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chameleonhub / chameleon-data

Repository for cleaning and adjusting BAHIS-related data
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BAHIS Data Pipeline

This repository contains the data pipeline for the BAHIS project. It is a collection of scripts that download data from the BAHIS postgreSQL database, process it, and export it as csv files that can be used by the dashboard.

Local Installation

First install pipenv. If you installed pipenv using sudo apt install pipenv and getting this error install using pip instead.

  1. pipenv install
  2. copy data from output to bahis-dash/exported_data/ if running the dashboard

If you get an error when running install like this:

Resolving dependencies...
✘ Locking Failed!

remove the Pipfile.lock file and run again.

Local development

Run pipenv run python pipeline.py. (If you get a Permission denied error you may need to run as sudo)

This will run a development server with hot reloading and other useful features.

Deployment

To run the system in a local "deployment" you can use the Dockerfile with docker build -t data . && docker run -p 80:80 --name bahis-data data:latest. Note this will fail if bahis_creds_file.cnf is not valid, i.e. points to a local postgreSQL instance. You will also need to make sure the backup sql file is in the input directory.

Cloud deployment is done (currently manually) using bahis-infra. Only the latest release will be deployed - releases are created automatically when a PR is successfully merged into main.

The following is a cronjob that is added to crontab in the docker that will run the scripts each night at 23:00:

0 23 * * * cd /home/app && sh nightly.sh >> log.txt

If you need to run the script immediately just run docker exec bahis-data sh nightly.sh from your terminal.

Known missing files

The following files are needed to run prep_data.py:

  1. newbahis_bahis_patient_registrydyncsv_live_table.csv;
  2. newbahis_bahis_species_table.csv;
  3. newbahis_bahis_diagnosis_table.csv;
  4. newbahis_geo_cluster.csv.

Put the stated files in the "output" folder.

Adding pipeline scripts

Add new pipelines scripts to the pipeline_scripts folder. The script should have a main() function that is called by pipeline.py. The main() function should read inputs from the input folder and save outputs to the output folder. We currently don't have chained pipelines.

Lookup tables

The file named "bahis_data_lovi_top_diagnosis.xlsx" contains the lookup table for correcting the spellings of diseases. Put this file in the "lookup" folder.