Opal 4.2 has been released. This version introduces R server clusters and DataSHIELD Profiles: Opal can now connect to different R servers (different R versions, different R packages installed).
A DataSHIELD profile:
- links to a R server cluster
- defines a DataSHIELD configuration (allowed functions and R options)
- can be restricted to some users/groups.
This is a major feature addition for making reproducible science. It solves the needs of:
- having different R server packages versions,
- facilitating base R upgrade,
- restricting access to packages in development.
Combined with containerized R servers, it is now easy to have several different R servers running in parallel and connected to the same Opal application. For DataSHIELD usage, the datashield/rock-base images are the recommended R servers with
dsBase package installed and can be used to build even more specific images.
DataSHIELD profiles can be declared at login time. To enable the profiles feature, latest client-side R packages DSI (1.3.0), DSOpal (1.3.0) and opalr (3.0.0) are required (and are backward compatible).
Connecting to a DataSHIELD profile only requires to declare the profile name. As an example, opal-demo.obiba.org server has the profiles
library(DSOpal) # declare login data with profile info builder <- DSI::newDSLoginBuilder() builder$append(server = "s1", user = "dsuser", password = "password", url = "https://opal-demo.obiba.org", profile = "omics") # profile parameter is optional ("default" is default value) builder$append(server = "s2", user = "dsuser", password = "password", url = "https://opal-demo.obiba.org") logindata <- builder$build() conns <- datashield.login(logindata) # list available profiles and current ones datashield.profiles(conns) # list packages in the current profiles datashield.pkg_status(conns) # list aggregate methods in the current profiles datashield.method_status(conns, type = "aggregate") datashield.logout(conns)
For DataSHIELD node administrators, profiles can be managed using R: see DataSHIELD Administration documentation.
This Opal release also comes with the new version of “R parser” that forbids subsets with brackets
, contact @swheater for more details.
See the complete release note.