This section introduces the typical OpenSAFELY workflow for a single research project.
The workflow consists of a number of key steps which may be iterated over as the code is developed and the study evolves. The following assumes that a well-defined and ethically-approved research agenda has been specified, with an accompanying study protocol, and all necessary permissions for accessing the OpenSAFELY platform are in place.
The workflow for a single study can typically be broken down into the following steps:
- Create a git repository from the template repository provided and clone it on your local machine. This repo will contain all the code relating to your project, and a history of its development over time.
- Write a Study Definition that specifies what data you want to extract from the database:
- specify the patient population (dataset rows) and variables (dataset columns)
- specify the expected distributions of these variables for use in dummy data
- specify (or create) the codelists required by the study definition, hosted by OpenCodelists, and import them to the repo.
- Generate dummy data based on the Study Definition, for writing and testing code.
- Develop analysis scripts using the dummy data in R, Stata, or Python. This will include:
- importing and processing the dataset(s) created by the cohort extractor
- importing any other external files needed for analysis
- generating analysis outputs like tables and figures
- generating log files to debug the scripts when they run on the real data.
- Test the code by running the analysis steps specified in the project pipeline, which specifies the execution order for data extracts and analyses and the outputs to be released.
- Execute the analysis on the real data via OpenSAFELY's jobs site. This will generate outputs on the secure server.
- Check the output for disclosivity within the server, and redact if necessary.
- Release the outputs via GitHub.
- Repeat and iterate steps 2 to 8 as necessary.
These steps should always proceed with frequent git commits and code reviews where appropriate. Steps 2-5 can all be progressed on your local machine without accessing the real data.
It is possible to automatically test that the analytical pipeline defined in step 5 can be successfully executed on dummy data, using the
opensafely run command.
This pipeline is also automatically tested against dummy data every time a new version of the study repository is saved ("pushed") to GitHub.
As well as your own Python, R or Stata scripts, other non-standard actions are available. For example, it's possible to run a matching routine that extracts a matched control population to the population defined in the study definition, without having to extract all candidate matches into a dataset first.