DatabaseConnector is part of the OHDSI Methods Library.
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)
Requires R. Also requires Java 1.6 or higher (Oracle Java is recommended. Issues have been reported when using GCJ.)
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.
To install the latest stable version, install from CRAN:
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.
DatabaseConnector is licensed under Apache License 2.0. The JDBC drivers fall under their own respective licenses.
DatabaseConnector is being developed in R Studio.