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‎.dockerignore

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node_modules

‎.env.development

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GEN3_COMMONS_NAME=gen3
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NEXT_PUBLIC_GEN3_API=https://localhost:3010
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NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010
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# set these if you want to use different endpoints
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#NEXT_PUBLIC_GEN3_GUPPY_API=

‎.env.production

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GEN3_COMMONS_NAME=gen3
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NEXT_PUBLIC_GEN3_API=https://localhost/
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NEXT_PUBLIC_GEN3_DOMAIN=https://localhost/

‎.eslintignore

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*.css
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node_modules

‎.eslintrc.js

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module.exports = {
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env: {
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browser: true,
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es2021: true,
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node: true,
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},
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extends: [
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'eslint:recommended',
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'plugin:jsx-a11y/recommended',
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'plugin:react/recommended',
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'plugin:react-hooks/recommended',
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'plugin:@typescript-eslint/recommended',
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'plugin:@next/next/recommended',
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'prettier',
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],
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parser: '@typescript-eslint/parser',
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parserOptions: {
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ecmaFeatures: {
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jsx: true,
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},
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ecmaVersion: 12,
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sourceType: 'module',
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},
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plugins: ['jsx-a11y', 'react', 'react-hooks', '@typescript-eslint'],
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rules: {
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'@typescript-eslint/no-explicit-any':['warn'],
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'no-underscore-dangle': 'off',
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'import/prefer-default-export': 'off',
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'linebreak-style': ['error', 'unix'],
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'@typescript-eslint/quotes': ['warn', 'single'],
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quotes: ['warn', 'single'],
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'jsx-quotes': ['warn', 'prefer-double'],
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semi: ['error', 'always'],
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'prefer-destructuring': ['error', { object: true, array: false }],
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'react/jsx-fragments': ['warn', 'element'],
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// disable these because we're using React 17+ with the jsx transform
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'react/jsx-uses-react': 'off',
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'react/react-in-jsx-scope': 'off',
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},
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overrides: [
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{
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files: ['**/*.tsx'],
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rules: {
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'react/prop-types': 'off',
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},
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},
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],
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settings: {
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react: {
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version: 'detect',
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},
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next: {
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rootDir: './',
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},
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},
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};

‎.eslintrc.json

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{
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"extends": "next/core-web-vitals"
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}

‎.github/workflows/ci.yaml

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name: CI
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on: push
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/[email protected]
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with:
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node-version: 20.11.0
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- name: install npm version
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run: npm install -g npm
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- name: Get Version
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run: npm -v
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- name: Install modules
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run: npm ci
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- name: Run ESLint
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run: npm run lint

‎.github/workflows/image_build_push.yaml

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name: Build Image and Push to Quay
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on: push
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jobs:
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Security:
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name: Security Pipeline
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uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
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with:
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python-poetry: 'false'
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secrets: inherit
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ci:
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name: Build Image and Push to Quay
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uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
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with:
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USE_QUAY_ONLY: true
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secrets:
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ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
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ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
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QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
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QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}

‎.gitignore

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# See https://help.github.com/articles/ignoring-files/ for more about ignoring files.
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# dependencies
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/node_modules
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/.pnp
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.pnp.js
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# testing
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/coverage
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# next.js
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/.next/
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/out/
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# production
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/build
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# misc
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.DS_Store
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*.pem
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# debug
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npm-debug.log*
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yarn-debug.log*
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yarn-error.log*
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# local env files
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.env*.local
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# vercel
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.vercel
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# typescript
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*.tsbuildinfo
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next-env.d.ts

‎.npmignore

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.DS_Store
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node_modules
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.next/cache/*

‎.nvmrc

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20

‎.pre-commit-config.yaml

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repos:
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- repo: [email protected]:Yelp/detect-secrets
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rev: v1.4.0
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hooks:
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- id: detect-secrets
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args: ['--baseline', '.secrets.baseline']
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exclude: 'package-lock.json'
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.5.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: no-commit-to-branch
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args: [--branch, develop, --branch, main, --pattern, release/.*]

