From 607be201ad2173ba2738488bcf6104f4b1b7b3e2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 22 Apr 2022 22:52:55 +0000 Subject: [PATCH 01/28] Bump nconf from 0.11.2 to 0.11.4 in /web/packages/api Bumps [nconf](https://github.com/flatiron/nconf) from 0.11.2 to 0.11.4. - [Release notes](https://github.com/flatiron/nconf/releases) - [Changelog](https://github.com/indexzero/nconf/blob/master/CHANGELOG.md) - [Commits](https://github.com/flatiron/nconf/compare/v0.11.2...v0.11.4) --- updated-dependencies: - dependency-name: nconf dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 14 +++++++------- web/packages/api/package.json | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index 31d6439f..d5d9e8c5 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -16,7 +16,7 @@ "method-override": "^3.0.0", "mocha": "^8.3.0", "morgan": "^1.10.0", - "nconf": "^0.11.2", + "nconf": "^0.11.4", "neo4j-driver": "^4.2.2", "python-shell": "^3.0.1", "swagger-jsdoc": "^6.0.6", @@ -1637,9 +1637,9 @@ } }, "node_modules/nconf": { - "version": "0.11.2", - "resolved": "https://registry.npmjs.org/nconf/-/nconf-0.11.2.tgz", - "integrity": "sha512-gDmn0Fgt0U0esRE8OCF72tO8AA9dtlG9eZhW4/Ex5hozNC2/LgdhWO4vKLGHNfTxcvsv6Aoxk/ROVYJD2SAdyg==", + "version": "0.11.4", + "resolved": "https://registry.npmjs.org/nconf/-/nconf-0.11.4.tgz", + "integrity": "sha512-YaDR846q11JnG1vTrhJ0QIlhiGY6+W1bgWtReG9SS3vkTl3AoNwFvUItdhG6/ZjGCfWpUVuRTNEBTDAQ3nWhGw==", "dependencies": { "async": "^1.4.0", "ini": "^2.0.0", @@ -4060,9 +4060,9 @@ "integrity": "sha512-a1cQNyczgKbLX9jwbS/+d7W8fX/RfgYR7lVWwWOGIPNgK2m0MWvrGF6/m4kk6U3QcFMnZf3RIhL0v2Jgh/0Uxw==" }, "nconf": { - "version": "0.11.2", - "resolved": "https://registry.npmjs.org/nconf/-/nconf-0.11.2.tgz", - "integrity": "sha512-gDmn0Fgt0U0esRE8OCF72tO8AA9dtlG9eZhW4/Ex5hozNC2/LgdhWO4vKLGHNfTxcvsv6Aoxk/ROVYJD2SAdyg==", + "version": "0.11.4", + "resolved": "https://registry.npmjs.org/nconf/-/nconf-0.11.4.tgz", + "integrity": "sha512-YaDR846q11JnG1vTrhJ0QIlhiGY6+W1bgWtReG9SS3vkTl3AoNwFvUItdhG6/ZjGCfWpUVuRTNEBTDAQ3nWhGw==", "requires": { "async": "^1.4.0", "ini": "^2.0.0", diff --git a/web/packages/api/package.json b/web/packages/api/package.json index 5f9eeed8..4f118119 100644 --- a/web/packages/api/package.json +++ b/web/packages/api/package.json @@ -31,7 +31,7 @@ "method-override": "^3.0.0", "mocha": "^8.3.0", "morgan": "^1.10.0", - "nconf": "^0.11.2", + "nconf": "^0.11.4", "neo4j-driver": "^4.2.2", "python-shell": "^3.0.1", "swagger-jsdoc": "^6.0.6", From 28e0280b00139a95fb3f22ef9b087527cb0a6b09 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 22 May 2022 04:45:36 +0000 Subject: [PATCH 02/28] Bump node-forge from 1.2.1 to 1.3.1 in /web/packages/app Bumps [node-forge](https://github.com/digitalbazaar/forge) from 1.2.1 to 1.3.1. - [Release notes](https://github.com/digitalbazaar/forge/releases) - [Changelog](https://github.com/digitalbazaar/forge/blob/main/CHANGELOG.md) - [Commits](https://github.com/digitalbazaar/forge/compare/v1.2.1...v1.3.1) --- updated-dependencies: - dependency-name: node-forge dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/app/package-lock.json | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/web/packages/app/package-lock.json b/web/packages/app/package-lock.json index 4edfb6a6..e7435468 100644 --- a/web/packages/app/package-lock.json +++ b/web/packages/app/package-lock.json @@ -14345,9 +14345,10 @@ } }, "node_modules/node-forge": { - "version": "1.2.1", + "version": "1.3.1", + "resolved": "https://registry.npmjs.org/node-forge/-/node-forge-1.3.1.tgz", + "integrity": "sha512-dPEtOeMvF9VMcYV/1Wb8CPoVAXtp6MKMlcbAt4ddqmGqUJ6fQZFXkNZNkNlfevtNkGtaSoXf/vNNNSvgrdXwtA==", "dev": true, - "license": "(BSD-3-Clause OR GPL-2.0)", "engines": { "node": ">= 6.13.0" } @@ -29235,7 +29236,9 @@ } }, "node-forge": { - "version": "1.2.1", + "version": "1.3.1", + "resolved": "https://registry.npmjs.org/node-forge/-/node-forge-1.3.1.tgz", + "integrity": "sha512-dPEtOeMvF9VMcYV/1Wb8CPoVAXtp6MKMlcbAt4ddqmGqUJ6fQZFXkNZNkNlfevtNkGtaSoXf/vNNNSvgrdXwtA==", "dev": true }, "node-int64": { From 5d1f406b1128e62e6c50b0f576abab6ae752789f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 20 Jul 2022 20:42:01 +0000 Subject: [PATCH 03/28] Bump terser from 5.11.0 to 5.14.2 in /web/packages/app Bumps [terser](https://github.com/terser/terser) from 5.11.0 to 5.14.2. - [Release notes](https://github.com/terser/terser/releases) - [Changelog](https://github.com/terser/terser/blob/master/CHANGELOG.md) - [Commits](https://github.com/terser/terser/commits) --- updated-dependencies: - dependency-name: terser dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/app/package-lock.json | 94 +++++++++++++++++++++++------- 1 file changed, 74 insertions(+), 20 deletions(-) diff --git a/web/packages/app/package-lock.json b/web/packages/app/package-lock.json index 8e92289a..cb263cbc 100644 --- a/web/packages/app/package-lock.json +++ b/web/packages/app/package-lock.json @@ -3303,6 +3303,20 @@ "node": ">=8" } }, + "node_modules/@jridgewell/gen-mapping": { + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.2.tgz", + "integrity": "sha512-mh65xKQAzI6iBcFzwv28KVWSmCkdRBWoOh+bYQGW3+6OZvbbN3TqMGo5hqYxQniRcH9F2VZIoJCm4pa3BPDK/A==", + "dev": true, + "dependencies": { + "@jridgewell/set-array": "^1.0.1", + "@jridgewell/sourcemap-codec": "^1.4.10", + "@jridgewell/trace-mapping": "^0.3.9" + }, + "engines": { + "node": ">=6.0.0" + } + }, "node_modules/@jridgewell/resolve-uri": { "version": "3.0.5", "license": "MIT", @@ -3310,13 +3324,33 @@ "node": ">=6.0.0" } }, + "node_modules/@jridgewell/set-array": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz", + "integrity": "sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw==", + "dev": true, + "engines": { + "node": ">=6.0.0" + } + }, + "node_modules/@jridgewell/source-map": { + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.2.tgz", + "integrity": "sha512-m7O9o2uR8k2ObDysZYzdfhb08VuEml5oWGiosa1VdaPZ/A6QyPkAJuwN0Q1lhULOf6B7MtQmHENS743hWtCrgw==", + "dev": true, + "dependencies": { + "@jridgewell/gen-mapping": "^0.3.0", + "@jridgewell/trace-mapping": "^0.3.9" + } + }, "node_modules/@jridgewell/sourcemap-codec": { "version": "1.4.11", "license": "MIT" }, "node_modules/@jridgewell/trace-mapping": { - "version": "0.3.4", - "license": "MIT", + "version": "0.3.14", + "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.14.tgz", + "integrity": "sha512-bJWEfQ9lPTvm3SneWwRFVLzrh6nhjwqw7TUFFBEMzwvg7t7PCDenf2lDwqo4NQXzdpgBXyFgDWnQA+2vkruksQ==", "dependencies": { "@jridgewell/resolve-uri": "^3.0.3", "@jridgewell/sourcemap-codec": "^1.4.10" @@ -18650,13 +18684,14 @@ } }, "node_modules/terser": { - "version": "5.11.0", + "version": "5.14.2", + "resolved": "https://registry.npmjs.org/terser/-/terser-5.14.2.tgz", + "integrity": "sha512-oL0rGeM/WFQCUd0y2QrWxYnq7tfSuKBiqTjRPWrRgB46WD/kiwHwF8T23z78H6Q6kGCuuHcPB+KULHRdxvVGQA==", "dev": true, - "license": "BSD-2-Clause", "dependencies": { + "@jridgewell/source-map": "^0.3.2", "acorn": "^8.5.0", "commander": "^2.20.0", - "source-map": "~0.7.2", "source-map-support": "~0.5.20" }, "bin": { @@ -18723,14 +18758,6 @@ "dev": true, "license": "MIT" }, - "node_modules/terser/node_modules/source-map": { - "version": "0.7.3", - "dev": true, - "license": "BSD-3-Clause", - "engines": { - "node": ">= 8" - } - }, "node_modules/test-exclude": { "version": "6.0.0", "dev": true, @@ -22124,14 +22151,43 @@ } } }, + "@jridgewell/gen-mapping": { + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/@jridgewell/gen-mapping/-/gen-mapping-0.3.2.tgz", + "integrity": "sha512-mh65xKQAzI6iBcFzwv28KVWSmCkdRBWoOh+bYQGW3+6OZvbbN3TqMGo5hqYxQniRcH9F2VZIoJCm4pa3BPDK/A==", + "dev": true, + "requires": { + "@jridgewell/set-array": "^1.0.1", + "@jridgewell/sourcemap-codec": "^1.4.10", + "@jridgewell/trace-mapping": "^0.3.9" + } + }, "@jridgewell/resolve-uri": { "version": "3.0.5" }, + "@jridgewell/set-array": { + "version": "1.1.2", + "resolved": "https://registry.npmjs.org/@jridgewell/set-array/-/set-array-1.1.2.tgz", + "integrity": "sha512-xnkseuNADM0gt2bs+BvhO0p78Mk762YnZdsuzFV018NoG1Sj1SCQvpSqa7XUaTam5vAGasABV9qXASMKnFMwMw==", + "dev": true + }, + "@jridgewell/source-map": { + "version": "0.3.2", + "resolved": "https://registry.npmjs.org/@jridgewell/source-map/-/source-map-0.3.2.tgz", + "integrity": "sha512-m7O9o2uR8k2ObDysZYzdfhb08VuEml5oWGiosa1VdaPZ/A6QyPkAJuwN0Q1lhULOf6B7MtQmHENS743hWtCrgw==", + "dev": true, + "requires": { + "@jridgewell/gen-mapping": "^0.3.0", + "@jridgewell/trace-mapping": "^0.3.9" + } + }, "@jridgewell/sourcemap-codec": { "version": "1.4.11" }, "@jridgewell/trace-mapping": { - "version": "0.3.4", + "version": "0.3.14", + "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.14.tgz", + "integrity": "sha512-bJWEfQ9lPTvm3SneWwRFVLzrh6nhjwqw7TUFFBEMzwvg7t7PCDenf2lDwqo4NQXzdpgBXyFgDWnQA+2vkruksQ==", "requires": { "@jridgewell/resolve-uri": "^3.0.3", "@jridgewell/sourcemap-codec": "^1.4.10" @@ -31892,12 +31948,14 @@ } }, "terser": { - "version": "5.11.0", + "version": "5.14.2", + "resolved": "https://registry.npmjs.org/terser/-/terser-5.14.2.tgz", + "integrity": "sha512-oL0rGeM/WFQCUd0y2QrWxYnq7tfSuKBiqTjRPWrRgB46WD/kiwHwF8T23z78H6Q6kGCuuHcPB+KULHRdxvVGQA==", "dev": true, "requires": { + "@jridgewell/source-map": "^0.3.2", "acorn": "^8.5.0", "commander": "^2.20.0", - "source-map": "~0.7.2", "source-map-support": "~0.5.20" }, "dependencies": { @@ -31908,10 +31966,6 @@ "commander": { "version": "2.20.3", "dev": true - }, - "source-map": { - "version": "0.7.3", - "dev": true } } }, From e4b0f4733db70e58669f160272e648f09975562d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 8 Nov 2022 11:10:20 +0000 Subject: [PATCH 04/28] Bump loader-utils in /web/packages/app Bumps [loader-utils](https://github.com/webpack/loader-utils) and [loader-utils](https://github.com/webpack/loader-utils). These dependencies needed to be updated together. Updates `loader-utils` from 2.0.0 to 2.0.3 - [Release notes](https://github.com/webpack/loader-utils/releases) - [Changelog](https://github.com/webpack/loader-utils/blob/v2.0.3/CHANGELOG.md) - [Commits](https://github.com/webpack/loader-utils/compare/v2.0.0...v2.0.3) Updates `loader-utils` from 1.4.0 to 2.0.3 - [Release notes](https://github.com/webpack/loader-utils/releases) - [Changelog](https://github.com/webpack/loader-utils/blob/v2.0.3/CHANGELOG.md) - [Commits](https://github.com/webpack/loader-utils/compare/v2.0.0...v2.0.3) --- updated-dependencies: - dependency-name: loader-utils dependency-type: indirect - dependency-name: loader-utils dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/app/package-lock.json | 55 ++++++++++++++++++++++++------ 1 file changed, 44 insertions(+), 11 deletions(-) diff --git a/web/packages/app/package-lock.json b/web/packages/app/package-lock.json index 8e92289a..839b7bd3 100644 --- a/web/packages/app/package-lock.json +++ b/web/packages/app/package-lock.json @@ -5879,9 +5879,10 @@ } }, "node_modules/babel-loader/node_modules/loader-utils": { - "version": "1.4.0", + "version": "1.4.1", + "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-1.4.1.tgz", + "integrity": "sha512-1Qo97Y2oKaU+Ro2xnDMR26g1BwMT29jNbem1EvcujW2jqt+j5COXyscjM7bLQkM9HaxI7pkWeW7gnI072yMI9Q==", "dev": true, - "license": "MIT", "dependencies": { "big.js": "^5.2.2", "emojis-list": "^3.0.0", @@ -13945,9 +13946,10 @@ } }, "node_modules/loader-utils": { - "version": "2.0.0", + "version": "2.0.3", + "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.3.tgz", + "integrity": "sha512-THWqIsn8QRnvLl0shHYVBN9syumU8pYWEHPTmkiVGd+7K5eFNVSY6AJhRvgGF70gg1Dz+l/k8WicvFCxdEs60A==", "dev": true, - "license": "MIT", "dependencies": { "big.js": "^5.2.2", "emojis-list": "^3.0.0", @@ -18634,6 +18636,18 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/tempy/node_modules/type-fest": { + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.16.0.tgz", + "integrity": "sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg==", + "dev": true, + "engines": { + "node": ">=10" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/terminal-link": { "version": "2.1.1", "dev": true, @@ -18926,11 +18940,14 @@ } }, "node_modules/type-fest": { - "version": "0.16.0", + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-2.19.0.tgz", + "integrity": "sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA==", "dev": true, - "license": "(MIT OR CC0-1.0)", + "optional": true, + "peer": true, "engines": { - "node": ">=10" + "node": ">=12.20" }, "funding": { "url": "https://github.com/sponsors/sindresorhus" @@ -23724,7 +23741,9 @@ } }, "loader-utils": { - "version": "1.4.0", + "version": "1.4.1", + "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-1.4.1.tgz", + "integrity": "sha512-1Qo97Y2oKaU+Ro2xnDMR26g1BwMT29jNbem1EvcujW2jqt+j5COXyscjM7bLQkM9HaxI7pkWeW7gnI072yMI9Q==", "dev": true, "requires": { "big.js": "^5.2.2", @@ -28998,7 +29017,9 @@ "dev": true }, "loader-utils": { - "version": "2.0.0", + "version": "2.0.3", + "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.3.tgz", + "integrity": "sha512-THWqIsn8QRnvLl0shHYVBN9syumU8pYWEHPTmkiVGd+7K5eFNVSY6AJhRvgGF70gg1Dz+l/k8WicvFCxdEs60A==", "dev": true, "requires": { "big.js": "^5.2.2", @@ -31881,6 +31902,14 @@ "temp-dir": "^2.0.0", "type-fest": "^0.16.0", "unique-string": "^2.0.0" + }, + "dependencies": { + "type-fest": { + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.16.0.tgz", + "integrity": "sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg==", + "dev": true + } } }, "terminal-link": { @@ -32067,8 +32096,12 @@ "dev": true }, "type-fest": { - "version": "0.16.0", - "dev": true + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-2.19.0.tgz", + "integrity": "sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA==", + "dev": true, + "optional": true, + "peer": true }, "type-is": { "version": "1.6.18", From 63b28235429506720e936a99db9e0f1cec44493a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 11 Nov 2022 04:17:05 +0000 Subject: [PATCH 05/28] Bump minimatch and mocha in /web/packages/api Bumps [minimatch](https://github.com/isaacs/minimatch) to 3.1.2 and updates ancestor dependency [mocha](https://github.com/mochajs/mocha). These dependencies need to be updated together. Updates `minimatch` from 3.0.4 to 3.1.2 - [Release notes](https://github.com/isaacs/minimatch/releases) - [Commits](https://github.com/isaacs/minimatch/compare/v3.0.4...v3.1.2) Updates `mocha` from 8.3.0 to 10.1.0 - [Release notes](https://github.com/mochajs/mocha/releases) - [Changelog](https://github.com/mochajs/mocha/blob/master/CHANGELOG.md) - [Commits](https://github.com/mochajs/mocha/compare/v8.3.0...v10.1.0) --- updated-dependencies: - dependency-name: minimatch dependency-type: indirect - dependency-name: mocha dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 514 +++++++++++++++-------------- web/packages/api/package.json | 2 +- 2 files changed, 259 insertions(+), 257 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index aa35b6f9..2ff3def6 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -15,7 +15,7 @@ "express": "^4.17.1", "lodash": "^4.17.21", "method-override": "^3.0.0", - "mocha": "^8.3.0", + "mocha": "^10.1.0", "morgan": "^1.10.0", "nconf": "^0.11.2", "neo4j-driver": "^4.2.2", @@ -119,11 +119,6 @@ "node": ">=6" } }, - "node_modules/@ungap/promise-all-settled": { - "version": "1.1.2", - "resolved": "https://registry.npmjs.org/@ungap/promise-all-settled/-/promise-all-settled-1.1.2.tgz", - "integrity": "sha512-sL/cEvJWAnClXw0wHk85/2L0G6Sj8UB0Ctc1TEMbKSsmpRosqhwj9gWgFRZSrBr2f9tiXISwNhCPmlfqUqyb9Q==" - }, "node_modules/abbrev": { "version": "1.1.1", "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.1.1.tgz", @@ -200,14 +195,6 @@ "node": ">=6" } }, - "node_modules/ansi-regex": { - "version": "3.0.1", - "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-3.0.1.tgz", - "integrity": "sha512-+O9Jct8wf++lXxxFc4hc8LsjaSq0HFzzL7cVsw8pRDIPdjKD2mT4ytDZlLuSBZ4cLKZFXIrMGO7DbQCtMJJMKw==", - "engines": { - "node": ">=4" - } - }, "node_modules/ansi-styles": { "version": "4.3.0", "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-4.3.0.tgz", @@ -220,9 +207,9 @@ } }, "node_modules/anymatch": { - "version": "3.1.1", - "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.1.tgz", - "integrity": "sha512-mM8522psRCqzV+6LhomX5wgp25YVibjh8Wj23I5RPkPppSVSjyKD2A2mBJmWGa+KN7f2D6LNh9jkBCeyLktzjg==", + "version": "3.1.2", + "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.2.tgz", + "integrity": "sha512-P43ePfOAIupkguHUycrc4qJ9kz8ZiuOUijaETwX7THt0Y/GNK7v0aa8rY816xWjZ7rJdA5XdMcpVFTKMq+RvWg==", "dependencies": { "normalize-path": "^3.0.0", "picomatch": "^2.0.4" @@ -479,15 +466,18 @@ } }, "node_modules/chalk": { - 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"string-width": { - "version": "2.1.1", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-2.1.1.tgz", - "integrity": "sha512-nOqH59deCq9SRHlxq1Aw85Jnt4w6KvLKqWVik6oA9ZklXLNIOlqg4F2yrT1MVaTjAqvVwdfeZ7w7aCvJD7ugkw==", - "requires": { - "is-fullwidth-code-point": "^2.0.0", - "strip-ansi": "^4.0.0" - } - }, - "strip-ansi": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-4.0.0.tgz", - "integrity": "sha1-qEeQIusaw2iocTibY1JixQXuNo8=", - "requires": { - "ansi-regex": "^3.0.0" - } - }, "strip-json-comments": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz", @@ -4843,22 +4861,6 @@ "resolved": "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz", "integrity": "sha1-IpnwLG3tMNSllhsLn3RSShj2NPw=" }, - "which": { - "version": "2.0.2", - "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz", - "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==", - "requires": { - "isexe": "^2.0.0" - } - }, - "wide-align": { - "version": "1.1.3", - "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.3.tgz", - "integrity": "sha512-QGkOQc8XL6Bt5PwnsExKBPuMKBxnGxWWW3fU55Xt4feHozMUhdUMaBCk290qpm/wG5u/RSKzwdAC4i51YigihA==", - "requires": { - "string-width": "^1.0.2 || 2" - } - }, "widest-line": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/widest-line/-/widest-line-3.1.0.tgz", @@ -4903,9 +4905,9 @@ } }, "workerpool": { - "version": "6.1.0", - "resolved": "https://registry.npmjs.org/workerpool/-/workerpool-6.1.0.tgz", - "integrity": "sha512-toV7q9rWNYha963Pl/qyeZ6wG+3nnsyvolaNUS8+R5Wtw6qJPTxIlOP1ZSvcGhEJw+l3HMMmtiNo9Gl61G4GVg==" + "version": "6.2.1", + "resolved": "https://registry.npmjs.org/workerpool/-/workerpool-6.2.1.tgz", + "integrity": "sha512-ILEIE97kDZvF9Wb9f6h5aXK4swSlKGUcOEGiIYb2OOu/IrDU9iwj0fD//SsA6E5ibwJxpEvhullJY4Sl4GcpAw==" }, "wrap-ansi": { "version": "7.0.0", diff --git a/web/packages/api/package.json b/web/packages/api/package.json index 16e5c3f1..3d24d92e 100644 --- a/web/packages/api/package.json +++ b/web/packages/api/package.json @@ -30,7 +30,7 @@ "express": "^4.17.1", "lodash": "^4.17.21", "method-override": "^3.0.0", - "mocha": "^8.3.0", + "mocha": "^10.1.0", "morgan": "^1.10.0", "nconf": "^0.11.2", "neo4j-driver": "^4.2.2", From 54396fada7b43627fb2f00fb584c26ffedcab3b2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 8 Dec 2022 10:22:47 +0000 Subject: [PATCH 06/28] Bump qs, body-parser and express in /web/packages/api Bumps [qs](https://github.com/ljharb/qs) to 6.11.0 and updates ancestor dependencies [qs](https://github.com/ljharb/qs), [body-parser](https://github.com/expressjs/body-parser) and [express](https://github.com/expressjs/express). These dependencies need to be updated together. Updates `qs` from 6.7.0 to 6.11.0 - [Release notes](https://github.com/ljharb/qs/releases) - [Changelog](https://github.com/ljharb/qs/blob/main/CHANGELOG.md) - [Commits](https://github.com/ljharb/qs/compare/v6.7.0...v6.11.0) Updates `body-parser` from 1.19.0 to 1.20.1 - [Release notes](https://github.com/expressjs/body-parser/releases) - [Changelog](https://github.com/expressjs/body-parser/blob/master/HISTORY.md) - [Commits](https://github.com/expressjs/body-parser/compare/1.19.0...1.20.1) Updates `express` from 4.17.1 to 4.18.2 - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](https://github.com/expressjs/express/compare/4.17.1...4.18.2) --- updated-dependencies: - dependency-name: qs dependency-type: indirect - dependency-name: body-parser dependency-type: direct:production - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 774 +++++++++++++++++++---------- web/packages/api/package.json | 4 +- 2 files changed, 520 insertions(+), 258 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index aa35b6f9..7df9f675 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -9,10 +9,10 @@ "version": "1.0.0", "license": "MIT", "dependencies": { - "body-parser": "^1.19.0", + "body-parser": "^1.20.1", "cors": "^2.8.5", "dotenv": "^8.2.0", - "express": "^4.17.1", + "express": "^4.18.2", "lodash": "^4.17.21", "method-override": "^3.0.0", "mocha": "^8.3.0", @@ -131,12 +131,12 @@ "dev": true }, "node_modules/accepts": { - "version": "1.3.7", - "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.7.tgz", - "integrity": "sha512-Il80Qs2WjYlJIBNzNkK6KYqlVMTbZLXgHx2oT0pU/fjRHyEp+PEfEPY0R3WCwAGVOtauxh1hOxNgIf5bv7dQpA==", + "version": "1.3.8", + "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.8.tgz", + "integrity": "sha512-PYAthTa2m2VKxuvSD3DPC/Gy+U+sOA1LAuT8mkmRuvw+NACSaeXEQ+NHcVF7rONl6qcaxV3Uuemwawk+7+SJLw==", "dependencies": { - "mime-types": "~2.1.24", - "negotiator": "0.6.2" + "mime-types": "~2.1.34", + "negotiator": "0.6.3" }, "engines": { "node": ">= 0.6" @@ -271,20 +271,34 @@ } }, "node_modules/body-parser": { - "version": "1.19.0", - "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.19.0.tgz", - "integrity": "sha512-dhEPs72UPbDnAQJ9ZKMNTP6ptJaionhP5cBb541nXPlW60Jepo9RV/a4fX4XWW9CuFNK22krhrj1+rgzifNCsw==", + "version": "1.20.1", + "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.20.1.tgz", + "integrity": "sha512-jWi7abTbYwajOytWCQc37VulmWiRae5RyTpaCyDcS5/lMdtwSz5lOpDE67srw/HYe35f1z3fDQw+3txg7gNtWw==", "dependencies": { - "bytes": "3.1.0", + "bytes": "3.1.2", "content-type": "~1.0.4", "debug": "2.6.9", - "depd": "~1.1.2", - "http-errors": "1.7.2", + "depd": "2.0.0", + "destroy": "1.2.0", + "http-errors": "2.0.0", "iconv-lite": "0.4.24", - "on-finished": "~2.3.0", - "qs": "6.7.0", - "raw-body": "2.4.0", - "type-is": "~1.6.17" + "on-finished": "2.4.1", + "qs": "6.11.0", + "raw-body": "2.5.1", + "type-is": "~1.6.18", + "unpipe": "1.0.0" + }, + "engines": { + "node": ">= 