DIZutils

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The R package DIZutils 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.

Installation

You can install DIZutils directly from CRAN:

install.packages("DIZutils")

The development version can be installed using

install.packages("remotes")
remotes::install_github("miracum/misc-dizutils", ref = "development")

Basic functions

db_connection

The function DIZutils::db_connection provides one simple interface for connecting to various types of databases. It reads necessary connection settings from the active environment (see below how to use the function set_env_vars to set environment variables).

The following database types are currently supported:

postgres

The following environment variables need to be set to the active environment in order to connect with a postgres database with “i2b2” as name of the database to connect with:

Variable Description
I2B2_HOST The hostname/ IP address of your pg instance.
I2B2_DBNAME The name of the pg-database.
I2B2_PORT The port, your pg postgres instance is running on.
I2B2_USER The name of the ‘I2B2_USER’.
I2B2_PASSWORD The password of the ‘I2B2_USER’ of your pg instance.

To establish the connection, please set those environment variables accordingly and execute the following command. The argument db_name is used to detect the corresponding environment variables and thus must match with the environment variables’ prefix.

db_con <- DIZutils::db_connection(
    system_name = "i2b2",
    db_type = "postgres"
  )

oracle

The following environment variables need to be set to the active environment in order to connect with an oracle database:

Variable Description
MYORACLEDB_HOST The hostname/ IP address of your oracle instance.
MYORACLEDB_DBNAME The name of the oracle-database.
MYORACLEDB_DRIVER The path to the oracle jdbc driver.
MYORACLEDB_SID The SID of the oracle-database.
MYORACLEDB_PORT The port, your oracle postgres instance is running on.
MYORACLEDB_USER The name of the ‘MYORACLEDB_USER’.
MYORACLEDB_PASSWORD The password of the ‘MYORACLEDB_USER’ of your oracle instance.

To establish the connection, please set those environment variables accordingly and execute the following command. The argument db_name is used to detect the corresponding environment variables and thus must match with the environment variables’ prefix. Furthermore, an ojdbc*.jar-file needs to be provided via the function’s lib_path argument.

db_con <- DIZutils::db_connection(
  system_name = "myoracledb",
  db_type = "oracle",
  lib_path = "path/to/ojdbc*.jar"
)

For further details on how to set the specific environment variables using a configuration file, please refer to the documentation in the DIZtools R package.

More Infos