Sprint Reporter

Validate submissions for the All of Us data sprints. Visit the website for the sprint specifications.

Requirements

Python 2.7.* (download from here and install)
pip (download get-pip.py and run python get-pip.py)

Installation / Configuration

Install requirements by running
```
 pip install -r requirements.txt
```
Update _settings.py and rename it to settings.py

reporter

python reporter.py

This module checks files for conformance to All of Us Data Sprint specifications. It attempts to read CSV files in a configured directory and load them into a configured database, thereby creating an instance of the OMOP Common Data Model (CDM).

Errors and issues encountered along the way are logged to a table pmi_spring_reporter_log. An abbreviated log is written to docs/_data/log.json to be presented on the website report page.

achilles

This runs an abbreviated version of Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES). It creates and populates ACHILLES_{analysis, results, results_derived, results_dist, HEEL_results}, tables which help to characterize an OMOP CDM instance.

Assumes conn_str in settings refers to a valid instance of OMOP CDM (e.g. reporter was run successfully).

python achilles.py

webapi

This module helps to automate the backend configuration of Atlas, a tool which enables researchers to conduct scientific analyses on data sets conforming to the OMOP CDM standard. It populates source and source_daimon tables so Atlas can be used to analyze datasets created by reporter and achilles.

Assumes webapi_conn_str_str in settings refers to a valid instance of the application database (see WebAPI).