ui

The user interface of Cellenics - cloud based Single Cell RNA seq Analysis web platform.

Development

Prerequisites

We highly recommend using VSCode for development, if you don't have it, make sure you get it installed. You will also need to install: homebrew, docker, node (version 14). You should also install the following packages:

• dbaeumer.vscode-eslint for syntax linting & format errors in VS Code,
• markis.code-coverage highlights which lines are covered in unit tests and which aren’t.

installing node 14 on macOS

Easiest way to do it is using homebrew. Instructions based on this SO answer.

brew install node@14

If you already have a newer node version installed, you have to unlink it, and link node@14, which creates symlinks in /usr/local/bin.

brew unlink node
brew link node@14

You may have to force the linking, with the --force and --overwrite options. (if you want you could use --dry-run to check what would be overwritten).

brew link node@14 --force --overwrite

Running locally

Make sure that you clone this repo and are in the ui folder. then simply do:

make install
make run

See more available commands like syntax checking with make help.

Note that since the UI is not connected to the backend, you should see an empty screen saying You are not connected to the backend. To get it running end-to-end locally with mocked dataset, you will need to set up and run each of these:

• API: https://github.com/hms-dbmi-cellenics/api
• Inframock: https://github.com/hms-dbmi-cellenics/inframock
• worker: https://github.com/hms-dbmi-cellenics/worker
• pipeline: https://github.com/hms-dbmi-cellenics/pipeline

Just follow the README of each of them for instructions on how to get it to run.

Once you have everything running on the backend, go to http://localhost:5000 in your browser. You will get redirected to an authentication page. You will have to create a staging account by clicking through "Sign up" link (even if you have an existing production account).

Remote debugging with VS Code

Remote debugging is enabled for all staging and production environments. For remote debugging, the best approach is to use VS Code's native debugger capatibilites.

First, you need to ensure you have the correct website to debug. You can go to .vscode/launch.json and find an object with the name set to Debug develop in Chrome.

You can edit the url to match your staged or production environment. Then you can use the VS Code debugger, select Debug develop in Chrome and start the debug session. A Chrome window should spin up and you can control it using the debugger in VS Code.

Note: For debugging to work reliably, the code used on the environment must be the same version as the code open in VS Code. This is needed so line numbers from VS Code can be mapped to remote code on the server.

Remote debugging with Chrome DevTools

Alternatively, you can use Google Chrome's built-in DevTools. When it is open (e.g. by clicking Inspect on an element), you can click on Sources > Filesystem. Click on Add Folder to Workspace and add this folder. You will be able to use Google Chrome's debugger to set breakpoints, inspect variables, similarly to VS Code.

In the DevTools, if you have the React and Redux Developer Tools installed, you can also run the React profiler and check the Redux history just as you would on a local development environment.

Note: For debugging to work reliably, the code added the the workspace must be the same version as the code on the environment.

How to run tests in debug mode

The workspace comes with a preset for debugging tests. You can enter the Debugger in Visual Studio Code, find Run and Debug and find the preset Test and debug. Running the debugger using this configuration will automatically launch the test suite and attach the VS Code debugger to it.

How to check bundle size

You can check for the size of the bundles served to the user and loaded onto the server by typing:

npm run analyze

Alternatively, you can use npm run analyze:server or npm run analyze:client to get information about bundle sizes for just server-side rendered and client-side scripts.

The script will produce HTML artifacts that will open in your default browser as a Voronoi treemap.

Browser cache

Browser cache enabled by default in production environment. This can be disabled by adding the entry "disableCache" to "true" via the console using the command:

localStorage.setItem("disableCache", "true")

Browser cache makes it hard to develop as it can hide changes from the backend, so cache is disabled by default in development. This can be changed by modifying disableCache in localStorage manually.

Troubleshooting

1. Error: listen EADDRINUSE: address already in use :::5000

   Starting on macOS 12 (Monterey) port 5000 is used by Airplay receiver. To be able to run the UI locally it has to be disabled, going to system Preferences > Sharing and unticking the Airplay Reciever service box.