FHIR JSON to XML parsing issue with fhir-net-api stu2

Question

I am using the library fhir-net-api dstu2 to parse incoming FHIR JSON from a Restful web service to XML in a biztalk pipeline component and then passing it to the XML disassembler for debatching in BizTalk. Most message go through without an issue but I am getting the following error on the occasional message.

"Invalid character in the given encoding. Line 1, position 12700.".

I have inspected the messages and cannot see any difference in the incoming JSON that would cause this error. Looking at the character position given in the error message, the XML output from the fhir-net-api shows the issue below. For some reason the library cuts the location short and puts in a bundle tag. <Bundle xmlns="http://hl7.org/fhir"><total value="9" />

Any thought on what is going on here or how to go about troubleshooting?

I cannot post the full messages but here are snippet of the problem area.

Input JSON snippet

"hospitalization": {"dischargeDiagnosis": [         {
        "reference": "#Reason",
        "display": "DWA-Discharged with Approval"
     }]},
     "location": [{"location": {"display": "SPH 4th Bunny Dr’s Clinic"}}],
     "serviceProvider": {"display": "FOO"}
  }},
  {"resource":       {
     "resourceType": "Encounter",
     "id": "FOO0009-394a-4c51",
     "extension":          [

Output XML snippet

<hospitalization>
    <dischargeDiagnosis>
        <reference value="#Reason" />
        <display value="DWA-Discharged with Approval" />
    </dischargeDiagnosis>
</hospitalization>
<location>
    <location>
        <display value="SPH 4<Bundle xmlns="http://hl7.org/fhir">
                        <total value="9" />
<entry>
    <resource>
        <Encounter>

EDIT - I isolated the problem resource and de-identified the message. Here is the full JSON message that causes the error above. I tried the FHIR JSON to XML notepad++ plugin and it serializes the message correctly.

Here is the code from the pipeline component.

     Hl7.Fhir.Serialization.ResourceReader resourceReader = new Hl7.Fhir.Serialization.ResourceReader(FhirJsonParser.CreateFhirReader(json), ParserSettings.Default);


  string resourceXmlString = Hl7.Fhir.Serialization.FhirSerializer.SerializeResourceToXml(resourceReader.Deserialize());

Here is the JSON that causes the issue

{
   "resourceType": "Bundle",
   "total": 1,
   "entry":    [
     {"resource":       {
         "resourceType": "Encounter",
         "id": "10000000-0000-0000-000-200000000",
         "extension":          [
                        {
               "url": "https://foo.org/documents/fhir/extensions/encounter-facility",
               "valueString": "St. Foo Hospital"
            },
                        {
               "url": "https://foo.org/documents/fhir/extensions/encounter-service",
               "valueString": "Foo PROGRAM/Foo ECHOCARDIOLOGY"
            },
                        {
               "url": "https://foo.org/documents/fhir/extensions/encounter-patienttype",
               "valueString": "Diagnostic - Outpatient"
            },
                        {
               "url": "https://foo.org/documents/fhir/extensions/encounter-documentcount",
               "valueInteger": 0
            },
                        {
               "url": "https://foo.org/documents/fhir/extensions/encounter-entitysourcesystem",
               "valueString": "CDR"
            },
                        {
               "url": "https://foo.org/documents/fhir/extensions/encounter-mrnid",
               "valueString": "10000000"
            }
         ],
         "identifier":          [
                        {
               "use": "official",
               "value": "1000000-5420-0000-0000-00000"
            },
                        {
               "use": "secondary",
               "value": "100000000000"
            }
         ],
         "patient": {"reference": "Patient/000000000"},
         "participant":          [
                        {
               "type": [               {
                  "coding": [                  {
                     "system": "http://hl7.org/fhir/v3/ParticipationType",
                     "code": "PRCP"
                  }],
                  "text": "Primary Care Physician"
               }],
               "individual": {"display": "Foo, Guy"}
            },
                        {
               "type": [               {
                  "coding": [                  {
                     "system": "http://hl7.org/fhir/v3/ParticipationType",
                     "code": "ATND"
                  }],
                  "text": "Attending Physician"
               }],
               "individual": {"display": "RFoo, JFoo L"}
            }
         ],
         "period":          {
            "start": "2015-10-27T13:59:00+00:00",
            "end": "2017-02-17T09:39:07+00:00"
         },
         "reason": [         {
            "coding": [            {
               "system": "http://www.ihtsdo.org/snomed-ct",
               "code": "33962009"
            }],
            "text": "ECHOCARDIOGRAM"
         }],
         "hospitalization": {"dischargeDiagnosis": [         {
            "reference": "#Reason",
            "display": "DWA-Discharged with Approval"
         }]},
         "location": [{"location": {"display": "SPH 4th Foo Dr’s Clinic"}}],
         "serviceProvider": {"display": "Foo_foo"}
      }}

   ]
}

I think the issue might be that the apostrophe in "Dr's" is hex E28099, right single quote, instead of the expected hex 27 apostrophe. — David
This leads to a second question of, is the hex value E28099 allowed in the FHIR JSON message. Should I send this issue back to the service provider or handle the bad data myself? — David

Ewout Kramer Ewout Kramer · Accepted Answer · 2017-10-23T10:08:33

the error message "Invalid character in the given encoding" does not appear in the FHIR .NET API's source code, it does however surface on google in the context of the .NET XmlReader. So, my first guess is that the json gets parsed ok (it's perfectly fine to have any Unicode character bar some in a json string), then turned into XML where the character is not being escaped. Then when BizTalk processes the XML, it runs into trouble.

Which is interesting, given the fact that I only use the .NET XML libraries to serialize to XML, so it should not generate illegal XML. Maybe -and this is on the BizTalk side- is there a setting to indicate the encoding used in the XML pipeline in BizTalk?

FHIR JSON to XML parsing issue with fhir-net-api stu2

1 Answers