Type:	Package
Title:	'DataSHIELD' Interface
Version:	1.7.1
Description:	'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package defines the API that is to be implemented by 'DataSHIELD' compliant data repositories.
Depends:	R (≥ 4.3), methods, progress, R6,
Imports:	cli
Suggests:	testthat (≥ 2.1.0)
License:	LGPL-2.1 | LGPL-3 [expanded from: LGPL (≥ 2.1)]
URL:	https://github.com/datashield/DSI/, https://datashield.github.io/DSI/, https://datashield.org/
BugReports:	https://github.com/datashield/DSI/issues
RoxygenNote:	7.3.2
Encoding:	UTF-8
Collate:	'DSObject.R' 'DSConnection.R' 'DSDriver.R' 'DSI-package.R' 'DSLoginBuilder.R' 'DSResult.R' 'datashield.aggregate.R' 'datashield.assign.R' 'datashield.connections.R' 'datashield.errorMessages.R' 'datashield.errors.R' 'datashield.list.R' 'datashield.login.R' 'datashield.logout.R' 'datashield.status.R' 'datashield.symbol.R' 'datashield.workspace.R' 'utils.R'
NeedsCompilation:	no
Packaged:	2024-11-03 08:25:02 UTC; yannick
Author:	Yannick Marcon [aut, cre], Amadou Gaye [ctb], Tim Cadman [ctb], Paul Burton [ctb]
Maintainer:	Yannick Marcon <yannick.marcon@obiba.org>
Repository:	CRAN
Date/Publication:	2024-11-03 08:50:02 UTC

DSI: 'DataSHIELD' Interface

Description

'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package defines the API that is to be implemented by 'DataSHIELD' compliant data repositories.

Author(s)

Maintainer: Yannick Marcon yannick.marcon@obiba.org (ORCID)

Other contributors:

• Amadou Gaye (ORCID) [contributor]

• Tim Cadman (ORCID) [contributor]

• Paul Burton [contributor]

See Also

Useful links:

• https://github.com/datashield/DSI/

• https://datashield.github.io/DSI/

• https://datashield.org/

• Report bugs at https://github.com/datashield/DSI/issues

Append error message to last errors vector

Description

Append error message to last errors vector

Usage

.appendError(name, msg, env = getOption("datashield.env", globalenv()))

Makes a single DSConnection-class object or a named list of DSConnection-class objects.

Description

Makes a single DSConnection-class object or a named list of DSConnection-class objects.

Usage

.asNamedListOfConnections(conns)

Makes a typical logindata data frame a list of resources named by the server in which they are defined. Makes a character vector of resource names a list named by the connections.

Description

Makes a typical logindata data frame a list of resources named by the server in which they are defined. Makes a character vector of resource names a list named by the connections.

Usage

.asNamedListOfResources(conns, value)

Makes a typical logindata data frame a list of tables named by the server in which they are defined. Makes a character vector of table names a list named by the connections.

Description

Makes a typical logindata data frame a list of tables named by the server in which they are defined. Makes a character vector of table names a list named by the connections.

Usage

.asNamedListOfTables(conns, value)

Makes a typical logindata data frame a list of items named by the server in which they are defined. Makes a character vector of item names a list named by the connections.

Description

Makes a typical logindata data frame a list of items named by the server in which they are defined. Makes a character vector of item names a list named by the connections.

Usage

.asNamedListOfValues(conns, value, colname = NULL)

Check if there are last errors

Description

Check if there are last errors

Usage

.checkLastErrors(env = getOption("datashield.env", globalenv()))

Clear some cache

Description

Clear some cache

Usage

.clearCache(env = getOption("datashield.env", globalenv()))

Clear last errors

Description

Clear last errors

Usage

.clearLastErrors(env = getOption("datashield.env", globalenv()))

Deparse language expression

Description

Deparse language expression

Usage

.deparse(expr)

Gets the DSConnection-class objects

Description

The function searches for a list containing object of type DSConnection-class in the current environment; if more than one list is found it return the lastest. This way no matter what the user calls his connection object list it will be captured.

Usage

.getDSConnections(env)

Arguments

Value

A list of DSConnection-class objects obtained after login into the servers

Get time to sleep depending on the numer of previous iterations

Description

Get time to sleep depending on the numer of previous iterations

Usage

.getSleepTime(checks)

Check if there are last errors

Description

Check if there are last errors

Usage

.hasLastErrors(name, env = getOption("datashield.env", globalenv()))

Check if a callback parameter is a valid function

Description

Check if a callback parameter is a valid function

Usage

.is.callback(cb)

Check if provided object is a S4 class instance and if this class inherits from DSConnection-class.

