Using the NHS LFPSE FHIR resource at https://psims-uat.azure-api.net/taxonomy/fhir/StructureDefinition/adverse-event-estimated-date-4 I want to save the StructureDefinition.Snapshot.Element list into my database so I can process it later.
To do this I had planned on using data serialisation. The serialisation and saving the database is working OK.
However, when I extract the string and attempt to deserialise it:
var snapshot = JsonConvert.DeserializeObject<StructureDefinition.SnapshotComponent>(mySnapshotString);
I get an error:
Newtonsoft.Json.JsonSerializationException: 'Cannot deserialize readonly or fixed size dictionary: Hl7.Fhir.Model.StructureDefinition+SnapshotComponent. Path 'element', line 1, position 11.'
I'm using Hl7.Fhir.STU3 and I've tried alternative serilialisation libraries too
FhirJsonSerializer - does not have a Deserialise methodJsonSerializer - same error as aboveHow can I deserialise the snapshot elements?
Example of the serialised snapshot element:
{
"element": [
{
"id": "Extension",
"path": {
"value": "Extension"
},
"short": {
"value": "Information about the estimated date/time of the event"
},
"definition": {
"value": "Information about the estimated date/time of the event"
},
"min": {
"value": 0
},
"max": {
"value": "1"
},
"base": {
"path": {
"value": "Element"
},
"min": {
"value": 0
},
"max": {
"value": "*"
}
},
"condition": [
{
"value": "ele-1"
}
],
"constraint": [
{
"key": {
"value": "ele-1"
},
"severity": {
"value": "error"
},
"human": {
"value": "All FHIR elements must have a @value or children"
},
"expression": {
"value": "hasValue() | (children().count() > id.count())"
},
"xpath": {
"value": "@value|f:*|h:div"
},
"source": {
"value": "Element"
}
},
{
"key": {
"value": "ext-1"
},
"severity": {
"value": "error"
},
"human": {
"value": "Must have either extensions or value[x], not both"
},
"expression": {
"value": "extension.exists() != value.exists()"
},
"xpath": {
"value": "exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])"
}
}
],
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "n/a"
}
},
{
"identity": {
"value": "rim"
},
"map": {
"value": "N/A"
}
}
]
},
{
"id": "Extension.id",
"path": {
"value": "Extension.id"
},
"representation": [
{
"value": "xmlAttr"
}
],
"short": {
"value": "xml:id (or equivalent in JSON)"
},
"definition": {
"value": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."
},
"min": {
"value": 0
},
"max": {
"value": "1"
},
"base": {
"path": {
"value": "Element.id"
},
"min": {
"value": 0
},
"max": {
"value": "1"
}
},
"type": [
{
"code": {
"value": "string"
}
}
],
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "n/a"
}
}
]
},
{
"id": "Extension.extension",
"path": {
"value": "Extension.extension"
},
"slicing": {
"discriminator": [
{
"type": {
"value": "value"
},
"path": {
"value": "url"
}
}
],
"description": {
"value": "Extensions are always sliced by (at least) url"
},
"rules": {
"value": "open"
}
},
"short": {
"value": "Additional Content defined by implementations"
},
"definition": {
"value": "May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."
},
"comment": {
"value": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."
},
"alias": [
{
"value": "extensions"
},
{
"value": "user content"
}
],
"min": {
"value": 0
},
"max": {
"value": "*"
},
"base": {
"path": {
"value": "Element.extension"
},
"min": {
"value": 0
},
"max": {
"value": "*"
}
},
"type": [
{
"code": {
"value": "Extension"
}
}
],
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "n/a"
}
}
]
},
{
"id": "Extension.extension:IncidentOccurredToday",
"path": {
"value": "Extension.extension"
},
"sliceName": {
"value": "IncidentOccurredToday"
},
"short": {
"value": "Indication of whether the event occurred today"
},
"definition": {
"value": "Indication of whether the event occurred today"
},
"comment": {
"value": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."
