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dependency maintenance #354

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Jul 11, 2023
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7 changes: 3 additions & 4 deletions .github/workflows/sbom.yml
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@nickgros nickgros Jul 11, 2023

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This workflow pushes a dependency list from our lockfile to a Microsoft tool that generates and reports security vulnerabilities. It's our workaround to get vulnerability alerts until GitHub supports Dependabot security updates for pnpm.

Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,10 @@ name: SBOM upload

on:
push:
branches: ["main"]
branches: ['main']

jobs:
SBOM-upload:

runs-on: ubuntu-latest
permissions:
id-token: write
Expand All @@ -28,6 +27,6 @@ jobs:
name: sbom
path: _manifest/spdx_2.2
- name: SBOM upload
uses: jhutchings1/spdx-to-dependency-graph[email protected].2
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original repo was archived and points to this new action

uses: advanced-security/spdx-dependency-submission[email protected].1
with:
filePath: "_manifest/spdx_2.2/"
filePath: '_manifest/spdx_2.2/'
79 changes: 35 additions & 44 deletions apps/SageAccountWeb/package.json
Original file line number Diff line number Diff line change
Expand Up @@ -5,48 +5,47 @@
"private": true,
"dependencies": {
"@emotion/core": "^11.0.0",
"@emotion/react": "^11.10.6",
"@emotion/styled": "^11.10.6",
"@mui/icons-material": "^5.11.16",
"@mui/material": "^5.11.16",
"@mui/system": "^5.11.16",
"@mui/utils": "^5.11.13",
"@emotion/react": "^11.11.1",
"@emotion/styled": "^11.11.0",
"@mui/icons-material": "^5.13.7",
"@mui/material": "^5.13.7",
"@mui/system": "^5.13.7",
"@mui/utils": "^5.13.7",
"lodash-es": "^4.17.21",
"plotly.js-basic-dist": "^2.22.0",
"plotly.js-basic-dist": "^2.24.3",
"react": "18.2.0",
"react-bootstrap": "^1.5.2",
"react-bootstrap": "^1.6.7",
"react-cookie": "4.0.0",
"react-dom": "18.2.0",
"react-easy-crop": "^4.2.0",
"react-query": "3.39.1",
"react-router-dom": "5.3.3",
"react-spinners": "^0.11.0",
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Dropped react-spinners as it is unused in this project.

"react-use": "^17.3.1",
"sass": "^1.30.0",
"react-easy-crop": "^4.7.5",
"react-query": "3.39.3",
"react-router-dom": "^5.3.4",
"react-use": "^17.4.0",
"sass": "^1.63.6",
"synapse-react-client": "workspace:*",
"universal-cookie": "^4.0.3"
"universal-cookie": "^4.0.4"
},
"devDependencies": {
"@sage-bionetworks/synapse-types": "workspace:*",
"@testing-library/react": "^13.3.0",
"@testing-library/react": "^13.4.0",
"@testing-library/user-event": "^14.4.3",
"@types/katex": "^0.5.0",
"@types/node": "^18.16.12",
"@types/plotly.js": "^2.12.18",
"@types/react": "18.0.17",
"@types/node": "^18.16.19",
"@types/plotly.js": "^2.12.22",
"@types/react": "18.0.27",
"@types/react-dom": "18.0.6",
"@types/react-easy-crop": "^2.0.0",
"@types/react-plotly.js": "^2.6.0",
"@types/react-router-dom": "^5.1.7",
"@types/react-router-dom": "^5.3.3",
"@types/react-tooltip": "^4.2.4",
"@vitest/coverage-c8": "^0.31.0",
"@vitest/ui": "^0.31.0",
"@vitest/coverage-c8": "^0.33.0",
"@vitest/ui": "^0.33.0",
"assert": "^2.0.0",
"buffer": "^6.0.3",
"https-browserify": "^1.0.0",
"identity-obj-proxy": "^3.0.0",
"jsdom": "^21.1.1",
"katex": "^0.10.0-rc.1",
"jsdom": "^21.1.2",
"katex": "^0.10.2",
"markdown-it": "^13.0.1",
"markdown-it-br": "^1.0.0",
"markdown-it-center-text": "^1.0.4",
Expand All @@ -56,27 +55,27 @@
"markdown-it-strikethrough-alt": "^1.0.0",
"markdown-it-sub-alt": "^1.0.0",
"markdown-it-sup-alt": "^1.0.2",
"markdown-it-synapse": "^1.1.7",
"markdown-it-synapse": "workspace:^",
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Using workspace markdown-it-synapse for devDependencies, but I think all of the apps are pulling an old version from CDN. Since the bundling strategy changed, that should be tackled separately