Description

Check if provided object is a S4 class instance and if this class inherits from DSConnection-class.

Usage

.isDSConnection(obj)

Create a new progress instance with default settings.

Description

Create a new progress instance with default settings.

Usage

.newProgress(
  format = "  :what [:bar] :percent /:elapsed",
  clear = getOption("datashield.progress.clear", FALSE),
  total,
  width = 100
)

Update and increment the progress status if option "datashield.progress" is TRUE.

Description

Update and increment the progress status if option "datashield.progress" is TRUE.

Usage

.tickProgress(progress, tokens = list())

Update the progress status if option "datashield.progress" is TRUE.

Description

Update the progress status if option "datashield.progress" is TRUE.

Usage

.updateProgress(progress, step, total, tokens = list())

DSConnection class

Description

This virtual class encapsulates the connection to a DataSHIELD-aware data repository, and it provides access to data assignments and aggregagtions etc.

Implementation note

Individual drivers are free to implement single or multiple simultaneous connections.

See Also

Other DS classes: DSDriver-class, DSObject-class, DSResult-class

Other DSConnection generics: dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1", 
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
con
dsDisconnect(con)

## End(Not run)

DSDriver class

Description

Base class for all DataSHIELD-aware data repositories drivers (e.g., Opal, ...). The virtual class 'DSDriver' defines the operations for creating connections.

See Also

Other DS classes: DSConnection-class, DSObject-class, DSResult-class

Other DSDriver generics: dsConnect(), dsGetInfo()

DataSHIELD login details builder

Description

DataSHIELD login details builder

DataSHIELD login details builder

Format

A R6 object of class DSLoginBuilder

Details

Helper class for creating a valid data frame that can be used to perform datashield.login. See also newDSLoginBuilder.

Methods

Public methods

• DSLoginBuilder$new()

• DSLoginBuilder$append()

• DSLoginBuilder$build()

• DSLoginBuilder$clone()

Method new()

Create a new DSLoginBuilder instance.

Usage

DSLoginBuilder$new(logins = NULL, .silent = FALSE)

Arguments

Returns

A DSLoginBuilder object.

Method append()

Append login information for a specific server.

Usage

DSLoginBuilder$append(
  server,
  url,
  table = "",
  resource = "",
  driver = "OpalDriver",
  user = "",
  password = "",
  token = "",
  options = "",
  profile = ""
)

Arguments

Method build()

Build the DSLoginBuilder instance.

Usage

DSLoginBuilder$build()

Returns

The DataSHIELD logindata data.frame

Method clone()

The objects of this class are cloneable with this method.

Usage

DSLoginBuilder$clone(deep = FALSE)

Arguments

DSObject class

Description

Base class for all other DataSHIELD classes (e.g., drivers, connections). This is a virtual Class: No objects may be created from it.

Details

More generally, DataSHIELD defines a very small set of classes and generics that allows users and applications perform meta-analysis with a common interface. The virtual classes are 'DSDriver' that individual drivers extend, 'DSConnection' that represent instances of DataSHIELD-aware data repository connections, and 'DSResult' that represent the result of a DataSHIELD operation. These three classes extend the basic class of 'DSObject', which serves as the root or parent of the class hierarchy.

Implementation notes

An implementation MUST provide methods for the following generics:

• dsGetInfo

It MAY also provide methods for:

• summary Print a concise description of the object. The default method invokes 'dsGetInfo(dsObj)' and prints the name-value pairs one per line. Individual implementations may tailor this appropriately.

See Also

Other DS classes: DSConnection-class, DSDriver-class, DSResult-class

Examples

## Not run: 
drv <- DSOpal::Opal()
con <- dsConnect(drv, 
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")

rs <- dsAssign(con, "Project.TableA")
is(drv, "DSObject")  ## True
is(con, "DSObject")  ## True
is(rs, "DSObject")   ## True

dsDisconnect(con)

## End(Not run)

DSResult class

Description

This virtual class describes the result and state of execution of a DataSHIELD request (aggregation or assignment).

Implementation notes

Individual drivers are free to allow single or multiple active results per connection.

The default show method displays a summary of the query using other DS generics.

See Also

Other DS classes: DSConnection-class, DSDriver-class, DSObject-class

Other DSResult generics: dsFetch(), dsGetInfo(), dsIsCompleted()

Data aggregation

Description

Aggregates the expression result using the specified aggregation method in the current Datashield session.