‎.prettierignore

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node_modules
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.next
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public
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dist

‎.prettierrc

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{
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"tabWidth": 2,
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"useTabs": false,
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"trailingComma": "all",
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"singleQuote": true
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}

‎.secrets.baseline

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{
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"version": "1.4.0",
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"plugins_used": [
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{
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"name": "ArtifactoryDetector"
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},
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{
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"name": "AWSKeyDetector"
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},
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{
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"name": "AzureStorageKeyDetector"
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},
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{
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"name": "Base64HighEntropyString",
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"limit": 4.5
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},
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{
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"name": "BasicAuthDetector"
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},
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{
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"name": "CloudantDetector"
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},
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{
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"name": "DiscordBotTokenDetector"
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},
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{
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"name": "GitHubTokenDetector"
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},
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{
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"name": "HexHighEntropyString",
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"limit": 3.0
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},
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{
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"name": "IbmCloudIamDetector"
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},
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{
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"name": "IbmCosHmacDetector"
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},
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{
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"name": "JwtTokenDetector"
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},
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{
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"name": "KeywordDetector",
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"keyword_exclude": ""
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},
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{
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"name": "MailchimpDetector"
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},
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{
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"name": "NpmDetector"
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},
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{
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"name": "PrivateKeyDetector"
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},
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{
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"name": "SendGridDetector"
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},
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{
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"name": "SlackDetector"
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},
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{
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"name": "SoftlayerDetector"
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},
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{
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"name": "SquareOAuthDetector"
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},
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{
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"name": "StripeDetector"
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},
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{
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"name": "TwilioKeyDetector"
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}
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],
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"filters_used": [
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{
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"path": "detect_secrets.filters.allowlist.is_line_allowlisted"
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},
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{
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"path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
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"min_level": 2
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},
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{
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"path": "detect_secrets.filters.heuristic.is_indirect_reference"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_likely_id_string"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_lock_file"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_potential_uuid"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_sequential_string"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_swagger_file"
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},
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{
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"path": "detect_secrets.filters.heuristic.is_templated_secret"
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}
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],
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"results": {},
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"generated_at": "2024-01-26T17:55:44Z"
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}

‎Dockerfile

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# docker build -t gen3ff .
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# docker run -p 3000:3000 -it gen3ff
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# for Macbook silicon M1/m2 uncomment the following lines and comment quay.io/cdis/ubuntu:20.04:
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#FROM arm64v8/ubuntu:20.04 as build
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FROM quay.io/cdis/ubuntu:20.04 AS build
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ARG NODE_VERSION=20
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ARG BASE_PATH
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ARG NEXT_PUBLIC_PORTAL_BASENAME
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ENV NPM_CONFIG_PREFIX=/home/node/.npm-global
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ENV PATH=$PATH:/home/node/.npm-global/bin
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WORKDIR /gen3
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RUN apt-get update && apt-get install -y --no-install-recommends \
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build-essential \
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libssl1.1 \
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libgnutls30 \
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ca-certificates \
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curl \
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git \
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gnupg \
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&& mkdir -p /etc/apt/keyrings \
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&& curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \
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&& echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_VERSION.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list \
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&& apt-get update \
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&& apt-get install -y nodejs \
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&& apt-get clean \
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&& npm install -g [email protected]
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RUN addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs
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COPY ./package.json ./package-lock.json ./
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COPY ./package-lock.json ./
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COPY ./src ./src
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COPY ./public ./public
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COPY ./config ./config
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COPY ./next.config.js ./
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COPY ./tsconfig.json ./
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COPY ./.env.development ./
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COPY ./.env.production ./
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COPY ./tailwind.config.js ./
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COPY ./postcss.config.js ./
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RUN npm ci
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RUN npm install \
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"@swc/core" \
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"@napi-rs/magic-string"
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RUN npm run build
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ENV PORT=80
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CMD ["npm", "run", "start"]

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