": + version "7.22.13" + resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.22.13.tgz#e3c1c099402598483b7a8c46a721d1038803755e" + integrity sha512-XktuhWlJ5g+3TJXc5upd9Ks1HutSArik6jf2eAjYFyIOf4ej3RN+184cZbzDvbPnuTJIUhPKKJE3cIsYTiAT3w== + dependencies: + "@babel/highlight" "^7.22.13" + chalk "^2.4.2" + "@babel/code-frame@^7.22.5": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.22.5.tgz#234d98e1551960604f1246e6475891a570ad5658" @@ -431,7 +439,7 @@ "@jridgewell/gen-mapping" "^0.3.2" jsesc "^2.5.1" -"@babel/generator@^7.22.5", "@babel/generator@^7.22.7": +"@babel/generator@^7.22.5": version "7.22.9" resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.22.9.tgz#572ecfa7a31002fa1de2a9d91621fd895da8493d" integrity sha512-KtLMbmicyuK2Ak/FTCJVbDnkN1SlT8/kceFTiuDiiRUUSMnHMidxSCdG4ndkTOHHpoomWe/4xkvHkEOncwjYIw== @@ -441,6 +449,16 @@ "@jridgewell/trace-mapping" "^0.3.17" jsesc "^2.5.1" +"@babel/generator@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/generator/-/generator-7.23.0.tgz#df5c386e2218be505b34837acbcb874d7a983420" + integrity sha512-lN85QRR+5IbYrMWM6Y4pE/noaQtg4pNiqeNGX60eqOfo6gtEj6uw/JagelB8vVztSd7R6M5n1+PQkDbHbBRU4g== + dependencies: + "@babel/types" "^7.23.0" + "@jridgewell/gen-mapping" "^0.3.2" + "@jridgewell/trace-mapping" "^0.3.17" + jsesc "^2.5.1" + "@babel/helper-annotate-as-pure@7.22.5", "@babel/helper-annotate-as-pure@^7.22.5": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.22.5.tgz#e7f06737b197d580a01edf75d97e2c8be99d3882" @@ -546,6 +564,11 @@ resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.18.9.tgz#0c0cee9b35d2ca190478756865bb3528422f51be" integrity sha512-3r/aACDJ3fhQ/EVgFy0hpj8oHyHpQc+LPtJoY9SzTThAsStm4Ptegq92vqKoE3vD706ZVFWITnMnxucw+S9Ipg== +"@babel/helper-environment-visitor@^7.22.20": + version "7.22.20" + resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.20.tgz#96159db61d34a29dba454c959f5ae4a649ba9167" + integrity sha512-zfedSIzFhat/gFhWfHtgWvlec0nqB9YEIVrpuwjruLlXfUSnA8cJB0miHKwqDnQ7d32aKo2xt88/xZptwxbfhA== + "@babel/helper-environment-visitor@^7.22.5": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/helper-environment-visitor/-/helper-environment-visitor-7.22.5.tgz#f06dd41b7c1f44e1f8da6c4055b41ab3a09a7e98" @@ -567,12 +590,13 @@ "@babel/template" "^7.22.5" "@babel/types" "^7.22.5" -"@babel/helper-hoist-variables@^7.18.6": - version "7.18.6" - resolved "https://registry.yarnpkg.com/@babel/helper-hoist-variables/-/helper-hoist-variables-7.18.6.tgz#d4d2c8fb4baeaa5c68b99cc8245c56554f926678" - integrity sha512-UlJQPkFqFULIcyW5sbzgbkxn2FKRgwWiRexcuaR8RNJRy8+LLveqPjwZV/bwrLZCN0eUHD/x8D0heK1ozuoo6Q== +"@babel/helper-function-name@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/helper-function-name/-/helper-function-name-7.23.0.tgz#1f9a3cdbd5b2698a670c30d2735f9af95ed52759" + integrity sha512-OErEqsrxjZTJciZ4Oo+eoZqeW9UIiOcuYKRJA4ZAgV9myA+pOXhhmpfNCKjEH/auVfEYVFJ6y1Tc4r0eIApqiw== dependencies: - "@babel/types" "^7.18.6" + "@babel/template" "^7.22.15" + "@babel/types" "^7.23.0" "@babel/helper-hoist-variables@^7.22.5": version "7.22.5" @@ -762,6 +786,11 @@ resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.19.1.tgz#7eea834cf32901ffdc1a7ee555e2f9c27e249ca2" integrity