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DataSHIELD Interface

The DataSHIELD Interface (DSI) defines a set of S4 classes and generic methods that can be implemented for accessing a data repository supporting the DataSHIELD infrastructure: controlled R commands to be executed on the server side are garanteeing that non disclosive information is returned to client side.

Learn more about DataSHIELD.

Class Structure

The DSI classes are:

• DSObject a common base class for all DSI,
• DSDriver drives the creation of a connection object,
• DSConnection allows the interaction with the remote server; DataSHIELD operations such as aggregation and assignment return a result object; DataSHIELD setup status check can be performed (dataset access, configuration comparision),
• DSResult wraps access to the result, which can be fetched either synchronously or asynchronously depending on the capabilities of the data repository server.

All classes are virtual: they cannot be instantiated directly and instead must be subclassed. See DSOpal for a reference implementation of DSI based on the Opal data warehouse. See also DSLite for a server-less implementation of DSI for local datasets.

These S4 classes and generic methods are meant to be used for implementing connection to a DataSHIELD-aware data repository.

Higher Level Functions

In addition to these S4 classes, DSI provides functions to handle a list of remote data repository servers:

• datashield.login and datashield.logout will make use of the DSDriver paradigm to create DSConnections to the data repositories,
• datashield.aggregate and datashield.assign will perform typical DataSHIELD operations on DSConnections, which result will be fetched through DSResult objects,
• datashield.connections, datashield.connections_default and datashield.connections_find are functions for managing the list of DSConnection objects that will be discovered and used by the client-side analytic functions.
• datashield.errors will report the last R errors that may have occurred after a datashield.assign or datashield.aggregate call.
• Other data management functions are provided by the DSConnection objects:
  • datashield.workspaces, datashield.workspace_save, datashield.workspace_restore and datashield.workspace_rm allow to manage R images of the remote DataSHIELD sessions (to speed up data analysis sessions),
  • datashield.symbols and datashield.symbol_rm offer a minimalistic management of the R symbols living in the remote DataSHIELD sessions,
  • datashield.tables, datashield.table_status list the tables and their accessibility across a set of data repositories,
  • datashield.resources, datashield.resource_status list the resources and their accessibility across a set of data repositories,
  • datashield.pkg_status, datashield.method_status and datashield.methods are utility functions to explore the DataSHIELD setup across a set of data repositories.
  • datashield.profiles lists the DataSHIELD profiles that can be selected at login time.

These datashield.* functions are meant to be used by DataSHIELD packages developers and users.

Options

Some options can be set to modify the behavior of the DSI:

• datashield.env is the R environment in which the DSConnection object list is to be looking for. Default value is the Global Environment: globalenv().
• datashield.progress is a logical to enable the visibility of the progress bars. Default value is TRUE.
• datashield.progress.clear is a logical to make the progress bar disappear after it has been completed. Default value is FALSE.
• datashield.errors.stop is a logical to alter error handling behavior: if TRUE an error is raised when at least one server has failed, otherwise a warning message is issued. Default value is TRUE.
• datashield.polling.sleep.0 time in seconds to wait before checking async calls completion, before ~1 second. Default value 50 milliseconds.
• datashield.polling.sleep.1 base time in seconds to wait before checking async calls completion, after ~1 second. Default value is 1 second.
• datashield.polling.sleep.10 time in seconds to wait before checking async calls completion, after ~10 seconds. Default value is x2 the base time (2 seconds).
• datashield.polling.sleep.60 time in seconds to wait before checking async calls completion, after ~1 minute. Default value is x10 the base time (10 seconds).
• datashield.polling.sleep.600 time in seconds to wait before checking async calls completion, after ~10 minutes. Default value is x60 the base time (1 minute).
• datashield.polling.sleep.3600 time in seconds to wait before checking async calls completion, after ~1 hour. Default value is x600 the base time (10 minutes).

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.