FiaB-Updates

A place to announce updates, security alerts, and patches to the FAIR-in-a-Box modules

NEW!! FAIR-in-a-Box Security Upgrades

With the arrival of ERDERA, we have improved the way we handle security upgrades on all FiaB components. The basic workflow is:

start the base image
open a shell into that base container
apt-get dist-upgrade   OR   apk upgrade
commit the patched image
upload the patched, timestamped image to the FAIR Data Systems GitHub
run Trivy to do a security audit on the patched version
write the trivy logs to a folder (in the FiaB installer folder) with the same timestamp, that you can access and determine the severity of any remaining security holes
close the container
git commit the patched installer file and the new logs

FAIR-in-a-Box

FiaB is a suite of Docker images, and an installer/bootstrapper, that results in an end-to-end pipeline for FAIRification of legacy clinical data, publishing of that data and its associated metadata,privacy-preserving query and exploration of data and metadata, and user management. The European Joint Programme on Rare Disease has defined three "levels" of access to data/metadata. L1 is access to metadata only, and is the minimal requried to be FAIR. L2 is discovery of resources based on data-level queries, but with only returning anonymous counts or yes/no. L3 is data-level query for the purpose of analytics, but without exposing patient-specific data.

The primary components of FAIR in a Box are

Function	Provided by	Source	License	Required/Optional
Installer	Bash script	run_me_to_install.sh	Open Source	Required L1
Authentication management	MongoDB	Mongodb 7.0 Docker image (mongo:7.0)	******	Required L1
Metadata Server	FAIR Data Point	fairdata/fairdatapoint:1.16.2 Docker image	Open source	Required L1
Metadata Client	FAIR Data Point Client	fairdata/fairdatapoint-client:1.16.3 Docker image	Open source	Required L1
Metadata and data storage	GraphDB	ontotext/graphdb:10.7.3	Commercial, free-for-limited-use	Required L1
Transformation trigger	CDE-Box_Daemon	markw/cde-box-daemon:0.5.4 Docker image	Open source	Optional; Required L2
Pre-transformation quality control	CARE-SM Toolkit	pabloalarconm/care-sm-toolkit:0.1.6	Open source	Optional; Required L2
Transformation	YARRRML-RML from RML.io	markw/yarrrml-rml-ejp:0.1.1 Docker image	Open source	Optional; Required L2
Privacy-preserving data-level discoveryn	Beacon2 from GA4GH Project	pabloalarconm/beacon-api4care-sm:0.2.2 Docker image	Open source	Optional; Required L2
Privacy-preserving analytical query	Shallot	markw/shallot:0.0.2 Docker image	Open source	Optional; Required L3