FHIR Chat · Extending canonical fails json schema

Stream: implementers

Topic: Extending canonical fails json schema

Mirjam Baltus (Jun 30 2021 at 16:10):

If you add an extension to a field of type canonical (FHIR R4), if I understand correctly for json this should go into '_fieldName' since canonical is a primitive type. However, if you validate this with the JSON schema, it fails. Is extending a canonical not allowed, or is the schema wrong? The Java validator does not complain.

Lloyd McKenzie (Jun 30 2021 at 18:27):

@Grahame Grieve

Grahame Grieve (Jun 30 2021 at 19:38):

the json schema is supposed to allow this. Please provide an example

Eric Haas (Jun 30 2021 at 19:48):

canonicals extensions worked for me in ImplementationGuide

Mirjam Baltus (Jun 30 2021 at 20:04):

Thanks, I will check to see how it was validated exactly. What I was told, is that the extension was set on the QuestionnaireResponse.questionnaire field and the error thrown on _questionnaire not being a known field.

Eric Haas (Jun 30 2021 at 23:13):

oops, I did not read this thoroughly. my example validated using fhir validator. Did not test with the json schema

Mirjam Baltus (Jul 01 2021 at 07:52):

@Ilya Sher Maybe you can elaborate on this?

Ilya Sher (Jul 01 2021 at 07:59):

I guess we wait for @Eric Haas to reproduce the issue with QuestionnaireResponse.questionnaire / QuestionnaireResponse._questionnaire and with JSON Schema

Ilya Sher (Jul 01 2021 at 08:56):

The code at https://github.com/awslabs/fhir-works-on-aws-routing/blob/mainline/src/router/validation/jsonSchemaValidator.ts fails with Failed to parse request body as JSON resource ...

Ilya Sher (personal account) (Jul 02 2021 at 10:11):

Waiting for update from @Eric Haas ... or anyone else :)

Eric Haas (Jul 03 2021 at 04:07):

I misunderstood the issue. I have not tried to use json schemas at all. So I am unable to comment

Lloyd McKenzie (Jul 03 2021 at 22:36):

@Grahame Grieve

Ilya Sher (Jul 05 2021 at 15:43):

Eric Haas said:

I misunderstood the issue. I have not tried to use json schemas at all. So I am unable to comment

... and then I misread your comment :)

Mirjam Baltus (Jul 07 2021 at 13:09):

@Grahame Grieve I've tried this with the Newtonsoft libraries for .Net, and do get an error as soon as I add an extension to the QuestionnaireResponse.questionnaire field. Without it, all works fine. Here is a QuestionnaireResponse that is valid according to both HAPI and Firely Server, but not against the schema:

{
  "resourceType": "QuestionnaireResponse",
  "_questionnaire": {
    "extension": [
      {
        "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
        "valueCode": "unknown"
      }
    ]
  },
  "status": "stopped"
}

Ilya Sher (Jul 28 2021 at 13:04):

Mirjam Baltus said:

Grahame Grieve I've tried this with the Newtonsoft libraries for .Net, and do get an error as soon as I add an extension to the QuestionnaireResponse.questionnaire field. Without it, all works fine. Here is a QuestionnaireResponse that is valid according to both HAPI and Firely Server, but not against the schema:
{
  "resourceType": "QuestionnaireResponse",
  "_questionnaire": {
    "extension": [
      {
        "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
        "valueCode": "unknown"
      }
    ]
  },
  "status": "stopped"
}

How should I proceed with that? Looks like bug in JSON schema. Should I open a Jira issue?

Lloyd McKenzie (Jul 28 2021 at 13:50):

Do you know what the schema should look like?

Ilya Sher (Jul 28 2021 at 14:33):

Lloyd McKenzie said:

Do you know what the schema should look like?

I have a guess. Add (just after "questionnaire": {...}):

"_questionnaire": {
          "description": "Extensions for questionnaire",
          "$ref": "#/definitions/Element"
        }

that's how extension for other elements of primitive types look.

Ilya Sher (Jul 28 2021 at 14:36):

Lloyd McKenzie said:

Do you know what the schema should look like?

There is also quite a few other elements with "$ref": "#/definitions/canonical" which don't have _myElementName extensions. I think maybe all of them.

Lloyd McKenzie (Jul 28 2021 at 14:51):

If you can test the solution, a change request would be most welcome.

Ilya Sher (Jul 29 2021 at 05:16):

Not sure yet. Meanwhile have a question - isn't this file generated?

Lloyd McKenzie (Jul 29 2021 at 13:15):

Yes

Lloyd McKenzie (Jul 29 2021 at 13:15):

So the fix would be to the generation algorithm

Ilya Sher (Aug 03 2021 at 11:03):

Lloyd McKenzie said:

So the fix would be to the generation algorithm

... and where that one is?

