config_funcs: Functions for configuring the gtox package

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

Functions for configuring the gtox package

Description

These functions are used to configure the gtox settings.

Load the current configuration file

Usage

gtoxConf(drvr = NULL, user = NULL, pass = NULL, host = NULL,
  db = NULL)

gtoxConfDefault()

gtoxConfList(show.pass = FALSE)

gtoxConfLoad(list.new = TRUE)

gtoxConfReset()

gtoxConfSave()

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 gtox database
show.pass	Logical, should the password be returned
list.new	Logical of length 1, should the new settings be printed?

Details

Currently, the gtox package only supports the "MariaDB" and "SQLite" 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 gtoxConf in the home directory, eg. TCPL_CONF=~/gtoxConf. Note, '~' may not indicate the home directory on every operating system. Once the environment variable is added, the user can change the settings using gtoxConf, then save the settings to the file given by the TCPL_CONF environment variable running gtoxConfSave().

Value

None

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

gtoxConfSave modifies the configuration file to reflect the current gtox settings.

gtoxConfList lists the values assigned to the gtox global options.

gtoxConfLoad updates the gtox settings to reflect the current configuration file.

gtoxConfDefault changes the options to reflect the default settings for the example SQLite database, but does not alter the configuration file.

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

Examples

gtoxConfList() # List configuration parameters


## Configure database
sqlite <- file.path(system.file(package="GladiaTOX"),
    "sql",
    "gladiatoxdb.sqlite")
gtoxConf(db=sqlite, user=NA, host=NA, drvr="SQLite")


## Configure database with default parameters
gtoxConfDefault()


## List configuration of database parameters
gtoxConfList()


## Set the environment variable pointing to the configuration file
Sys.setenv(TCPL_CONF=file.path(system.file(package="GladiaTOX"),"gtoxConf"))

## Configure database
gtoxConfLoad()


## Set the environment variable pointing to the configuration file
Sys.setenv(TCPL_CONF=file.path(system.file(package="GladiaTOX"),"gtoxConf"))

## Configure database
gtoxConfReset()


## Set the environment variable pointing to the configuration file
Sys.setenv(TCPL_CONF=file.path(system.file(package="GladiaTOX"),"gtoxConf"))

## Configure database
gtoxConfSave()

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.