Missing support for externalized content when using HAPI FHIR

[jkiddo]

The functionality here:

clinical-reasoning/cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/cql2elm/content/BaseFhirLibrarySourceProvider.java

Line 49 in f4843b3

return new ByteArrayInputStream(attachmentAdapter.getData());

is missing HAPI FHIR support when used together with the externalized content feature as documented here: https://smilecdr.com/docs/fhir_repository/binary_data.html#externalized-binary-storage as it missing to look up the HAPI FHIR defined extension on the data field if used. Example of piece of data as follows:

{
    "resourceType": "Library",
    "id": "14",
    "meta": {
        "versionId": "1",
        "lastUpdated": "2024-06-09T20:52:41.320+02:00"
    },
    "url": "http:https://trifork.com/Library/LastDueDate",
    "identifier": [
        {
            "use": "official",
            "value": "LastDueDate"
        }
    ],
    "version": "1.0.0",
    "name": "LastDueDate",
    "status": "active",
    "experimental": false,
    "type": {
        "coding": [
            {
                "system": "http:https://terminology.hl7.org/CodeSystem/library-type",
                "code": "logic-library",
                "display": "Logic Library"
            }
        ]
    },
    "date": "2024-06-06",
    "content": [
        {
            "contentType": "text/cql",
            "_data": {
                "extension": [
                    {
                        "url": "http:https://hapifhir.io/fhir/StructureDefinition/externalized-binary-id",
                        "valueString": "N7UFAtfVcrpt88IJZCdQFqCDFimQf3mlHuHQbvWLupfiEcIOQNRZ515N2a1V89d1TQg2afKf3kY7WtsKxO1OsYVAz7kMlOsVyUZG"
                    }
                ]
            },
            "size": 386
        }
    ]
}

[jkiddo]

I guess one way to fix it would be to extract this

clinical-reasoning/cqf-fhir-cql/src/main/java/org/opencds/cqf/fhir/cql/Engines.java

Line 189 in d45dc73

public static AdapterFactory getAdapterFactory(FhirContext fhirContext) {

and let the adaptors from the factory do the lifting. Then everything else could be left untouched.

[jkiddo]

@barhodes I can do a PR that fixes it but it will have quite the impact on the current architecture. Due the static design on CqlEngine and the switch statements for obtaining a AdapterFactory I'd prefer a discussion before heading into a PR adventure. I did the original design on e.g. https://github.com/hapifhir/hapi-fhir-jpaserver-starter/blob/master/src/main/java/ca/uhn/fhir/jpa/starter/annotations/OnEitherVersion.java and I would suggest to head the same direction - having the version of the AdaptorFactories being bound to configs outside the CqlEngine - or at least injected into it. There isn't many Spring annotations in the existing codebase and I assume you guys would prefer it stays that way? Preferrably and overall I would suggest let the specific AdaptorFactory be constructed by Spring and let that be arried through the different places. Let me know what you think.