Demonstrator for the BBMRI.it Pilot project

This project is a demonstrator of the usage of the profiled FHIR BBMRI.it consent resource. It provides a series of sample resources, including Consent, that can be loaded into a FHIR server and then queried via CQL.

Provided resources

The following examples of resources are provided in the examples/ folder:

• Person
• Organization (for Biobanks and Collections)
• Condition
• Specimen
• Consent

Requirements

• Install and run the Samply FHIR server (via docker compose)
• Install the blazectl command line tool and set the related blazectl command in the path
• Python 3.x
• Python packages: requests

Installation and run

First, load the fhir resources, launcing the .sh script;

./load_examples.sh

Then, run the cql query, launching the python script:

python3 run_cql_query.py

You can modufy the variables in the script:

• CCEs: can be edited by adding or removing one or more conditions of use
• CQL_QUERY_CONTEXT: if set to Patient, then the query provides the count or the detail of the Patients whose samples satisfy the CCEs; if set to Specimen, then the query provides the count or the detail of the Specimens that satisfy the CCEs.
• CQL_QUERY_GRANULARITY: can be set to RESOURCE or COUNT, depending on whether you want the detail of the resources or just their count.