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The Readme for the whole VRNetzer platform is HERE

Analytics Module

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.

Installing and running locally (mac/linux/windows)

  1. 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.
  2. Clone this repository git clone git@github.com:menchelab/Analytics_Module.git
  3. Navigate to the repo cd dataserver
  4. Install dependencies pip install -r requirements.txt
  5. Run the server with python3 app.py
  6. 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)
  7. Optionally, configure it as a development environment, which would make the server reload with every code change. export FLASK_ENV=development
  8. 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.
  9. 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/.

Uploading a Layout / File structure

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

Data types of each column :

  • 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)