Initial commit

.dockerignore

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+node_modules

.env.development

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

.env.production

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

.eslintignore

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+*.css
+node_modules

.eslintrc.js

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

.eslintrc.json

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

.github/workflows/ci.yaml

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

.github/workflows/image_build_push.yaml

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+name: Build Image and Push to Quay
+
+on: push
+
+jobs:
+  Security:
+    name: Security Pipeline
+    uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
+    with:
+      python-poetry: 'false'
+    secrets: inherit
+  ci:
+    name: Build Image and Push to Quay
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      USE_QUAY_ONLY: true
+    secrets:
+      ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
+      ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
+      QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
+      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.
+
+# dependencies
+/node_modules
+/.pnp
+.pnp.js
+
+# testing
+/coverage
+
+# next.js
+/.next/
+/out/
+
+# production
+/build
+
+# misc
+.DS_Store
+*.pem
+
+# debug
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+
+# local env files
+.env*.local
+
+# vercel
+.vercel
+
+# typescript
+*.tsbuildinfo
+next-env.d.ts

.npmignore

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+.DS_Store
+node_modules
+.next/cache/*

.nvmrc

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+20

.pre-commit-config.yaml

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

.prettierignore

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+node_modules
+.next
+public
+dist

.prettierrc

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

.secrets.baseline

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

Dockerfile

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