DatabaseConnector

DatabaseConnector is part of the OHDSI Methods Library.

Introduction

This R package provides function for connecting to various DBMSs.

Features

• Create connections to the various database platforms:
  • MicrosoftSQL Server
  • Oracle
  • PostgresSql
  • Microsoft Parallel Data Warehouse (a.k.a. Analytics Platform System)
  • Amazon Redshift
  • Apache Impala
  • Google BigQuery
  • IBM Netezza
  • SQLite
• Statements for executing queries with
  • Error reporting to file
  • Progress reporting
  • Multiple statements per query
• Support for fetching data to ffdf objects
• Insert data frame to a database table
• Supports the DBI interface
• Integrates with RStudio's Connections tab

Examples

connectionDetails <- createConnectionDetails(dbms="postgresql", 
                                             server="localhost",
                                             user="root",
                                             password="blah",
                                             schema="cdm_v4")
conn <- connect(connectionDetails)
querySql(conn,"SELECT COUNT(*) FROM person")
disconnect(conn)

## regular data insert
insertTable(connection = connection, 
            tableName = "scratch.somedata", 
            data = data, 
            dropTableIfExists = TRUE, 
            createTable = TRUE, 
            tempTable = FALSE, 
            useMppBulkLoad = FALSE)
            
## bulk data insert with Redshift or PDW
insertTable(connection = connection, 
            tableName = "scratch.somedata", 
            data = data, 
            dropTableIfExists = TRUE, 
            createTable = TRUE, 
            tempTable = FALSE, 
            useMppBulkLoad = TRUE)

Technology

DatabaseConnector is an R package using Java's JDBC drivers.

System Requirements

Requires R. Also requires Java 1.6 or higher (Oracle Java is recommended. Issues have been reported when using GCJ.)

Dependencies

Please note that this package requires Java to be installed. If you don't have Java already installed on your computed (on most computers it already is installed), go to java.com to get the latest version.

To be able to use Windows authentication for SQL Server, you have to install the JDBC driver. Download the .exe from Microsoft and run it, thereby extracting its contents to a folder. In the extracted folder you will find the file sqljdbc_4.0/enu/auth/x64/sqljdbc_auth.dll (64-bits) or sqljdbc_4.0/enu/auth/x86/sqljdbc_auth.dll (32-bits), which needs to be moved to location on the system path, for example to c:/windows/system32. If you not have write access to any folder in the system path, you can also specify the path to the folder containing the dll by setting the environmental variable PATH_TO_AUTH_DLL, so for example Sys.setenv("PATH_TO_AUTH_DLL" = "c:/temp").

DatabaseConnector also depends on the OHDSI DatabaseConnectorJars and SqlRender packages.

For Redshift Bulk Mpp inserts, the cloudyR aws S3 package is required.

Getting Started

To install the latest stable version, install from CRAN:

install.packages("DatabaseConnector")

To install the latest development version, install from GitHub:

install.packages("devtools")
devtools::install_github("ohdsi/DatabaseConnectorJars")
devtools::install_github("ohdsi/DatabaseConnector")

To download and use the JDBC drivers for BigQuery, Impala, or Netezza, see these instructions.

User Documentation

• Vignette: Using DatabaseConnector
• Package manual: DatabaseConnector manual

Support

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

DatabaseConnector is licensed under Apache License 2.0. The JDBC drivers fall under their own respective licenses.

Development

DatabaseConnector is being developed in R Studio.

Development status

Stable. The code is actively being used in several projects.

Acknowledgements

• This project is supported in part through the National Science Foundation grant IIS 1251151.