olm is a tool to operate on linelists provided from Global.health
(G.h). Linelists are epidemiological datasets with information about a
disease outbreak organised into one row per case. Currently it supports
generating briefing reports, fetching linelists and checking linelists
against a provided schema.
Installation can be done via pip
git clone https://github.com/globaldothealth/olm && cd olm
python3 -m venv .venv
source .venv/bin/activate
pip install .Recommended method is to use uv
git clone https://github.com/globaldothealth/olm && cd olm
uv sync
uv run olmolm is customised for Global.health usage, so may not work on
arbitrary line lists. Outbreak reports are generated using
presets. To see a list of presets:
$ uv run olm list
marburg Marburg 2023 [GHL2023.D11.1D60.1]
mpox-2024 Mpox 2024 [GHL2024.D11.1E71]To generate a report for a particular outbreak, run
uv run olm report <outbreak> [<url>]where <url> is the data link on the outbreak information
page. By default
olm will use the latest data file specified in the outbreak
configuration to build the report.