Usage

datashield.aggregate(
  conns,
  expr,
  async = TRUE,
  success = NULL,
  error = NULL,
  errors.print = getOption("datashield.errors.print", FALSE)
)

Arguments

Value

The result of the aggregation

Examples

## Not run: 
# call aggregate function on server side asynchronously
# i.e. each study connection will process the request in parallel
result <- datashield.aggregate(conns, expr = quote(someFunction(D, 123)))

# call aggregate function on server side synchronously, i.e. each study 
# connection will be called, one after the other, in a blocking way 
result <- datashield.aggregate(conns, expr = quote(someFunction(D, 123)), async = FALSE)

# call aggregate functions that are defined in the provided named list. 
# Connections are filtered by the list names.
result <- datashield.aggregate(conns,
  list(server1=quote(someFunction(D, 123)), server2=quote(someFunction(G, 456))))

# call aggregate function with callback functions
result <- datashield.aggregate(conns, expr = quote(someFunction(D, 123)),
  success = function(server, res) {
    # do something with server's result value
  },
  error = function(server, error) {
    # do something with server's error message
  })

## End(Not run)

Data assignment (table or expression result)

Description

Assign a table or an expression result to a R symbol in the Datashield R session. Note that usage of usage of respectively datashield.assign.table or datashield.assign.expr should be preferred for readability.

Usage

datashield.assign(
  conns,
  symbol,
  value,
  variables = NULL,
  missings = FALSE,
  identifiers = NULL,
  id.name = NULL,
  async = TRUE,
  success = NULL,
  error = NULL
)

Arguments

Examples

## Not run: 
# assign a list of variables from table CNSIM1
datashield.assign(conn, symbol="D", value="CNSIM.CNSIM1",
  variables=list("GENDER","LAB_GLUC"))

# assign all the variables matching 'LAB' from table CNSIM1
datashield.assign(conn, symbol="D", value="CNSIM.CNSIM1",
  variables="name().matches('LAB_')")

# do assignment with callback functions
datashield.assign(conns, "D",
  list(server1="CNSIM.CNSIM1", server2="CNSIM.CNSIM2"),
  success = function(server) {
    # do something with server's success
  },
  error = function(server, error) {
    # do something with server's error message
  })

## End(Not run)

Expression result assignment

Description

Assign the result of the execution of an expression to a R symbol in the Datashield R session.

Usage

datashield.assign.expr(
  conns,
  symbol,
  expr,
  async = TRUE,
  success = NULL,
  error = NULL,
  errors.print = getOption("datashield.errors.print", FALSE)
)

Arguments

Examples

## Not run: 
# assign an expression to G asynchronously
datashield.assign.expr(conns, symbol = "G", expr = quote(as.numeric(D$GENDER)))

# assign an expression to G synchronously
datashield.assign.expr(conns, symbol = "G", expr = quote(as.numeric(D$GENDER)), async = FALSE)

# assign the expressions that are defined in the provided named list.
# Connections are filtered by the list names.
datashield.assign.expr(conns, "G",
  list(server1=quote(as.numeric(D$GENDER)), server2=quote(as.numeric(D$SEX))))

# do assignment with callback functions
datashield.assign.expr(conns, symbol = "G", expr = quote(as.numeric(D$GENDER)),
  success = function(server) {
    # do something with server's success
  },
  error = function(server, error) {
    # do something with server's error message
  })

## End(Not run)

Resource assignment

Description

Assign a resource object of class 'ResourceClient' to a R symbol in the Datashield R session.

Usage

datashield.assign.resource(
  conns,
  symbol,
  resource,
  async = TRUE,
  success = NULL,
  error = NULL,
  errors.print = getOption("datashield.errors.print", FALSE)
)

Arguments

Examples

## Not run: 
# assign a resource asynchronously
datashield.assign.resource(conn, symbol="rsrc", resource="RSRC.CNSIM1")

# assign a resource synchronously
datashield.assign.resource(conn, symbol="rsrc", resource="RSRC.CNSIM1", async = FALSE)

# assign the tables that are defined in the logindata ('server' and 'resource' columns are
# expected) data frame that is used in datashield.login() function. Connections names
# and server names must match.
datashield.assign.resource(conns, "rsrc", logindata)

# assign the resources that are defined in the provided named list.
# Connections are filtered by the list names.
datashield.assign.resource(conns, "rsrc",
  list(server1="RSRC.CNSIM1", server2="RSRC.CNSIM2"))

# do assignment with callback functions
datashield.assign.resource(conn, symbol="rsrc",
  resource = list(server1="RSRC.CNSIM1", server2="RSRC.CNSIM2"),
  success = function(server) {
    # do something with server's success
  },
  error = function(server, error) {
    # do something with server's error message
  })

## End(Not run)

Table assignment

Description

Assign a table to a R symbol in the Datashield R session.

