before running collect.py

[2533245542]

Hi,

In order to run collect.py, it seems I need to have a psql database setup with mimic-iv FHIR loaded.

I have installed psql and have mimic-iv FHIR downloaded and unzip and stored in a folder.

Do you know how to load them into a database called 'mimiciv_fhir'?

[Adibvafa]

@mahshidaln Could you review?

[zzadxz]

Hi @2533245542!

I went through the setup, and here’s what worked for me to get collect.py up and running smoothly. Since collect.py relies on data from the MIMIC-IV FHIR dataset, I had to need to first load the data into PostgreSQL. I made a PR with an updated README that explains how to load the dataset mimic-iv FHIR (and how to download it properly). I added the files inside of the path odyssey under a folder named physionet.org and inside of it you can find ~/odyssey/physionet.org/files/mimic-iv-fhir-demo/2.0/mimic-fhir/Condition.ndjson and other .ndjson files. The script that I added load_ndjson_to_postgres.py loads everything properly and handles the formatting of these .ndjson files. I also added the unpacked physionet.org to .gitignore so that future users and contribtuers don't accidentally commit this HUGE database :)
Hope this helps!