Missing elements `status` & `occurence` in `immunization` resource

[j-frei]

Describe the bug In our setup, the output JSON file bundle-*.json (retrieved by odm2fhir_online.sh) contains the following entry.

{
  "fullUrl": "urn:uuid:*a-uuid*",
  "resource": {
    "resourceType": "Immunization",
    "id": "*a-uuid*",
    "meta": {
      "profile": [ "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/immunization" ]
    },
    "vaccineCode": {
      "coding": [ {
        "system": "http://snomed.info/sct",
        "code": "261665006",
        "display": "Unknown (qualifier value)"
      } ]
    },
    "patient": {
      "reference": "Patient/*a-patient-uuid*"
    },
    "protocolApplied": [ {
      "targetDisease": [ {
        "coding": [ {
          "system": "http://snomed.info/sct",
          "code": "6142004"
        } ]
      } ],
      "_doseNumberString": {
        "extension": [ {
          "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
          "valueCode": "unknown"
        } ]
      }
    } ]
  },
  "request": {
    "method": "POST",
    "url": "Immunization"
  }
}

It seems that the resource lacks the required properties status and a occurrence-property.

The error message (HTTP Code 400) looks like this:

{"resourceType":"OperationOutcome","issue":[{"severity":"fatal","code":"invalid","details":{"text":"FHIRProvider: Missing required element: 'status' [Bundle.entry[46]]"},"expression":["Bundle.entry[46]"]}]}

We are using the Docker instance of the IBM FHIR server (As docker-compose https://git.rz.uni-augsburg.de/freijoha/ibm-fhir-server) . The FHIR server version was set to 4.5.4.

Is this expected? Is there a potential misconfiguration of our local REDCap instance that is responsible for this?

[cerbelding]

Thank you for your report.

I assume the answer of this particular question was "unknown"?

For "Yes" the Status is already set to "COMPLETED" for "No" to "NOTDONE" I just added "NOTDONE" to all Immunizations with "Unknown", as this is the definition here.

The Fix will be published in the next version of the app.

[j-frei]

Thank you for your reply.

Unfortunately, I have no further knowledge of the details of our local REDCap testing instance. But it seems that you have already found the root of our initial problem.

Similar to "status" in "immunization" we are also facing issues with missing "occurrence" properties.

Old error log:

[cerbelding]

Which FHIR-Ressource should this be? (Bundle.entry[47])?

The occurence-property is filled using the field impfungen_XXXXX_datum maybe this field is malformed in your CDISC-ODM or not answered?

[j-frei]

The resource looks like this:

"resource": {
      "resourceType": "Immunization",
      "id": "*a-uuid*",
      "meta": {
        "profile": [ "https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/immunization" ]
      },
      "vaccineCode": {
        "coding": [ {
          "system": "http://snomed.info/sct",
          "code": "some-snomed-code",
          "display": "Unknown (qualifier value)"
        } ]
      },
      "patient": {
        "reference": "Patient/*a-patient-uuid*"
      },
      "protocolApplied": [ {
        "targetDisease": [ {
          "coding": [ {
            "system": "http://snomed.info/sct",
            "code": "some-snomed-code"
          } ]
        } ],
        "_doseNumberString": {
          "extension": [ {
            "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
            "valueCode": "unknown"
          } ]
        }
      } ]
    },

It seems plausible that this field has not been answered in our ODM. Is it required to be answered in order to convert it to a valid FHIR format?

[cerbelding]

Yes, according to the FHIR-Profile https://simplifier.net/forschungsnetzcovid-19/immunization , occurence is mandatory item. Maybe we can use some sort of default-occurence for unanswered *_datum-fields.

[cerbelding]

Issue will be closed as status & occurence of immunization-resource were already fixed in version 0.3.0.