Usage

datashield.assign.table(
  conns,
  symbol,
  table,
  variables = NULL,
  missings = FALSE,
  identifiers = NULL,
  id.name = NULL,
  async = TRUE,
  success = NULL,
  error = NULL,
  errors.print = getOption("datashield.errors.print", FALSE)
)

Arguments

Examples

## Not run: 
# assign a list of variables from table CNSIM1
datashield.assign.table(conn, symbol="D", table="CNSIM.CNSIM1",
  variables=list("GENDER","LAB_GLUC"))

# assign all the variables matching 'LAB' from table CNSIM1
datashield.assign.table(conn, symbol="D", table="CNSIM.CNSIM1",
  variables="name().matches('LAB_')")

# assign the tables that are defined in the logindata ('server' and 'table' columns are
# expected) data frame that is used in datashield.login() function. Connections
# are filtered by the list names.
datashield.assign.table(conns, "D", logindata)

# assign the tables that are defined in the provided named list.
# Connections are filtered by the list names.
datashield.assign.table(conns, "D",
  list(server1="CNSIM.CNSIM1", server2="CNSIM.CNSIM2"))

# do assignment with callback functions
datashield.assign.table(conns, "D",
  list(server1="CNSIM.CNSIM1", server2="CNSIM.CNSIM2"),
  success = function(server) {
    # do something with server's success
  },
  error = function(server, error) {
    # do something with server's error message
  })

## End(Not run)

List the DSConnection objects in the analytic environment

Description

This function identifies and prints all DSConnection-class objects in the analytic environment. If there are no DSConnection servers in the analytic environment datashield.connections reminds the user that they have to login to a valid set of DataSHIELD aware servers. If there is only one set of DSConnections, it copies that one set and names the copy 'default.connections'. This default set will then be used by default by all subsequent calls to client-side functions. If there is more than one set of DSConnections in the analytic environment, datashield.connections tells the user that they can either explicitly specify the DSConnections to be used by each client-side function by providing an explicit "datasources=" argument for each call, or can alternatively use the datashield.connections_default function to specify a default set of DSConnections to be used by all client-side calls unless over-ruled by the 'datasources=' argument.

Usage

datashield.connections(env = getOption("datashield.env", globalenv()))

Arguments

Value

Returns a list of DSConnection-class objects and advises the user how best to respond depending whether there are zero, one or multiple connections detected.

See Also

Other Connections management: datashield.connections_default(), datashield.connections_find()

Set or get the default list of DSConnection objects in the analytic environment

Description

By default if there is only one set of DSConnection-class objects that is available for analysis, all DataSHIELD client-side functions will use that full set of DSConnections unless the 'datasources=' argument has been set and specifies that a particular subset of those DSConnections should be used instead. The correct identification of the full single set of opals is based on the datashield.connections_find function. To illustrate, if the single set of Opals is called 'study.opals' and consists of six servers numbered studies[1] to studies[6] then all client-side functions will use data from all six of these 'studies' unless, say, datasources=studies[c(2,5)] is declared and only data from the second and fifth studies will then be used. On the other hand, if there is more than one set of DSConnections in the analytic environment client-side functions will be unable to determine which set to use. The function datashield.connections_find has therefore been written so that if one of the DSConnection sets is called 'default.connections' then that set - i.e. 'default.connections' - will be selected by default by all DataSHIELD client-side functions. If there is more than one set of DSConnections in the analytic environment and NONE of these is called 'default.connections', the function datashield.connections_find will fail. Therefore datashield.connections_default copies the provided set of DSConnections as 'default.connections'. This set will then be selected by default by all client-side functions, unless it is deleted and an alternative set of DSConnections is copied and named 'default.connections'. Regardless how many sets of DSConnections exist and regardless whether any of them may be called 'default.connections', the 'datasources=' argument overrides the defaults and allows the user to base his/her analysis on any set of DSConnections and any subset of those DSConnections.

Usage

datashield.connections_default(
  name = NULL,
  env = getOption("datashield.env", globalenv())
)

Arguments

Value

The 'default.connections' value from the analytic environment or NULL if the 'default.connections' symbol is not defined.

