Lightweight DataSHIELD server-side component

DSLiteServer mimics a DataSHIELD server by holding datasets and exposing DataSHIELD-like functions: aggregate and assign. A DataSHIELD session is a R environment where the assignment and the operations happen.

See also

Other server-side items: newDSLiteServer()

Methods

Public methods

• DSLiteServer$new()

• DSLiteServer$config()

• DSLiteServer$profile()

• DSLiteServer$strict()

• DSLiteServer$home()

• DSLiteServer$workspaces()

• DSLiteServer$workspace_save()

• DSLiteServer$workspace_restore()

• DSLiteServer$workspace_rm()

• DSLiteServer$aggregateMethods()

• DSLiteServer$aggregateMethod()

• DSLiteServer$assignMethods()

• DSLiteServer$assignMethod()

• DSLiteServer$options()

• DSLiteServer$option()

• DSLiteServer$newSession()

• DSLiteServer$hasSession()

• DSLiteServer$getSession()

• DSLiteServer$getSessionIds()

• DSLiteServer$getSessionData()

• DSLiteServer$closeSession()

• DSLiteServer$tableNames()

• DSLiteServer$hasTable()

• DSLiteServer$resourceNames()

• DSLiteServer$hasResource()

• DSLiteServer$symbols()

• DSLiteServer$symbol_rm()

• DSLiteServer$assignTable()

• DSLiteServer$assignResource()

• DSLiteServer$assignExpr()

• DSLiteServer$aggregate()

• DSLiteServer$clone()

---

Method new()

Create new DSLiteServer instance. See defaultDSConfiguration function for including or excluding packages when discovering the DataSHIELD configuration from the DataSHIELD server-side packages (meta-data from the DESCRIPTION files).

Usage

DSLiteServer$new(
  tables = list(),
  resources = list(),
  config = DSLite::defaultDSConfiguration(),
  strict = TRUE,
  home = file.path(tempdir(), ".dslite"),
  profile = "default"
)

Arguments

tables

A named list of data.frames representing the harmonized tables.

resources

A named list of resourcer::Resource objects representing accessible data or computation resources.

config

The DataSHIELD configuration. Default is to discover it from the DataSHIELD server-side R packages.

strict

Logical to specify whether the DataSHIELD configuration must be strictly applied. Default is TRUE.

home

Folder location where are located the session work directory and where to read and dump workspace images.

profile

The DataSHIELD profile name, used to give a name to the DS configuration. Default is "default". Default is in a hidden folder of the R session's temporary directory.

Returns

A DSLiteServer object

---

Method config()

Get or set the DataSHIELD configuration.

Usage

DSLiteServer$config(value)

Arguments

value

The DataSHIELD configuration: aggregate/assign methods in data frames and a named list of options.

Returns

The DataSHIELD configuration, if no parameter is provided.

---

Method profile()

Get or set the DataSHIELD profile name.

Usage

DSLiteServer$profile(value)

Arguments

value

The DataSHIELD profile name.

Returns

The DataSHIELD profile, if no parameter is provided.

---

Method strict()

Get or set the level of strictness (stop when function call is not configured)

Usage

DSLiteServer$strict(value)

Arguments

value

The strict logical field.

Returns

The strict field if no parameter is provided.

---

Method home()

Get or set the home folder location where are located the session work directories and where to read and dump workspace images.

Usage

DSLiteServer$home(value)

Arguments

value

The path to the home folder.

Returns

The home folder path if no parameter is provided.

---

Method workspaces()

List the saved workspaces in the home folder.

Usage

DSLiteServer$workspaces(prefix = NULL)

Arguments

prefix

Filter workspaces starting with provided prefix (optional).

---

Method workspace_save()

Save the session's workspace image identified by the sid identifier with the provided name in the home folder.

Usage

DSLiteServer$workspace_save(sid, name)

Arguments

sid,

Session ID

name

The name to be given to the workspace's image.

---

Method workspace_restore()

Restore a saved session's workspace image into the session identified by the sid identifier with the provided name in the home folder.

Usage

DSLiteServer$workspace_restore(sid, name)

Arguments

sid,

Session ID

name

The name of the workspace's image to restore.

---

Method workspace_rm()

Remove the workspace image with the provided name from the home folder.

Usage

DSLiteServer$workspace_rm(name)

Arguments

name

The name of the workspace.

---

Method aggregateMethods()

Get or set the aggregate methods.

Usage

DSLiteServer$aggregateMethods(value)

Arguments

value

A data.frame with columns: name (the client function call), value (the translated server call), package (relevant when extracted from a DataSHIELD server-side package), version (relevant when extracted from a DataSHIELD server-side package), type ("aggregate"), class ("function" for package functions or "script" for custom scripts).

Returns

The aggregate methods when no parameter is provided.

