datashield.login {opal}R Documentation

Logs in and assigns variables to R

Description

This function allows for clients to login to opal servers and (optionaly) assign all the data or specific variables from Opal tables to R dataframes. The assigned dataframes (one for each opal server) are named 'D' (by default).

Usage

datashield.login(logins = NULL, assign = FALSE, variables = NULL,
  symbol = "D", directory = "~/.ssh",
  username = getOption("datashield.username"),
  password = getOption("datashield.password"),
  opts = getOption("datashield.opts", list()), restore = NULL)

Arguments

logins

A dataframe table that holds login details. This table holds five elements required to login to the servers where the data to analyse is stored. The expected column names are 'server' (the server name), 'url' (the opal url), 'user' (the user name or the certificate file path), 'password' (the user password or the private key file path), 'table' (the fully qualified name of the table in opal), 'options' (the SSL options). An additional column 'identifiers' can be specified for identifiers mapping (from Opal 2.0). See also the documentation of the examplar input table logindata for details of the login elements.

assign

A boolean which tells whether or not data should be assigned from the opal table to R after login into the server(s).

variables

Specific variables to assign. If assign is set to FALSE this argument is ignored otherwise the specified variables are assigned to R. If no variables are specified (default) the whole opal's table is assigned.

symbol

A character, the name of the dataframe to which the opal's table will be assigned after login into the server(s).

directory

A character that indicates the location of the key pairs files (certificate and private key). If the default location is the users '.ssh' directory.

username

Default user name to be used in case it is not specified in the logins structure.

password

Default user password to be used in case it is not specified in the logins structure.

opts

Default SSL options to be used in case it is not specified in the logins structure.

restore

The workspace name to restore (optional).

Value

object(s) of class opal

Author(s)

Gaye, A.

Examples

## Not run: 

#### The below examples illustrate an analysises that use test/simulated data ####

# build your data.frame
server <- c("study1", "study2")
url <- c("https://some.opal.host:8443","https://another.opal.host")
user <- c("user1", "datashield-certificate.pem")
password <- c("user1pwd", "datashield-private.pem")
table <- c("store.Dataset","foo.DS")
options <- c("","c(ssl.verifyhost=2,ssl.verifypeer=1)")
logindata <- data.frame(server,url,user,password,table)

# or load the data.frame that contains the login details
data(logindata)

# Example 1: just login (default)
opals <- datashield.login(logins=logindata)

# Example 2: login and assign the whole dataset
opals <- datashield.login(logins=logindata,assign=TRUE)

# Example 3: login and assign specific variable(s)
myvar <- list("LAB_TSC")
opals <- datashield.login(logins=logindata,assign=TRUE,variables=myvar)

## End(Not run)


[Package opal version 2.6.0 ]