Lloyd McKenzie (Aug 03 2021 at 13:21):

Here, I believe: https://github.com/HL7/kindling/blob/main/src/main/java/org/hl7/fhir/definitions/generators/specification/json/SchemaGenerator.java

Ilya Sher (Aug 09 2021 at 10:55):

Meanwhile checked whether other elements have the same issue. Apparently only "canonical" type has the issue:

[
  {
    "resourceType": "ActivityDefinition",
    "element": "library",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ActivityDefinition",
    "element": "profile",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ActivityDefinition",
    "element": "transform",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "CapabilityStatement",
    "element": "instantiates",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "CapabilityStatement",
    "element": "imports",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "CapabilityStatement",
    "element": "implementationGuide",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "CarePlan",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ChargeItem",
    "element": "definitionCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ChargeItemDefinition",
    "element": "partOf",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ChargeItemDefinition",
    "element": "replaces",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "CodeSystem",
    "element": "valueSet",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "CodeSystem",
    "element": "supplements",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "Communication",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "DeviceRequest",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ExampleScenario",
    "element": "workflow",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ExampleScenario_Instance",
    "element": "resourceType",
    "should_have_extension": false,
    "has_extenstion": true,
    "track_of_refs": []
  },
  {
    "resourceType": "FamilyMemberHistory",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "GraphDefinition",
    "element": "profile",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "Measure",
    "element": "library",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "MeasureReport",
    "element": "measure",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "MessageDefinition",
    "element": "replaces",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "MessageDefinition",
    "element": "base",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "MessageDefinition",
    "element": "parent",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "MessageDefinition",
    "element": "graph",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "MessageHeader",
    "element": "definition",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "NutritionOrder",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "OperationDefinition",
    "element": "base",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "OperationDefinition",
    "element": "inputProfile",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "OperationDefinition",
    "element": "outputProfile",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "PlanDefinition",
    "element": "library",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "Procedure",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "Questionnaire",
    "element": "derivedFrom",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "QuestionnaireResponse",
    "element": "questionnaire",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ResearchDefinition",
    "element": "library",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ResearchElementDefinition",
    "element": "library",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "SearchParameter",
    "element": "derivedFrom",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "ServiceRequest",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "StructureDefinition",
    "element": "baseDefinition",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "StructureMap",
    "element": "import",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  },
  {
    "resourceType": "Task",
    "element": "instantiatesCanonical",
    "should_have_extension": true,
    "has_extenstion": false,
    "track_of_refs": [
      "#/definitions/canonical"
    ]
  }
]

This was generated by the script I wrote. It is at https://github.com/ngs-lang/nsd/blob/df1e69f22458713a29291449c008f820ec988768/fhir/check-schema-extensions.ngs

Last updated: Apr 12 2022 at 19:14 UTC

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FHIR Chat · Extending canonical fails json schema · implementers

Stream: implementers

Topic: Extending canonical fails json schema

Mirjam Baltus (Jun 30 2021 at 16:10):

Lloyd McKenzie (Jun 30 2021 at 18:27):

Grahame Grieve (Jun 30 2021 at 19:38):

Eric Haas (Jun 30 2021 at 19:48):

Mirjam Baltus (Jun 30 2021 at 20:04):

Eric Haas (Jun 30 2021 at 23:13):

Mirjam Baltus (Jul 01 2021 at 07:52):

Ilya Sher (Jul 01 2021 at 07:59):

Ilya Sher (Jul 01 2021 at 08:56):

Ilya Sher (personal account) (Jul 02 2021 at 10:11):

Eric Haas (Jul 03 2021 at 04:07):

Lloyd McKenzie (Jul 03 2021 at 22:36):

Ilya Sher (Jul 05 2021 at 15:43):

Mirjam Baltus (Jul 07 2021 at 13:09):

Ilya Sher (Jul 28 2021 at 13:04):

Lloyd McKenzie (Jul 28 2021 at 13:50):

Ilya Sher (Jul 28 2021 at 14:33):

Ilya Sher (Jul 28 2021 at 14:36):

Lloyd McKenzie (Jul 28 2021 at 14:51):

Ilya Sher (Jul 29 2021 at 05:16):

Lloyd McKenzie (Jul 29 2021 at 13:15):

Lloyd McKenzie (Jul 29 2021 at 13:15):

Ilya Sher (Aug 03 2021 at 11:03):

Lloyd McKenzie (Aug 03 2021 at 13:21):

Ilya Sher (Aug 09 2021 at 10:55):