sha512-awrNfaMtnHUr653GgGEs++LlAvW6w+DcPrOliSMXWCKo597CwL5Acf/wWdNkf/tfEQE3mjkeD1YOVZOUV/od1w== +"@babel/helper-validator-identifier@^7.22.20": + version "7.22.20" + resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.20.tgz#c4ae002c61d2879e724581d96665583dbc1dc0e0" + integrity sha512-Y4OZ+ytlatR8AI+8KZfKuL5urKp7qey08ha31L8b3BwewJAoJamTzyvxPR/5D+KkdJCGPq/+8TukHBlY10FX9A== + "@babel/helper-validator-identifier@^7.22.5": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/helper-validator-identifier/-/helper-validator-identifier-7.22.5.tgz#9544ef6a33999343c8740fa51350f30eeaaaf193" @@ -823,6 +852,15 @@ chalk "^2.0.0" js-tokens "^4.0.0" +"@babel/highlight@^7.22.13": + version "7.22.20" + resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.22.20.tgz#4ca92b71d80554b01427815e06f2df965b9c1f54" + integrity sha512-dkdMCN3py0+ksCgYmGG8jKeGA/8Tk+gJwSYYlFGxG5lmhfKNoAy004YpLxpS1W2J8m/EK2Ew+yOs9pVRwO89mg== + dependencies: + "@babel/helper-validator-identifier" "^7.22.20" + chalk "^2.4.2" + js-tokens "^4.0.0" + "@babel/highlight@^7.22.5": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/highlight/-/highlight-7.22.5.tgz#aa6c05c5407a67ebce408162b7ede789b4d22031" @@ -837,7 +875,12 @@ resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.20.7.tgz#66fe23b3c8569220817d5feb8b9dcdc95bb4f71b" integrity sha512-T3Z9oHybU+0vZlY9CiDSJQTD5ZapcW18ZctFMi0MOAl/4BjFF4ul7NVSARLdbGO5vDqy9eQiGTV0LtKfvCYvcg== -"@babel/parser@^7.22.5", "@babel/parser@^7.22.7": +"@babel/parser@^7.22.15", "@babel/parser@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.23.0.tgz#da950e622420bf96ca0d0f2909cdddac3acd8719" + integrity sha512-vvPKKdMemU85V9WE/l5wZEmImpCtLqbnTvqDS2U1fJ96KrxoW7KrXhNsNCblQlg8Ck4b85yxdTyelsMUgFUXiw== + +"@babel/parser@^7.22.5": version "7.22.7" resolved "https://registry.yarnpkg.com/@babel/parser/-/parser-7.22.7.tgz#df8cf085ce92ddbdbf668a7f186ce848c9036cae" integrity sha512-7NF8pOkHP5o2vpmGgNGcfAeCvOYhGLyA3Z4eBQkT1RJlWu47n63bCs93QfJ2hIAFCil7L5P2IWhs1oToVgrL0Q== @@ -1750,35 +1793,28 @@ "@babel/parser" "^7.20.7" "@babel/types" "^7.20.7" -"@babel/traverse@^7.10.3", "@babel/traverse@^7.14.0", "@babel/traverse@^7.16.8", "@babel/traverse@^7.20.10", "@babel/traverse@^7.20.12", "@babel/traverse@^7.20.5", "@babel/traverse@^7.20.7": - version "7.20.12" - resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.20.12.tgz#7f0f787b3a67ca4475adef1f56cb94f6abd4a4b5" - integrity sha512-MsIbFN0u+raeja38qboyF8TIT7K0BFzz/Yd/77ta4MsUsmP2RAnidIlwq7d5HFQrH/OZJecGV6B71C4zAgpoSQ== +"@babel/template@^7.22.15": + version "7.22.15" + resolved "https://registry.yarnpkg.com/@babel/template/-/template-7.22.15.tgz#09576efc3830f0430f4548ef971dde1350ef2f38" + integrity sha512-QPErUVm4uyJa60rkI73qneDacvdvzxshT3kksGqlGWYdOTIUOwJ7RDUL8sGqslY1uXWSL6xMFKEXDS3ox2uF0w== dependencies: - "@babel/code-frame" "^7.18.6" - "@babel/generator" "^7.20.7" - "@babel/helper-environment-visitor" "^7.18.9" - "@babel/helper-function-name" "^7.19.0" - "@babel/helper-hoist-variables" "^7.18.6" - "@babel/helper-split-export-declaration" "^7.18.6" - "@babel/parser" "^7.20.7" - "@babel/types" "^7.20.7" - debug "^4.1.0" - globals "^11.1.0" + "@babel/code-frame" "^7.22.13" + "@babel/parser" "^7.22.15" + "@babel/types" "^7.22.15" -"@babel/traverse@^7.22.5", "@babel/traverse@^7.22.6": - version "7.22.8" - resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.22.8.tgz#4d4451d31bc34efeae01eac222b514a77aa4000e" - integrity sha512-y6LPR+wpM2I3qJrsheCTwhIinzkETbplIgPBbwvqPKc+uljeA5gP+3nP8irdYt1mjQaDnlIcG+dw8OjAco4GXw== +"@babel/traverse@^7.10.3", "@babel/traverse@^7.14.0", "@babel/traverse@^7.16.8", "@babel/traverse@^7.20.10", "@babel/traverse@^7.20.12", "@babel/traverse@^7.20.5", "@babel/traverse@^7.20.7", "@babel/traverse@^7.22.5", "@babel/traverse@^7.22.6": + version "7.23.2" + resolved "https://registry.yarnpkg.com/@babel/traverse/-/traverse-7.23.2.tgz#329c7a06735e144a506bdb2cad0268b7f46f4ad8" + integrity sha512-azpe59SQ48qG6nu2CzcMLbxUudtN+dOM9kDbUqGq3HXUJRlo7i8fvPoxQUzYgLZ4cMVmuZgm8vvBpNeRhd6XSw== dependencies: - "@babel/code-frame" "^7.22.5" - "@babel/generator" "^7.22.7" - "@babel/helper-environment-visitor" "^7.22.5" - "@babel/helper-function-name" "^7.22.5" + "@babel/code-frame" "^7.22.13" + "@babel/generator" "^7.23.0" + "@babel/helper-environment-visitor" "^7.22.20" + "@babel/helper-function-name" "^7.23.0" "@babel/helper-hoist-variables" "^7.22.5" "@babel/helper-split-export-declaration" "^7.22.6" - "@babel/parser" "^7.22.7" - "@babel/types" "^7.22.5" + "@babel/parser" "^7.23.0" + "@babel/types" "^7.23.0" debug "^4.1.0" globals "^11.1.0" @@ -1791,6 +1827,15 @@ "@babel/helper-validator-identifier" "^7.19.1" to-fast-properties "^2.0.0" +"@babel/types@^7.22.15", "@babel/types@^7.23.0": + version "7.23.0" + resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.23.0.tgz#8c1f020c9df0e737e4e247c0619f58c68458aaeb" + integrity sha512-0oIyUfKoI3mSqMvsxBdclDwxXKXAUA8v/apZbc+iSyARYou1o8ZGDxbUYyLFoW2arqS2jDGqJuZvv1d/io1axg== + dependencies: + "@babel/helper-string-parser" "^7.22.5" + "@babel/helper-validator-identifier" "^7.22.20" + to-fast-properties "^2.0.0" + "@babel/types@^7.22.5": version "7.22.5" resolved "https://registry.yarnpkg.com/@babel/types/-/types-7.22.5.tgz#cd93eeaab025880a3a47ec881f4b096a5b786fbe" From 30ffa5edf6a2c2bc4d04af5dbf06f6bce4c4749c Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Tue, 17 Oct 2023 10:25:04 -0500 Subject: [PATCH 6/9] Implement suggestions from code review --- server/app/jobs/set_allele_registry_id_single_variant.rb | 8 ++++---- server/app/jobs/set_allele_registry_ids.rb | 4 ++-- server/app/jobs/update_allele_registry_ids.rb | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/server/app/jobs/set_allele_registry_id_single_variant.rb b/server/app/jobs/set_allele_registry_id_single_variant.rb index 7aefeba9a..eaa760866 100644 --- a/server/app/jobs/set_allele_registry_id_single_variant.rb +++ b/server/app/jobs/set_allele_registry_id_single_variant.rb @@ -7,14 +7,14 @@ def perform(variant) allele_registry_id = get_allele_registry_id(variant) if allele_registry_id == '_:CA' && old_allele_registry_id != 'unregistered' variant.allele_registry_id = 'unregistered' - variant.save + variant.save! elsif allele_registry_id.present? && allele_registry_id != '_:CA' && allele_registry_id != old_allele_registry_id variant.allele_registry_id = allele_registry_id - variant.save + variant.save! add_allele_registry_link(allele_registry_id) elsif old_allele_registry_id.present? && allele_registry_id.nil? - variant.allele_registry_id = None - variant.save + variant.allele_registry_id = nil + variant.save! end unless Variant.where(allele_registry_id: old_allele_registry_id).exists? if old_allele_registry_id != '_:CA' and old_allele_registry_id != 'undefined' diff --git a/server/app/jobs/set_allele_registry_ids.rb b/server/app/jobs/set_allele_registry_ids.rb index a652fefba..55fc573c9 100644 --- a/server/app/jobs/set_allele_registry_ids.rb +++ b/server/app/jobs/set_allele_registry_ids.rb @@ -7,10 +7,10 @@ def perform allele_registry_id = get_allele_registry_id(v) if allele_registry_id == '_:CA' v.allele_registry_id = 'unregistered' - v.save + v.save! elsif allele_registry_id.present? v.allele_registry_id = allele_registry_id - v.save + v.save! add_allele_registry_link(allele_registry_id) end end diff --git a/server/app/jobs/update_allele_registry_ids.rb b/server/app/jobs/update_allele_registry_ids.rb index c6fa32334..840c70332 100644 --- a/server/app/jobs/update_allele_registry_ids.rb +++ b/server/app/jobs/update_allele_registry_ids.rb @@ -9,14 +9,14 @@ def perform if allele_registry_id != old_allele_registry_id || old_allele_registry_id == '_:CA' if allele_registry_id == '_:CA' v.allele_registry_id = 'unregistered' - v.save + v.save! elsif allele_registry_id.present? v.allele_registry_id = allele_registry_id - v.save + v.save! add_allele_registry_link(allele_registry_id) elsif old_allele_registry_id.present? && allele_registry_id.nil? - v.allele_registry_id = None - v.save + v.allele_registry_id = nil + v.save! end #delete the linkout if no other variant has this allele registry ID unless Variant.where(allele_registry_id: old_allele_registry_id).exists? From ed99c7e60f083b140c914ff6756683463bc5541e Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 19 Oct 2023 14:03:04 -0500 Subject: [PATCH 7/9] Fix COSMIC linkouts --- .../variants/my-variant-info/my-variant-info.component.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/app/components/variants/my-variant-info/my-variant-info.component.html b/client/src/app/components/variants/my-variant-info/my-variant-info.component.html index 429bf75a2..0039fcb55 100644 --- a/client/src/app/components/variants/my-variant-info/my-variant-info.component.html +++ b/client/src/app/components/variants/my-variant-info/my-variant-info.component.html @@ -83,7 +83,7 @@ {{ variantInfo.cosmicId }} From 484a24dd2f936e68db27b9dfb6972e58f4799b07 Mon Sep 17 00:00:00 2001 From: Joshua McMichael Date: Thu, 19 Oct 2023 14:04:08 -0500 Subject: [PATCH 8/9] fix welcome page news item text Removed '(HTML)' string from headline. --- client/src/app/views/welcome/welcome.component.