"markdown-it-synapse-heading": "^1.0.1",
"markdown-it-synapse-math": "^3.0.4",
"markdown-it-synapse-math": "^3.0.5",
"markdown-it-synapse-table": "^1.0.6",
"memfs": "^3.4.7",
"memfs": "^3.5.3",
"path-browserify": "^1.0.1",
"pluralize": "^8.0.0",
"prettier": "^2.6.2",
"prettier": "^2.8.8",
"process": "^0.11.10",
"source-map-explorer": "^2.5.2",
"source-map-explorer": "^2.5.3",
"stream-browserify": "^3.0.0",
"stream-http": "^3.2.0",
"timers-browserify": "^2.0.12",
"tslib": "^2.3.1",
"type-fest": "^3.7.2",
"typescript": "5.0.4",
"url": "^0.11.0",
"util": "^0.12.4",
"vite": "^4.3.4",
"tslib": "^2.6.0",
"type-fest": "^3.13.0",
"typescript": "5.1.6",
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Upgraded TS everywhere

"url": "^0.11.1",
"util": "^0.12.5",
"vite": "^4.4.2",
"vite-config": "workspace:*",
"vitest": "^0.31.0",
"vitest": "^0.33.0",
"whatwg-fetch": "^3.6.2"
},
"scripts": {
Expand All @@ -103,14 +102,6 @@
"last 1 safari version"
]
},
"resolutions": {
"js-yaml": "3.13.1",
"react": "18.2.0",
"react-hot-toast": "2.2.0",
"@types/react": "18.0.17",
"@types/react-dom": "18.0.6",
"minimatch": "^3.1.2"
},
Comment on lines -106 to -113
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According to the output of pnpm install, these resolution entries are ignored. Only the base package.json resolutions are used.

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See docs for overrides: https://pnpm.io/package_json#pnpmoverrides - this is the same feature, just a different property name.

