mandarvaze / fhir-assignment

Requirements

• Docker
• Python 3.8

Get the code and data files

$ git clone [e-mail]:mandarvaze/fhir-assignment.git
$ cd fhir-assignment
# Ignore the following warning if you are not using direnv
# `direnv: error /private/tmp/fhir-assignment/.envrc is blocked. Run `direnv allow` to approve its content`
$ mkdir data

Download the data files

Download these files in the data folder we created in the previous step

1. https://github.com/smart-on-fhir/flat-fhir-files/blob/master/r3/Patient.ndjson
2. https://github.com/smart-on-fhir/flat-fhir-files/blob/master/r3/Observation.ndjson
3. https://github.com/smart-on-fhir/flat-fhir-files/blob/master/r3/Encounter.ndjson
4. https://github.com/smart-on-fhir/flat-fhir-files/blob/master/r3/Procedure.ndjson

Setup

# Make sure you are back to folder where you cloned the code
python -m venv .venv-prometheus
source .venv-prometheus/bin/activate
pip install -r requirements.txt
pre-commit install  # Only for development

Start postgres

• make start-pgsql (To start in the background)
• make pgsql (To start in the foreground - sometimes this is helpful to troubleshoot)
• if/when required - stop postgres via make stop-pgsql
• Use docker ps to ensure that postgres has actually started (or stopped)

Usage

1. First import the data into the database

$ python main.py -i

This step can take really long time, but it shows progress via "one dot per record" - so you won't think it had hung. I will optimize this part later.

2. Now you can generate the report

$ python main.py -r