---

Method aggregateMethod()

Get or set an aggregate method.

Usage

DSLiteServer$aggregateMethod(name, value)

Arguments

name

The client function call.

value

The translated server call: either a package function reference or function expression. Remove the method when NULL.

Returns

The aggregate method when no value parameter is provided.

---

Method assignMethods()

Get or set the assign methods.

Usage

DSLiteServer$assignMethods(value)

Arguments

value

A data.frame with columns: name (the client function call), value (the translated server call), package (relevant when extracted from a DataSHIELD server-side package), version (relevant when extracted from a DataSHIELD server-side package), type ("assign"), class ("function" for package functions or "script" for custom scripts).

Returns

The assign methods when no parameter is provided.

---

Method assignMethod()

Get or set an assign method.

Usage

DSLiteServer$assignMethod(name, value)

Arguments

name

The client function call

value

The translated server call: either a package function reference or function expression. Remove the method when NULL.

Returns

The assign method when no value parameter is provided.

---

Method options()

Get or set the DataSHIELD R options that are applied when a new DataSHIELD session is started.

Usage

DSLiteServer$options(value)

Arguments

value

A named list of options.

Returns

The R options when no parameter is provided.

---

Method option()

Get or set a R option.

Usage

DSLiteServer$option(key, value)

Arguments

key

The R option's name.

value

The R option's value. Remove the option when NULL.

Returns

The R option's value when only key parameter is provided.

---

Method newSession()

Create a new DataSHIELD session (contained execution environment), apply options that are defined in the DataSHIELD configuration and restore workspace image if restore workspace name argument is provided.

Usage

DSLiteServer$newSession(restore = NULL, profile = NULL)

Arguments

restore

The workspace image to be restored (optional).

profile

The requested profile name (optional). If provided, new session creation will fail in case it does not match the server's profile name.

---

Method hasSession()

Check a DataSHIELD session is alive.

Usage

DSLiteServer$hasSession(sid)

Arguments

sid

The session ID.

---

Method getSession()

Get the DataSHIELD session's environment.

Usage

DSLiteServer$getSession(sid)

Arguments

sid

The session ID.

---

Method getSessionIds()

Get the DataSHIELD session IDs.

Usage

DSLiteServer$getSessionIds()

---

Method getSessionData()

Get the symbol value from the DataSHIELD session's environment.

Usage

DSLiteServer$getSessionData(sid, symbol)

Arguments

sid

The session ID.

symbol

The symbol name.

---

Method closeSession()

Destroy DataSHIELD session and save workspace image if save workspace name argument is provided.

Usage

DSLiteServer$closeSession(sid, save = NULL)

Arguments

sid

The session ID.

save

The name of the workspace image to be saved (optional).

---

Method tableNames()

List the names of the tables that can be assigned.

Usage

DSLiteServer$tableNames()

---

Method hasTable()

Check a table exists.

Usage

DSLiteServer$hasTable(name)

Arguments

name

The table name to be looked for.

---

Method resourceNames()

List the names of the resources (resourcer::Resource objects) that can be assigned.

Usage

DSLiteServer$resourceNames()

---

Method hasResource()

Check a resource (resourcer::Resource object) exists.

Usage

DSLiteServer$hasResource(name)

Arguments

name

The resource name to be looked for.

---

Method symbols()

List the symbols living in a DataSHIELD session.

Usage

DSLiteServer$symbols(sid)

Arguments

sid

The session ID.

---

Method symbol_rm()

Remove a symbol from a DataSHIELD session.

Usage

DSLiteServer$symbol_rm(sid, name)

Arguments

sid

The session ID.

name

The symbol name.

---

Method assignTable()

Assign a table to a symbol in a DataSHIELD session. Filter table columns with the variables names provided.

Usage

DSLiteServer$assignTable(sid, symbol, name, variables = NULL, id.name = NULL)

Arguments

sid

The session ID.

symbol

The symbol to be assigned.

name

The table's name.

variables

The variable names to be filtered in (optional).

id.name

The column name to be used for the entity's identifier (optional).

---

Method assignResource()

Assign a resource as a resourcer::ResourceClient object to a symbol in a DataSHIELD session.

Usage

DSLiteServer$assignResource(sid, symbol, name)

Arguments

sid

The session ID.

symbol

The symbol name.

name

The name of the resource.

---

Method assignExpr()

Evaluate an assignment expression in a DataSHIELD session.

Usage

DSLiteServer$assignExpr(sid, symbol, expr)

Arguments

sid

The session ID.

symbol

The symbol name.

expr

The R expression to evaluate.

---

Method aggregate()

Evaluate an aggregate expression in a DataSHIELD session.

Usage

DSLiteServer$aggregate(sid, expr)

Arguments

sid

The session ID.

expr

The R expression to evaluate.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DSLiteServer$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.