README.md

In DIZutils: Utilities for 'DIZ' R Package Development

DIZutils

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 (via the R package RPostgres)
• oracle (via the R packages RJDBC and DBI)

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. | | I2B2_SCHEMA | (optional) The database schema on which queries should be performed. |

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

• about MIRACUM: https://www.miracum.org/
• about the Medical Informatics Initiative: https://www.medizininformatik-initiative.de/en/start

DIZutils documentation built on Jan. 23, 2023, 5:42 p.m.