The R package DIZtools provides utility functions used
for the R package development infrastructure inside the data integration
centers (‘DIZ’) to standardize and facilitate repetitive tasks such as
setting up a database connection or issuing notification messages and to
avoid redundancy.
:bulb: DIZtools contains all “lightweighted” functions
of DIZutils
making it a lot quicker to install, while DIZutils
has a lot of dependencies and system requirements.
You can install DIZtools directly from CRAN:
install.packages("DIZtools")The development version can be installed using
install.packages("remotes")
remotes::install_github("miracum/misc-diztools", ref = "dev")In order to set up a database connection using the function
DIZutils::db_connection, one needs to provide the required
connection settings via environment variables. To facilitate the process
of making such environment variables available within the current R
session, the function DIZtools::setenv_file works as a
wrapper function around the base R method Sys.setenv. It
takes the file name of a text file with the definitions of the
environment variables as input, and sets those environment variables
within the current R session.
DIZtools::setenv_file("path/to/envfile")The design of the envfile is based on the
.env file for defining environment variables when using
docker-compose commands. See here (currently,
neither empty lines nor the using of comments (‘#’) is being supported
by DIZtools::setenv_file).
To create an envfile for connecting with an i2b2
database, the following exemplary definitions of environment variables
should be written to a simple textfile, e.g. named envfile,
which can then be passed as argument to
DIZtools::setenv_file.
I2B2_HOST=123.45.56.8
I2B2_PORT=5432
I2B2_DBNAME=i2b2
I2B2_USER=user
I2B2_PASSWORD=password