readepi (version 1.0.4)

read_rdbms: Import data from relational database management systems (RDBMS).

Description

The function assumes the user has read access to the database. Importing data from RDBMS requires the installation of the appropriate driver that is compatible with the server version hosting the database. For more details, see the Installing drivers on how to install the driver.

Usage

read_rdbms(login, query)

Value

A data.frame with the requested data as specified in the query

argument.

Arguments

login

The connection object obtained from the login() function.

query

An SQL query or a list with the following elements:

1. table: a string with the table name

2. fields: a vector of column names. When specified, only those columns will be returned. Default is NULL.

3. filter: an expression or a vector of values used to filter the rows from the table of interest. This should be of the same length as the value for the 'select'. Default is NULL.

Examples

if (FALSE) {
  # establish the connection to the database
  rdbms_login <- login(
    from = "mysql-rfam-public.ebi.ac.uk",
    type = "mysql",
    user_name = "rfamro",
    password = "",
    driver_name = "",
    db_name = "Rfam",
    port = 4497
  )

  # import data where query parameters are specified as a list
  authors_list <- read_rdbms(
    login = rdbms_login,
    query = list(table = "author", fields = NULL, filter = NULL)
  )

  # import data where query parameters is within an SQL query
  authors_list <- read_rdbms(
    login = rdbms_login,
    query = "select * from author"
  )
}