Skip to content

Latest commit

 

History

History
80 lines (56 loc) · 2.97 KB

README.md

File metadata and controls

80 lines (56 loc) · 2.97 KB
Raw

OpenSAFELY cohort extractor tool

This tool supports the authoring of OpenSAFELY-compliant research, by:

  • Allowing developers to generate random data based on their study expectations. They can then use this as input data when developing analytic models.
  • Supporting downloading of codelist CSVs from the OpenSAFELY codelists repository, for incorporation into the study definition
  • Providing tools to understand and visualise the properties of real data, without having direct access to it

It is also the mechanism by which cohorts are extracted from live database backends within the OpenSAFELY framework.

To install the latest released version:

pip install --upgrade opensafely-cohort-extractor

To discover its options:

cohortextractor --help

It is designed to be run within an OpenSAFELY-compliant research repository. You can find a template repository to get you started here.

The tool has a remote subcommand which triggers jobs to be scheduled to run elsewhere, via a job server. If you set the environment variable OPENSAFELY_REMOTE_WEBHOOK, this hook will be supplied to the job server, which will POST a message to that URL when a job has finished.

For developers

Run tests

You can run everything in docker with ./run.sh pytest.

You can also run the tests in your own virtualenv, but either way you will (probably) still want to use docker to run a SQL Server instance:

  • Start an mssql server with docker-compose up
  • Set up a virtualenv and pip install -r requirements.txt
  • py.test tests/

Note: if you change the database schema be sure to docker-compose stop && docker-compose rm before re-running tests to ensure they are recreated.

Make releases

To make a release, when you merge to the main branch, at least one of your commits must contain a conventional commit prefixed fix:, perf: or feat: (patch, patch, and minor releases, respectively); or a final line starting BREAKING CHANGE: (major release).

Other types are ignored, but you might as well use them: docs, style, refactor, ci, revert are likely to be the most common, but there's a full list here

About the OpenSAFELY framework

The OpenSAFELY framework is a new secure analytics platform for electronic health records research in the NHS.

Instead of requesting access for slices of patient data and transporting them elsewhere for analysis, the framework supports developing analytics against dummy data, and then running against the real data within the same infrastructure that the data is stored. Read more at OpenSAFELY.org.

The framework is under fast, active development to support rapid analytics relating to COVID19; we're currently seeking funding to make it easier for outside collaborators to work with our system.