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DataSHIELD4J

Build Status

DataSHIELD core classes for implementing the DataSHIELD platform in a data repository.

Reference implementation is Opal.

Learn more about DataSHIELD.

See also DataSHIELD Interface (DSI) for identifying the web services needed to implement the DataSHIELD platform.

DataSHIELD Core

This package defines the core classes of the DataSHIELD configuration, mainly:

  • methods (the allowed functions, either package specific or scripted)
  • method types (either assignment, or aggregation)
  • options (the options set at session start)

These classes are not bound to a specific implementation language, despite only R is used at the moment.

DataSHIELD R

Each DataSHIELD request must be parsed to identify and resolve the function calls and the allowed language elements. This package provides an R parser, based on a subset of the R language. This parser is to be used to secure the access to the data and to apply the DataSHIELD configuration before forwarding the request to the R server session.

The R parser comes with several versions (which R parser version to be used must be specified):

Parser Version Description
v1 The original R parser (since ds4j 1.0.0), used until Opal 4.1.
v2 The most recent R parser (since ds4j 2.0.0), more restrictive regarding the R subset syntax (square brackets are not allowed). Default R parser since Opal 4.2.

What is currently NOT included (because it is too data repository specific):

  • R server session management
  • data assignment from database to the R session
  • DataSHIELD related web services

Usage

Maven

Available in OBiBa's Maven repository: https://obiba.jfrog.io/artifactory/libs-release-local/

  <dependency>
    <groupId>org.obiba.datashield</groupId>
    <artifactId>ds4j-core</artifactId>
    <version>${ds4j.version}</version>
  </dependency>
  <dependency>
    <groupId>org.obiba.datashield</groupId>
    <artifactId>ds4j-r</artifactId>
    <version>${ds4j.version}</version>
  </dependency>

Java

You can use the helper classes to define your DSConfiguration and store it in a file or a database.

The entry point class is the RScriptGeneratorFactory that makes a RScriptGenerator object. This object will validate the submitted R code and will rewrite the function calls according to the DataSHIELD configuration (aggregate and assign function name mapping).

When receiving an R script request, and using the DSConfiguration, follow this example code:

// * rParserVersion: one of "v1" (legacy) or "v2" (recommended)
// * dsConfig: a DSConfiguration object
// * dsEnv: a DSEnvironment object that defines the allowed function calls
//   and the mapping of these functions to internal ones
// * script: the submitted R script
DSEnvironment dsEnv = dsConfig.getEnvironment(DSMethodType.ASSIGN); // or DSMethodType.AGGREGATE
RScriptGenerator rScriptGenerator = RScriptGeneratorFactory.make(rParserVersion, dsEnv, script);

// script was validated, rewrite it with internal functions
String scriptToExec = rScriptGenerator.toScript();