From 0b0d9d3f5f88cc204f37ac836d0d571cdd55b754 Mon Sep 17 00:00:00 2001 From: Swaathik Date: Tue, 14 Apr 2026 15:31:50 +0100 Subject: [PATCH 01/19] Update vite to v8 --- package.json | 2 +- yarn.lock | 573 +++++++++++++++++++++------------------------------ 2 files changed, 237 insertions(+), 338 deletions(-) diff --git a/package.json b/package.json index 41483db..f8cf7dd 100644 --- a/package.json +++ b/package.json @@ -71,7 +71,7 @@ "svg-inline-loader": "0.8.2", "typescript": "5.9.3", "typescript-eslint": "8.56.1", - "vite": "7.3.1", + "vite": "8.0.8", "vite-plugin-dts": "4.5.4", "vite-plugin-env-compatible": "2.0.1", "vite-plugin-html": "3.2.2", diff --git a/yarn.lock b/yarn.lock index e652bac..6b5d76b 100644 --- a/yarn.lock +++ b/yarn.lock @@ -958,6 +958,14 @@ resolved "https://registry.yarnpkg.com/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz#75a2e8b51cb758a7553d6804a5932d7aace75c39" integrity 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"https://registry.yarnpkg.com/lightningcss-win32-arm64-msvc/-/lightningcss-win32-arm64-msvc-1.32.0.tgz#4f30ba3fa5e925f5b79f945e8cc0d176c3b1ab38" + integrity sha512-8SbC8BR40pS6baCM8sbtYDSwEVQd4JlFTOlaD3gWGHfThTcABnNDBda6eTZeqbofalIJhFx0qKzgHJmcPTnGdw== + +lightningcss-win32-x64-msvc@1.32.0: + version "1.32.0" + resolved "https://registry.yarnpkg.com/lightningcss-win32-x64-msvc/-/lightningcss-win32-x64-msvc-1.32.0.tgz#141aa5605645064928902bb4af045fa7d9f4220a" + integrity sha512-Amq9B/SoZYdDi1kFrojnoqPLxYhQ4Wo5XiL8EVJrVsB8ARoC1PWW6VGtT0WKCemjy8aC+louJnjS7U18x3b06Q== + +lightningcss@^1.32.0: + version "1.32.0" + resolved "https://registry.yarnpkg.com/lightningcss/-/lightningcss-1.32.0.tgz#b85aae96486dcb1bf49a7c8571221273f4f1e4a9" + integrity sha512-NXYBzinNrblfraPGyrbPoD19C1h9lfI/1mzgWYvXUTe414Gz/X1FD2XBZSZM7rRTrMA8JL3OtAaGifrIKhQ5yQ== + dependencies: + detect-libc "^2.0.3" + optionalDependencies: + lightningcss-android-arm64 "1.32.0" + lightningcss-darwin-arm64 "1.32.0" + lightningcss-darwin-x64 "1.32.0" + lightningcss-freebsd-x64 "1.32.0" + lightningcss-linux-arm-gnueabihf "1.32.0" + lightningcss-linux-arm64-gnu "1.32.0" + lightningcss-linux-arm64-musl "1.32.0" + lightningcss-linux-x64-gnu "1.32.0" + lightningcss-linux-x64-musl "1.32.0" + lightningcss-win32-arm64-msvc "1.32.0" + lightningcss-win32-x64-msvc "1.32.0" + lines-and-columns@^1.1.6: version "1.2.4" resolved "https://registry.yarnpkg.com/lines-and-columns/-/lines-and-columns-1.2.4.tgz#eca284f75d2965079309dc0ad9255abb2ebc1632" @@ -7371,6 +7276,11 @@ picomatch@^4.0.2, picomatch@^4.0.3: resolved "https://registry.yarnpkg.com/picomatch/-/picomatch-4.0.3.tgz#796c76136d1eead715db1e7bad785dedd695a042" integrity sha512-5gTmgEY/sqK6gFXLIsQNH19lWb4ebPDLA4SdLP7dsWkIXHWlG66oPuVvXSGFPppYZz8ZDZq0dYYrbHfBCVUb1Q== +picomatch@^4.0.4: + version "4.0.4" + resolved "https://registry.yarnpkg.com/picomatch/-/picomatch-4.0.4.tgz#fd6f5e00a143086e074dffe4c924b8fb293b0589" + integrity sha512-QP88BAKvMam/3NxH6vj2o21R6MjxZUAd6nlwAS/pnGvN9IVLocLHxGYIzFhg6fUQ+5th6P4dv4eW9jX3DSIj7A== + pidtree@^0.3.0: version "0.3.1" resolved "https://registry.yarnpkg.com/pidtree/-/pidtree-0.3.1.tgz#ef09ac2cc0533df1f3250ccf2c4d366b0d12114a" @@ -7421,10 +7331,10 @@ possible-typed-array-names@^1.0.0: resolved "https://registry.yarnpkg.com/possible-typed-array-names/-/possible-typed-array-names-1.1.0.tgz#93e3582bc0e5426586d9d07b79ee40fc841de4ae" integrity sha512-/+5VFTchJDoVj3bhoqi6UeymcD00DAwb1nJwamzPvHEszJ4FpF6SNNbUbOS8yI56qHzdV8eK0qEfOSiodkTdxg== -postcss@^8.5.6: - version "8.5.8" - resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.5.8.tgz#6230ecc8fb02e7a0f6982e53990937857e13f399" - integrity sha512-OW/rX8O/jXnm82Ey1k44pObPtdblfiuWnrd8X7GJ7emImCOstunGbXUpp7HdBrFQX6rJzn3sPT397Wp5aCwCHg== +postcss@^8.5.8: + version "8.5.9" + resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.5.9.tgz#f6ee9e0b94f0f19c97d2f172bfbd7fc71fe1cca4" + integrity sha512-7a70Nsot+EMX9fFU3064K/kdHWZqGVY+BADLyXc8Dfv+mTLLVl6JzJpPaCZ2kQL9gIJvKXSLMHhqdRRjwQeFtw== dependencies: nanoid "^3.3.11" picocolors "^1.1.1" @@ -7760,6 +7670,30 @@ robust-predicates@^3.0.2: resolved "https://registry.yarnpkg.com/robust-predicates/-/robust-predicates-3.0.2.tgz#d5b28528c4824d20fc48df1928d41d9efa1ad771" integrity sha512-IXgzBWvWQwE6PrDI05OvmXUIruQTcoMDzRsOd5CDvHCVLcLHMTSYvOK5Cm46kWqlV3yAbuSpBZdJ5oP5OUoStg== +rolldown@1.0.0-rc.15: + version "1.0.0-rc.15" + resolved "https://registry.yarnpkg.com/rolldown/-/rolldown-1.0.0-rc.15.tgz#ea3526443b2dbe834e9f8f6c1fde6232ec687170" + integrity sha512-Ff31guA5zT6WjnGp0SXw76X6hzGRk/OQq2hE+1lcDe+lJdHSgnSX6nK3erbONHyCbpSj9a9E+uX/OvytZoWp2g== + dependencies: + "@oxc-project/types" "=0.124.0" + "@rolldown/pluginutils" "1.0.0-rc.15" + optionalDependencies: + "@rolldown/binding-android-arm64" "1.0.0-rc.15" + "@rolldown/binding-darwin-arm64" "1.0.0-rc.15" + "@rolldown/binding-darwin-x64" "1.0.0-rc.15" + "@rolldown/binding-freebsd-x64" "1.0.0-rc.15" + "@rolldown/binding-linux-arm-gnueabihf" "1.0.0-rc.15" + "@rolldown/binding-linux-arm64-gnu" "1.0.0-rc.15" + "@rolldown/binding-linux-arm64-musl" "1.0.0-rc.15" + "@rolldown/binding-linux-ppc64-gnu" "1.0.0-rc.15" + "@rolldown/binding-linux-s390x-gnu" "1.0.0-rc.15" + "@rolldown/binding-linux-x64-gnu" "1.0.0-rc.15" + "@rolldown/binding-linux-x64-musl" "1.0.0-rc.15" + "@rolldown/binding-openharmony-arm64" "1.0.0-rc.15" + "@rolldown/binding-wasm32-wasi" "1.0.0-rc.15" + "@rolldown/binding-win32-arm64-msvc" "1.0.0-rc.15" + "@rolldown/binding-win32-x64-msvc" "1.0.0-rc.15" + rollup-plugin-visualizer@7.0.0: version "7.0.0" resolved "https://registry.yarnpkg.com/rollup-plugin-visualizer/-/rollup-plugin-visualizer-7.0.0.tgz#7abacfae91efeda6f2e0a445f97a9997249e884c" @@ -7770,40 +7704,6 @@ rollup-plugin-visualizer@7.0.0: source-map "^0.7.4" yargs "^18.0.0" -rollup@^4.43.0: - version "4.59.0" - resolved "https://registry.yarnpkg.com/rollup/-/rollup-4.59.0.tgz#cf74edac17c1486f562d728a4d923a694abdf06f" - integrity sha512-2oMpl67a3zCH9H79LeMcbDhXW/UmWG/y2zuqnF2jQq5uq9TbM9TVyXvA4+t+ne2IIkBdrLpAaRQAvo7YI/Yyeg== - dependencies: - "@types/estree" "1.0.8" - optionalDependencies: - "@rollup/rollup-android-arm-eabi" "4.59.0" - "@rollup/rollup-android-arm64" "4.59.0" - "@rollup/rollup-darwin-arm64" "4.59.0" - "@rollup/rollup-darwin-x64" "4.59.0" - "@rollup/rollup-freebsd-arm64" "4.59.0" - "@rollup/rollup-freebsd-x64" "4.59.0" - "@rollup/rollup-linux-arm-gnueabihf" "4.59.0" - "@rollup/rollup-linux-arm-musleabihf" "4.59.0" - "@rollup/rollup-linux-arm64-gnu" "4.59.0" - "@rollup/rollup-linux-arm64-musl" "4.59.0" - "@rollup/rollup-linux-loong64-gnu" "4.59.0" - "@rollup/rollup-linux-loong64-musl" "4.59.0" - "@rollup/rollup-linux-ppc64-gnu" "4.59.0" - "@rollup/rollup-linux-ppc64-musl" "4.59.0" - "@rollup/rollup-linux-riscv64-gnu" "4.59.0" - "@rollup/rollup-linux-riscv64-musl" "4.59.0" - "@rollup/rollup-linux-s390x-gnu" "4.59.0" - "@rollup/rollup-linux-x64-gnu" "4.59.0" - "@rollup/rollup-linux-x64-musl" "4.59.0" - "@rollup/rollup-openbsd-x64" "4.59.0" - "@rollup/rollup-openharmony-arm64" "4.59.0" - "@rollup/rollup-win32-arm64-msvc" "4.59.0" - "@rollup/rollup-win32-ia32-msvc" "4.59.0" - "@rollup/rollup-win32-x64-gnu" "4.59.0" - "@rollup/rollup-win32-x64-msvc" "4.59.0" - fsevents "~2.3.2" - run-applescript@^7.0.0: version "7.1.0" resolved "https://registry.yarnpkg.com/run-applescript/-/run-applescript-7.1.0.tgz#2e9e54c4664ec3106c5b5630e249d3d6595c4911" @@ -8910,16 +8810,15 @@ vite-plugin-svgo@2.0.0: dependencies: svgo "3.3.2" -vite@7.3.1: - version "7.3.1" - resolved "https://registry.yarnpkg.com/vite/-/vite-7.3.1.tgz#7f6cfe8fb9074138605e822a75d9d30b814d6507" - integrity sha512-w+N7Hifpc3gRjZ63vYBXA56dvvRlNWRczTdmCBBa+CotUzAPf5b7YMdMR/8CQoeYE5LX3W4wj6RYTgonm1b9DA== +vite@8.0.8: + version "8.0.8" + resolved "https://registry.yarnpkg.com/vite/-/vite-8.0.8.tgz#4e26a9bba77c4b27a00b6b10100a7dab48d546a3" + integrity sha512-dbU7/iLVa8KZALJyLOBOQ88nOXtNG8vxKuOT4I2mD+Ya70KPceF4IAmDsmU0h1Qsn5bPrvsY9HJstCRh3hG6Uw== dependencies: - esbuild "^0.27.0" - fdir "^6.5.0" - picomatch "^4.0.3" - postcss "^8.5.6" - rollup "^4.43.0" + lightningcss "^1.32.0" + picomatch "^4.0.4" + postcss "^8.5.8" + rolldown "1.0.0-rc.15" tinyglobby "^0.2.15" optionalDependencies: fsevents "~2.3.3" From 63e8315bf1b9a5644ee5431c6e82bae7b1d68b8b Mon Sep 17 00:00:00 2001 From: Daniel Rice Date: Thu, 16 Apr 2026 14:34:00 +0100 Subject: [PATCH 02/19] Security audit. --- .github/workflows/test-and-deploy.yml | 1 + .gitignore | 15 +- eslint.config.mjs | 10 +- index.html | 4 + package.json | 1 + scripts/clearCDNcaches.sh | 2 +- .../alphamissense-pathogenicity-adapter.ts | 6 +- src/protvista-uniprot-structure.ts | 10 +- src/protvista-uniprot.ts | 2 +- src/tooltips/feature-tooltip.ts | 62 +- src/tooltips/interpro-tooltip.ts | 15 +- src/tooltips/ptm-tooltip.ts | 12 +- src/tooltips/rna-editing-tooltip.ts | 17 +- src/tooltips/structure-tooltip.ts | 10 +- src/tooltips/variation-tooltip.ts | 27 +- src/utils/security.ts | 49 + tsconfig.json | 2 +- vite.config.mjs | 2 +- yarn.lock | 2269 +++++++++-------- 19 files changed, 1305 insertions(+), 1211 deletions(-) create mode 100644 src/utils/security.ts diff --git a/.github/workflows/test-and-deploy.yml b/.github/workflows/test-and-deploy.yml index e073af8..107c314 