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DataSHIELD Interface Python

This DataSHIELD Client Interface is a Python port of the original DataSHIELD Client Interface written in R (DSI). The provided interface 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.

Configuration

The search path for the DataSHIELD configuration file is the following:

  1. User general location: ~/.config/datashield/config.yaml
  2. Current project specific location: ./.datashield/config.yaml

The configurations are merged: any existing entry is replaced by the new one (for instance server names must be unique).

The format of the DataSHIELD configuration file is:

servers:
  - name: server1
    url: https://opal-demo.obiba.org
    user: dsuser
    password: P@ssw0rd
  - name: server2
    url: https://opal.example.org
    token: your-access-token-here
    profile: default
  - name: server3
    url: https://study.example.org/opal
    user: dsuser
    password: P@ssw0rd
    profile: custom
    driver: datashield_opal.OpalDriver

Each server entry in the list must have:

  • name: Unique identifier for the server
  • url: The server URL
  • Authentication: Either user and password, or token (recommended)
  • profile: DataSHIELD profile name (optional, defaults to "default")
  • driver: Connection driver class name (optional, defaults to "datashield_opal.OpalDriver")