nzwang / text2brain_server

Webserver of text2brain for predicting brain activation maps from free-form text query

Text2Brain Web Server

A webpage that deploys Text2Brain model for predicting brain activation maps from free-form text query. The webpage is built with Flask + SQLite + AngularJS + Redis + RQ.

---

Broad picture

The setup is largely similar to this RealPython tutorial (we highly recommend going through this tutorial). Essentially there are two main python files, app.py is the Flask web server and worker.py performs the inference. app.py receives input query, which is then passed to a job that is queued by Redis and run in the background by worker.py without interfering with new web requests.

---

How to run

Requirements:

• Install virtualenv and install python 3.6.14
• Create a virtual environment with venv and install packages under requirements.txt
• Install sqlite
• Install redis
• Download checkpoints from Google Drive and do tar -xzvf text2brain_checkpoint.tar.gz
• Download uncased SciBert pretrained model from AllenAI S3 and unzip into scibert_scivocab_uncased directory

How to run locally in debug mode:

• Set the environment variables required by config.py
• Initialize the database from app import db; db.create_all()
• Run the worker python worker.py
• Run the web server on another terminal window/tab python app.py

---

Bugs and Questions

Please contact Gia at [email protected]