See Also

Other Connections management: datashield.connections(), datashield.connections_find()

Search for DSConnection objects in the analytic environment

Description

If the user does not set the argument 'datasources' in the client side analysis functions, this function is called to search for DSConnection-class objects in the environment (default environment is the Global one). If one set of DSConnection objects is found, it is assigned to 'default.connections' symbol in the analytic environment. If more than one set of DSConnection objects is found and none of them is called 'default.connections', the function stops and suggests user to use the datashield.connections_default function.

Usage

datashield.connections_find(env = getOption("datashield.env", globalenv()))

Arguments

Value

Returns a list of DSConnection-class objects or stops the process

See Also

Other Connections management: datashield.connections(), datashield.connections_default()

datashield.errorMessages

Description

Retrieve and display DataSHIELD errors in CLI format

Usage

datashield.errorMessages()

Details

This function retrieves the last errors occurred in a DataSHIELD session and displays them in a formatted manner using bullet points.

Value

NULL if no errors are found, otherwise prints the errors.

datashield.errors

Description

Retrieve and display the last errors occurred in a DataSHIELD session.

Usage

datashield.errors()

Value

NULL if no errors are found, otherwise a list containing the errors for each server.

Logs in a DataSHIELD R sessions and optionaly assigns variables to R

Description

This function allows for clients to login to data repository servers and (optionaly) assign all the data or specific variables from the data repositories tables to R data frames. The assigned dataframes (one for each data repository) are named 'D' (by default). Different login strategies are supported: using a certificate/private key pair (2-way SSL encryption mechanism), using user credentials (user name and password) or using a personal access token (could be combined with a user name, depending on the data repository system).

Usage

datashield.login(
  logins = NULL,
  assign = FALSE,
  variables = NULL,
  missings = FALSE,
  symbol = "D",
  id.name = NULL,
  opts = getOption("datashield.opts", list()),
  restore = NULL,
  failSafe = FALSE
)

Arguments

Value

object(s) of class DSConnection

Examples

## Not run: 

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

# build your data.frame
builder <- newDSLoginBuilder()
builder$append(server="server1", url="https://opal-demo.obiba.org",
               table="datashield.CNSIM1", resource="datashield.CNSIM1r",
               user="dsuser", password="password",
               options="list(ssl_verifyhost=0,ssl_verifypeer=0)")
builder$append(server="server2", url="dslite.server",
               table="CNSIM2", resource="CNSIM2r", driver="DSLiteDriver")
builder$append(server="server3", url="https://molgenis.example.org",
               table="CNSIM3", resource="CNSIM3r", token="123456789", driver="MolgenisDriver")
builder$append(server="server4", url="dslite.server",
               table="CNSIM4", resource="CNSIM4r", driver="DSLiteDriver")
logindata <- builder$build()

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

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

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

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

# Example 4: ignore with a warning message servers for which connection cannot be established
connections <- datashield.login(logins=logindata, failSafe=TRUE)

# note that the asignment information can also be provided afterwards
builder <- newDSLoginBuilder()
builder$append(server="server1", url="https://opal-demo.obiba.org",
               user="dsuser", password="password")
builder$append(server="server2", url="https://opal-test.obiba.org",
               token="123456789")
logindata <- builder$build()
connections <- datashield.login(logins=logindata)
datashield.assign.table(connections, symbol = "D",
                        table = list(server1 = "CNSIM.CNSIM1",
                                     server2 = "CNSIM.CNSIM2"))
datashield.assign.resource(connections, symbol = "rsrc",
                           resource = list(server1 = "res.CNSIM1",
                                        server2 = "res.CNSIM2"))

## End(Not run)

Logout from DataSHIELD R sessions

Description

Clear the Datashield R sessions and logout from DataSHIELD data repositories.

Usage

datashield.logout(conns, save = NULL)

Arguments

Status of the DataSHIELD methods

Description

Get the status of the DataSHIELD methods in the different data repositories to check if any method is missing.

Usage

datashield.method_status(conns, type = "aggregate")

Arguments

Value

Methods availability on each server.

List of DataSHIELD methods

Description

Get the list of all the DataSHIELD methods from the different data repositories.

Usage

datashield.methods(conns, type = "aggregate")

Arguments

Value

Methods details from all the servers.

Check server-side package minimum version

Description

Check for each of the server, accessible through provided DSConnection-class objects, whether the installed

Usage

datashield.pkg_check(
  conns,
  name,
  version,
  env = getOption("datashield.env", globalenv())
)

Arguments

Status of the DataSHIELD packages

Description

Get the status of the DataSHIELD packages in the different data repositories to check if any package is missing.