0.8", + "npm": "1.2.8000 || >= 1.4.16" + } + }, + "node_modules/body-parser/node_modules/on-finished": { + "version": "2.4.1", + "resolved": "https://registry.npmjs.org/on-finished/-/on-finished-2.4.1.tgz", + "integrity": "sha512-oVlzkg3ENAhCk2zdv7IJwd/QUD4z2RxRwpkcGY8psCVcCYZNq4wYnVWALHM+brtuJjePWiYF/ClmuDr8Ch5+kg==", + "dependencies": { + "ee-first": "1.1.1" }, "engines": { "node": ">= 0.8" @@ -416,9 +430,9 @@ "integrity": "sha512-qhAVI1+Av2X7qelOfAIYwXONood6XlZE/fXaBSmW/T5SzLAmCgzi+eiWE7fUvbHaeNBQH13UftjpXxsfLkMpgw==" }, "node_modules/bytes": { - 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"body-parser": "^1.19.0", + "body-parser": "^1.20.1", "cors": "^2.8.5", "dotenv": "^8.2.0", - "express": "^4.17.1", + "express": "^4.18.2", "lodash": "^4.17.21", "method-override": "^3.0.0", "mocha": "^8.3.0", From a33fda251c5a4b09fb9d94b73650ad89863cd6db Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 8 Dec 2022 13:07:05 +0000 Subject: [PATCH 07/28] Bump decode-uri-component from 0.2.0 to 0.2.2 in /web/packages/app Bumps [decode-uri-component](https://github.com/SamVerschueren/decode-uri-component) from 0.2.0 to 0.2.2. - [Release notes](https://github.com/SamVerschueren/decode-uri-component/releases) - [Commits](https://github.com/SamVerschueren/decode-uri-component/compare/v0.2.0...v0.2.2) --- updated-dependencies: - dependency-name: decode-uri-component dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/app/package-lock.json | 46 ++++++++++++++++++++++++------ 1 file changed, 38 insertions(+), 8 deletions(-) diff --git a/web/packages/app/package-lock.json b/web/packages/app/package-lock.json index 8e92289a..f541537d 100644 --- a/web/packages/app/package-lock.json +++ b/web/packages/app/package-lock.json @@ -7538,9 +7538,10 @@ "license": "MIT" }, "node_modules/decode-uri-component": { - "version": "0.2.0", + "version": "0.2.2", + "resolved": "https://registry.npmjs.org/decode-uri-component/-/decode-uri-component-0.2.2.tgz", + "integrity": "sha512-FqUYQ+8o158GyGTrMFJms9qh3CqTKvAqgqsTnkLI8sKu0028orqBhxNMFkFen0zGyg6epACD32pjVk58ngIErQ==", "dev": true, - "license": "MIT", "engines": { "node": ">=0.10" } @@ -18634,6 +18635,18 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/tempy/node_modules/type-fest": { + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.16.0.tgz", + "integrity": "sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg==", + "dev": true, + "engines": { + "node": ">=10" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/terminal-link": { "version": "2.1.1", "dev": true, @@ -18926,11 +18939,14 @@ } }, "node_modules/type-fest": { - "version": "0.16.0", + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-2.19.0.tgz", + "integrity": "sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA==", "dev": true, - "license": "(MIT OR CC0-1.0)", + "optional": true, + "peer": true, "engines": { - "node": ">=10" + "node": ">=12.20" }, "funding": { "url": "https://github.com/sponsors/sindresorhus" @@ -24861,7 +24877,9 @@ "dev": true }, "decode-uri-component": { - "version": "0.2.0", + "version": "0.2.2", + "resolved": "https://registry.npmjs.org/decode-uri-component/-/decode-uri-component-0.2.2.tgz", + "integrity": "sha512-FqUYQ+8o158GyGTrMFJms9qh3CqTKvAqgqsTnkLI8sKu0028orqBhxNMFkFen0zGyg6epACD32pjVk58ngIErQ==", "dev": true }, "dedent": { @@ -31881,6 +31899,14 @@ "temp-dir": "^2.0.0", "type-fest": "^0.16.0", "unique-string": "^2.0.0" + }, + "dependencies": { + "type-fest": { + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.16.0.tgz", + "integrity": "sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg==", + "dev": true + } } }, "terminal-link": { @@ -32067,8 +32093,12 @@ "dev": true }, "type-fest": { - "version": "0.16.0", - "dev": true + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-2.19.0.tgz", + "integrity": "sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA==", + "dev": true, + "optional": true, + "peer": true }, "type-is": { "version": "1.6.18", From 67fae3830e695ee0302655d98c35ad8a8101648b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 14 Dec 2022 03:01:47 +0000 Subject: [PATCH 08/28] Bump express from 4.17.1 to 4.17.3 in /web/packages/api Bumps [express](https://github.com/expressjs/express) from 4.17.1 to 4.17.3. - [Release notes](https://github.com/expressjs/express/releases) - [Changelog](https://github.com/expressjs/express/blob/master/History.md) - [Commits](https://github.com/expressjs/express/compare/4.17.1...4.17.3) --- updated-dependencies: - dependency-name: express dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 421 ++++++++++++++++------------- web/packages/api/package.json | 2 +- 2 files changed, 239 insertions(+), 184 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index aa35b6f9..3e736009 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -12,7 +12,7 @@ "body-parser": "^1.19.0", "cors": "^2.8.5", "dotenv": "^8.2.0", - "express": "^4.17.1", + "express": "^4.17.3", "lodash": "^4.17.21", "method-override": "^3.0.0", "mocha": "^8.3.0", @@ -131,12 +131,12 @@ "dev": true }, "node_modules/accepts": { - "version": "1.3.7", - "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.7.tgz", - "integrity": "sha512-Il80Qs2WjYlJIBNzNkK6KYqlVMTbZLXgHx2oT0pU/fjRHyEp+PEfEPY0R3WCwAGVOtauxh1hOxNgIf5bv7dQpA==", + "version": "1.3.8", + "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.8.tgz", + "integrity": "sha512-PYAthTa2m2VKxuvSD3DPC/Gy+U+sOA1LAuT8mkmRuvw+NACSaeXEQ+NHcVF7rONl6qcaxV3Uuemwawk+7+SJLw==", "dependencies": { - "mime-types": "~2.1.24", - "negotiator": "0.6.2" + "mime-types": "~2.1.34", + "negotiator": "0.6.3" }, "engines": { "node": ">= 0.6" @@ -271,20 +271,20 @@ } }, "node_modules/body-parser": { - "version": "1.19.0", - "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.19.0.tgz", - "integrity": "sha512-dhEPs72UPbDnAQJ9ZKMNTP6ptJaionhP5cBb541nXPlW60Jepo9RV/a4fX4XWW9CuFNK22krhrj1+rgzifNCsw==", + "version": "1.19.2", + "resolved": "https://registry.npmjs.org/body-parser/-/body-parser-1.19.2.tgz", + "integrity": "sha512-SAAwOxgoCKMGs9uUAUFHygfLAyaniaoun6I8mFY9pRAJL9+Kec34aU+oIjDhTycub1jozEfEwx1W1IuOYxVSFw==", "dependencies": { - "bytes": "3.1.0", + "bytes": "3.1.2", "content-type": "~1.0.4", "debug": "2.6.9", "depd": "~1.1.2", - "http-errors": "1.7.2", + "http-errors": "1.8.1", "iconv-lite": "0.4.24", "on-finished": "~2.3.0", - "qs": "6.7.0", - "raw-body": "2.4.0", - "type-is": "~1.6.17" + "qs": "6.9.7", + "raw-body": "2.4.3", + "type-is": "~1.6.18" }, "engines": { "node": ">= 0.8" @@ -416,9 +416,9 @@ "integrity": "sha512-qhAVI1+Av2X7qelOfAIYwXONood6XlZE/fXaBSmW/T5SzLAmCgzi+eiWE7fUvbHaeNBQH13UftjpXxsfLkMpgw==" }, "node_modules/bytes": { - 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"serve-static": "1.14.1", - "setprototypeof": "1.1.1", + "safe-buffer": "5.2.1", + "send": "0.17.2", + "serve-static": "1.14.2", + "setprototypeof": "1.2.0", "statuses": "~1.5.0", "type-is": "~1.6.18", "utils-merge": "1.0.1", @@ -923,6 +942,25 @@ "node": ">= 0.10.0" } }, + "node_modules/express/node_modules/safe-buffer": { + "version": "5.2.1", + "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.2.1.tgz", + "integrity": "sha512-rp3So07KcdmmKbGvgaNxQSJr7bGVSVk5S9Eq1F+ppbRo70+YeaDxkw5Dd8NPN+GD6bjnYm2VuPuCXmpuYvmCXQ==", + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/feross" + }, + { + "type": "patreon", + "url": "https://www.patreon.com/feross" + }, + { + "type": "consulting", + "url": "https://feross.org/support" + } + ] + }, "node_modules/fill-range": { "version": "7.0.1", "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz", @@ -972,9 +1010,9 @@ } }, "node_modules/forwarded": { - "version": "0.1.2", - "resolved": "https://registry.npmjs.org/forwarded/-/forwarded-0.1.2.tgz", - 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"integrity": "sha1-Yzwsg+PaQqUC9SRmAiSA9CCCYd4=" + "version": "2.0.4", + "resolved": "https://registry.npmjs.org/inherits/-/inherits-2.0.4.tgz", + "integrity": "sha512-k/vGaX4/Yla3WzyMCvTQOXYeIHvqOKtnqBduzTHpzpQZzAskKMhZ2K+EnBiSM9zGSoIFeMpXKxa4dYeZIQqewQ==" }, "ini": { "version": "2.0.0", @@ -4026,16 +4081,16 @@ "integrity": "sha512-x0Vn8spI+wuJ1O6S7gnbaQg8Pxh4NNHb7KSINmEWKiPE4RKOplvijn+NkmYmmRgP68mc70j2EbeTFRsrswaQeg==" }, "mime-db": { - "version": "1.45.0", - "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.45.0.tgz", - "integrity": "sha512-CkqLUxUk15hofLoLyljJSrukZi8mAtgd+yE5uO4tqRZsdsAJKv0O+rFMhVDRJgozy+yG6md5KwuXhD4ocIoP+w==" + "version": "1.52.0", + "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.52.0.tgz", + "integrity": "sha512-sPU4uV7dYlvtWJxwwxHD0PuihVNiE7TyAbQ5SWxDCB9mUYvOgroQOwYQQOKPJ8CIbE+1ETVlOoK1UC2nU3gYvg==" }, "mime-types": { - "version": "2.1.28", - "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.1.28.tgz", - "integrity": "sha512-0TO2yJ5YHYr7M2zzT7gDU1tbwHxEUWBCLt0lscSNpcdAfFyJOVEpRYNS7EXVcTLNj/25QO8gulHC5JtTzSE2UQ==", + "version": "2.1.35", + "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.1.35.tgz", + "integrity": "sha512-ZDY+bPm5zTTF+YpCrAU9nK0UgICYPT0QtT1NZWFv4s++TNkcgVaT0g6+4R2uI4MjQjzysHB1zxuWL50hzaeXiw==", "requires": { - "mime-db": "1.45.0" + "mime-db": "1.52.0" } }, "mimic-response": { @@ -4153,9 +4208,9 @@ } }, "negotiator": { - "version": "0.6.2", - "resolved": "https://registry.npmjs.org/negotiator/-/negotiator-0.6.2.tgz", - "integrity": "sha512-hZXc7K2e+PgeI1eDBe/10Ard4ekbfrrqG8Ep+8Jmf4JID2bNg7NvCPOZN+kfF574pFQI7mum2AUqDidoKqcTOw==" + "version": "0.6.3", + "resolved": "https://registry.npmjs.org/negotiator/-/negotiator-0.6.3.tgz", + "integrity": "sha512-+EUsqGPLsM+j/zdChZjsnX51g4XrHFOIXwfnCVPGlQk/k5giakcKsuxCObBRu6DSm9opw/O6slWbJdghQM4bBg==" }, "neo4j-driver": { "version": "4.2.2", @@ -4338,11 +4393,11 @@ "dev": true }, "proxy-addr": { - "version": "2.0.6", - "resolved": "https://registry.npmjs.org/proxy-addr/-/proxy-addr-2.0.6.tgz", - "integrity": "sha512-dh/frvCBVmSsDYzw6n926jv974gddhkFPfiN8hPOi30Wax25QZyZEGveluCgliBnqmuM+UJmBErbAUFIoDbjOw==", + "version": "2.0.7", + "resolved": "https://registry.npmjs.org/proxy-addr/-/proxy-addr-2.0.7.tgz", + "integrity": "sha512-llQsMLSUDUPT44jdrU/O37qlnifitDP+ZwrmmZcoSKyLKvtZxpyV0n2/bD/N4tBAAZ/gJEdZU7KMraoK1+XYAg==", "requires": { - "forwarded": "~0.1.2", + "forwarded": "0.2.0", "ipaddr.js": "1.9.1" } }, @@ -4382,9 +4437,9 @@ "integrity": "sha512-TWeotuxe1auhXa5bGRScxnc2J+0r41NBntSa6RYZtMBLtAEsvCboKrEbW6DvASosWQepVkhZZlT3B5Ei766G+Q==" }, "qs": { - "version": "6.7.0", - "resolved": "https://registry.npmjs.org/qs/-/qs-6.7.0.tgz", - "integrity": "sha512-VCdBRNFTX1fyE7Nb6FYoURo/SPe62QCaAyzJvUjwRaIsc+NePBEniHlvxFmmX56+HZphIGtV0XeCirBtpDrTyQ==" + "version": "6.9.7", + "resolved": "https://registry.npmjs.org/qs/-/qs-6.9.7.tgz", + "integrity": "sha512-IhMFgUmuNpyRfxA90umL7ByLlgRXu6tIfKPpF5TmcfRLlLCckfP/g3IQmju6jjpu+Hh8rA+2p6A27ZSPOOHdKw==" }, "randombytes": { "version": "2.1.0", @@ -4400,12 +4455,12 @@ "integrity": "sha512-Hrgsx+orqoygnmhFbKaHE6c296J+HTAQXoxEF6gNupROmmGJRoyzfG3ccAveqCBrwr/2yxQ5BVd/GTl5agOwSg==" }, "raw-body": { - "version": "2.4.0", - "resolved": "https://registry.npmjs.org/raw-body/-/raw-body-2.4.0.tgz", - "integrity": "sha512-4Oz8DUIwdvoa5qMJelxipzi/iJIi40O5cGV1wNYp5hvZP8ZN0T+jiNkL0QepXs+EsQ9XJ8ipEDoiH70ySUJP3Q==", + "version": "2.4.3", + "resolved": "https://registry.npmjs.org/raw-body/-/raw-body-2.4.3.tgz", + "integrity": "sha512-UlTNLIcu0uzb4D2f4WltY6cVjLi+/jEN4lgEUj3E04tpMDpUlkBo/eSn6zou9hum2VMNpCCUone0O0WeJim07g==", "requires": { - "bytes": "3.1.0", - "http-errors": "1.7.2", + "bytes": "3.1.2", + "http-errors": "1.8.1", "iconv-lite": "0.4.24", "unpipe": "1.0.0" } @@ -4541,9 +4596,9 @@ } }, "send": { - "version": "0.17.1", - "resolved": "https://registry.npmjs.org/send/-/send-0.17.1.tgz", - "integrity": "sha512-BsVKsiGcQMFwT8UxypobUKyv7irCNRHk1T0G680vk88yf6LBByGcZJOTJCrTP2xVN6yI+XjPJcNuE3V4fT9sAg==", + "version": "0.17.2", + "resolved": "https://registry.npmjs.org/send/-/send-0.17.2.tgz", + "integrity": "sha512-UJYB6wFSJE3G00nEivR5rgWp8c2xXvJ3OPWPhmuteU0IKj8nKbG3DrjiOmLwpnHGYWAVwA69zmTm++YG0Hmwww==", "requires": { "debug": "2.6.9", "depd": "~1.1.2", @@ -4552,18 +4607,18 @@ "escape-html": "~1.0.3", "etag": "~1.8.1", "fresh": "0.5.2", - "http-errors": "~1.7.2", + "http-errors": "1.8.1", "mime": "1.6.0", - "ms": "2.1.1", + "ms": "2.1.3", "on-finished": "~2.3.0", "range-parser": "~1.2.1", "statuses": "~1.5.0" }, "dependencies": { "ms": { - "version": "2.1.1", - "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.1.tgz", - "integrity": "sha512-tgp+dl5cGk28utYktBsrFqA7HKgrhgPsg6Z/EfhWI4gl1Hwq8B/GmY/0oXZ6nF8hDVesS/FpnYaD/kOWhYQvyg==" + "version": "2.1.3", + "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz", + "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==" } } }, @@ -4576,20 +4631,20 @@ } }, "serve-static": { - "version": "1.14.1", - "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.14.1.tgz", - "integrity": "sha512-JMrvUwE54emCYWlTI+hGrGv5I8dEwmco/00EvkzIIsR7MqrHonbD9pO2MOfFnpFntl7ecpZs+3mW+XbQZu9QCg==", + "version": "1.14.2", + "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.14.2.tgz", + "integrity": "sha512-+TMNA9AFxUEGuC0z2mevogSnn9MXKb4fa7ngeRMJaaGv8vTwnIEkKi+QGvPt33HSnf8pRS+WGM0EbMtCJLKMBQ==", "requires": { "encodeurl": "~1.0.2", "escape-html": "~1.0.3", "parseurl": "~1.3.3", - "send": "0.17.1" + "send": "0.17.2" } }, "setprototypeof": { - "version": "1.1.1", - "resolved": "https://registry.npmjs.org/setprototypeof/-/setprototypeof-1.1.1.tgz", - "integrity": "sha512-JvdAWfbXeIGaZ9cILp38HntZSFSo3mWg6xGcJJsd+d4aRMOqauag1C63dJfDw7OaMYwEbHMOxEZ1lqVRYP2OAw==" + "version": "1.2.0", + "resolved": "https://registry.npmjs.org/setprototypeof/-/setprototypeof-1.2.0.tgz", + "integrity": "sha512-E5LDX7Wrp85Kil5bhZv46j8jOeboKq5JMmYM3gVGdGH8xFpPWXUMsNrlODCrkoxMEeNi/XZIwuRvY4XNwYMJpw==" }, "signal-exit": { "version": "3.0.3", @@ -4704,9 +4759,9 @@ } }, "toidentifier": { - "version": "1.0.0", - "resolved": "https://registry.npmjs.org/toidentifier/-/toidentifier-1.0.0.tgz", - "integrity": "sha512-yaOH/Pk/VEhBWWTlhI+qXxDFXlejDGcQipMlyxda9nthulaxLZUNcUqFxokp0vcYnvteJln5FNQDRrxj3YcbVw==" + "version": "1.0.1", + "resolved": "https://registry.npmjs.org/toidentifier/-/toidentifier-1.0.1.tgz", + "integrity": "sha512-o5sSPKEkg/DIQNmH43V0/uerLrpzVedkUh8tGNvaeXpfpuwjKenlSox/2O/BTlZUtEe+JG7s5YhEz608PlAHRA==" }, "touch": { "version": "3.1.0", diff --git a/web/packages/api/package.json b/web/packages/api/package.json index 16e5c3f1..827e0a35 100644 --- a/web/packages/api/package.json +++ b/web/packages/api/package.json @@ -27,7 +27,7 @@ "body-parser": "^1.19.0", "cors": "^2.8.5", "dotenv": "^8.2.0", - "express": "^4.17.1", + "express": "^4.17.3", "lodash": "^4.17.21", "method-override": "^3.0.0", "mocha": "^8.3.0", From ac950657759664dd72afabb2bd7f2a501bdd8e4a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 7 Jan 2023 23:12:40 +0000 Subject: [PATCH 09/28] Bump json5 in /web/packages/app Bumps [json5](https://github.com/json5/json5) and [json5](https://github.com/json5/json5). These dependencies needed to be updated together. Updates `json5` from 2.2.0 to 2.2.3 - [Release notes](https://github.com/json5/json5/releases) - [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md) - [Commits](https://github.com/json5/json5/compare/v2.2.0...v2.2.3) Updates `json5` from 1.0.1 to 2.2.3 - [Release notes](https://github.com/json5/json5/releases) - [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md) - [Commits](https://github.com/json5/json5/compare/v2.2.0...v2.2.3) --- updated-dependencies: - dependency-name: json5 dependency-type: indirect - dependency-name: json5 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/app/package-lock.json | 74 +++++++++++++++++++++--------- 1 file changed, 53 insertions(+), 21 deletions(-) diff --git a/web/packages/app/package-lock.json b/web/packages/app/package-lock.json index 8e92289a..62e0c1c5 100644 --- a/web/packages/app/package-lock.json +++ b/web/packages/app/package-lock.json @@ -5868,9 +5868,10 @@ } }, "node_modules/babel-loader/node_modules/json5": { - "version": "1.0.1", + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/json5/-/json5-1.0.2.tgz", + "integrity": "sha512-g1MWMLBiz8FKi1e4w0UyVL3w+iJceWAFBAaBnnGKOpNa5f8TLktkbre1+s6oICydWAm+HRUGTmI+//xv2hvXYA==", "dev": true, - "license": "MIT", "dependencies": { "minimist": "^1.2.0" }, @@ -13750,11 +13751,9 @@ "license": "MIT" }, "node_modules/json5": { - "version": "2.2.0", - "license": "MIT", - "dependencies": { - "minimist": "^1.2.5" - }, + "version": "2.2.3", + "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz", + "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==", "bin": { "json5": "lib/cli.js" }, @@ -14272,6 +14271,7 @@ }, "node_modules/minimist": { "version": "1.2.5", + "dev": true, "license": "MIT" }, "node_modules/mkdirp": { @@ -18634,6 +18634,18 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/tempy/node_modules/type-fest": { + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.16.0.tgz", + "integrity": "sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg==", + "dev": true, + "engines": { + "node": ">=10" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } + }, "node_modules/terminal-link": { "version": "2.1.1", "dev": true, @@ -18864,9 +18876,10 @@ } }, "node_modules/tsconfig-paths/node_modules/json5": { - "version": "1.0.1", + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/json5/-/json5-1.0.2.tgz", + "integrity": "sha512-g1MWMLBiz8FKi1e4w0UyVL3w+iJceWAFBAaBnnGKOpNa5f8TLktkbre1+s6oICydWAm+HRUGTmI+//xv2hvXYA==", "dev": true, - "license": "MIT", "dependencies": { "minimist": "^1.2.0" }, @@ -18926,11 +18939,14 @@ } }, "node_modules/type-fest": { - "version": "0.16.0", + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-2.19.0.tgz", + "integrity": "sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA==", "dev": true, - "license": "(MIT OR CC0-1.0)", + "optional": true, + "peer": true, "engines": { - "node": ">=10" + "node": ">=12.20" }, "funding": { "url": "https://github.com/sponsors/sindresorhus" @@ -23717,7 +23733,9 @@ }, "dependencies": { "json5": { - "version": "1.0.1", + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/json5/-/json5-1.0.2.tgz", + "integrity": "sha512-g1MWMLBiz8FKi1e4w0UyVL3w+iJceWAFBAaBnnGKOpNa5f8TLktkbre1+s6oICydWAm+HRUGTmI+//xv2hvXYA==", "dev": true, "requires": { "minimist": "^1.2.0" @@ -28864,10 +28882,9 @@ "dev": true }, "json5": { - "version": "2.2.0", - "requires": { - "minimist": "^1.2.5" - } + "version": "2.2.3", + "resolved": "https://registry.npmjs.org/json5/-/json5-2.2.3.tgz", + "integrity": "sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg==" }, "jsonfile": { "version": "6.1.0", @@ -29204,7 +29221,8 @@ } }, "minimist": { - "version": "1.2.5" + "version": "1.2.5", + "dev": true }, "mkdirp": { "version": "0.5.5", @@ -31881,6 +31899,14 @@ "temp-dir": "^2.0.0", "type-fest": "^0.16.0", "unique-string": "^2.0.0" + }, + "dependencies": { + "type-fest": { + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-0.16.0.tgz", + "integrity": "sha512-eaBzG6MxNzEn9kiwvtre90cXaNLkmadMWa1zQMs3XORCXNbsH/OewwbxC5ia9dCxIxnTAsSxXJaa/p5y8DlvJg==", + "dev": true + } } }, "terminal-link": { @@ -32026,7 +32052,9 @@ }, "dependencies": { "json5": { - "version": "1.0.1", + "version": "1.0.2", + "resolved": "https://registry.npmjs.org/json5/-/json5-1.0.2.tgz", + "integrity": "sha512-g1MWMLBiz8FKi1e4w0UyVL3w+iJceWAFBAaBnnGKOpNa5f8TLktkbre1+s6oICydWAm+HRUGTmI+//xv2hvXYA==", "dev": true, "requires": { "minimist": "^1.2.0" @@ -32067,8 +32095,12 @@ "dev": true }, "type-fest": { - "version": "0.16.0", - "dev": true + "version": "2.19.0", + "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-2.19.0.tgz", + "integrity": "sha512-RAH822pAdBgcNMAfWnCBU3CFZcfZ/i1eZjwFU/dsLKumyuuP3niueg2UAukXYF0E2AAoc82ZSSf9J0WQBinzHA==", + "dev": true, + "optional": true, + "peer": true }, "type-is": { "version": "1.6.18", From 464f87065d2972f5ceb33bfafd4d774bcc3b5368 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 3 Feb 2023 18:47:05 +0000 Subject: [PATCH 10/28] Bump http-cache-semantics from 4.1.0 to 4.1.1 in /web/packages/api Bumps [http-cache-semantics](https://github.com/kornelski/http-cache-semantics) from 4.1.0 to 4.1.1. - [Release notes](https://github.com/kornelski/http-cache-semantics/releases) - [Commits](https://github.com/kornelski/http-cache-semantics/compare/v4.1.0...v4.1.1) --- updated-dependencies: - dependency-name: http-cache-semantics dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index aa35b6f9..1719d0cb 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -1134,9 +1134,9 @@ } }, "node_modules/http-cache-semantics": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/http-cache-semantics/-/http-cache-semantics-4.1.0.tgz", - "integrity": "sha512-carPklcUh7ROWRK7Cv27RPtdhYhUsela/ue5/jKzjegVvXDqM2ILE9Q2BGn9JZJh1g87cp56su/FgQSzcWS8cQ==", + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/http-cache-semantics/-/http-cache-semantics-4.1.1.tgz", + "integrity": "sha512-er295DKPVsV82j5kw1Gjt+ADA/XYHsajl82cGNQG2eyoPkvgUhX+nDIyelzhIWbbsXP39EHcI6l5tYs2FYqYXQ==", "dev": true }, "node_modules/http-errors": { @@ -3741,9 +3741,9 @@ "integrity": "sha512-F/1DnUGPopORZi0ni+CvrCgHQ5FyEAHRLSApuYWMmrbSwoN2Mn/7k+Gl38gJnR7yyDZk6WLXwiGod1JOWNDKGw==" }, "http-cache-semantics": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/http-cache-semantics/-/http-cache-semantics-4.1.0.tgz", - "integrity": "sha512-carPklcUh7ROWRK7Cv27RPtdhYhUsela/ue5/jKzjegVvXDqM2ILE9Q2BGn9JZJh1g87cp56su/FgQSzcWS8cQ==", + "version": "4.1.1", + "resolved": "https://registry.npmjs.org/http-cache-semantics/-/http-cache-semantics-4.1.1.tgz", + "integrity": "sha512-er295DKPVsV82j5kw1Gjt+ADA/XYHsajl82cGNQG2eyoPkvgUhX+nDIyelzhIWbbsXP39EHcI6l5tYs2FYqYXQ==", "dev": true }, "http-errors": { From d56c0b08c6577ffac75880299a1f2efe1955392d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 11 Feb 2023 18:15:46 +0000 Subject: [PATCH 11/28] Bump cacheable-request and nodemon in /web/packages/api Removes [cacheable-request](https://github.com/jaredwray/cacheable-request). It's no longer used after updating ancestor dependency [nodemon](https://github.com/remy/nodemon). These dependencies need to be updated together. Removes `cacheable-request` Updates `nodemon` from 2.0.7 to 2.0.20 - [Release notes](https://github.com/remy/nodemon/releases) - [Commits](https://github.com/remy/nodemon/compare/v2.0.7...v2.0.20) --- updated-dependencies: - dependency-name: cacheable-request dependency-type: indirect - dependency-name: nodemon dependency-type: direct:development ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 1873 +++------------------------- web/packages/api/package.json | 2 +- 2 files changed, 175 insertions(+), 1700 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index aa35b6f9..d8d2546c 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -26,7 +26,7 @@ "xml2js": "^0.4.23" }, "devDependencies": { - "nodemon": "^2.0.7" + "nodemon": "^2.0.20" } }, "node_modules/@apidevtools/json-schema-ref-parser": { @@ -98,27 +98,6 @@ "resolved": "https://registry.npmjs.org/@jsdevtools/ono/-/ono-7.1.3.tgz", "integrity": "sha512-4JQNk+3mVzK3xh2rqd6RB4J46qUR19azEHBneZyTZM+c456qOrbbM/5xcR8huNCCcbVt7+UmizG6GuUvPvKUYg==" }, - "node_modules/@sindresorhus/is": { - "version": "0.14.0", - "resolved": "https://registry.npmjs.org/@sindresorhus/is/-/is-0.14.0.tgz", - "integrity": "sha512-9NET910DNaIPngYnLLPeg+Ogzqsi9uM4mSboU5y6p8S5DzMTVEsJZrawi+BoDNUVBa2DhJqQYUFvMDfgU062LQ==", - "dev": true, - "engines": { - "node": ">=6" - } - }, - "node_modules/@szmarczak/http-timer": { - "version": "1.1.2", - "resolved": "https://registry.npmjs.org/@szmarczak/http-timer/-/http-timer-1.1.2.tgz", - "integrity": "sha512-XIB2XbzHTN6ieIjfIMV9hlVcfPU26s2vafYWQcZHWXHOxiaRZYEDKEwdl129Zyg50+foYV2jCgtrqSA6qNuNSA==", - "dev": true, - "dependencies": { - "defer-to-connect": "^1.0.1" - }, - "engines": { - "node": ">=6" - } - }, "node_modules/@ungap/promise-all-settled": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/@ungap/promise-all-settled/-/promise-all-settled-1.1.2.tgz", @@ -142,56 +121,6 @@ "node": ">= 0.6" } }, - "node_modules/ansi-align": { - "version": "3.0.0", - "resolved": "https://registry.npmjs.org/ansi-align/-/ansi-align-3.0.0.tgz", - "integrity": "sha512-ZpClVKqXN3RGBmKibdfWzqCY4lnjEuoNzU5T0oEFpfd/z5qJHVarukridD4juLO2FXMiwUQxr9WqQtaYa8XRYw==", - "dev": true, - "dependencies": { - "string-width": "^3.0.0" - } - }, - "node_modules/ansi-align/node_modules/ansi-regex": { - 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}, - "node_modules/ansi-align/node_modules/strip-ansi": { - "version": "5.2.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-5.2.0.tgz", - "integrity": "sha512-DuRs1gKbBqsMKIZlrffwlug8MHkcnpjs5VPmL1PAh+mA30U0DTotfDZ0d2UUsXpPmPmMMJ6W773MaA3J+lbiWA==", - "dev": true, - "dependencies": { - "ansi-regex": "^4.1.0" - }, - "engines": { - "node": ">=6" - } - }, "node_modules/ansi-colors": { "version": "4.1.1", "resolved": "https://registry.npmjs.org/ansi-colors/-/ansi-colors-4.1.1.tgz", @@ -220,9 +149,9 @@ } }, "node_modules/anymatch": { - "version": "3.1.1", - "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.1.tgz", - "integrity": "sha512-mM8522psRCqzV+6LhomX5wgp25YVibjh8Wj23I5RPkPppSVSjyKD2A2mBJmWGa+KN7f2D6LNh9jkBCeyLktzjg==", + "version": "3.1.3", + "resolved": "https://registry.npmjs.org/anymatch/-/anymatch-3.1.3.tgz", + "integrity": "sha512-KMReFUr0B4t+D+OBkjR3KYqvocp2XaSzO55UcB6mgQMd3KbcE+mWTyvVV7D/zsdEbNnV6acZUutkiHQXvTr1Rw==", "dependencies": { "normalize-path": "^3.0.0", "picomatch": "^2.0.4" @@ -290,106 +219,6 @@ "node": ">= 0.8" } }, - 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"node": ">=8" - } - }, "node_modules/brace-expansion": { "version": "1.1.11", "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.11.tgz", @@ -423,48 +252,6 @@ "node": ">= 0.8" } }, - "node_modules/cacheable-request": { - "version": "6.1.0", - "resolved": "https://registry.npmjs.org/cacheable-request/-/cacheable-request-6.1.0.tgz", - "integrity": "sha512-Oj3cAGPCqOZX7Rz64Uny2GYAZNliQSqfbePrgAQ1wKAihYmCUnraBtJtKcGR4xz7wF+LoJC+ssFZvv5BgF9Igg==", - "dev": true, - "dependencies": { - "clone-response": "^1.0.2", - "get-stream": "^5.1.0", - "http-cache-semantics": "^4.0.0", - "keyv": "^3.0.0", - "lowercase-keys": "^2.0.0", - "normalize-url": "^4.1.0", - "responselike": "^1.0.2" - }, - "engines": { - "node": ">=8" - } - }, - "node_modules/cacheable-request/node_modules/get-stream": { - "version": "5.2.0", - "resolved": "https://registry.npmjs.org/get-stream/-/get-stream-5.2.0.tgz", - "integrity": "sha512-nBF+F1rAZVCu/p7rjzgA+Yb4lfYXrpl7a6VmJrU8wF9I1CKvP/QwPNZHnOlwbTkY6dvtFIzFMSyQXbLoTQPRpA==", - "dev": true, - "dependencies": { - "pump": "^3.0.0" - }, - "engines": { - "node": ">=8" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - }, - "node_modules/cacheable-request/node_modules/lowercase-keys": { - "version": "2.0.0", - "resolved": "https://registry.npmjs.org/lowercase-keys/-/lowercase-keys-2.0.0.tgz", - "integrity": "sha512-tqNXrS78oMOE73NMxK4EMLQsQowWf8jKooH9g7xPavRT706R6bkQJ6DY2Te7QukaZsulxa30wQ7bk0pm4XiHmA==", - "dev": true, - "engines": { - "node": ">=8" - } - }, "node_modules/call-me-maybe": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/call-me-maybe/-/call-me-maybe-1.0.1.tgz", @@ -521,24 +308,6 @@ "fsevents": "~2.3.1" } }, - "node_modules/ci-info": { - "version": "2.0.0", - "resolved": "https://registry.npmjs.org/ci-info/-/ci-info-2.0.0.tgz", - "integrity": "sha512-5tK7EtrZ0N+OLFMthtqOj4fI2Jeb88C4CAZPu25LDVUgXJ0A3Js4PMGqrn0JU1W0Mh1/Z8wZzYPxqUrXeBboCQ==", - "dev": true - }, - "node_modules/cli-boxes": { - "version": "2.2.1", - 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"integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg==", - "dev": true - }, - "string-width": { - "version": "4.2.0", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.0.tgz", - "integrity": "sha512-zUz5JD+tgqtuDjMhwIg5uFVV3dtqZ9yQJlZVfq4I01/K5Paj5UHj7VyrQOJvzawSVlKpObApbfD0Ed6yJc+1eg==", - "dev": true, - "requires": { - "emoji-regex": "^8.0.0", - "is-fullwidth-code-point": "^3.0.0", - "strip-ansi": "^6.0.0" - } - }, - "strip-ansi": { - "version": "6.0.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.0.tgz", - "integrity": "sha512-AuvKTrTfQNYNIctbR1K/YGTR1756GycPsg7b9bdV9Duqur4gv6aKqHXah67Z8ImS7WEz5QVcOtlfW2rZEugt6w==", - "dev": true, - "requires": { - "ansi-regex": "^5.0.0" - } - } - } - }, "workerpool": { "version": "6.1.0", "resolved": "https://registry.npmjs.org/workerpool/-/workerpool-6.1.0.tgz", @@ -4952,24 +3445,6 @@ "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, - "write-file-atomic": { - "version": "3.0.3", - "resolved": "https://registry.npmjs.org/write-file-atomic/-/write-file-atomic-3.0.3.tgz", - "integrity": "sha512-AvHcyZ5JnSfq3ioSyjrBkH9yW4m7Ayk8/9My/DD9onKeu/94fwrMocemO2QAJFAlnnDN+ZDS+ZjAR5ua1/PV/Q==", - "dev": true, - "requires": { - "imurmurhash": "^0.1.4", - "is-typedarray": "^1.0.0", - "signal-exit": "^3.0.2", - "typedarray-to-buffer": "^3.1.5" - } - }, - "xdg-basedir": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/xdg-basedir/-/xdg-basedir-4.0.0.tgz", - "integrity": "sha512-PSNhEJDejZYV7h50BohL09Er9VaIefr2LMAf3OEmpCkjOi34eYyQYAXUTjEQtZJTKcF0E2UKTh+osDLsgNim9Q==", - "dev": true - }, "xml2js": { "version": "0.4.23", "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.4.23.tgz", diff --git a/web/packages/api/package.json b/web/packages/api/package.json index 16e5c3f1..884006cf 100644 --- a/web/packages/api/package.json +++ b/web/packages/api/package.json @@ -41,6 +41,6 @@ "xml2js": "^0.4.23" }, "devDependencies": { - "nodemon": "^2.0.7" + "nodemon": "^2.0.20" } } From 8e5add3ac26b8803a5dcb4c11371b92fde02f871 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Mar 2023 00:14:17 +0000 Subject: [PATCH 12/28] Bump minimist from 1.2.5 to 1.2.8 in /web/packages/api Bumps [minimist](https://github.com/minimistjs/minimist) from 1.2.5 to 1.2.8. - [Release notes](https://github.com/minimistjs/minimist/releases) - [Changelog](https://github.com/minimistjs/minimist/blob/main/CHANGELOG.md) - [Commits](https://github.com/minimistjs/minimist/compare/v1.2.5...v1.2.8) --- updated-dependencies: - dependency-name: minimist dependency-type: indirect ... Signed-off-by: dependabot[bot] --- web/packages/api/package-lock.json | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/web/packages/api/package-lock.json b/web/packages/api/package-lock.json index aa35b6f9..28d4aa04 100644 --- a/web/packages/api/package-lock.json +++ b/web/packages/api/package-lock.json @@ -1547,10 +1547,13 @@ } }, "node_modules/minimist": { - "version": "1.2.5", - "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.5.tgz", - "integrity": "sha512-FM9nNUYrRBAELZQT3xeZQ7fmMOBg6nWNmJKTcgsJeaLstP/UODVpGsr5OhXhhXg6f+qtJ8uiZ+PUxkDWcgIXLw==", - "dev": true + "version": "1.2.8", + "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz", + "integrity": "sha512-2yyAR8qBkN3YuheJanUpWC5U3bb5osDywNB8RzDVlDwDHbocAJveqqj1u8+SVD7jkWT4yvsHCpWqqWqAxb0zCA==", + "dev": true, + "funding": { + "url": "https://github.com/sponsors/ljharb" + } }, "node_modules/mocha": { "version": "8.3.0", @@ -4053,9 +4056,9 @@ } }, "minimist": { - "version": "1.2.5", - "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.5.tgz", - "integrity": "sha512-FM9nNUYrRBAELZQT3xeZQ7fmMOBg6nWNmJKTcgsJeaLstP/UODVpGsr5OhXhhXg6f+qtJ8uiZ+PUxkDWcgIXLw==", + "version": "1.2.8", + "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz", + "integrity": "sha512-2yyAR8qBkN3YuheJanUpWC5U3bb5osDywNB8RzDVlDwDHbocAJveqqj1u8+SVD7jkWT4yvsHCpWqqWqAxb0zCA==", "dev": true }, "mocha": { From 504b43e723aeca3f7bc88d81e053a8a74f8461c2 Mon Sep 17 00:00:00 2001 From: Joe Romano Date: Fri, 2 Jun 2023 10:24:53 -0400 Subject: [PATCH 13/28] Update setup.py Bump Scipy version to something that works on M2 macos. --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index cf77c68c..5978c02f 100644 --- a/setup.py +++ b/setup.py @@ -46,7 +46,7 @@ def get_docs_url(): install_requires=[ 'ablog==0.10.19', 'numpy==1.21.2', - 'scipy==1.7.1', + 'scipy==1.10.1', 'pandas==1.3.3', 'mysqlclient==2.0.3', 'neo4j==4.3.4', From c294ca491d9cce69a04b83e1d396a221f98f5575 Mon Sep 17 00:00:00 2001 From: Joe Romano Date: Tue, 11 Jul 2023 09:51:03 -0400 Subject: [PATCH 14/28] Update README.md Updated README.md to reflect my updated academic status. --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 6ee19e3d..a0ad18d6 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ A modern data infrastructure for AI research in computational toxicology. ComptoxAI is a collection of resources made to enable a diverse range of artificial intelligence applications for computational toxicology