initEnvironment: Initialize the environment.

In sendigR: Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

Initialize the environment.

Description

Open or create a SEND database and return a token for the open database connection.

Usage

initEnvironment(
  dbType = NULL,
  dbPath = NULL,
  dbCreate = FALSE,
  dbUser = NULL,
  dbPwd = NULL,
  dbSchema = NULL,
  ctFile = NULL
)

Arguments

dbType	Mandatory, character The type of database, valid values (case insensitive): 'sqlite' 'oracle'
dbPath	Mandatory, character The path to the database (path to file or another kind of db reference)
dbCreate	Mandatory, boolean If TRUE, a new database is to be created - this is only valid for dbType 'sqlite'
dbUser	Mandatory, character - if login credentials are required for the specific db type The user name to be used for login to database.
dbPwd	Mandatory, character - if login credentials are required for the specific db type The password to be used for login to database.
dbSchema	Optional, character The table owner of the SEND table in the specific database. This parameter is only relevant to specify if it is necessary to prefix table names with schema in SQL statements i the database.
ctFile	Optional, character. Name (full path) of CDISC CT file in Excel xls format to be imported. Only relevant to use if another CDISC CT version than the version included in packages is wanted.

Details

If the function is executed with parameter dbCreate=FALSE (default), a connection to the specified database is opened. Dependent of the type of database (parameter dbType), a login using specified user credentials (parameters dbUser and dbPwd) may be done.
The database must contain a set of tables representing the SEND domains compliant with SEND IG version 3.0 and/on 3.1.

If the function is executed with parameter dbCreate=TRUE, an empty database is created and opened. This is only supported for a SQLite database, i.e. parameter dbType='sqlite'. The SEND domain tables may then be created by execution of the function dbCreateSchema.

Besides the open database connection, a set of CDISC SEND controlled terminology values are imported. If parameter ctFile is specified with a path to an Excel file containing a CDISC SEND ct version downloaded from https://evs.nci.nih.gov/ftp1/CDISC/SEND/, the content from this file is imported and used by some of the package's functions. Else a set of CDISC SEND CT values which are included in the packages is used by the package's functions. It's the newest CDISC SEND CT version at the time of the build of the current version of the package which is included.

Value

The function returns a token which is a data structure describing the open database connection. This token must be given as input parameter to all functions accessing the actual database.

Examples

## Not run: 
db <- initEnvironment(dbType='sqlite',
                      dbPath='//servername/SendData/db/send.db',
                      ctFile='//servername/SendData/metadata/SEND_Terminology_2019-12-27.xls')
db <- initEnvironment(dbType='oracle',
                      dbPath='dbserver:1521/send_db',
                      dbUser='ME',
                      dbPwd='mypassword',
                      dbSchema = 'send',
                      ctFile='//servername/SendData/metadata/SEND_Terminology_2019-12-27.xls')

## End(Not run)

sendigR documentation built on Aug. 18, 2022, 9:07 a.m.