Usage

datashield.pkg_status(conns)

Arguments

Value

Packages status for each server.

List of DataSHIELD profiles

Description

Get the list of all the DataSHIELD profiles from the different data repositories: available ones and currently applied to each connection.

Usage

datashield.profiles(conns)

Arguments

Value

Profiles details from all the servers.

Status of some resources

Description

Get whether some identified resources are accessible in each of the data repositories.

Usage

datashield.resource_status(conns, resource)

Arguments

Value

Resource status for each server.

List of the resources

Description

Get the list of all the resources from the different data repositories.

Usage

datashield.resources(conns)

Arguments

Value

Resource unique names from all the servers.

Examples

## Not run: 
  datashield.resources(conns)

## End(Not run)

Remove a R symbol

Description

Remove a symbol from the current Datashield session.

Usage

datashield.rm(conns, symbol)

Arguments

List R symbols

Description

Get the R symbols available after the datashield.assign calls in the Datashield R session.

Usage

datashield.symbols(conns)

Arguments

Status of some tables

Description

Get whether some identified tables are accessible in each of the data repositories.

Usage

datashield.table_status(conns, table)

Arguments

Value

Table status for each server.

List of the tables

Description

Get the list of all the tables from the different data repositories.

Usage

datashield.tables(conns)

Arguments

Value

Table unique names from all the servers.

Examples

## Not run: 
  datashield.tables(conns)

## End(Not run)

Restore saved workspace to the current DataSHIELD R session

Description

Restore the state of a previously saved DataSHIELD R session (the workspace saved with datashield.workspace_save) with the provided name from each data repository. Note that when restoring a workspace, any existing symbol or file with same name will be overridden.

Usage

datashield.workspace_restore(conns, ws)

Arguments

Remove a DataSHIELD workspace

Description

Remove in each data repository the workspace with the provided name.

Usage

datashield.workspace_rm(conns, ws)

Arguments

Save DataSHIELD R session to a workspace

Description

Save the current state of the DataSHIELD R session in a workspace with the provided name in each data repository. The workspace can be restored on the next datashield.login or with datashield.workspace_restore.

Usage

datashield.workspace_save(conns, ws)

Arguments

List saved DataSHIELD R workspaces

Description

Get the list of R workspaces that were saved during a Datashield R session.

Usage

datashield.workspaces(conns)

Arguments

Aggregate data

Description

Aggregate some data from the DataSHIELD R session using a valid R expression. The aggregation expression must satisfy the data repository's DataSHIELD configuration.

Usage

dsAggregate(conn, expr, async = TRUE)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignTable(con, "D", "test.CNSIM")
dsAggregate(con, as.symbol("meanDS(D$WEIGHT)"))
dsDisconnect(con)

## End(Not run)

Assign an expression result

Description

Assign the result of the evaluation of an expression to a symbol the DataSHIELD R session The assignment expression must satisfy the data repository's DataSHIELD configuration.

Usage

dsAssignExpr(conn, symbol, expr, async = TRUE)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignExpr(con, "C", as.symbol("c(1, 2, 3)"))
dsDisconnect(con)

## End(Not run)

Assign a resource object

Description

Assign a resource object of class 'ResourceClient' from the data repository to a symbol in the DataSHIELD R session. The resource reference to be assigned must exist (i.e. proper permissions apply) for the DataSHIELD user.

Usage

dsAssignResource(conn, symbol, resource, async = TRUE)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignResource(con, "D", "test.CNSIM")
dsDisconnect(con)

## End(Not run)

Assign a data table

Description

Assign a data table from the data repository to a symbol in the DataSHIELD R session. The table to be assigned must exist (i.e. proper permissions apply) for the DataSHIELD user.

Usage

dsAssignTable(
  conn,
  symbol,
  table,
  variables = NULL,
  missings = FALSE,
  identifiers = NULL,
  id.name = NULL,
  async = TRUE
)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignTable(con, "D", "test.CNSIM")
dsDisconnect(con)

## End(Not run)

Create a connection to a DataSHIELD-aware data repository

Description

Connect to a data repository going through the appropriate authentication procedure. Some implementations may allow you to have multiple connections open, so you may invoke this function repeatedly assigning its output to different objects. The authentication mechanism is left unspecified, so check the documentation of individual drivers for details.

Usage

dsConnect(drv, name, restore = NULL, ...)

