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• how to install Opal
• integration of Opal with R and DataSHEILD
• how to administer Opal

DataSHIELD Administration

DataSHIELD administration instructions are also available from the OBiBa wiki.

Installing the DataSHIELD packages in Opal

Installation of the DataSHIELD server packages is done through Opal. Packages can be installed using the Opal web interface, or from R using the opaladmin library.

Using the Opal web interface

1. Go to Administration > DataSHIELD.

2. Select '+ Add Package'.

3. On the pop-up window, select 'Install all'.

4. Once the packages are installed, you will see them listed in a table under 'Packages'.

5. For each package in the table, select 'Publish Methods' in the 'Actions' column.

Using R

You will need a computer with R to act as the client, to send commands to your Opal server(s). Alternatively you can use the server itself as the client and connect over localhost.

The instructions below are based on using the server as a client. The only part you need to change to do this from a separate client computer, is the url in the opal.login function. By giving the opal.login function a list of urls, you can administer more than one opal server at once.

1. Install the opaladmin R package

While logged in to the server (as any user):

$ R
> install.packages('opaladmin', repos='http://cran.obiba.org', dependencies=TRUE)

2. Log in to Opal

Use the dsadmin.* set of functions to install the DataSHIELD server packages and publish their methods:

> library(opaladmin)
> o<-opal.login('administrator', 'password', url='http://localhost:8080')
> dsadmin.install_package(o, 'dsBase')
> dsadmin.install_package(o, 'dsStats')
> dsadmin.install_package(o, 'dsGraphics')
> dsadmin.install_package(o, 'dsModelling')
> dsadmin.set_package_methods(o, 'dsBase')
> dsadmin.set_package_methods(o, 'dsStats')
> dsadmin.set_package_methods(o, 'dsGraphics')
> dsadmin.set_package_methods(o, 'dsModelling')
> opal.logout(o)

Server-side R DataSHIELD package manuals

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