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DEVELOPERS.md

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For statisticians

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. Until then, be warned that these instructions are preliminary, you will almost certainly need more support from the OpenSAFELY team to get running, and the framework API is changing quickly. In other words, if you'd like to work with us at this stage, get in touch before writing too much code.

Currently there is a single backend implemented for the data, for running analytics against TPP SystmOne records. Other backends are under development.

This repository contains everything needed to:

  • Define a set of covariates needed for your model
  • Generate an input dataset from dummy data against which you can develop your model
  • Request that the model be run against the live data

You will need access to a dummy dataset to do this; get in touch to request credentials. Our first analyses are with Stata - you will, therefore, also need a licenced copy of Stata (see below for information about the Docker version)

Until we have developed a deployment framework, you should use this repository as a template when you create a new Github Repo. When you do so, for the automated tests to run, you should also add two Secrets to the settings for your repo:

  • DOCKER_GITHUB_TOKEN: a token generated using your Github account (see instructions in "Running the model against real data", below)
  • DUMMY_DATABASE_URL: the URL / credentials for the dummy database, which the database manager should share with you (or someone else on the team)

The entrypoint of your model must be called model.do and it must live in the analysis/ folder.

Your model must start by importing the dataset, which will be called input.csv and be in the same folder.

For portability, the recommended way of starting your model is:

import delimited `c(pwd)'/analysis/input.csv

Defining covariates

At the moment, this involves writing some simple Python code.

This must live in a file at analysis/study_definition.py. Until more documentation is written, refer to the sample one provided here for inspiration; or, if you're feeling adventurous, search the tests (in tests/) for StudyDefinition examples.

Generating dummy data

On Windows

You'll want to install a couple of things:

  • This ODBC driver from Microsoft
  • The latest run.exe from here
    • This must be copied to and run from the root folder of your research repository
    • Note that if you're testing a new branch with new runner functionality, you'll need to download the latest run.exe that is tagged with that branch name from the Releases section of github

You need to obtain the "database URL", which includes a username and password. When running outside the secure environment, obtain a URL that gives you access to the publicly-available dummy dataset.

Now double-click run.exe, and it will use your covariate definitions in analysis/study_definition.py to generate a data file at analysis/input.csv

You can now use Stata as you usually would, with your code entrypoint in analysis/model.do.

Using docker and the command line

Python 3.8 is assumed:

  • Install Docker
  • python run.py generate_cohort --docker --database-url <DATABASE_URL>

Using plain python

  • Install ODBC Driver 17 for SQL Server for your platform
  • Set up a Python 3.8 virtual environment
  • pip install -r requirements.txt
  • python run.py --help

Running the model

There are three ways to run your model:

  • Directly in your usual development environent. For example, if you have Stata installed locally, just open model.do and run as normal
  • Via the runner tool:
    • Select the run option and tell it where your Stata application is
    • Leave the Stata location blank, and the tool will attempt to use Docker to run the model

For the last option, you will need to provide docker with credentials to access the Docker version of Stata. It's password-protected as it includes licensed software -- if you are a third party outside the OpenSAFELY collaborative, you'll need to purchase your own Stata licence, and we will help you set up your own docker version.

We use the Github Docker package repository, so you'll need to add a Personal Access Token with permissions to read packages. visit your personal Github "settings" page, find the Developer > Developer Settings > Personal Access Tokens, and add a token there (any name will do) with the permission read:packages. Take a note of the token (you only get a chance to see it once!).

Now run

docker login docker.pkg.github.com -u <YourGithubUsername> --password <PersonalAccessToken>

You can check this worked by running

docker pull docker.pkg.github.com/ebmdatalab/stata-docker-runner/stata-mp:latest
  • Run run.py run --analysis to run the model. Its output is streamed to stdout, and saved in model.log

For developers

Run tests

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

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: until we make this cleaner... if you change the database schema be sure to docker rm stata-docker_sql_1 before restarting.