Arguments

See Also

dsDisconnect to disconnect from a data repository.

Other DSDriver generics: DSDriver-class, dsGetInfo()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
con
dsListTables(con)
dsDisconnect(con)

## End(Not run)

Disconnect (close) a connection

Description

This closes the connection, discards all pending work, and frees resources (e.g., memory, sockets).

Usage

dsDisconnect(conn, save = NULL)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsDisconnect(con)

## End(Not run)

Get the raw result

Description

Wait for the result to be available and fetch the result from a previous assignment or aggregation operation that may have been run asynchronously, in which case it is a one-shot call. When the assignment or aggregation operation was not asynchronous, the result is wrapped in the object and can be fetched multiple times.

Usage

dsFetch(res)

Arguments

See Also

Other DSResult generics: DSResult-class, dsGetInfo(), dsIsCompleted()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignExpr(con, "C", as.symbol("c(1, 2, 3)"))
res <- dsAggregate(con, as.symbol("length(C)"))
length <- dsFetch(res)
dsDisconnect(con)

## End(Not run)

Get DataSHIELD-aware data repository metadata

Description

Get DataSHIELD-aware data repository metadata

Usage

dsGetInfo(dsObj, ...)

Arguments

Value

a named list

Implementation notes

For 'DSDriver' subclasses, this should include the version of the package ('driver.version') and the version of the underlying client library ('client.version').

For 'DSConnection' objects this should report the version of the data repository application ('repo.version') and its name ('repo.name'), the database name ('dbname'), username, ('username'), host ('host'), port ('port'), etc. It MAY also include any other arguments related to the connection (e.g., thread id, socket or TCP connection type). It MUST NOT include the password.

For 'DSResult' objects, this should include the R expression being executed (an expression object tailored by the implementation of DSI) and if the query is complete (a result object tailored by the implementation of DSI).

See Also

Other DSDriver generics: DSDriver-class, dsConnect()

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Other DSResult generics: DSResult-class, dsFetch(), dsIsCompleted()

Check remote resource exists

Description

Check if a remote resource reference exists in the data repository. Returns a logical indicating the existence of a remote resource accessible through this connection.

Usage

dsHasResource(conn, resource)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsHasResource(con, "test.CNSIM")
dsDisconnect(con)

## End(Not run)

Check remote table exists

Description

Check if a remote table exists in the data repository. Returns a logical indicating the existence of a remote table accessible through this connection.

Usage

dsHasTable(conn, table)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsHasTable(con, "test.CNSIM")
dsDisconnect(con)

## End(Not run)

Asynchronous result support

Description

When a DSResult-class object is returned on aggregation or assignment operation, the raw result can be accessed asynchronously, allowing parallelization of DataSHIELD calls over multpile servers. The returned named list of logicals will specify if asynchronicity is supported for: aggregation operation ('aggregate'), table assignment operation ('assignTable'), resource assignment operation ('assignResource') and expression assignment operation ('assignExpr').

Usage

dsIsAsync(conn)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsIsAsync(con)
dsDisconnect(con)

## End(Not run)

Get whether the operation is completed

Description

Get whether the result from a previous assignment or aggregation operation was completed, either with a successful status or a failed one. This call must not wait for the completion, immediate response is expected. Once the result is identified as being completed, the raw result the operation can be get directly.

Usage

dsIsCompleted(res)

Arguments

Value

A logical

See Also

Other DSResult generics: DSResult-class, dsFetch(), dsGetInfo()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignExpr(con, "C", as.symbol("c(1, 2, 3)"))
res <- dsAggregate(con, as.symbol("length(C)"), async = TRUE)
completed <- dsIsCompleted(res)
while (!completed) {
  Sys.sleep(1)
  completed <- dsIsCompleted(res)
}
length <- dsFetch(res)
dsDisconnect(con)

## End(Not run)

Keep a connection alive

Description

As the DataSHIELD sessions are working in parallel, this function helps at keeping idle connections alive while others are working. Any communication failure must be silently processed.

Usage

dsKeepAlive(conn)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsKeepAlive(con)
dsDisconnect(con)

## End(Not run)

Get the DataSHIELD methods

Description

Get the list of DataSHIELD methods that have been configured on the remote data repository.

Usage

dsListMethods(conn, type = "aggregate")

Arguments

Value

A data.frame with columns: name, type ('aggregate' or 'assign'), class ('function' or 'script'), value, package, version.

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListMethods(con)
dsDisconnect(con)

## End(Not run)

Get the DataSHIELD packages

Description

Get the list of DataSHIELD packages with their version, that have been configured on the remote data repository.

