"This does not appear to be a FHIR resource" when validating Patient

[Gatoke]

Hello. I need to check if incoming Patient with profile https://www.fhir.org/guides/argonaut/r2/StructureDefinition-argo-patient.html is valid.

- I created a class which implements IValidationSupport
- I override "fetchResource" method which returns custom StructureDefinition from a file (https://www.fhir.org/guides/argonaut/r2/StructureDefinition-argo-patient.html).

(my JPA Server is configured for DSTU2, but I've made a simple mapper - ca.uhn Patient to org.hl7 Patient)

- When I receive request I am passing org.hl7 Patient to the validator

private ValidationResult validatePatient(final Patient patient) {
    final FhirValidator fhirValidator = FhirContext.forDstu2Hl7Org().newValidator();
    final FhirInstanceValidator fhirInstanceValidator = new FhirInstanceValidator(new MyValidationSupport());
    fhirValidator.registerValidatorModule(fhirInstanceValidator);

    return fhirValidator.validateWithResult(mapper.toHl7Org(patient));
}

Now the problem is - the whole method always returns false with a message "This does not appear to be a FHIR resource (unknown namespace/name 'http://hl7.org/fhir::Patient')".

I've tested it with random Patient from hapi test server and with official Argonaut example: https://www.fhir.org/guides/argonaut/r2/Patient-peter-chalmers.json

Does anyone know what am I doing wrong?

[James Agnew]

Hmm. I'm not sure where that error message is coming from..

You could try putting a breakpoint in the constructor(s) of the following class:

org.hl7.fhir.utilities.validation.ValidationMessage

This should help at least pinpoint that, and then you could work backwards to see why it's being generated.

Cheers,

James

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[Avanti Sunil Kopulwar]

Hello,

I am also getting the similar error while validating the FHIR resource against the custom profile.

Can you please share the solution or your observation?

Thanks,

Avanti

[fan yihui]

Hi

I have same problem when validate a resource against custom profile. Do you have the solution?

Regards,

Yihui

[Elano]

Hi everybody,

does anyone know the solution of this problem? Zihui, did you find a way to solve this issue?

Thanks

Elano

[Yuriy Flyud]

Adding this dependency helped me:

<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>${hapi_version}</version>
</dependency>

[Marc Dumontier]

I added the dependency but I still get this error message when validating against a profile

--

This does not appear to be a FHIR resource (unknown namespace/name 'http://hl7.org/fhir::Patient')

[Elano]

Hi Marc,

Here is the list of the dependencies (gradle) I am using:

// https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-base
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-base', version: '5.2.0'

// https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-client
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-client', version: '5.2.0'

// https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-structures-r4
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-structures-r4', version: '5.2.0'

// https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-validation-resources-r4
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-validation-resources-r4', version: '5.2.0'

// https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/hapi-fhir-validation
compile group: 'ca.uhn.hapi.fhir', name: 'hapi-fhir-validation', version: '5.2.0'

// https://mvnrepository.com/artifact/ca.uhn.hapi.fhir/org.hl7.fhir.utilities
compile group: 'ca.uhn.hapi.fhir', name: 'org.hl7.fhir.utilities', version: '5.2.0'

for me, it is working now.

[Marc Dumontier]

Thanks

I have the same set of packages via maven

The code is really just based on what's in the documentation..I'm using a downloaded profile XML I published to simplifier.net

FhirContext ctx = FhirContext.forR4();

IParser parser = ctx.newXmlParser();

StructureDefinition sd = (StructureDefinition) parser.parseResource(

new FileInputStream(new File("/home/marc/Downloads/MyPatient.StructureDefinition.xml")));

List<StructureDefinition> definitions = new ArrayList<StructureDefinition>();

definitions.add(sd);

IValidationSupport valSupport = new MyValidationSupport(ctx, definitions);

ValidationSupportChain validationSupportChain = new ValidationSupportChain(valSupport,

new InMemoryTerminologyServerValidationSupport(ctx), new CommonCodeSystemsTerminologyService(ctx));

FhirValidator validator = ctx.newValidator();

IValidatorModule module = new FhirInstanceValidator(validationSupportChain);

validator.registerValidatorModule(module);

// Pass a resource instance as input to be validated

Patient resource = new Patient();

resource.addName().setFamily("Simpson").addGiven("Homer");

resource.getMeta().addProfile("http://inputhealth.com/fhir/StructureDefinition/MyPatient");

ValidationResult result = validator.validateWithResult(resource);

System.out.println("validation result = " + result.isSuccessful());

for (SingleValidationMessage msg : result.getMessages()) {

System.out.println(msg.getMessage());

}

---

validation result = false

This does not appear to be a FHIR resource (unknown namespace/name 'http://hl7.org/fhir::Patient')

[James Agnew]

I notice in that code snippet you don't have DefaultProfileValidationSupport as a part of your chain. I don't know for sure that this is the cause, but it may help unless your custom provider is also serving up the base definitions.

Cheers,

James

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[Marc Dumontier]

Thanks James

So for reference to anyone else in the future..here's a working snippet of the most basic profile validator for a profile downloaded from simplifier (messy code version :P)

public static void main(String[] args) throws Exception {

String profileSnapshotXml = "my-profile.xml";

String profileUrl = "http://my.profile.url/xx";

FhirContext ctx = FhirContext.forR4();

IParser parser = ctx.newXmlParser();

StructureDefinition sd = (StructureDefinition) parser.parseResource(

new FileInputStream(new File(profileSnapshotXml)));

PrePopulatedValidationSupport prePopulatedValidationSupport = new PrePopulatedValidationSupport(ctx);

prePopulatedValidationSupport.addStructureDefinition(sd);

ValidationSupportChain validationSupportChain = 

new ValidationSupportChain(new DefaultProfileValidationSupport(ctx), prePopulatedValidationSupport);

FhirValidator validator = ctx.newValidator();

validator.registerValidatorModule(new FhirInstanceValidator(validationSupportChain));

Patient resource = new Patient();

resource.addName().setFamily("Simpson").addGiven("Homer");

resource.getMeta().addProfile(profileUrl);

ValidationResult result = validator.validateWithResult(resource);

IParser jParser = ctx.newJsonParser().setPrettyPrint(true);

System.out.println(jParser.encodeResourceToString(validator.validateWithResult(resource).toOperationOutcome()));

}

[Andrey Pismenetsky]

Good day. I am working with R4 validation against my test structure definition at the moment. The structure definition is at the simplifier.net.  There is an example in 12.2.3 Running the Validator part of HAPI FHIR documentation. According to this snippets I can add my profile to ValidationOptions object and then call validateWithResult method. I.e.:

/*
 * Note: You can also explicitly declare a profile to validate against
 * using the block below.
 */
// ValidationResult result = validator.validateWithResult(obs, new ValidationOptions().addProfile("https://fhir.simplifier.net/…/StructureDefinition/aaaaaaaa-bbbb-cccc-dddd-eeeeeeeeeeee"));

But this part of the code is under comment. What does it mean ?  Does it mean that this approach is wrong  and it is  better to use Marc's approach ?

Kind regards

Andrii

среда, 24 февраля 2021 г. в 22:56:23 UTC+2, Marc Dumontier: