News

collect Opal 4.0 Released

We are pleased to announce that Opal 4.0 is now available. Opal is OBiBa’s core data management application for biobanks.

This release of Opal integrates with the Rock R server which is a modern implementation of a R server with a REST API, built-in security and the capability of scaling horizontaly: Opal can connect with multiple R servers, grouped in a cluster. This allows to balance the load of the analysis between multiple computation nodes. This fully integrates with the DataSHIELD federated analysis platform.

R servers

Additional features implemented:

  • import/export data in RDS format (single serialized R object, see base::readRDS documentation), also available as import/export python commands,
  • new Resource permissions python commands for adding/deleting permissions on a project's resources,
  • the R REST API now returns either binary serialized R objects (as before) or JSON serialized R objects, which makes the Opal's R service usable by non-R clients,
  • R markdown report additional files (R script to source, subsection of R markdown, images etc.) are supported for building complex reports.

Breaking changes

Despite Opal is backward compatible with the legacy R servers, some breaking changes are expected with this release:.

  • R based plugins need to be upgraded. This will be done automatically by Opal (requires internet connection),
  • opalr needs to be upgraded to its latest version (otherwise JSON serialized R objects will be returned). Use the following R command:

install.packages("opalr")

This release was possible thanks to the funding of the EUCAN-Connect program.

See Opal documentation for installation and operation instructions. We recommend to have a look at the section about Docker Image Installation .