Datman's Configuration Files

Overview

Datman's configuration is managed by two types of yaml configuration files:

1. A site wide configuration file (tigrlab_config.yaml in our case)
2. Study configuration files (each named ${study_name}_settings.yml in our lab)

The site wide config file holds settings that affect every study and holds default configuration that can be overridden by the study config files. The study config file holds study specific overrides of defaults, details of the expected data in each scan session, and settings to use for the nightly pipelines. In our lab, we store all of our config files at /archive/code/config.

Datman finds the configuration files by looking for the shell variables DM_CONFIG, which should be the full path to your site wide config file, and DM_SYSTEM, which should be the name of a system configured in the site wide config file's SystemSettings block.

NOTE: Settings in the config files are case sensitive. If Datman complains about a 'KeyError' for any settings that you've defined double check your spelling and case.

Overriding default settings

Redefining the same setting in a 'more specific' context will, for most settings in the config files, override any default settings defined elsewhere.

From most specific settings to least it goes:

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Inside a 'Site' block in the study config file

⬇️

Top level of the same study config file

⬇️

Inside the site wide config file

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Or to put it another way: you can override defaults for almost any setting just for one specific site, or for a whole study.

There are some special cases, though, which are mentioned in the Site Config and Study Config pages in sections where the defaults of these special cases are typically defined.