FHIR CodeSystem Fixes

[jamlung-ri]

On today's OCL Dev call, we talked through some of the issues that prevented the FHIR IG Publisher from generating a FHIR IG. The diffs of manual changes that I had to make can be found here and here.

Changes needed to OCL's FHIR Core CodeSystem:

• “Count” field does not count inactive codes, but OCL FHIR Core does return inactive values (which was pointed out via the FHIR Validator)
  - Solution: "Count" needs to count all codes, whether active or inactive.
• “Null” fields are intended to be excluded in FHIR e.g. "definition": null (see second-to-last paragraph on this page)
• Concept Property’s “value” should be “valueString”
• Had to add a whole new property -- "content": "complete" (FHIR Spec)
• "type": "coding" -> "type": "Coding" (FHIR Spec)

I am attaching the current OCL FHIR CodeSystem resource and the one that I hand-edited, for reference in a comment below

[jamlung-ri]

Current OCL FHIR Core's CodeSystem:

{
    "resourceType": "CodeSystem",
    "url": "http://smart.who.int/immunizations-measles/CodeSystem/VaccineProducts",
    "title": "Vaccine Product codes CodeSet",
    "status": "active",
    "id": "VaccineProducts",
    "language": "en",
    "count": 2,
    "property": [
        {
            "code": "conceptclass",
            "uri": "https://api.staging.openconceptlab.org/orgs/OCL/sources/Classes/concepts",
            "description": "Standard list of concept classes.",
            "type": "string"
        },
        {
            "code": "datatype",
            "uri": "https://api.staging.openconceptlab.org/orgs/OCL/sources/Datatypes/concepts",
            "description": "Standard list of concept datatypes.",
            "type": "string"
        },
        {
            "code": "inactive",
            "uri": "http://hl7.org/fhir/concept-properties",
            "description": "True if the concept is not considered active.",
            "type": "coding"
        }
    ],
    "meta": {
        "lastUpdated": "2024-02-23T20:43:22.381603Z"
    },
    "version": "0.1.0",
    "name": "VaccineProducts",
    "description": "0.1.0",
    "publisher": "WHO",
    "experimental": true,
    "caseSensitive": true,
    "concept": [
        {
            "code": "7680007030014",
            "display": "M-M-RvaxPRO",
            "definition": null,
            "designation": [
                {
                    "language": "en",
                    "value": "M-M-RvaxPRO",
                    "use": null
                }
            ],
            "property": [
                {
                    "code": "conceptclass",
                    "value": "Drug"
                },
                {
                    "code": "datatype",
                    "value": "None"
                }
            ]
        },
        {
            "code": "20009060%2F2",
            "display": "Serum Institute of India Measles vaccine",
            "definition": null,
            "designation": [
                {
                    "language": "en",
                    "value": "Serum Institute of India Measles vaccine",
                    "use": null
                }
            ],
            "property": [
                {
                    "code": "conceptclass",
                    "value": "Drug"
                },
                {
                    "code": "datatype",
                    "value": "None"
                }
            ]
        },
        {
            "code": "1",
            "display": "Serum Institute of India Measles vaccine",
            "definition": null,
            "designation": [
                {
                    "language": "en",
                    "value": "Serum Institute of India Measles vaccine",
                    "use": null
                }
            ],
            "property": [
                {
                    "code": "conceptclass",
                    "value": "Drug"
                },
                {
                    "code": "datatype",
                    "value": "None"
                },
                {
                    "code": "inactive",
                    "value": true
                }
            ]
        }
    ],
    "identifier": [
        {
            "system": "https://api.staging.openconceptlab.org",
            "value": "/orgs/WHO-Smart-Guidelines/CodeSystem/VaccineProducts/",
            "type": {
                "text": "Accession ID",
                "coding": [
                    {
                        "system": "http://hl7.org/fhir/v2/0203",
                        "code": "ACSN",
                        "display": "Accession ID"
                    }
                ]
            }
        }
    ]
}

[jamlung-ri]

Manually edited CodeSystem resource that worked with FHIR IG Publisher:

{
    "resourceType": "CodeSystem",
    "url": "http://smart.who.int/immunizations-measles/CodeSystem/VaccineProducts",
    "title": "Vaccine Product codes CodeSet",
    "status": "active",
    "id": "VaccineProducts",
    "language": "en",
    "count": 2,
    "property": [
        {
            "code": "conceptclass",
            "uri": "https://api.staging.openconceptlab.org/orgs/OCL/sources/Classes/concepts",
            "description": "Standard list of concept classes.",
            "type": "string"
        },
        {
            "code": "datatype",
            "uri": "https://api.staging.openconceptlab.org/orgs/OCL/sources/Datatypes/concepts",
            "description": "Standard list of concept datatypes.",
            "type": "string"
        },
        {
            "code": "inactive",
            "uri": "http://hl7.org/fhir/concept-properties",
            "description": "True if the concept is not considered active.",
            "type": "Coding"
        }
    ],
    "meta": {
        "lastUpdated": "2024-02-23T20:43:22.381603Z"
    },
    "version": "0.1.0",
    "name": "VaccineProducts",
    "description": "0.1.0",
    "publisher": "WHO",
    "content": "complete",
    "experimental": true,
    "caseSensitive": true,
    "concept": [
        {
            "code": "7680007030014",
            "display": "M-M-RvaxPRO",
            "designation": [
                {
                    "language": "en",
                    "value": "M-M-RvaxPRO"
                }
            ],
            "property": [
                {
                    "code": "conceptclass",
                    "valueString": "Drug"
                },
                {
                    "code": "datatype",
                    "valueString": "None"
                }
            ]
        },
        {
            "code": "20009060%2F2",
            "display": "Serum Institute of India Measles vaccine",
            "designation": [
                {
                    "language": "en",
                    "value": "Serum Institute of India Measles vaccine"
                }
            ],
            "property": [
                {
                    "code": "conceptclass",
                    "valueString": "Drug"
                },
                {
                    "code": "datatype",
                    "valueString": "None"
                }
            ]
        },
        {
            "code": "1",
            "display": "Serum Institute of India Measles vaccine",
            "designation": [
                {
                    "language": "en",
                    "value": "Serum Institute of India Measles vaccine"
                }
            ],
            "property": [
                {
                    "code": "conceptclass",
                    "valueString": "Drug"
                },
                {
                    "code": "datatype",
                    "valueString": "None"
                },
                {
                    "code": "inactive",
                    "valueString": true
                }
            ]
        }
    ],
    "identifier": [
        {
            "system": "https://api.staging.openconceptlab.org",
            "value": "/orgs/WHO-Smart-Guidelines/CodeSystem/VaccineProducts/",
            "type": {
                "text": "Accession ID",
                "coding": [
                    {
                        "system": "http://hl7.org/fhir/v2/0203",
                        "code": "ACSN",
                        "display": "Accession ID"
                    }
                ]
            }
        }
    ]
}

[rkorytkowski]

@jamlung-ri the changes should be deployed to QA in a few minutes, see https://ci.openmrs.org/browse/OCL-OCLAPI2-1991

[jamlung-ri]

Awesome, I tested this in QA and the diff is looking exactly how I expected!

And then it worked when testing against the FHIR IG Publisher! See this page for the new and improved CodeSystem, entirely created from OCL with no manual alterations: https://jamlung-ri.github.io/smart-catopia-measles/CodeSystem-VaccineProducts.html and https://github.com/jamlung-ri/smart-catopia-measles/blob/main/input/resources/CodeSystem-VaccineProducts.json

@rkorytkowski This should be ready to deploy to other environments.