config_funcs: Functions for configuring the tcpl package

In tcpl: ToxCast Data Analysis Pipeline

Functions for configuring the tcpl package

Description

These functions are used to configure the tcpl settings.

Usage

tcplConf(drvr = NULL, user = NULL, pass = NULL, host = NULL, db = NULL, ...)

tcplConfDefault()

tcplConfExample()

tcplConfList(show.pass = FALSE)

tcplConfLoad(list.new = TRUE)

tcplConfReset()

tcplConfSave()

Arguments

drvr	Character of length 1, which database driver to use
user	Character of length 1, the database server username
pass	Character of length 1, the database server password
host	Character of length 1, the database server
db	Character of length 1, the name of the tcpl database
...	Additional arguments that should be passed to dbConnect function
show.pass	Logical, should the password be returned
list.new	Logical of length 1, should the new settings be printed?

Details

Currently, the tcpl package only supports the "MySQL" and "tcplLite" database drivers.

The settings can be stored in a configuration file to make the using the package more user-friendly. To create the configuration file, the user must first create a system environment variable ('TCPL_CONF') that points to to the file. There is more information about system environment variables in Startup and Sys.getenv. Briefly, the user needs to modify the '.Renviron' file in their home directory. If the file does not exist, create it, and add the following line:

TCPL_CONF=path/to/confFile.conf

Here 'path/to/confFile.conf' can be any path to a file. One suggestion would be to include .tcplConf in the home directory, e.g. TCPL_CONF=~/.tcplConf. Note, '~' may not indicate the home directory on every operating system. Once the environment variable is added, the user can change the settings using tcplConf, then save the settings to the file given by the TCPL_CONF environment variable running tcplConfSave().

tcplConf changes options to set the tcpl-specific options, most importantly to configure the connection to the tcpl databases. tcplConf will only change non-null values, and can be used to change a single value if needed.

tcplConfSave modifies the configuration file to reflect the current tcpl settings.

tcplConfList lists the values assigned to the tcpl global options.

tcplConfLoad updates the tcpl settings to reflect the current configuration file.

tcplConfDefault changes the options to reflect the default settings for the example tcplLite database, i.e. local directory, but does not alter the configuration file.

tcplConfReset is used to generate the initial configuration script, and can be used to reset or regenerate the configuration script by the user.

tcpl documentation built on Oct. 7, 2023, 1:06 a.m.