Bump the npm_and_yarn group across 1 directory with 2 updates

.dockerignore

@@ -0,0 +1 @@
+node_modules

.env.development

@@ -1,6 +1,2 @@
 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=
+NEXT_PUBLIC_GEN3_API=https://prometheus.data-commons.org

.env.production

@@ -1,3 +1,2 @@
 GEN3_COMMONS_NAME=gen3
-NEXT_PUBLIC_GEN3_API=https://localhost/
-NEXT_PUBLIC_GEN3_DOMAIN=https://localhost/
+NEXT_PUBLIC_GEN3_API=https://prometheus.data-commons.org

.eslintrc.js

@@ -0,0 +1,55 @@
+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: {
+    '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

@@ -0,0 +1,3 @@
+{
+  "extends": "next/core-web-vitals"
+}

.github/workflows/ci.yaml

@@ -4,13 +4,16 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-node@v3
-      with:
-        node-version: 20
-    - name: Setup npm
-      run: npm install -g [email protected]
-    - name: Install modules
-      run: npm ci
-    - name: Run ESLint
-      run: npm run lint
+      - 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

.npmignore

@@ -0,0 +1,3 @@
+.DS_Store
+node_modules
+.next/cache/*

.nvmrc

@@ -0,0 +1 @@
+20

.prettierignore

@@ -0,0 +1,4 @@
+node_modules
+.next
+public
+dist

.prettierrc

@@ -0,0 +1,6 @@
+{
+  "tabWidth": 2,
+  "useTabs": false,
+  "trailingComma": "all",
+  "singleQuote": true
+}

Dockerfile

@@ -3,12 +3,10 @@
 # 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
+FROM quay.io/cdis/ubuntu:20.04 AS build
 
 ARG NODE_VERSION=20
 
-ENV DEBIAN_FRONTEND=noninteractive
-
 ARG BASE_PATH
 ARG NEXT_PUBLIC_PORTAL_BASENAME
 ENV NPM_CONFIG_PREFIX=/home/node/.npm-global
@@ -24,20 +22,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     curl \
     git \
     gnupg \
-    nginx \
-    python3 \
-    time \
-    vim \
     && 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 \
-    && rm -rf /var/src/apt/lists/* \
-    && ln -sf /dev/stdout /var/log/nginx/access.log \
-    && ln -sf /dev/stderr /var/log/nginx/error.log \
-    && npm install -g [email protected]
+    && npm install -g [email protected]
 
 RUN  addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs
 COPY ./package.json ./package-lock.json ./

config/gen3/colors.json

@@ -1,9 +1,10 @@
 {
-  "primary": "#345948",
-  "secondary": "#BF7E06",
-  "accent": "#8C0404",
-  "base": "#CCCCCC",
-  "accentWarm": "#594B04",
-  "accentCool": "#908719",
-  "chart": "#0d95A1"
+  "primary": "#3283C8",
+  "secondary": "#3283C8",
+  "accent": "#b75113",
+  "base": "#c0c0c0",
+  "accentWarm": "#25869b",
+  "accentCool": "#1f839b",
+  "chart": "#0d95A1",
+  "table": "#c0c0c0"
 }

config/gen3/crosswalk.json

@@ -0,0 +1,38 @@
+{
+  "showSubmittedIdInTable": false,
+  "mapping": {
+    "source": {
+      "id": "prom",
+      "label": "PROMETHEUS",
+      "description": "PROject for Military Exposures and Toxin History Evaluation in US Service Members"
+    },
+    "external": [
+      {
+        "id": "PROMETHEUS",
+        "label": "PROMETHEUS",
+        "dataPath": "crosswalk->subject->https://prometheus.data-commons.org->case_id->value"
+      },
+      {
+        "id": "GDC",
+        "label": "GDC",
+        "dataPath": "crosswalk->subject->https://portal.gdc.cancer.gov->submitter_id->value",
+        "description": "A repository and computational platform for cancer researchers who need to understand cancer, its clinical progression, and response to therapy."
+      },
+      {
+        "id": "PDC",
+        "label": "PDC",
+        "dataPath": "crosswalk->subject->https://proteomic.datacommons.cancer.gov->case_id->value"
+      },
+      {
+        "id": "BLOODPAC",
+        "label": "BLOODPAC",
+        "dataPath": "crosswalk->subject->https://data.bloodpac.org->subject.subject_id->value"
+      },
+      {
+        "id": "dbGaP",
+        "label": "dbGaP",
+        "dataPath": "crosswalk->subject->https://www.ncbi.nlm.nih.gov->dbgap_subject_id->value"
+      }
+    ]
+  }
+}

config/gen3/dictionary.json

@@ -0,0 +1,4 @@
+{
+"showGraph": false,
+"showDownloads": false
+}