Usage

dsListPackages(conn)

Arguments

Value

A data.frame with columns: name, version.

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListPackages(con)
dsDisconnect(con)

## End(Not run)

Get the DataSHIELD profiles

Description

Get the list of DataSHIELD profiles that have been configured on the remote data repository.

Usage

dsListProfiles(conn)

Arguments

Value

A list containing the "available" character vector of profile names and the "current" profile (in case a default one was assigned).

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListProfiles(con)
dsDisconnect(con)

## End(Not run)

List remote resources

Description

List remote resources from the data repository. Returns the unquoted names of remote resources accessible through this connection.

Usage

dsListResources(conn)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListResources(con)
dsDisconnect(con)

## End(Not run)

List symbols

Description

After assignments have been performed, some symbols live in the DataSHIELD R session on the server side.

Usage

dsListSymbols(conn)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignTable(con, "D", "test.CNSIM")
dsListSymbols(con)
dsDisconnect(con)

## End(Not run)

List remote tables

Description

List remote tables from the data repository. Returns the unquoted names of remote tables accessible through this connection.

Usage

dsListTables(conn)

Arguments

Value

A character vector of table names.

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListTables(con)
dsDisconnect(con)

## End(Not run)

Get the DataSHIELD workspaces

Description

Get the list of DataSHIELD workspaces, that have been saved on the remote data repository.

Usage

dsListWorkspaces(conn)

Arguments

Value

A data.frame with columns: name, lastAccessDate, size.

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListWorkspaces(con)
dsDisconnect(con)

## End(Not run)

Restore a saved DataSHIELD R session (a workspace) into the current DataSHIELD R session

Description

Restore a saved DataSHIELD R session from the remote data repository. When restoring a workspace, any existing symbol or file with same name will be overridden.

Usage

dsRestoreWorkspace(conn, name)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRmSymbol(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsListWorkspaces(con)
dsRestoreWorkspace(con, "foo")
dsDisconnect(con)

## End(Not run)

Remove a symbol

Description

After removal, the data identified by the symbol will not be accessible in the DataSHIELD R session on the server side.

Usage

dsRmSymbol(conn, symbol)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmWorkspace(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsAssignTable(con, "D", "test.CNSIM")
dsRmSymbol(con, "D")
dsDisconnect(con)

## End(Not run)

Remove a DataSHIELD workspace

Description

Remove a DataSHIELD workspace from the remote data repository. Ignore if no such workspace exists.

Usage

dsRmWorkspace(conn, name)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsSaveWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsSaveWorkspace(con, "foo")
dsListWorkspaces(con)
dsRmWorkspace(con, "foo")
dsListWorkspaces(con)
dsDisconnect(con)

## End(Not run)

Save the DataSHIELD R session in a workspace

Description

Save the DataSHIELD R session in a workspace on the remote data repository.

Usage

dsSaveWorkspace(conn, name)

Arguments

See Also

Other DSConnection generics: DSConnection-class, dsAggregate(), dsAssignExpr(), dsAssignResource(), dsAssignTable(), dsDisconnect(), dsGetInfo(), dsHasResource(), dsHasTable(), dsIsAsync(), dsKeepAlive(), dsListMethods(), dsListPackages(), dsListProfiles(), dsListResources(), dsListSymbols(), dsListTables(), dsListWorkspaces(), dsRestoreWorkspace(), dsRmSymbol(), dsRmWorkspace()

Examples

## Not run: 
con <- dsConnect(DSOpal::Opal(), "server1",
  username = "dsuser", password = "password", url = "https://opal-demo.obiba.org")
dsSaveWorkspace(con, "foo")
dsListWorkspaces(con)
dsDisconnect(con)

## End(Not run)

Create a new DataSHIELD login details builder

Description

Shortcut function to create a new DSLoginBuilder instance. The data frame that is being built can be used to perform datashield.login.

Usage

newDSLoginBuilder(logins = NULL, .silent = FALSE)

Arguments

Examples

{
  builder <- newDSLoginBuilder()
  builder$append(server="server1", url="https://opal-demo.obiba.org", table="datashield.CNSIM1",
    user="administrator", password="password")
  builder$append(server="server2", url="dslite.server", table="CNSIM2")
  builder$append(server="server3", url="http://molgenis.example.org", table="CNSIM3",
   token="123456789")
  builder$append(server="server4", url="dslite.server", table="CNSIM4")
  logindata <- builder$build()
}