├── .dockerignore ├── .env-example ├── .env-test ├── .flake8 ├── .github ├── dependabot.yml └── workflows │ ├── build_and_publish.yaml │ ├── emis_trino_version_check.yaml │ └── test_runner.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── DEVELOPERS.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── ROADMAP.md ├── certs ├── directoraccess-cert.emishealthinsights.co.uk │ ├── 1.crt │ ├── 2.crt │ └── get_certs.sh └── providerplus.emishealthinsights.co.uk │ ├── 1.crt │ ├── 2.crt │ └── get_certs.sh ├── cohortextractor ├── VERSION ├── __init__.py ├── codelistlib.py ├── cohortextractor.py ├── csv_utils.py ├── custom_medication_dictionary.csv ├── dashboards │ ├── __init__.py │ ├── vaccinations.py │ ├── vaccinations_combine.py │ └── vaccinations_extract.py ├── date_expressions.py ├── emis_backend.py ├── exceptions.py ├── expectation_generators.py ├── expressions.py ├── log_utils.py ├── measure.py ├── mssql_utils.py ├── pandas_utils.py ├── patients.py ├── process_covariate_definitions.py ├── study_definition.py ├── therapeutics_utils.py ├── tpp_backend.py ├── trino_utils.py ├── uk_population_bands_2018.csv ├── update_custom_medication_dictionary.py ├── update_vmp_mapping.py └── validate_dummy_data.py ├── dependencies.txt ├── docker-compose.yml ├── mssql ├── entrypoint.sh └── setup.sql ├── pyproject.toml ├── pytest.ini ├── requirements.dev.in ├── requirements.dev.txt ├── requirements.prod.txt ├── run.sh ├── setup.py ├── starburst └── etc │ ├── catalog │ └── mssql.properties │ ├── config.properties │ ├── jvm.config │ ├── log.properties │ └── node.properties └── tests ├── __init__.py ├── conftest.py ├── dashboards ├── __init__.py ├── test_vaccinations.py ├── test_vaccinations_combine.py └── test_vaccinations_extract.py ├── emis_backend_setup.py ├── fixtures ├── dummy-data │ ├── dummy-data.csv │ ├── extra-column.csv │ ├── invalid-bool.csv │ ├── invalid-date-yyyy-mm-dd.csv │ ├── invalid-date-yyyy-mm.csv │ ├── invalid-date-yyyy.csv │ ├── invalid-int.csv │ └── missing-column.csv ├── studies │ ├── test_params │ │ ├── analysis │ │ │ └── study_definition.py │ │ └── codelists │ │ │ └── .gitkeep │ ├── test_patients_from_file │ │ ├── analysis │ │ │ └── study_definition_controls.py │ │ ├── codelists │ │ │ └── .gitkeep │ │ └── output │ │ │ └── matched_matches.csv │ ├── test_smoketest │ │ ├── analysis │ │ │ └── study_definition.py │ │ └── codelists │ │ │ ├── codelists.txt │ │ │ ├── opensafely-asthma-inhaler-salbutamol-medication.csv │ │ │ ├── opensafely-chronic-cardiac-disease.csv │ │ │ └── opensafely-chronic-liver-disease.csv │ └── test_suppresses_small_numbers │ │ ├── analysis │ │ └── study_definition.py │ │ └── codelists │ │ ├── codelists.txt │ │ └── opensafely-chronic-liver-disease.csv └── therapeutic_risk_groups │ └── risk_groups.txt ├── helpers.py ├── test_codelistlib.py ├── test_cohortextractor.py ├── test_date_expressions.py ├── test_emis_backend.py ├── test_expectation_generators.py ├── test_expressions.py ├── 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