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For developers

Run cohortextractor commands

Run cohortextractor commands in Docker with ./run.sh cohortextractor --help.

If you need to point cohortextractor to a study, then you can set the WORKSPACE env var

WORKSPACE=/path/to/study ./run.sh ...

Run tests

Docker

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

If using MacOS Docker Desktop, you should increase Settings->Resources->Memory to at least 4GB.

Linux

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 and server with docker-compose up
  • install system dependencies
# mssql tools
sudo su
apt-get install -y gnupg && \
  curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add - && \
  curl https://packages.microsoft.com/config/ubuntu/20.04/prod.list > /etc/apt/sources.list.d/mssql-release.list && \
  apt-get update && \
  ACCEPT_EULA=Y apt-get install -y msodbcsql17 && \
  ACCEPT_EULA=Y apt-get install -y mssql-tools
export PATH=$PATH:/opt/mssql-tools/bin
  • Set up virtual env: make devenv - Note: if not on linux, you may need to install ctds manually
  • 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.

macOS

Running the tests in your own virtualenv on macOS is not advised, because of a hard-to-debug issue with OpenSSL and Microsoft's ODBC driver for SQL Server. Whilst the installation instructions are clear, there are several known issues that you should be aware of. Hic sunt dracones.

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

Debugging pymssql

To get query logs from pymssql, we can set an envvar: TDSDUMP=stdout. You can just set this when using local venv, or uncomment the line in docker-compose.yaml if using run.sh.

It's useful when disabling pytest's output/log capturing:

./run.sh pytest -s --log-cli-level=INFO

Ths output is very verbose, so this grep filter might help filter out the noise (note: there are tab characters in there).

grep -vE '^([a-z]+\.[ch]:|[0-9a-f]{4} | | .*[:=].*)' | grep -v -e '^[[:space:]]*$'