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Yan Xu
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Add webapp
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‎.gitignore

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**/work/**
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*/logs/*
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**/ec_info/*
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.nf-test*
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.nf-test*
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.DS_Store
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.env
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io
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node_modules

‎.vscode/settings.json

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{
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"editor.codeActionsOnSave": {
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"source.fixAll.eslint": "explicit"
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},
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"eslint.validate": ["javascript"],
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"editor.defaultFormatter": "rvest.vs-code-prettier-eslint",
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"editor.formatOnPaste": false, // required
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"editor.formatOnType": false, // required
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"editor.formatOnSave": true, // optional
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"editor.formatOnSaveMode": "file", // required to format on save
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"files.autoSave": "onFocusChange", // optional but recommended
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"vs-code-prettier-eslint.prettierLast": false, // set as "true" to run 'prettier' last not first
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"files.eol": "\n",
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}

‎installation/README.md

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## INSTALLATION PREREQUISITES
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### Install Node20
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https://nodejs.org/dist/latest-v20.x/
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### Install pm2
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`npm install pm2@latest -g`
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### Install MongoDB Community Edition
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https://docs.mongodb.com/manual/installation/#mongodb-community-edition-installation-tutorials
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## INSTALL webapp
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1. Move/copy EDGEv3 folder to the installation directory
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2. Inside EDGEv3/installation folder, run the installation script
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`./install.sh`
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3. Create environment variables
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The web client and web server each rely on environment variables for their configuration.
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You can define those environment variables in `.env` files.
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Here's how you can define them in `.env` files:
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- Populate the "client build" environment configuration file (i.e. `webapp/client/.env`).
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You can initialize it based upon the corresponding development/production example file:
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```shell
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cp webapp/client/.env.development.example \
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webapp/client/.env
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```
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> Those environment variables are used within `webapp/client/src/config.js`.
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- Populate the server environment configuration file (i.e. `webapp/server/.env`).
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You can initialize it based upon the corresponding development/production example file:
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```shell
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cp webapp/server/.env.development.example \
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webapp/server/.env
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```
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> Those environment variables are used within `webapp/server/config.js`.
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## START webapp
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1. Start MongoDB if it's not started yet
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2. Inside EDGEv3 folder, run the pm2 start command
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`pm2 start pm2.config.js`
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## STOP webapp
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pm2 stop all

‎installation/install.sh

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#!/bin/bash
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echo "Install LANL EDGE webapp..."
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pwd=$PWD
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app_home="$(dirname "$pwd")"
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#create upload/log/projects/public directories, skip this step for reinstallation
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io_home=$app_home/io
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if [ ! -d $io_home ]; then
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echo "Create directories"
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mkdir ${io_home}
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dirs=(
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"upload"
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"upload/files"
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"upload/tmp"
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"log"
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"projects"
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"public"
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"sra"
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"db"
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"nextflow"
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"nextflow/work"
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)
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for dir in "${dirs[@]}"
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do
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mkdir ${io_home}/${dir}
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done
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test_data_home=$app_home/workflows/Nextflow/test_data
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if [ -d $test_data_home ]; then
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ln -s ${test_data_home} ${io_home}/public/test_data
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fi
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fi
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echo "Setup LANL EDGE webapp ..."
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#build client
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echo "build client..."
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cd $app_home/webapp/client
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npm install --legacy-peer-deps
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npm run build
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#build server
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echo "build server..."
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cd $app_home/webapp/server
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npm install
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echo "LANL EDGE webapp successfully installed!"
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echo "To start the webapp in EDGEv3's root directory:"
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echo "pm2 start pm2.config.js"

‎pm2.config.js

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/**
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* This is a PM2 configuration file.
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*
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* References:
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* - https://pm2.keymetrics.io/docs/usage/application-declaration/
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* - https://pm2.keymetrics.io/docs/usage/environment/
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*/
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module.exports = {
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apps: [
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{
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name: "appserver",
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script: "server.js",
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instances: 4,
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exec_mode: "cluster",
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cwd: "./webapp/server",
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node_args: "--max_old_space_size=1024",
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max_memory_restart: "150M"
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},
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{
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name: "cronserver",
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script: "cronServer.js",
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cwd: "./webapp/server",
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node_args: "--max_old_space_size=1024",
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max_memory_restart: "150M"
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}
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]
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}

