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https://github.com/JacobGrisham/Synthetic-Biology-LIMS
(In development) Microservices full-stack single-page web app built with Typescript, React, Redux, Styled Components (for CSS-in-JS), Python, Django, Redis, and PostgreSQL. Separate servers for LIMS and Payments hosted on AWS EC2 instances with Kubernetes and circleci CI/CD. Database hosted on AWS DynamoDB. CDN through AWS Cloudfront and DNS through Google Domains.
https://github.com/JacobGrisham/Synthetic-Biology-LIMS
circleci django django-rest-framework docker docker-compose full-stack-web-development kubernetes lims microservices-architecture postgresql python react redis redux rest-api restful-api styled-components synbio synthetic-biology typescript
Last synced: about 1 month ago
JSON representation
(In development) Microservices full-stack single-page web app built with Typescript, React, Redux, Styled Components (for CSS-in-JS), Python, Django, Redis, and PostgreSQL. Separate servers for LIMS and Payments hosted on AWS EC2 instances with Kubernetes and circleci CI/CD. Database hosted on AWS DynamoDB. CDN through AWS Cloudfront and DNS through Google Domains.
- Host: GitHub
- URL: https://github.com/JacobGrisham/Synthetic-Biology-LIMS
- Owner: JacobGrisham
- Created: 2021-06-14T04:11:32.000Z (about 3 years ago)
- Default Branch: master
- Last Pushed: 2024-05-07T22:17:55.000Z (4 months ago)
- Last Synced: 2024-05-07T23:28:12.018Z (4 months ago)
- Topics: circleci, django, django-rest-framework, docker, docker-compose, full-stack-web-development, kubernetes, lims, microservices-architecture, postgresql, python, react, redis, redux, rest-api, restful-api, styled-components, synbio, synthetic-biology, typescript
- Language: TypeScript
- Homepage:
- Size: 1.47 MB
- Stars: 8
- Watchers: 2
- Forks: 2
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Synthetic Biology Laboratory Information Management System (LIMS)
[](https://app.circleci.com/pipelines/github/JacobGrisham/Synthetic-Biology-LIMS)
[](https://www.codacy.com/gh/JacobGrisham/Synthetic-Biology-LIMS/dashboard?utm_source=github.com&utm_medium=referral&utm_content=JacobGrisham/Synthetic-Biology-LIMS&utm_campaign=Badge_Grade)
[](https://codecov.io/gh/JacobGrisham/Synthetic-Biology-LIMS)
[](https://pyup.io/repos/github/JacobGrisham/Synthetic-Biology-LIMS/)
[](https://pyup.io/repos/github/JacobGrisham/Synthetic-Biology-LIMS/)
[](https://gitmoji.dev)
[](https://semantic-release.gitbook.io/semantic-release/)
## 🎓 [Final Project](https://cs50.harvard.edu/web/2020/projects/final/capstone/) for [Harvard's Web Programming with Python and Javascript CS50W hosted on eDX](https://www.edx.org/course/cs50s-web-programming-with-python-and-javascript)
## 💡Lessons Learned
- Gathering business requirements and scoping project feature development
- Prototyping Single Page Application User Interface in AdobeXD
- Creating new, meaningful SVG illustrations by combining and altering existing free SVG illustrations
- Architected SQL Database to Boyce-Codd Normal form in UML
- Using PostgreSQL with Django
- Implementing JSON Web Token authentication with Redis in Django
- Designing an API, especially in Django using django-rest-framework
- Implementing React Hooks
- Implementing complex state management in Redux
- Writing React and Redux in Typescript
- Integration testing React and Redux with Jest and react-testing-library
- End to end automation testing with Cypress
- Unit and Integration testing Django with pytest
- Behavioral Driven Testing: test the expected result, not the implementation details
- Implementing Test Driven Development: write tests as you go
- Implementing Domain Driven Development: start and finish features based on user stories
- Working with python virtual environment (virtualenv) for python dependency management
- Dockerizing the development environment for coordinating the following services: Django, PostgreSQL, Redis, and React
- Setting up linting with Prettier and Husky
- Setting up standardized commit messages with gitmoji
- Compressing files with Webpack and zipping files with brotli
## 🛠 Technologies
|Protoyping|Graphic Design|Front-End |Back-End |Database |Deployment |Testing |
-----------|------------- | -----------------| ---------------------- | -------- | ---------------- | ---------------------- |
|Adobe XD |Adobe XD |React |Python3 |PostgreSQL|Git |Jest |
|. |Freepik |Redux |Django |Redis |circleci |React Testing Library |
|. |. |Typescript |Django Rest Framework |. |Docker |Cypress |
|. |. |ES6 |*Celery* |. |*Kubernetes* |PyTest |
|. |. |React Router |. |. |*AWS Lambda* |. |
|. |. |Formik |. |. |*AWS Aurora* |. |
|. |. |Styled Components |. |. |*AWS API Gateway* |. |
|. |. |Material UI |. |. |. |. |
- note that *italicized* text indicates that the technology has not been applied yet
## ⚖️ Methodology
- Single Page Application for a better user experience.
- Separated front-end and back-end to avoid a monolithic architecture and to lay the foundation of a microservices architecture.
- Microservices architecture for decoupled business logic and more flexibility for adaptations in the future.
