README.md

The frontend for the fragalysis tool

• React, Redux and built using Webpack

XCHEM FRAGALYSIS Frontend Dev environment setup

Background

The stack consists of three services, running as containers: -

• a MySQL database
• a neo4j graph database
• the fraglaysis stack
• a transient data loader container

The stack is formed from code resident in a number of repositories. Begin by forking repositories you anticipate editing (although you really want to consider forking all the repositories as this is a relatively low-cost operation).

The repositories are:

• xchem/fragalysis
• xchem/fragalysis-frontend
• xchem/fragalysis-backend
• xchem/fragalysis-stack
• xchem/fragalysis-loader

Prerequisites

• Docker
• Git
• NodeJS (v12)
• Yarn
• Some target data

Setup

Start with creating project directory, e.g.

mkdir fragalysis

Clone repositories

Note: You might want to work on frontend fork.

# git clone https://github.com/xchem/fragalysis-frontend.git
git clone https://github.com/pavol-brunclik-m2ms/fragalysis-frontend.git

Note: Fork if any work is expected.

Optional

git clone https://github.com/xchem/fragalysis-backend.git
git clone https://github.com/xchem/fragalysis-loader.git
git clone https://github.com/xchem/fragalysis-stack.git

Mandatory

# git clone https://github.com/xchem/dls-fragalysis-stack-openshift.git (Did not contain 'loader' image)
git clone https://github.com/InformaticsMatters/dls-fragalysis-stack-openshift.git

Build the images locally

Optional

pushd fragalysis-backend || exit
docker build . -t xchem/fragalysis-backend:latest
popd || exit

pushd fragalysis-loader || exit
docker build . -t xchem/fragalysis-loader:latest
popd || exit

pushd fragalysis-stack || exit
docker build . -t xchem/fragalysis-stack:latest
popd || exit

Mandatory

pushd dls-fragalysis-stack-openshift/images/loader || exit
docker build . -f Dockerfile-local -t loader:latest
popd || exit

Optional

pushd dls-fragalysis-stack-openshift/images/graph || exit
docker build . -t xchem/graph:latest
popd || exit

Create some key data directories

Note: The data/input/django_data directory will need to be populated with EXAMPLE data before you can launch the application.

mkdir -p data/input/django_data
mkdir -p data/mysql/data
mkdir -p data/neo4j/data
mkdir -p data/neo4j/logs
mkdir -p data/stack/media
mkdir -p data/stack/logs

Modify fragalysis-frontend/docker-compose.dev.yml file to look at right loader

• ../data folders

• DATA_ORIGIN: EXAMPLE -> will look for EXAMPLE folder in ../data/input/django_data/EXAMPLE

• You can create the EXAMPLE folder in /data/input/django_data/ and then place target data within to test.

cd fragalysis-frontend/
yarn

Start webpack dev server:

yarn start

Start the fragalysis stack within /fragalysis-frontend:

docker-compose -f docker-compose.dev.yml up

Optionally use docker-compose.localhost.yml up and add a -d flag to start silently.

Please wait, it takes a minute until all containers are fully started.

Test if we are running at http://localhost:8080

If needed stop containers

docker-compose -f docker-compose.dev.yml down

React webpack hot reloading

Inspired by https://owais.lone.pw/blog/webpack-plus-reactjs-and-django/ and https://github.com/gaearon/react-hot-boilerplate/ and webpack-contrib/webpack-hot-middleware#255

Notes

To connect to web_dock container

docker exec -it web_dock /bin/bash

IDEs

WebStorm, PhpStorm

Please install following extension Prettier

Go to: Preferences, Tools, File watchers
Add Prettier
Prettier reccomended settings: Files to watch - Scope - All changed files

During the commit in this IDE, check Run Git hooks

Visual Studio Code

Please install following extensions

Prettier - Code formatter https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode

ES-lint https://marketplace.visualstudio.com/items?itemName=dbaeumer.vscode-eslint

Environments

to activate GitHub api create .env file and following environment variable

GITHUB_API_TOKEN=myGitHubToken

To create .env with token right away:

echo "GITHUB_API_TOKEN=myGitHubToken" > .env