},
"alias": [
{
"value": "extensions"
},
{
"value": "user content"
}
],
"min": {
"value": 0
},
"max": {
"value": "1"
},
"base": {
"path": {
"value": "Element.extension"
},
"min": {
"value": 0
},
"max": {
"value": "*"
}
},
"type": [
{
"code": {
"value": "Extension"
}
}
],
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "n/a"
}
}
]
},
{
"id": "Extension.extension:IncidentOccurredToday.id",
"path": {
"value": "Extension.extension.id"
},
"representation": [
{
"value": "xmlAttr"
}
],
"short": {
"value": "xml:id (or equivalent in JSON)"
},
"definition": {
"value": "unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."
},
"min": {
"value": 0
},
"max": {
"value": "1"
},
"base": {
"path": {
"value": "Element.id"
},
"min": {
"value": 0
},
"max": {
"value": "1"
}
},
"type": [
{
"code": {
"value": "string"
}
}
],
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "n/a"
}
}
]
},
{
"id": "Extension.extension:IncidentOccurredToday.extension",
"path": {
"value": "Extension.extension.extension"
},
"slicing": {
"discriminator": [
{
"type": {
"value": "value"
},
"path": {
"value": "url"
}
}
],
"description": {
"value": "Extensions are always sliced by (at least) url"
},
"rules": {
"value": "open"
}
},
"short": {
"value": "Additional Content defined by implementations"
},
"definition": {
"value": "May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."
},
"comment": {
"value": "There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."
},
"alias": [
{
"value": "extensions"
},
{
"value": "user content"
}
],
"min": {
"value": 0
},
"max": {
"value": "0"
},
"base": {
"path": {
"value": "Element.extension"
},
"min": {
"value": 0
},
"max": {
"value": "*"
}
},
"type": [
{
"code": {
"value": "Extension"
}
}
],
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "n/a"
}
}
]
},
{
"id": "Extension.extension:IncidentOccurredToday.url",
"path": {
"value": "Extension.extension.url"
},
"representation": [
{
"value": "xmlAttr"
}
],
"short": {
"value": "identifies the meaning of the extension"
},
"definition": {
"value": "Source of the definition for the extension code - a logical name or a URL."
},
"comment": {
"value": "The definition may point directly to a computable or human-readable definition of the extensibility codes, or it may be a logical URI as declared in some other specification. The definition SHALL be a URI for the Structure Definition defining the extension."
},
"min": {
"value": 1
},
"max": {
"value": "1"
},
"base": {
"path": {
"value": "Extension.url"
},
"min": {
"value": 1
},
"max": {
"value": "1"
}
},
"type": [
{
"code": {
"value": "uri"
}
}
],
"fixed": {
"value": "IncidentOccurredToday"
},
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "N/A"
}
}
]
},
{
"id": "Extension.extension:IncidentOccurredToday.valueCode",
"path": {
"value": "Extension.extension.valueCode"
},
"short": {
"value": "Value of extension"
},
"definition": {
"value": "Value of extension - may be a resource or one of a constrained set of the data types (see Extensibility in the spec for list)."
},
"min": {
"value": 0
},
"max": {
"value": "1"
},
"base": {
"path": {
"value": "Extension.value[x]"
},
"min": {
"value": 0
},
"max": {
"value": "1"
}
},
"type": [
{
"code": {
"value": "code"
}
}
],
"binding": {
"strength": {
"value": "required"
},
"description": {
"value": "Indication of whether the event occurred today"
},
"valueSet": {
"reference": {
"value": "https://psims-uat.azure-api.net/taxonomy/fhir/ValueSet/yes-no-unknown-codes-4"
}
}
},
"mapping": [
{
"identity": {
"value": "rim"
},
"map": {
"value": "N/A"
}
}
]
}
]
}
Following on from the answer from @Mirjan-Baltus the exact answers for me was:
var options = new JsonSerializerOptions().ForFhir();
var snapshot = System.Text.Json.JsonSerializer.Deserialize<StructureDefinition.SnapshotComponent>(structureDefinition.Snapshot, options);
The ForFhir() is explained in the Fhir.ly docs here and we use the overloaded version without the Assembly reference and it pickup the respective Fhir assembly being used (which in my case is hl7.fhir.stu3)