gCMAPWeb (version 1.12.0)

validate_config_file: Validation of gCMAPWeb configuration file

Description

This function validates the content of the gCMAPWeb configuration file.

Usage

validate_config_file(config.file.path)

Arguments

config.file.path

full path to gCMAPWeb configuration file (in yaml format)

Value

Information from a valid configuration file is returned as a nested list. Invalid entries in the config file with cause an error.

Details

Verifies that 1. all required fields are present 2. at least one species has been defined 3. all supported annotation packages are available 4. all cmaps have unique labels 5. each supported species has at least one associated reference dataset

Examples

## read the example configuration yaml file without validation
library(yaml)
conf1 <- yaml.load_file( system.file("config", "config.yml",
             package="gCMAPWeb") )
## read the example configuration file and validate that
## all required information is provided and valid
conf2 <- validate_config_file( system.file("config", "config.yml",
             package="gCMAPWeb") )
identical( conf1, conf2)