- React for front-end for the component-based approach to writing code, one-way data flow, and virtual document-object-model (DOM). Chose React over Angular and Vue since I have the most experience with React.
- Redux for managing state in React since this is a large application and managing React states would become unweidly in the long run.
- React and Redux both written in Typescript to leverage static typing for a more secure and well-tested application.
- Styled Components for styling for leveraging the power and benefits of CSS-in-JS.
- Django RESTful API for back-end. Django-rest-framework to simplify Create, Read, Update, and Delete routes. I've built a Django REST API without the help of a framework and there are no benefits to building routes at a lower level.
- Celery for asynchronous operations within Python since Django asynchronous support is still just for views (as of v3.1).
- SQL Database for leveraging the benefits of relational databases
- PostgreSQL as the Relational Database Management System (RDBMS) since it has more features integrations in Django
- Docker containerization of the application while in development mode because there are four different services and docker-compose provides automation for starting and ending the services.
- circleci for continuous integration and continuous delivery since I have the most experience with circleci. Considered using Jenkins, but my focus as a Web Developer is not DevOps.
## ⚙️ Features
- Manage user groups
- Manage chemical/biological inventory
- Manage protocols
- Manage projects (made up of protocols)
- Manage jobs (completing the protocol in a project)
- Manage products (output from a job)
## 📐 Tests
- Interactive code coverage diagram on [codecov](https://codecov.io/gh/JacobGrisham/Synthetic-Biology-LIMS). The code coverage takes into account both the Django unit tests and the React unit/integration tests.
- [Django unit](https://app.circleci.com/pipelines/github/JacobGrisham/Synthetic-Biology-LIMS/50/workflows/d5bd12a2-0792-49e8-b318-54b0cb35f843/jobs/117/tests) and the [React unit/integration](https://app.circleci.com/pipelines/github/JacobGrisham/Synthetic-Biology-LIMS/50/workflows/d5bd12a2-0792-49e8-b318-54b0cb35f843/jobs/116/tests) junit.xml test reports and code coverage artifacts automatically uploaded to circleci.
## 🚀 Getting Started
### System requirements:
- Make sure you have [PostgreSQL](https://www.postgresql.org/download/) installed and running on your computer. If you installed PostgreSQL with [Homebrew](https://brew.sh/), then you can start PostgreSQL with `brew services start postgresql`
- Make sure you have [Redis](https://redis.io/download) installed and running on your computer. If you installed Redis with [Homebrew](https://brew.sh/), then you can start Redis with `brew services start redis`
- Create an .env file in the root directory with the following key: `ENV_API_SERVER=http://127.0.0.1`
- Create an .env file in the django-backend directory with the following keys:
```
DJANGO_ENV=
DEBUG=
SECRET_KEY=
DJANGO_ALLOWED_HOSTS=www.example.com localhost 127.0.0.1 [::1]
DJANGO_ADMIN_USER=
DJANGO_ADMIN_EMAIL=
DJANGO_ADMIN_PASSWORD=
DATABASE=postgres
DB_DATABASE=db.postgresql
DB_USER=postgres_user
DB_PASSWORD=
DB_HOST=
DB_PORT=5432
JWT=
REDIS_URL=
```
- Create an .env file in the postgres directory with the following keys:
```
POSTGRES_USER=
POSTGRES_PASSWORD=
```
### To run this project on your system with Docker:
- Make sure you have Docker installed and running on your computer
- In your terminal, navigate to the root of this repository and run
docker-compose up (Docker will automatically run docker-compose up --build for the first setup phase)
**⚠️ Important:** if you are getting conflict errors, you should run `docker stop ` that is already running in the background.
**⚠️ Important:** if you are getting other errors, you should run `docker-compose down` to bring everything down, and start over.
### To run this project on your system manually (without Docker):
- Ensure that python3, python3-pip, and python3-venv are installed on your system
- (For first time running this application) run
python3 -m venv venv to create the virtual environment. Navigate to the directory django-backend and run source venv/bin/activate to activate the virtual environment. (For first time running this application) Run pip install -r requirements.txt to install the django dependencies
- (If you need to set up local database) Navigate to the directory django-backend and run
python3 manage.py migrate and then python3 manage.py makemigrations
- While still in the django-backend directory, run
python3 manage.py runserver to start the server
- (For first time running this application) Navigate to the directory react-frontend/frontend and run
npm install to install the react dependencies
- Open a new terminal tab or window, navigate to the directory react-frontend/frontend, and run
npm start
- To view the application in a web browser, visit http://localhost:3000
### To contribute to this project on your system:
- Ensure that `git lfs` is installed on your system. Download the extension here [git-lfs.github.com](https://git-lfs.github.com/).
- To make git commits, navigate to the root directory, add files to git staging with `git add `, and then run `git commit` to activate the [Gitmoji](https://gitmoji.dev) interactive prompt in your terminal. Here's a preview of the [interactive prompt](https://www.npmjs.com/package/gitmoji-cli). After completing the prompt, exit with `:wq`
- If making README.md updates, be sure to add `[skip ci]` to the git commit message in order to prevent running unneccessary tests in continuous integration and deployment.
## 🔒 License
Copyright Notice and Statement: currently not offering any license. Permission only to view and download. Refer to [choose a license](https://choosealicense.com/no-permission/) for more info.