This project is humble attempt of BioHackathon Team #6 to solve sample management problem faced by many lab scientists working hardly to gather all sample data and figure out connections between them.
Aim of this project is to..
Click here to check Presentation from the St. Jude BioHackathon 2022.
Example Demo app:
To get a local copy up and running follow these simple example steps:
Once docker is installed, clone the repo on you local folder:
git clone https://github.com/stjude-biohackathon/SJHack2022_Project6.git
Go to the repo root and run this docker commands to build image (will take few minute for first time, should be faster on sunsequent run):
cd SJHack2022_Project6
docker-compose build
Start database container first using following command:
docker-compose up db
Once you see following LOG in terminal, go to next step:
db_1 | LOG: database system is ready to accept connections
Open new terminal tab and start Django app container using following command:
docker-compose up backend
Once you see following LOG in terminal, the backend app is ready!
web_1 | Starting development server at http://0.0.0.0:8000/
web_1 | Quit the server with CONTROL-C.
To load the database to the Django backend go to this url: http://localhost:8000/ It will take sometime to load the page as it's working on loading data from csv files to database. Once dtatabse is loaded, the page will show how many records and tables are loaded to database.
Open new terminal tab and start React app container using following command:
docker-compose up frontend
Once you see following LOG in terminal, the frontend app is ready!
sjhack2022_project6-frontend-1 |
sjhack2022_project6-frontend-1 | webpack 5.72.0 compiled with 1 warning in 522 ms
frontend app can be accessed at: http://localhost:3000/
Note: Following steps are temporary till users can upload their own data from frontend page. (ETA feature release - April 30, 2022)
To upload your own data, convert all your excel to 1 CSV file per table.
Copy all your CSV files to backend/raw_data/
folder.
To repopulate database with your csv files, go to http://localhost:8000/ and Click "Update Database" button. The page will looks like this:
It will take sometime to load the page as it's working on loading data from csv files to database. Once dtatabse is loaded, the page will show how many records and tables are loaded to database.
To see your data on frontend go to this url: http://localhost:3000/
As this Application is using Docker, it's easy to deploy it to any server or cloud service like AWS. Detailed instrunction on deployment will be available soon.