100644 --- a/.github/workflows/test-and-deploy.yml +++ b/.github/workflows/test-and-deploy.yml @@ -2,6 +2,7 @@ name: Test and Deploy on: push: + branches: [main] pull_request: permissions: diff --git a/.gitignore b/.gitignore index f9bfde4..9654821 100644 --- a/.gitignore +++ b/.gitignore @@ -7,4 +7,17 @@ dist/ node_modules/ *.log .yalc/ -yalc.lock \ No newline at end of file +yalc.lock + +# Security: prevent accidental commit of secrets and credentials +.env +.env.* +.env.local +.env.*.local +*.pem +*.key +*.pfx +*.p12 +*.cert +.aws/ +credentials.json \ No newline at end of file diff --git a/eslint.config.mjs b/eslint.config.mjs index adc2f08..38f4927 100644 --- a/eslint.config.mjs +++ b/eslint.config.mjs @@ -2,6 +2,7 @@ import js from '@eslint/js'; import ts from 'typescript-eslint'; import tsParser from '@typescript-eslint/parser'; import tsPlugin from '@typescript-eslint/eslint-plugin'; +import noUnsanitized from 'eslint-plugin-no-unsanitized'; import prettier from 'eslint-config-prettier'; import globals from 'globals'; @@ -26,15 +27,20 @@ export default [ plugins: { '@typescript-eslint': tsPlugin, + 'no-unsanitized': noUnsanitized, }, - /* start with the plugin’s own recommended rules… */ + /* start with the plugin's own recommended rules... */ rules: { ...tsPlugin.configs.recommended.rules, - /* …then apply your custom tweaks */ + /* ...then apply your custom tweaks */ '@typescript-eslint/explicit-module-boundary-types': 'off', '@typescript-eslint/no-explicit-any': 'off', + + /* Security: flag unsafe DOM manipulation */ + 'no-unsanitized/method': 'warn', + 'no-unsanitized/property': 'warn', }, }, ]; diff --git a/index.html b/index.html index d3e9846..f0f0653 100644 --- a/index.html +++ b/index.html @@ -6,6 +6,10 @@ protvista-uniprot + diff --git a/package.json b/package.json index 41483db..3164d76 100644 --- a/package.json +++ b/package.json @@ -63,6 +63,7 @@ "babel-jest": "30.2.0", "eslint": "10.0.2", "eslint-config-prettier": "10.1.8", + "eslint-plugin-no-unsanitized": "^4.1.5", "eslint-plugin-prettier": "5.5.5", "globals": "17.3.0", "jest": "30.2.0", diff --git a/scripts/clearCDNcaches.sh b/scripts/clearCDNcaches.sh index 355a9c6..8fa9029 100755 --- a/scripts/clearCDNcaches.sh +++ b/scripts/clearCDNcaches.sh @@ -1,7 +1,7 @@ #!/bin/sh curl -X POST \ - http://purge.jsdelivr.net \ + https://purge.jsdelivr.net \ -H 'cache-control: no-cache' \ -H 'content-type: application/json' \ -d '{ diff --git a/src/adapters/alphamissense-pathogenicity-adapter.ts b/src/adapters/alphamissense-pathogenicity-adapter.ts index 165b0b0..b54f65d 100644 --- a/src/adapters/alphamissense-pathogenicity-adapter.ts +++ b/src/adapters/alphamissense-pathogenicity-adapter.ts @@ -47,6 +47,10 @@ const parseCSV = (rawText: string): string => { if (i === 0 || !row) { continue; } + const match = row.match(cellSplitter); + if (!match) { + continue; + } const [ , wildType, @@ -54,7 +58,7 @@ const parseCSV = (rawText: string): string => { mutated, pathogenicityScore, pathogenicityLabel, - ] = row.match(cellSplitter); + ] = match; const