README.md

IeDEA Pregnancy Registry

Collection of scripts and documentation for the pregnancy-registry

These utilities generate the cohorts for both AMPATH and FACES Encounters mapped to their respectice concept dictionaries, and then serialize those cohorts to the import format expected by INC Research who runs an OC Database to store the results.

Overview

Installation

Configuration

Two database connections are required to run this utility. One of them is for the local storage of exported pregnancy items. Initially this database will need to be synced to create the tables.

The second database connection will be to the OpenMRS MySQL instance to pull data from. This can be a production DB, or preferably a clone of production used for reporting tasks. This connection can be read only (preferably).

These connections are specified in pregreg/secure.py. This contains database credentials and should only be readable by the user running the reports. Alternatively, this file is a regular python source, so if you prefer to read credentials from an environment variable, keyring, or that store that can also be done.

DATABASES = {
    'apr_db': {
        'ENGINE': 'django.db.backends.mysql',
        'NAME': 'apr_db',
        'USER': 'apruser',
        'PASSWORD': '********',
        'HOST': 'localhost',   # Or an IP Address that your DB is hosted on
        'PORT': '3306',
    },
    'amrs_db': {
        'ENGINE': 'django.db.backends.mysql',
        'NAME': 'amrs',
        'USER': 'amrs_user',
        'PASSWORD': '********',
        'HOST': 'openmrs.ampath.org',
        'PORT': '3306',
    },
    'faces_openmrs_db': {
        'ENGINE': 'django.db.backends.mysql',
        'NAME': 'openmrs',
        'USER': 'faces_user',
        'PASSWORD': '********',
        'HOST': 'openmrs.faces.org',
        'PORT': '3306',
    },
}

Usage

To run the cohort for a given set of months use the below syntax. The following will generate the cohort entries for January, February, and March 2014.

generate_cohort 2014 1,2,3

To export the results in OC format after they have been generated, the following command is used. This will generate the report for February 2014 and write it to a file in your working directory called export-file.txt.

generate_report 2014 2 export-file.txt