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/app/views/welcome/welcome.component.ts b/client/src/app/views/welcome/welcome.component.ts index 6a31cc8a9..95f3242e9 100644 --- a/client/src/app/views/welcome/welcome.component.ts +++ b/client/src/app/views/welcome/welcome.component.ts @@ -47,7 +47,7 @@ export class WelcomeComponent implements OnInit { imageUrl: 'assets/images/2023-CGC-hackathon-attendees.jpg', }, { - title: 'Introducing Molecular Profiles (HTML)', + title: 'Introducing Molecular Profiles', date: '2023-01-09', htmlText: `Today we have rolled out support for a new core concept in CIViC: Molecular Profiles. Molecular Profiles are logical combinations of one or more CIViC Variants. While most Molecular Profiles will consist of a single Variant (“Simple”) they will also allow users to build “Complex” (multi-variant) Molecular Profiles to associate Evidence with. These complex profiles expand the CIViC data model to allow for clinical significance to be evaluated within contexts such as variant co-occurrence or mutual exclusivity. Going forward, Evidence will be associated with a Molecular Profile rather than directly with a Variant. If you have any questions about this change, please feel free to contact us. We have also prepared a video explaining this new feature.`, link: { From 30ab9f164df9d4671a34ad9defa17e9b68075570 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Fri, 20 Oct 2023 08:56:57 -0500 Subject: [PATCH 9/9] Exclude EID to be revised from duplication check --- .../app/graphql/mutations/suggest_evidence_item_revision.rb | 2 +- .../app/models/input_adaptors/evidence_item_input_adaptor.rb | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/server/app/graphql/mutations/suggest_evidence_item_revision.rb b/server/app/graphql/mutations/suggest_evidence_item_revision.rb index eb51e1b45..78e819332 100644 --- a/server/app/graphql/mutations/suggest_evidence_item_revision.rb +++ b/server/app/graphql/mutations/suggest_evidence_item_revision.rb @@ -39,7 +39,7 @@ def ready?(organization_id: nil, id:, fields:, **kwargs) @evidence_item = evidence_item - input_errors = InputAdaptors::EvidenceItemInputAdaptor.check_input_for_errors(evidence_input_object: fields) + input_errors = InputAdaptors::EvidenceItemInputAdaptor.check_input_for_errors(evidence_input_object: fields, revised_eid: id) if input_errors.any? raise GraphQL::ExecutionError, input_errors.join('|') diff --git a/server/app/models/input_adaptors/evidence_item_input_adaptor.rb b/server/app/models/input_adaptors/evidence_item_input_adaptor.rb index 7133f3b98..f7c99be45 100644 --- a/server/app/models/input_adaptors/evidence_item_input_adaptor.rb +++ b/server/app/models/input_adaptors/evidence_item_input_adaptor.rb @@ -10,7 +10,7 @@ def perform EvidenceItem.new(self.class.evidence_fields(input)) end - def self.check_input_for_errors(evidence_input_object: ) + def self.check_input_for_errors(evidence_input_object: , revised_eid: nil) errors = [] fields = evidence_input_object @@ -20,6 +20,9 @@ def self.check_input_for_errors(evidence_input_object: ) query_fields.delete(:phenotype_ids) eid_query = EvidenceItem.where(query_fields) + if revised_eid.present? + eid_query = eid_query.where.not(id: revised_eid) + end if eid = eid_query.first if eid.therapy_ids.sort == fields.therapy_ids.sort && eid.phenotype_ids.sort == fields.phenotype_ids.sort