‎webapp/README.md

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# Development
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## Dependencies
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* node.js v20
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* MongoDB
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## Install the webapp
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cd installation
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./install-local.sh
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## Start api server
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cd webapp/server
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(change NODE_ENV=prod to NODE_ENV=dev in .env)
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npm start
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## Start ui client
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cd webapp/client
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npm start
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## View the website
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http://localhost:3000
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## Note
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- Have to restart the client when any changes made in client/.env.
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- Have to restart the server when any changes made in server code or server/.env.
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#### Restart api server
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cd webapp/server
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use Ctrl-C to stop the webapp server
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npm start
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#### Restart ui client
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cd webapp/client
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use Ctrl-C to stop the webapp client
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npm start
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‎webapp/client/.browserslistrc

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# https://github.com/browserslist/browserslist#readme
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[production]
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>0.2%
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not dead
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not op_mini all
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[development]
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last 1 chrome version
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last 1 firefox version
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last 1 safari version

‎webapp/client/.editorconfig

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# Editor configuration, see http://editorconfig.org
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root = true
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[*]
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charset = utf-8
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end_of_line = lf
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indent_size = 2
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indent_style = space
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insert_final_newline = true
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trim_trailing_whitespace = true
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[*.md]
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max_line_length = off
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trim_trailing_whitespace = false

‎webapp/client/.env.development.example

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# EDGE
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VITE_NAME=EDGE V3
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VITE_EMAIL_NOTIFICATION_ENABLED=false
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VITE_FILEUPLOAD_ENABLED=true
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VITE_API_URL=http://localhost:5000
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# ORCiD login
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VITE_IS_ORCID_AUTH_ENABLED=false
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VITE_ORCID_CLIENT_ID=<Your ORCiD client id>

‎webapp/client/.env.production.example

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# EDGE
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VITE_NAME=EDGE V3
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VITE_FILEUPLOAD_ENABLED=true
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# ORCiD login
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VITE_IS_ORCID_AUTH_ENABLED=false
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VITE_ORCID_CLIENT_ID=<Your ORCiD client id>

‎webapp/client/.eslintrc.js

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module.exports = {
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// parser: '@typescript-eslint/parser', // Specifies the ESLint parser
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parserOptions: {
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ecmaVersion: 2020, // Allows for the parsing of modern ECMAScript features
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sourceType: 'module', // Allows for the use of imports
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ecmaFeatures: {
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jsx: true, // Allows for the parsing of JSX
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},
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},
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settings: {
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react: {
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version: 'detect', // Tells eslint-plugin-react to automatically detect the version of React to use
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},
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},
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extends: [
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'plugin:react/recommended', // Uses the recommended rules from @eslint-plugin-react
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'plugin:prettier/recommended', // Enables eslint-plugin-prettier and eslint-config-prettier. This will display prettier errors as ESLint errors. Make sure this is always the last configuration in the extends array.
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],
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plugins: ['react', 'react-hooks'],
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rules: {
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// Place to specify ESLint rules. Can be used to overwrite rules specified from the extended configs
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// e.g. "@typescript-eslint/explicit-function-return-type": "off",
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},
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}

‎webapp/client/.gitattributes

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# Enforce Unix newlines
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* text=auto eol=lf

‎webapp/client/.gitignore

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# See https://help.github.com/ignore-files/ for more about ignoring files.
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# dependencies
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/node_modules
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# testing
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/coverage
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# production
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/build
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# misc
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.eslintcache
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.DS_Store
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.idea
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.env.local
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.env.development.local
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.env.test.local
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.env.production.local
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npm-debug.log*
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yarn-debug.log*
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yarn-error.log*

‎webapp/client/.prettierignore

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build/

‎webapp/client/.prettierrc.js

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module.exports = {
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semi: false,
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trailingComma: 'all',
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singleQuote: true,
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printWidth: 100,
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tabWidth: 2,
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}

‎webapp/client/index.html

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta name="description" content="LANL EDGE V3">
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<meta name="author" content="LANL EDGE Bioinformatics Team">
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<meta name="keyword" content="Bootstrap,Admin,Template,Open,Source,CSS,SCSS,HTML,RWD,Dashboard,React">
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<title>EDGE</title>
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<base href="/">
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<link rel="manifest" src="/manifest.json">
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<link rel="shortcut icon" src="/favicon.ico">
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</head>
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<body>
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<noscript>
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You need to enable JavaScript to run this app
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</noscript>
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<div id="root"></div>
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<script type="module" src="/src/index.js"></script>
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<!-- built files will be auto injected -->
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</body>
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</html>

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