The Readme for the whole VRNetzer platform is HERE
The Analytics Module is a flexible interface between the MySQL database containing network data and the VR-based front end. It is implemented in Flask, a minimalist Python-based framework for web development.
- Make sure you are running Python 3 (we tested with 3.6 and up), preferably in a virtual environment. If using Windows check out the guide at: https://flask.palletsprojects.com/en/1.1.x/installation/ for instructions about how to get a virtualenv set up right.
- Clone this repository
git clone git@github.com:menchelab/Analytics_Module.git - Navigate to the repo
cd dataserver - Install dependencies
pip install -r requirements.txt - Run the server with
python3 app.py - If it doesn't work set your flask environment
export FLASK_APP=app(note that you can also use app_lite if you don't want the API) - Optionally, configure it as a development environment, which would
make the server reload with every code change.
export FLASK_ENV=development - Configure your database file. To do this, copy db_config_template.py to db_config.py and fill in your database locations, usernames, and passwords.
- Finally, spin up the server:
flask run. The output message in the console will tell you the web address for the server, typically http://127.0.0.1:1337/.
The file format for uploading a new layout into VR should be a .csv with the following structure. The file should be composed of nine columns with the following content: ID | X | Y | Z | R | G | B | A | Layout type
- ID = string of gene IDs
- X, Y, Z = floats of coordinates
- R, G, B = color values as integer in the range of 0 - 255
- A = opacity values as integer (100 = full saturated; 128 - 200 = glowing)
- Namespace of layout = string with layout type (same value for each row, for nodes in a layout)