data. This repository contains all of the code that comprises the overall ComptoxAI project, including code related to the database, website, REST API, graph machine learning toolkit, and other miscellaneous utilities. -ComptoxAI is maintained by [Joseph D. Romano, PhD](http://jdr.bio), who is a postdoctoral researcher at the [University of Pennsylvania](https://upenn.edu) in the [Institute for Biomedical Informatics](https://ibi.med.upenn.edu/) and the [Center of Excellence in Environmental Toxicology](http://ceet.upenn.edu/). +ComptoxAI is maintained by [the Romano Lab](http://romanolab.org) at the [University of Pennsylvania](https://upenn.edu) in the [Institute for Biomedical Informatics](https://ibi.med.upenn.edu/) and the [Center of Excellence in Environmental Toxicology](http://ceet.upenn.edu/). ### Funding @@ -25,4 +25,4 @@ We welcome collaborations and contributions from third-party developers. Please ### License -ComptoxAI is offered under a dual-license model, including an open-source option via the GNU GPLv3. See [LICENSE](LICENSE) for details. \ No newline at end of file +ComptoxAI is offered under a dual-license model, including an open-source option via the GNU GPLv3. See [LICENSE](LICENSE) for details. From cb46dbaa6bd3f232b5a96665e47d254ca9d2deb5 Mon Sep 17 00:00:00 2001 From: yunchae-kim Date: Tue, 18 Jul 2023 11:28:51 -0400 Subject: [PATCH 15/28] [#43] Refer to GitHub issue... The CSS styling issues that resulted in subject headers (ex. "Relationships," "Paths") having too little margin between each other. The update adds a CSS class "subject-container" to add margin to each subject div. The update changes package.json in order to fix dependency errors with using "react-d3-graph." d3 version 5.5.0 was added as a dependency. Closes-Bug: #43 --- web/packages/app/package.json | 1 + web/packages/app/src/App.css | 7 +- .../app/src/components/ChemicalSearch.js | 525 +++++++++--------- .../app/src/components/DatasetBuilder.js | 102 ++-- .../app/src/components/ExpandNetwork.js | 231 ++++---- .../app/src/components/NodeResults.js | 69 ++- web/packages/app/src/components/NodeSearch.js | 113 ++-- web/packages/app/src/components/PathSearch.js | 127 +++-- .../app/src/components/RelationshipSearch.js | 74 +-- .../app/src/components/ShortestPath.js | 242 ++++---- 10 files changed, 802 insertions(+), 689 deletions(-) diff --git a/web/packages/app/package.json b/web/packages/app/package.json index 87451ef1..9d6abd82 100644 --- a/web/packages/app/package.json +++ b/web/packages/app/package.json @@ -13,6 +13,7 @@ "bootstrap": "^4.6.0", "endent": "^2.1.0", "prop-types": "^15.7.2", + "d3": "^5.5.0", "react": "^17.0.2", "react-bootstrap": "^1.5.2", "react-d3-graph": "^2.6.0", diff --git a/web/packages/app/src/App.css b/web/packages/app/src/App.css index 21d5d5d7..8c9159b6 100644 --- a/web/packages/app/src/App.css +++ b/web/packages/app/src/App.css @@ -101,6 +101,11 @@ h2 { margin-right: 24px; } +.subject-container { + margin-top: 2rem; + margin-bottom: 2rem; +} + #marvin-bottom-controls { margin-left: 18px; margin-right: 18px; @@ -133,4 +138,4 @@ h2 { #structure-search-button { margin-left: 6px; -} \ No newline at end of file +} diff --git a/web/packages/app/src/components/ChemicalSearch.js b/web/packages/app/src/components/ChemicalSearch.js index 2ee46244..11ce072f 100644 --- a/web/packages/app/src/components/ChemicalSearch.js +++ b/web/packages/app/src/components/ChemicalSearch.js @@ -1,308 +1,299 @@ import React, { useReducer, Fragment } from 'react'; import { - Accordion, - AccordionDetails, - AccordionSummary, - Box, - Button, - Collapse, - IconButton, - Paper, - Skeleton, - Table, - TableBody, - TableCell, - TableContainer, - TableHead, - TableRow, - TextField, - Typography + Accordion, + AccordionDetails, + AccordionSummary, + Box, + Button, + Collapse, + IconButton, + Paper, + Skeleton, + Table, + TableBody, + TableCell, + TableContainer, + TableHead, + TableRow, + TextField, + Typography, } from '@mui/material'; import ExpandMoreIcon from '@mui/icons-material/ExpandMore'; -import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown' -import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp' +import KeyboardArrowDownIcon from '@mui/icons-material/KeyboardArrowDown'; +import KeyboardArrowUpIcon from '@mui/icons-material/KeyboardArrowUp'; import ChemicalizeMarvinJs from './marvin/client'; import { useRunStructureSearchQuery } from '../features/comptoxApiSlice'; import { setSearch } from '../features/nodeSlice'; import { useAppDispatch } from '../redux/hooks'; - const TEST_DATA = [ - { - "DSSTox_Compound_id": "DTXCID904115", - "DSSTox_Substance_id": "DTXSID2024115", - "CASRN": "64-18-6", - "QC_Level": "DSSTox_Low", - "Preferred_name": "Formic acid", - "Mol_Weight": "46.0250000000", - "Mol_Formula": "CH2O2", - "Monoisotopic_Mass": "46.0054793040", - "Dashboard_URL": "https://comptox.epa.gov/dashboard/DTXSID2024115", - "dissimilarity": "0.0", - "SIMILARITY": "1.000" - }, - { - "DSSTox_Compound_id": "DTXCID10161515", - "DSSTox_Substance_id": "DTXSID90239024", - "CASRN": "925-94-0", - "QC_Level": "Public_Medium", - "Preferred_name": "Formic (2H)acid", - "Mol_Weight": "47.0310000000", - "Mol_Formula": "CHDO2", - "Monoisotopic_Mass": "47.0117560500", - "Dashboard_URL": "https://comptox.epa.gov/dashboard/DTXSID90239024", - "dissimilarity": "0.0", - "SIMILARITY": "1.000" - }, - { - "DSSTox_Compound_id": "DTXCID7023801", - "DSSTox_Substance_id": "DTXSID9043801", - "CASRN": "463-79-6", - "QC_Level": "DSSTox_High", - "Preferred_name": "Carbonic acid", - "Mol_Weight": "62.0240000000", - "Mol_Formula": "CH2O3", - "Monoisotopic_Mass": "62.0003939240", - "Dashboard_URL": "https://comptox.epa.gov/dashboard/DTXSID9043801", - "dissimilarity": "0.16666669", - "SIMILARITY": "0.833" - } -] - + { + DSSTox_Compound_id: 'DTXCID904115', + DSSTox_Substance_id: 'DTXSID2024115', + CASRN: '64-18-6', + QC_Level: 'DSSTox_Low', + Preferred_name: 'Formic acid', + Mol_Weight: '46.0250000000', + Mol_Formula: 'CH2O2', + Monoisotopic_Mass: '46.0054793040', + Dashboard_URL: 'https://comptox.epa.gov/dashboard/DTXSID2024115', + dissimilarity: '0.0', + SIMILARITY: '1.000', + }, + { + DSSTox_Compound_id: 'DTXCID10161515', + DSSTox_Substance_id: 'DTXSID90239024', + CASRN: '925-94-0', + QC_Level: 'Public_Medium', + Preferred_name: 'Formic (2H)acid', + Mol_Weight: '47.0310000000', + Mol_Formula: 'CHDO2', + Monoisotopic_Mass: '47.0117560500', + Dashboard_URL: 'https://comptox.epa.gov/dashboard/DTXSID90239024', + dissimilarity: '0.0', + SIMILARITY: '1.000', + }, + { + DSSTox_Compound_id: 'DTXCID7023801', + DSSTox_Substance_id: 'DTXSID9043801', + CASRN: '463-79-6', + QC_Level: 'DSSTox_High', + Preferred_name: 'Carbonic acid', + Mol_Weight: '62.0240000000', + Mol_Formula: 'CH2O3', + Monoisotopic_Mass: '62.0003939240', + Dashboard_URL: 'https://comptox.epa.gov/dashboard/DTXSID9043801', + dissimilarity: '0.16666669', + SIMILARITY: '0.833', + }, +]; class StructureEditor extends React.Component { - componentDidMount() { - ChemicalizeMarvinJs.createEditor("#marvin-editor").then(function (marvin) { - function handleMolChange() { - marvin.exportStructure("mol").then(function (mol) { - document.getElementById("current-mol").innerHTML = mol; - }) - } + componentDidMount() { + ChemicalizeMarvinJs.createEditor('#marvin-editor').then(function (marvin) { + function handleMolChange() { + marvin.exportStructure('mol').then(function (mol) { + document.getElementById('current-mol').innerHTML = mol; + }); + } - marvin.importStructure("name", "arachidonic acid"); + marvin.importStructure('name', 'arachidonic acid'); - marvin.on("molchange", handleMolChange); - }); - } + marvin.on('molchange', handleMolChange); + }); + } - render() { - return ( -
- ); - } + render() { + return ( +
+ ); + } } - const StructureResultsRow = (props) => { - const { row } = props; - const [open, setOpen] = React.useState(false); - const dispatch = useAppDispatch(); + const { row } = props; + const [open, setOpen] = React.useState(false); + const dispatch = useAppDispatch(); - const handleNodeSearch = event => { - dispatch(setSearch({ - searchType: 'dsstox', - params: { - dtxsid: row.DSSTox_Substance_id - } - })); - } - - return ( - - - - setOpen(!open)} - > - {open ? : } - - - {row.Preferred_name} - {row.DSSTox_Substance_id} - {row.Mol_Formula} - {row.SIMILARITY} - {row.Mol_Weight} - - - - - - - - - - - + const handleNodeSearch = (event) => { + dispatch( + setSearch({ + searchType: 'dsstox', + params: { + dtxsid: row.DSSTox_Substance_id, + }, + }) ); -} + }; + + return ( + + + + setOpen(!open)} + > + {open ? : } + + + + {row.Preferred_name} + + {row.DSSTox_Substance_id} + {row.Mol_Formula} + {row.SIMILARITY} + {row.Mol_Weight} + + + + + + + + + + + + ); +}; const StructureResultsTable = (props) => { - const rows = props.data; + const rows = props.data; - return ( - - - - - - Chemical name - DSSTox ID - Molecular formula - Similarity score - MW - - - - {rows.map((row) => ( - - ))} - -
- - ); -} + return ( + + + + + + Chemical name + DSSTox ID + Molecular formula + Similarity score + MW + + + + {rows.map((row) => ( + + ))} + +
+ + ); +}; const setCurrentMolReducer = (state, event) => { - return event; -} + return event; +}; const StructureSearchControls = (props) => { - const [currentMolData, setCurrentMolData] = useReducer(setCurrentMolReducer, ""); + const [currentMolData, setCurrentMolData] = useReducer( + setCurrentMolReducer, + '' + ); - const skip = (currentMolData === "") ? true : false; + const skip = currentMolData === '' ? true : false; - const { data, error, isLoading, isUninitialized } = useRunStructureSearchQuery(currentMolData, { - skip + const { data, error, isLoading, isUninitialized } = + useRunStructureSearchQuery(currentMolData, { + skip, }); - const handleStructureQuery = (event) => { - const current_mol = document.getElementById("current-mol").innerHTML - setCurrentMolData(current_mol); - } - - return ( -
-
- - - } - aria-controls="panel1a-content" - id="panel1a-header" - > - Show structure information - - - MOL structure document: - - - - -
+ const handleStructureQuery = (event) => { + const current_mol = document.getElementById('current-mol').innerHTML; + setCurrentMolData(current_mol); + }; + + return ( +
+
+ + } + aria-controls="panel1a-content" + id="panel1a-header" + > + Show structure information + + + MOL structure document: + + + + +
+ + {error ? ( + <>Error! + ) : isUninitialized ? ( + <> + Draw a structure and click "Search for Structure" + + + + + + ) : isLoading ? ( + <> + Loading... + - {error ? ( - <>Error! - ) : isUninitialized ? ( - <> - Draw a structure and click "Search for Structure" - - - - - - - ) : isLoading ? ( - <> - Loading... - - {Array.from(new Array(6)).map((i, idx) => ( - - - - ))} - - - ) : data ? ( - <> - - - ) : null} + {Array.from(new Array(6)).map((i, idx) => ( + + + + ))} -
- ); - -} + + ) : data ? ( + <> + + + ) : null} + +
+ ); +}; const ChemicalSearch = (props) => { - return ( -
-