position = +positionString; const index = position - 1; if (!positions[index]) { diff --git a/src/protvista-uniprot-structure.ts b/src/protvista-uniprot-structure.ts index 4f8d57f..d64eca3 100644 --- a/src/protvista-uniprot-structure.ts +++ b/src/protvista-uniprot-structure.ts @@ -348,9 +348,10 @@ const sourceDownloadLink = (downloadUrl: string) => `; -const foldseekLink = (accession: string, sourceDB: string) => - html` { + const params = new URLSearchParams({ accession, source: sourceDB }); + return html` ${svg`${unsafeHTML(externalLinkIcon)}`} `; +}; const styleId = 'protvista-styles'; @@ -587,7 +589,7 @@ class ProtvistaUniprotStructure extends LitElement { if (!document.getElementById(styleId)) { const styleTag = document.createElement('style'); styleTag.id = styleId; - styleTag.innerHTML = ` + styleTag.textContent = ` ${loaderStyles.toString()} ${this.cssStyle} `; diff --git a/src/protvista-uniprot.ts b/src/protvista-uniprot.ts index 411d352..450c8c0 100644 --- a/src/protvista-uniprot.ts +++ b/src/protvista-uniprot.ts @@ -123,7 +123,7 @@ class ProtvistaUniprot extends LitElement { addStyles() { // We are not using static get styles() as we are not using the shadowDOM because of Mol* const styleTag = document.createElement('style'); - styleTag.innerHTML = `${protvistaStyles.toString()} ${loaderStyles.toString()}`; + styleTag.textContent = `${protvistaStyles.toString()} ${loaderStyles.toString()}`; document.querySelector('head')?.append(styleTag); } diff --git a/src/tooltips/feature-tooltip.ts b/src/tooltips/feature-tooltip.ts index 6e9aeb5..d5c3765 100644 --- a/src/tooltips/feature-tooltip.ts +++ b/src/tooltips/feature-tooltip.ts @@ -1,4 +1,5 @@ import ecoMap from '../adapters/config/evidence'; +import { escapeHtml, sanitizeUrl } from '../utils/security'; import { acetylate, phosphorylate, @@ -46,15 +47,15 @@ const unimodIdMapping = { const formatSource = (source) => { if (source.name?.toLowerCase() === 'PubMed'.toLowerCase()) { - return `${source.id} (${source.name} EuropePMC)`; + return `${escapeHtml(source.id)} (${escapeHtml(source.name)} EuropePMC)`; } - const sourceLink = ` ${source.id}`; + const sourceLink = ` ${escapeHtml(source.id)}`; if (source.name) { // Temporary until we get the expected value as 'PeptideAtlas' instead of 'HppPeptideAtlas' if (source.name.startsWith('Hpp')) { - return `${sourceLink} (${source.name.slice(3)})`; + return `${sourceLink} (${escapeHtml(source.name.slice(3))})`; } - return `${sourceLink} (${source.name})`; + return `${sourceLink} (${escapeHtml(source.name)})`; } return sourceLink; }; @@ -66,8 +67,8 @@ export const getEvidenceFromCodes = (evidenceList) => { .map((ev) => { const ecoMatch = ecoMap.find((eco) => eco.name === ev.code); if (!ecoMatch) return ``; - return `
  • ${ - ecoMatch.shortDescription + return `
  • ${ + escapeHtml(ecoMatch.shortDescription) }: ${ev.source ? formatSource(ev.source) : ''}
    • `; }) .join('')} @@ -78,10 +79,10 @@ export const formatXrefs = (xrefs) => { return ``; @@ -99,13 +100,14 @@ const getPTMEvidence = (ptms, taxId) => { return `