Initial Setup - dondi/GRNsight GitHub Wiki

These instructions assume that you already have the following installed:

• A code editor such as Visual Studio Code (VS Code)
  • Note that GRNsight uses Prettier for code formatting. Prettier can be installed as an extension from inside VS Code. Once it is installed, go to File > Preferences > Settings > Editor: Default Formatter and select Prettier from the dropdown menu. The GRNsight code formatting conventions are stored in the GitHub repository. Code formatting can be invoked manually in VS Code by pressing Alt-Shift-F or you can have it format automatically by going to File > Preferences > Settings and checking the box for Editor: Format on Save.
• Git
• Node.js/NPM LTS v18.20.8 (Node.js) & v10.8.2 (NPM)
  • As of this writing, the GRNsight server uses Node.js 18.19.1 (and npm version 9.2.0), but v18.20.8 is what is currently available. GRnsight also runs on recent versions except Node 17 due to a one-time issue regarding SSL. Changing to Node 16 and below or Node 18 or above addresses this.
  • To install, go to https://nodejs.org/en/download/
  • NPM is bundled with node.js
  • GRNsight may need to run on a different version of node than is used for your other projects. Follow these instructions to make a temporary switch to a different version of node.
• PostgreSQL
  • As of this writing, the GRNsight server uses PostgreSQL v16.8, but more recent versions should work.
• Python is required for the loading scripts used to load data into the database

The first step to being able to view and edit the code on this project as well as run the application is to clone this repository, either by downloading the zip of the files or by using the following git command in your command line:

git clone https://github.com/dondi/GRNsight.git

Before running the applications for the first time, you must first install the dependencies using npm.

Navigate to the directory that contains the GRNsight project (substitute <GRNsight folder> accordingly in the commands below) and install the project’s dependencies.

cd <GRNsight folder>
npm install

When running GRNsight on platforms other than macOS, you may see this error:

npm WARN optional SKIPPING OPTIONAL DEPENDENCY: [email protected] (node_modules/nodemon/node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for [email protected]: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})

As stated by the warning, this is an optional dependency, and thus is not an issue when running GRNsight.

1. In order to run the local GRNsight application, you need to set up a local copy of the GRNsight database. Instructions are located here.

   1. After installing your local database, you will want to either add a password to your default user postgres, or create a new user or superuser with a password if this was not done during the installation process. This is necessary so that GRNsight can use these credentials to log in to your database to perform database calls.

      • [OPTION 1]: Adding a password to default user postgres

        1. To edit the default user postgres, in Terminal type the following (replacing with your chosen password).

            sudo -u postgres psql -c "ALTER USER postgres PASSWORD '<new-password>';"
           

      • [OPTION 2]: Creating a new user with a password

        1. To add a new user, in Terminal type the following (replacing with your chosen username and with your chosen password).

            sudo -u postgres psql -c "CREATE ROLE <username> SUPERUSER LOGIN PASSWORD '<new-password>';"
           

      • On MacOs if you receive the error in your terminal psql: FATAL: role "postgres" does not exist, then try this solution from Stack Overflow(https://stackoverflow.com/questions/15301826/psql-fatal-role-postgres-does-not-exist?page=2&tab=scoredesc#tab-top):

        • sudo -u postgres createuser -s postgres

2. After you have a local instance of the GRNsight database on your machine, you will need to configure the environment variables for GRNsight to access your database.

   1. Navigate to the top-level GRNsight directory and create a file named .env.

   2. Inside the .env file add the following lines, replacing the and with the requested information.

       DB_USERNAME=<user>
       DB_PASSWORD=<password>
      

0. Start the database server (to be fleshed out)

1. Navigate to the GRNsight directory and enter the following in Terminal

   cd <GRNsight folder>
   npm run start-dev
   

   • If you run into the following error:

     TypeError [ERR_INVALID_ARG_TYPE]: The "options.cwd" property must be of type string or an instance of Buffer or URL. Received function wrappedCwd
     

     ...run this command:

     npm install --save-dev [email protected]
     

   • If that causes the following error:

     Error: Cannot find module 'C:\Users\kdahlqui\Desktop\GRNsight\node_modules\parallelshell\index.js'
     

     ...delete node-options from inside the GRNsight folder and run npm install

   • If you receive a Google Analytics error, delete the node-modules folder from the GRNsight folder and run npm update

2. In a web browser, navigate to localhost:5001 to access the running local GRNsight application. This will provide you with a view of the current state of the GRNsight site as the code on your computer produces it.

• Compatibility note: On recent versions of macOS, a service called “AirPlay Receiver” has been added which happens to use port 5000, the same port used by the GRNsight local dev server. As such, in order to allow the local dev server to run, “AirPlay Receiver” needs to be disabled in System Preferences > Sharing while GRNsight development is taking place

There are some commands that you only need to use once, but there are also commands that you have to use it every time you run it.

• Change the version of npm: export PATH="your path to node@version"

• Running GRNsight in developed mode

  cd <GRNsight folder>
  npm run start-dev
  

• Starting the database: pg_ctl start -D location-of-cluster

• Stopping the database: pg_ctl stop -D location-of-cluster