https://github.com/menchelab/analytics_module
Flask-based server handling data requests from the UI Module (VRNetzer)
https://github.com/menchelab/analytics_module
Last synced: about 1 year ago
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Flask-based server handling data requests from the UI Module (VRNetzer)
- Host: GitHub
- URL: https://github.com/menchelab/analytics_module
- Owner: menchelab
- License: mit
- Created: 2019-10-09T12:02:54.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2023-05-01T22:15:57.000Z (about 3 years ago)
- Last Synced: 2025-03-29T06:43:22.570Z (about 1 year ago)
- Language: Python
- Homepage:
- Size: 20.5 MB
- Stars: 2
- Watchers: 3
- Forks: 4
- Open Issues: 11
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Metadata Files:
- Readme: readme.md
- License: LICENSE
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README
The Readme for the whole VRNetzer platform is [HERE](https://github.com/menchelab/vrnetzer)
# 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.
1. Clone this repository `git clone git@github.com:menchelab/Analytics_Module.git`
1. Navigate to the repo `cd dataserver`
1. Install dependencies `pip install -r requirements.txt`
1. Run the server with `python3 app.py`
3. 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)
1. Optionally, configure it as a development environment, which would
make the server reload with every code change. `export FLASK_ENV=development`
1. 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.
1. 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)