2014 i2b2 NLP Sandbox Data Node

This NLP Sandbox Data Node contains the data from the 2014 i2b2 NLP De-identification Challenge.

Introduction

Specifications

TBA

Deploy using Docker

1. Create the file that contains the future environment variables

    cp .env.sample .env
   

2. In .env, set the values of SYNAPSE_USERNAME and SYNAPSE_APIKEY with the credentials of a Synapse account. This information is required to enable the Data Node to download the 2014 i2b2 data from Synapse in order to populate the Data Node database.

3. Export the variables defined in .env to environment variables

    export $(grep -v '^#' .env | xargs -d '\n')
   

4. Start the Data Node web service (RESP API)

    docker-compose up
   

5. In your browser, go to the web service documentation page http://localhost:8080/api/v1/ui/ to check that the web service of the Data Node started successfully.

Access logs

The current logs are saved to /var/log/app/current.

$ docker exec data-node-api cat /var/log/app/current
2020-09-25 23:33:39.809826500  Starting data node server
2020-09-25 23:33:40.436453500   * Serving Flask app "__main__" (lazy loading)
2020-09-25 23:33:40.436461500   * Environment: production
2020-09-25 23:33:40.436462500     WARNING: This is a development server. Do not use it in a production deployment.
2020-09-25 23:33:40.436463500     Use a production WSGI server instead.
2020-09-25 23:33:40.436464500   * Debug mode: off

Follow the logs using docker logs

docker logs --follow data-node-api