SDC spec implementation as microservice

The whole SDC specification you can find here http://hl7.org/fhir/uv/sdc/

Upgrading to 3.x.x

CONSTRAINT_LEGACY_BEHAVIOR and EXTRACT_SOURCE_QUERIES_LEGACY_BEHAVIOR are gone, and both now behave as False did:

• an itemConstraint expression states what must hold, and the submission is refused when it evaluates to false. Expressions written for the legacy behaviour describe the error instead, and have to be negated;
• source queries are loaded for the constraint check only, so mappers receive the $extract parameters alone.

Setting either variable no longer has any effect.

JUTE_SERVICE=aidbox is gone too: JUTE mappers always run through a JUTE service, and the app refuses to start while the variable still says aidbox. Leaving JUTE_SERVICE or FHIRPATH_MAPPING_SERVICE unset is fine — extraction then refuses only the mappers that would have needed the missing service.

Further plans:

• JUTE-based population
• Observation-based population
• Observation-based extraction
• Definition-based extraction

Tests

To run tests locally, copy .env.tpl to .env and specify TESTS_AIDBOX_LICENSE.

Build images using docker compose -f docker-compose.tests.yaml build.

After that, just start ./run_test.sh or ./run_test.sh tests/test_base.py (if you want to run the particular file/test). The first run may take about a minute because it prepares the db and devbox.

If you have updated some requirements, you need to re-run docker compose -f docker-compose.tests.yaml build