System Configuration
Common configuration information
ConfigParser
For parsing all of the system configurations we use
slightly modified version of ConfigParser
which you can find here. All of the
configurations follows the general INI format for which you can see more
here.
In all configuration files you can add [DEFAULT]
section which is supported
by the ConfigParser
.
Interpolation
You can use interpolation values when specifying filepaths. You can use for
this purpose work_dir
and wd
which are added by a parsers to all of the
configurations as default values for all of the sections. Path of the
work_dir
and wd
is the same is the path to the directory containing the
configuration file.
Selectors
Configuration files may contain nested values whose root name is called a “selector” (e.g. sel.val1, sel.val2). Selectors are essentially just nested dictionaries. We will refer to the dictionaries nested within as “entries”. Selectors and their contents are parsed as a Python dictionary. You can see an example of a selector in the people group configuration here.
Common documentation information
Within the configuration documentation, some properties have miscellaneous information about them defined below the property signature. This information can be about entries such as default values and environment overrides. Currently, there are:
DEFAULT
- This information option defines default value of the property which is set in the code.
ENVIRONMENT OVERRIDE
- This information option defines name of the environment variable which can override property from the configuration.
- DAE Configuration
- Studies and Datasets DB configuration
- GenomesDB configuration
- Genomic Scores Configuration
- Annotation Configuration
- Phenotype Database Configuration
- Phenotype Regression Configuration
- Gene Info Configuration
- Default Configuration
- Study and Dataset Configuration
- Allowed Configuration Values