Chemical Search

-

Find chemicals by drawing a molecular structure.

- - -
- ); -} - + return ( +
+

Chemical Search

+

+ Find chemicals by drawing a molecular structure. +

+ + +
+ ); +}; export default ChemicalSearch; diff --git a/web/packages/app/src/components/DatasetBuilder.js b/web/packages/app/src/components/DatasetBuilder.js index 07ad7610..ca17e4cf 100644 --- a/web/packages/app/src/components/DatasetBuilder.js +++ b/web/packages/app/src/components/DatasetBuilder.js @@ -8,27 +8,33 @@ import { InputLabel, MenuItem, Select, - TextField + TextField, } from '@mui/material'; import Autocomplete from '@mui/material/Autocomplete'; const qsarBuilderConfig = require('../data/qsar_params_data.json'); const DatasetBuilderQueryForm = (props) => { - - const [chemListValue, setChemListValue] = useState({'acronym': '', 'name': ''}); - const [assayValue, setAssayValue] = useState({'assayId': '', 'assayName': ''}); - const [checkedState, setCheckedState] = useState({ checkedIncludeDiscovery: true }); + const [chemListValue, setChemListValue] = useState({ acronym: '', name: '' }); + const [assayValue, setAssayValue] = useState({ assayId: '', assayName: '' }); + const [checkedState, setCheckedState] = useState({ + checkedIncludeDiscovery: true, + }); const [formatValue, setFormatValue] = useState('json'); - const handleSubmit = event => { + const handleSubmit = (event) => { event.preventDefault(); // Open new tab with API URL (should we refactor to use Redux or is this good enough?) - window.open(`https://comptox.ai/api/datasets/makeQsarDataset?assay=${assayValue.assayId}&chemList=${chemListValue.acronym}`); - } + window.open( + `https://comptox.ai/api/datasets/makeQsarDataset?assay=${assayValue.assayId}&chemList=${chemListValue.acronym}` + ); + }; const handleToggleCheckbox = (event) => { - setCheckedState({ ...checkedState, [event.target.name]: event.target.checked }); + setCheckedState({ + ...checkedState, + [event.target.name]: event.target.checked, + }); }; const handleChangeFormat = (event) => { @@ -37,9 +43,7 @@ const DatasetBuilderQueryForm = (props) => { return (
- - { }} value={chemListValue || null} options={qsarBuilderConfig.chemicalLists} - getOptionLabel={(option) => option.name ? (option.name + " (n=" + option.num_chems + ")") : ''} - isOptionEqualToValue={(option, value) => option.acronym === value.acronym} - renderInput={(params) => } + getOptionLabel={(option) => + option.name ? option.name + ' (n=' + option.num_chems + ')' : '' + } + isOptionEqualToValue={(option, value) => + option.acronym === value.acronym + } + renderInput={(params) => ( + + )} /> @@ -74,13 +88,25 @@ const DatasetBuilderQueryForm = (props) => { }} value={assayValue || null} options={qsarBuilderConfig.assays} - getOptionLabel={(option) => option.assayId ? (option.assayName + " (id: " + option.assayId + ")") : ''} - isOptionEqualToValue={(option, value) => option.assayId === value.assayId} - renderInput={(params) => } + getOptionLabel={(option) => + option.assayId + ? option.assayName + ' (id: ' + option.assayId + ')' + : '' + } + isOptionEqualToValue={(option, value) => + option.assayId === value.assayId + } + renderInput={(params) => ( + + )} /> -
+
{ /> } label="Include 'discovery' dataset of chemicals with unknown assay activity" - style={{ marginBottom: 6}} + style={{ marginBottom: 6 }} /> -
+
Format - + (Results will open in a new tab) -
); -} +}; const DatasetBuilder = (props) => { const { config, chemLists } = props; - return( -
+ return ( +

Build QSAR Dataset

-

Build a new dataset to use in Quantitative Structure-Activity Relationship modeling.

