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Table of Contents
Info

The logic

The environment that you have set up places a number of virtual machines on your computer.

The virtual machines play the role of the servers of different cohorts; they have Opal and R installed and each contain some simulated test data.

Your machine, the host, plays the role of the client; that is, the computer that is conducting the analysis.

The DataSHIELD code is also split into client and server packages. The DataSHIELD client packages are installed in R on your machine (so that it can act as a client), and the DataSHIELD server packages are installed in R on each of the virtual machines.

  • Modifying the client packages therefore involves downloading the DataSHIELD source code to your machine, making your changes, and the installing the changed client packages on your machine.
  • Modifying the server packages also involves downloading the DataSHIELD source code to your machine and making your changes. However the changed server packages must be installed on each of your virtual machines.

Download the DataSHIELD code

DataSHIELD code is stored publicly on github, a copy can be downloaded using git.

Install git

Code Block
sudo apt-get install git
Info

Now read the Using Git page

Clone the DataSHIELD repositories

DataSHIELD code is broken down into a number of client and server packages:

Client side packages
Server side packages
  • dsbase
  • dsmodelling
    If you want to download everything, then simply 'clone' all of these repositories. This creates a local copy of the code on your machine.
Code Block
mkdir dsdev
cd dsdev
git clone https://github.com/datashield/dsbaseclient.git
git clone https://github.com/datashield/dsmodellingclient.git
git clone https://github.com/datashield/dsbase.git
git clone https://github.com/datashield/dsmodelling.git

Installing the client side packages

When we installed the DataSHIELD client packages in order to 'play' with DataSHIELD, we did this by running R and then using the install.packages command, specifically we told R to get the DataSHIELD client packages from the OBiBa website.

...

You are now able to use your modified client code to run analyses on the virtual machines.

Installing Server Side DataSHIELD packages on the virtual servers

Official Packages

The official DataSHIELD packages can be installed in their current state through the Opal web interface:

...

If you select to install them all, this will install dsbase and dsmodelling.

Public In-development Packages

Any packages (each package is its own git repository) in the DataSHIELD github project can be installed on the virtual servers from within an R instance running on the host (that is to say, from the computer acting as the client or 'analysis computer').

...

This would install the package on all the virtual machines.

Private Packages

Installing you own local modified versions of the DataSHIELD server code is a little more involved.

Installing modified versions of the server code

Our aim is to take the DataSHIELD server source code that we have been modifying on our own computer and to install it on each of the virtual machines. As such, this means you will need to repeat this process on each of the virtual machines you are using.

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