SGD Website Project

This project is a frontend webaplication used for the SGD Nextgen Redesign. It retreives data in JSON format from SGDBackend, then creates the pages of the website.

Building the app

Prerequisities, node.js > 4.2.0 and python 2.7.x. o manage python dependencies, configure a virtualenv for this project. See virtualenv guide.

Node packages issues and versions

You may run into issues with node version. Currently the build is using Node v6.10.2. Make sure you're on this version. We're working migrate packages management to yarn and webpack so all these legacy version issues might be resolved once we make that switch. See requirements below:

1. Ruby version, point to ruby-2.3
2. Node version, point to v6.10.2
3. Bower version, point to v1.8.4(latest). Run the following commands: $ npm install -g bower $ bower install

To build the application and install dependencies.

$ make build

Set configuration variables in src/sgd/frontend/config.py, which doesn't exist at first, and is in the .gitignore. To create with default values, run

$ cp src/sgd/frontend/default_config.py src/sgd/frontend/config.py

To run off of a different backend: Set the backend_url parameter in the config file to the URL of the new backend.

To start the application:

$ make run

Deploying Assets

In production, assets are served from Amazon Cloudfront. Before deploying to a server, be sure to run

$ make deploy-assets

and then commit changes to git.

Using the Development Task

In the production buildout, asset preparation tasks run from start to finish. In development, however, there is an option to compile these assets, and then recompile them automatically when changes have been made. To use this task, run:

$ grunt dev

This will compile the JSX files and the SASS files in the client directory. If you make any changes to these files while this task is running, they will automatically recompile. Optionally, if you are using Chrome, you can install the live reload plugin, which will reload the browser once the changed files have finished compiling. Another difference between the development and production compile is that the bundled application.js file will be unminified with source maps, to help debug. To stop this task, type ctrl + c.

Browserify

The bundled application.js is compiled using browserify. Future client dependencies should be installed with NPM, and required using the CommonJS style.

JSX and React

Many of the files that compose the bundled application.js are JSX files, compiled using the harmony option, which allows some ES6 features. Future additions to the client/jsx directory should also have a .jsx extension. JSX features are optional in a JSX file. While using supported ES6 features is encouraged, it is possible to write plain JavaScript in a JSX file.

Some pages are written using the react framework. The react components are stored in the client/jsx/components directory, and future react components should follow.

Testing

Unit tests are in the test directory, and can be run with

$ make tests

Integration tests are run using ghost inspector. The tests are configured using their service.

Make sure the ghost inspector variables are in dev_deploy_variables.sh. To run the tests on a remote server, run

$ make ghost

By default, it will run with the start URL set to http://yeastgenome.org. To run against another URL

$ START_URL=http://myserver.com make ghost

This task will not send any alerts if it fails. If you want to run with alerts (like maybe after a production deploy). For this task, the credentials are configured in prod_deploy_variables.sh.

$ make ghost-with-alert

Test Locally

First, download ngrok (add URL) and start your ngrok server https://ngrok.com/download This will tunnel requests from bgrok to your local development environment.

Then, run

$ make ghost-local

Docker

In the top level directory there is the Dockerfile for making a docker image for the Frontend.

This Dockerfile uses multiple FROM for different stages. This allows us to build containers for different purposes, namely development and production. See https://docs.docker.com/develop/develop-images/multistage-build/

The image is based on Ubuntu 20.04 and building the image installs python 3.8, pip, ruby, node, and npm. All dependencies for the front end are then installed and pserve can then be run.

Build the image from exactly what's on the local host filesystem (make sure you're in the top level repository directory):

docker build --rm --target base -t frontend .

This will copy the contents of the repo into the image including the dev_deploy_variables.sh file. This will be used to run the dev frontend.

Running the image by default will start server by running source dev_deploy_variables.sh && pserve sgdfrontend_development.ini internally.

To run:

docker run --rm -it -p 6545:6545 frontend

will serve the front end, and going to localhost:6545 will show the locally running front end on docker.

To build the image with the local host directory mounted into the container, run with:

docker build --rm -t frontend .

This implicitely builds the vagrant stage (explicit with --target vagrant). This creates a vagrant user and installs SSH for usage with Vagrant (see next section).

Vagrant

Vagrant (https://www.vagrantup.com/) is a tool that lets you run run and operate inside a virtual machine, or, in our case, docker container. This allows a consistent development environment that will also look like production. This works because when developing with Vagrant on the docker container, we're using the container that defines the environment for the frontend.

Using a mounted directory (through docker) we can run anything we need in the container, but operated on files on the host machine, which are version controlled. Vagrant simply makes this easy to do.

Using Vagrant with Docker

• Install Vagrant at https://www.vagrantup.com/

• Vagrant is configured with the Vagrantfile which defines how vagrant should run the docker container.

• To start and build the container with vagrant:

$ vagrant up

This will build the docker image using the Dockerfile, link the SGDFrontend directory to /frontend in the container, and start the container.

• Login with SSH into the container with:

$ vagrant ssh

Developing in the container

Once logged in, cd into the frontend directory:

vagrant@d66e7945ee02:~$ cd /frontend
vagrant@d66e7945ee02:/frontend$ 

Note: Running an ls here will show your local files on your host machine, not the docker container because of the mount.

To run the frontend server:

vagrant@d66e7945ee02:/frontend$ . dev_deploy_variables.sh && pserve sgdfrontend_development.ini 
Starting server in PID 229.
Serving on http://0.0.0.0:6545

This message is internal to the docker container, and we mapped port 6545 out to 6546. So on your host machine browser, navigating to localhost:6546 should show the frontend hosted on your docker image, from the running docker image.

You can edit files and make changes on your host machine and see changes reflected since the docker image is mounting and then running your host files.