+

+ + Build a new dataset to use in Quantitative Structure-Activity + Relationship modeling. + +

-
+
- - - +
); -} +}; export default DatasetBuilder; diff --git a/web/packages/app/src/components/ExpandNetwork.js b/web/packages/app/src/components/ExpandNetwork.js index 4e74f2bf..8cb39b17 100644 --- a/web/packages/app/src/components/ExpandNetwork.js +++ b/web/packages/app/src/components/ExpandNetwork.js @@ -1,14 +1,14 @@ import React from 'react'; import { - Accordion, - AccordionDetails, - AccordionSummary, - Button, - Dialog, - DialogContent, - DialogContentText, - TextField, - Typography + Accordion, + AccordionDetails, + AccordionSummary, + Button, + Dialog, + DialogContent, + DialogContentText, + TextField, + Typography, } from '@mui/material'; import FileCopyIcon from '@mui/icons-material/FileCopy'; import ExpandMoreIcon from '@mui/icons-material/ExpandMore'; @@ -17,112 +17,131 @@ import { useAppSelector } from '../redux/hooks'; import endent from 'endent'; - const ExpandNetwork = (props) => { - const expandNetworkNode = useAppSelector((state) => state.modules.expandNetworkNode); + const expandNetworkNode = useAppSelector( + (state) => state.modules.expandNetworkNode + ); + + const selectedNodeId = expandNetworkNode ? expandNetworkNode : null; - const selectedNodeId = expandNetworkNode ? expandNetworkNode : null; - - const expandNetworkCypherQuery = selectedNodeId ? endent(`CALL apoc.path.spanningTree( + const expandNetworkCypherQuery = selectedNodeId + ? endent(`CALL apoc.path.spanningTree( ${selectedNodeId}, { maxLevel: 3 }) YIELD path - RETURN path;`) : "Find a node in the search interface and select 'Expand Network'." - - const [popupOpen, setPopupOpen] = React.useState(false); - - const handleCopyCypher = () => { - // see: https://stackoverflow.com/a/58406346/1730417 - let selBox = document.createElement('textarea'); - selBox.style.position = 'fixed'; - selBox.style.left = '0'; - selBox.style.top = '0'; - selBox.style.opacity = '0'; - selBox.value = expandNetworkCypherQuery; - document.body.appendChild(selBox); - selBox.focus(); - selBox.select(); - document.execCommand('copy'); - document.body.removeChild(selBox); - setPopupOpen(true); - }; + RETURN path;`) + : "Find a node in the search interface and select 'Expand Network'."; + + const [popupOpen, setPopupOpen] = React.useState(false); + + const handleCopyCypher = () => { + // see: https://stackoverflow.com/a/58406346/1730417 + let selBox = document.createElement('textarea'); + selBox.style.position = 'fixed'; + selBox.style.left = '0'; + selBox.style.top = '0'; + selBox.style.opacity = '0'; + selBox.value = expandNetworkCypherQuery; + document.body.appendChild(selBox); + selBox.focus(); + selBox.select(); + document.execCommand('copy'); + document.body.removeChild(selBox); + setPopupOpen(true); + }; - const handleClose = () => { - setPopupOpen(false); - }; + const handleClose = () => { + setPopupOpen(false); + }; - const openInNewTab = (url) => { - const newWindow = window.open(url, '_blank', 'noopener,noreferrer'); - if (newWindow) newWindow.opener = null; - }; + const openInNewTab = (url) => { + const newWindow = window.open(url, '_blank', 'noopener,noreferrer'); + if (newWindow) newWindow.opener = null; + }; - return( -
-
-

Expand a network around a query node

-

Create a Cypher query that builds a spanning tree outward from a starting node, showing their local neighborhood in the overall knowledge graph.

- - } - aria-controls="shortestpathhelp-content" - id="shortestpathhelp-header" - > - Usage instructions - - -
    -
  1. Find a node using the search feature at the top of the page, and click "Expand Network".
    2. -
  2. Click the "Copy Database Query" button below to copy the query to your clipboard.
    3. -
  3. Click the "Open Database Browser" button below to open the Neo4j interface.
    4. -
  4. Paste the contents in the query bar and run the search.
    5. -
- - - - - - - - Cypher database query copied to the clipboard. - - -
-
- ); -} + return ( +
+
+

Expand a network around a query node

+

+ + Create a Cypher query that builds a spanning tree outward from a + starting node, showing their local neighborhood in the overall + knowledge graph. + +

+ + } + aria-controls="shortestpathhelp-content" + id="shortestpathhelp-header" + > + Usage instructions + + +
    +
  1. + Find a node using the search feature at the top of the page, and + click "Expand Network". +
    2. +
  2. + Click the "Copy Database Query" button below to copy the query + to your clipboard. +
    3. +
  3. + Click the "Open Database Browser" button below to open the Neo4j + interface. +
    4. +
  4. Paste the contents in the query bar and run the search.
    5. +
+ + + + + + + + + Cypher database query copied to the clipboard. + + + +
+
+ ); +}; export default ExpandNetwork; diff --git a/web/packages/app/src/components/NodeResults.js b/web/packages/app/src/components/NodeResults.js index 5b3172bf..1ca0b7b7 100644 --- a/web/packages/app/src/components/NodeResults.js +++ b/web/packages/app/src/components/NodeResults.js @@ -1,65 +1,76 @@ import React from 'react'; import { Map } from 'react-lodash'; -import { - Button, - Paper -} from '@mui/material'; +import { Button, Paper } from '@mui/material'; import { useAppSelector, useAppDispatch } from '../redux/hooks'; import NodeResult from './NodeResult'; -import { useFetchChemicalByDtsxidQuery, useSearchNodesQuery } from '../features/comptoxApiSlice'; +import { + useFetchChemicalByDtsxidQuery, + useSearchNodesQuery, +} from '../features/comptoxApiSlice'; import { setSearch } from '../features/nodeSlice'; - const NodeResults = (props) => { const { config } = props; const dispatch = useAppDispatch(); const searchParams = useAppSelector((state) => state.node.searchParams); - const dsstoxResults = useFetchChemicalByDtsxidQuery(searchParams.params.dtxsid, { - skip: !(searchParams.searchType === 'dsstox') - }); - const nodeResults = useSearchNodesQuery([ - searchParams.params.label, - searchParams.params.field, - searchParams.params.value - ], { - skip: !(searchParams.searchType === 'node') - }); + const dsstoxResults = useFetchChemicalByDtsxidQuery( + searchParams.params.dtxsid, + { + skip: !(searchParams.searchType === 'dsstox'), + } + ); + const nodeResults = useSearchNodesQuery( + [ + searchParams.params.label, + searchParams.params.field, + searchParams.params.value, + ], + { + skip: !(searchParams.searchType === 'node'), + } + ); - const searchResults = (searchParams.searchType === 'dsstox') ? dsstoxResults : nodeResults; + const searchResults = + searchParams.searchType === 'dsstox' ? dsstoxResults : nodeResults; const handleResetNodeSearch = () => { - dispatch(setSearch({ - searchType: null, - params: {} - })) - } + dispatch( + setSearch({ + searchType: null, + params: {}, + }) + ); + }; return ( -
+

Search Results

{searchResults.isError ? ( - <>Error - the requested node was not found. Please try again with a new query. + <> + Error - the requested node was not found. Please try again with a new + query. + ) : searchResults.isUninitialized ? ( <>Please enter a search query and click "Search" to find nodes. ) : searchResults.isLoading ? ( <>Loading... ) : searchResults.data ? (
- ( + iteratee={(r) => ( { ) : null}
); -} +}; -export default NodeResults; \ No newline at end of file +export default NodeResults; diff --git a/web/packages/app/src/components/NodeSearch.js b/web/packages/app/src/components/NodeSearch.js index f4188274..9bf3615d 100644 --- a/web/packages/app/src/components/NodeSearch.js +++ b/web/packages/app/src/components/NodeSearch.js @@ -6,7 +6,7 @@ import { Select, MenuItem, FormControl, - InputLabel + InputLabel, } from '@mui/material'; import makeStyles from '@mui/styles/makeStyles'; @@ -16,9 +16,9 @@ import { setSearch } from '../features/nodeSlice'; const formReducer = (state, event) => { return { ...state, - [event.name]: event.value - } -} + [event.name]: event.value, + }; +}; const useStyles = makeStyles((theme) => ({ root: { @@ -32,68 +32,70 @@ const NodeSearch = (props) => { const { config } = props; const [formData, setFormData] = useReducer(formReducer, {}); const dispatch = useAppDispatch(); - - const classes = useStyles() - const handleSubmit = event => { + const classes = useStyles(); + + const handleSubmit = (event) => { event.preventDefault(); - dispatch(setSearch({ - searchType: 'node', - params: { - label: formData.nodeType, - field: formData.nodeField, - value: formData.nodeValue - } - })); - } - - const handleChange = event => { + dispatch( + setSearch({ + searchType: 'node', + params: { + label: formData.nodeType, + field: formData.nodeField, + value: formData.nodeValue, + }, + }) + ); + }; + + const handleChange = (event) => { setFormData({ name: event.target.name, value: event.target.value, }); - } + }; const handleReset = () => { setFormData({ name: 'nodeType', - value: '' - }) + value: '', + }); setFormData({ name: 'nodeField', - value: '' - }) + value: '', + }); setFormData({ name: 'nodeValue', - value: '' - }) - } + value: '', + }); + }; - const handleLoadExampleQuery = event => { + const handleLoadExampleQuery = (event) => { setFormData({ name: 'nodeType', - value: 'Gene' + value: 'Gene', }); setFormData({ name: 'nodeField', - value: 'geneSymbol' + value: 'geneSymbol', }); setFormData({ name: 'nodeValue', - value: 'CYP2E1' + value: 'CYP2E1', }); - } + }; - const fetchNodeFields = selectedNodeLabel => { + const fetchNodeFields = (selectedNodeLabel) => { if (selectedNodeLabel === undefined) { - return [] + return []; } else { - return config.nodeConfig.nodeLabelProperties[selectedNodeLabel] + return config.nodeConfig.nodeLabelProperties[selectedNodeLabel]; } - } + }; - return( -
+ return ( +

Nodes

Search @@ -107,9 +109,12 @@ const NodeSearch = (props) => {
-
- + Node Type - - + + Node Field - + { name="nodeValue" value={formData.nodeValue || ''} /> - -
+ +
- -
- ) -} + ); +}; export default NodeSearch; diff --git a/web/packages/app/src/components/PathSearch.js b/web/packages/app/src/components/PathSearch.js index dfe2e61b..4a5333db 100644 --- a/web/packages/app/src/components/PathSearch.js +++ b/web/packages/app/src/components/PathSearch.js @@ -1,30 +1,35 @@ import React from 'react'; -import { Graph } from "react-d3-graph"; -import { Box, Button, Typography } from "@mui/material"; +import { Graph } from 'react-d3-graph'; +import { Box, Button, Typography } from '@mui/material'; import { useAppDispatch, useAppSelector } from '../redux/hooks'; import { useFindPathByNodeIdsQuery } from '../features/comptoxApiSlice'; -import { setPathEndNodeId, setPathEndNodeName, setPathStartNodeName, setPathStartNodeId } from '../features/pathSlice'; +import { + setPathEndNodeId, + setPathEndNodeName, + setPathStartNodeName, + setPathStartNodeId, +} from '../features/pathSlice'; const graphConfig = { directed: true, initialZoom: 2, node: { - color: "#216a05", - labelProperty: "name", - } + color: '#216a05', + labelProperty: 'name', + }, }; const colorMap = { - "Chemical": '#e53935', - "Gene": '#c158dc', - "Pathway": '#6f74dd', - "KeyEvent": '#039be5', - "MolecularInitiatingEvent": '#4ebaaa', - "AdverseOutcome": '#aee571', - "AOP": '#fdd835', - "Assay": '#8eacbb', -} + Chemical: '#e53935', + Gene: '#c158dc', + Pathway: '#6f74dd', + KeyEvent: '#039be5', + MolecularInitiatingEvent: '#4ebaaa', + AdverseOutcome: '#aee571', + AOP: '#fdd835', + Assay: '#8eacbb', +}; const PathSearch = (props) => { const pathStartId = useAppSelector((state) => state.path.pathStartNodeId); @@ -34,91 +39,103 @@ const PathSearch = (props) => { const dispatch = useAppDispatch(); - const skip = ((!pathStartId) || (!pathEndId)) ? true : false; - - const { data = [], error, isLoading, isUninitialized } = useFindPathByNodeIdsQuery([pathStartId, pathEndId], { + const skip = !pathStartId || !pathEndId ? true : false; + + const { + data = [], + error, + isLoading, + isUninitialized, + } = useFindPathByNodeIdsQuery([pathStartId, pathEndId], { skip, }); const nodes = data.nodes ? data.nodes : []; const relationships = data.relationships ? data.relationships : []; - const nodes_parsed = nodes.map(n => ({ + const nodes_parsed = nodes.map((n) => ({ id: n.id, name: n.name, nodeType: n.labels[0], color: colorMap[n.labels[0]], })); - const links_parsed = relationships.map(r => ({ + const links_parsed = relationships.map((r) => ({ source: r.source, - target: r.target + target: r.target, })); const parsed_data = { nodes: nodes_parsed, - links: links_parsed + links: links_parsed, }; const handleClearPathSearch = () => { - dispatch(setPathStartNodeId(null)) - dispatch(setPathEndNodeId(null)) - dispatch(setPathStartNodeName('')) - dispatch(setPathEndNodeName('')) - } + dispatch(setPathStartNodeId(null)); + dispatch(setPathEndNodeId(null)); + dispatch(setPathStartNodeName('')); + dispatch(setPathEndNodeName('')); + }; const handleLoadExamplePath = () => { - dispatch(setPathStartNodeId(660070)) - dispatch(setPathEndNodeId(723548)) - dispatch(setPathStartNodeName("cytochrome P450 family 2 subfamily E member 1")) - dispatch(setPathEndNodeName("Capsaicin")) - } + dispatch(setPathStartNodeId(660070)); + dispatch(setPathEndNodeId(723548)); + dispatch( + setPathStartNodeName('cytochrome P450 family 2 subfamily E member 1') + ); + dispatch(setPathEndNodeName('Capsaicin')); + }; - return( -