"lint-staged": {
"*.{js,jsx,ts,tsx,json,yml,scss,css,md}": "prettier --config .prettierrc --write"
}
Expand Down
74 changes: 33 additions & 41 deletions apps/portals/package.json
Original file line number Diff line number Diff line change
Expand Up @@ -4,27 +4,27 @@
"private": true,
"type": "module",
"dependencies": {
"@emotion/react": "^11.10.6",
"@emotion/styled": "^11.10.6",
"@mui/icons-material": "^5.11.16",
"@mui/material": "^5.11.16",
"@sage-bionetworks/react-base-table": "^1.13.2",
"@emotion/react": "^11.11.1",
"@emotion/styled": "^11.11.0",
"@mui/icons-material": "^5.13.7",
"@mui/material": "^5.13.7",
"@sage-bionetworks/react-base-table": "^1.13.4",
"clone-deep": "^4.0.1",
"dayjs": "^1.11.6",
"dayjs": "^1.11.9",
"lodash": "^4.17.21",
"lodash-es": "^4.17.21",
"plotly.js-basic-dist": "^2.22.0",
"plotly.js-basic-dist": "^2.24.3",
"react": "^18.2.0",
"react-bootstrap": "^1.5.2",
"react-bootstrap": "^1.6.7",
"react-cookie": "4.0.0",
"react-dom": "^18.2.0",
"react-plotly.js": "^2.6.0",
"react-query": "3.39.1",
"react-router-dom": "^5.3.3",
"react-query": "3.39.3",
"react-router-dom": "^5.3.4",
"react-spinners": "^0.13.8",
"react-switch": "^7.0.0",
"react-use": "^17.3.1",
"sass": "^1.30.0",
"react-use": "^17.4.0",
"sass": "^1.63.6",
"synapse-react-client": "workspace:*"
},
"scripts": {
Expand All @@ -43,25 +43,25 @@
"devDependencies": {
"@sage-bionetworks/synapse-types": "workspace:*",
"@testing-library/jest-dom": "^5.16.5",
"@testing-library/react": "^13.3.0",
"@testing-library/react": "^13.4.0",
"@testing-library/user-event": "^14.4.3",
"@types/katex": "^0.5.0",
"@types/lodash": "^4.14.191",
"@types/node": "^18.16.12",
"@types/plotly.js": "^2.12.18",
"@types/react": "^18.0.17",
"@types/react-dom": "^18.0.6",
"@types/lodash": "^4.14.195",
"@types/node": "^18.16.19",
"@types/plotly.js": "^2.12.22",
"@types/react": "18.0.27",
"@types/react-dom": "^18.2.6",
"@types/react-plotly.js": "^2.6.0",
"@types/react-router-dom": "^5.3.3",
"@vitest/coverage-c8": "^0.31.0",
"@vitest/ui": "^0.31.0",
"@vitest/utils": "^0.31.1",
"@vitest/coverage-c8": "^0.33.0",
"@vitest/ui": "^0.33.0",
"@vitest/utils": "^0.33.0",
"assert": "^2.0.0",
"buffer": "^6.0.3",
"https-browserify": "^1.0.0",
"identity-obj-proxy": "^3.0.0",
"jsdom": "^21.1.1",
"katex": "^0.10.0-rc.1",
"jsdom": "^21.1.2",
"katex": "^0.10.2",
"markdown-it": "^13.0.1",
"markdown-it-br": "^1.0.0",
"markdown-it-center-text": "^1.0.4",
Expand All @@ -71,26 +71,26 @@
"markdown-it-strikethrough-alt": "^1.0.0",
"markdown-it-sub-alt": "^1.0.0",
"markdown-it-sup-alt": "^1.0.2",
"markdown-it-synapse": "^1.1.10",
"markdown-it-synapse": "workspace:^",
"markdown-it-synapse-heading": "^1.0.1",
"markdown-it-synapse-math": "^3.0.4",
"markdown-it-synapse-math": "^3.0.5",
"markdown-it-synapse-table": "^1.0.6",
"memfs": "^3.4.7",
"memfs": "^3.5.3",
"path-browserify": "^1.0.1",
"pluralize": "^8.0.0",
"postcss-normalize": "^10.0.1",
"process": "^0.11.10",
"source-map-explorer": "^2.5.2",
"source-map-explorer": "^2.5.3",
"stream-browserify": "^3.0.0",
"stream-http": "^3.2.0",
"timers-browserify": "^2.0.12",
"tslib": "^2.3.1",
"typescript": "5.0.4",
"url": "^0.11.0",
"util": "^0.12.4",
"vite": "^4.3.4",
"tslib": "^2.6.0",
"typescript": "5.1.6",
"url": "^0.11.1",
"util": "^0.12.5",
"vite": "^4.4.2",
"vite-config": "workspace:*",
"vitest": "^0.31.0",
"vitest": "^0.33.0",
"whatwg-fetch": "^3.6.2"
},
"browserslist": {
Expand All @@ -108,13 +108,5 @@
"last 1 firefox version",
"last 1 safari version"
]
},
"resolutions": {
"goober": "2.1.9",
"js-yaml": "3.13.1",
"react": "18.2.0",
"react-hot-toast": "2.2.0",
"@types/react": "^18.0.17",
"minimatch": "^3.1.2"
}
}
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