Validator is not finding reference to CodeableConcepts

[jorgealarco]

Hi,

I am using the validator to create a bunch of unit tests for conformance with the UK Core IG. I am trying the custom loading for the StructureDefinitions, CodeSystems and ValueSets of the FHIR R4 plus the corresponding resources of the UK Core IG.

Despite of having loaded all the resources, I am still getting warnings when validating the resource. I decided to custom load the FHIR R4 resources instead of using the pre-loaded data of the ParseConformance constructor in case there was an issue with the default data. I made sure the ValueSets are loaded before the StructureDefinitions as well, but I am still getting:

{
        location: 'Patient.contact[0].relationship[0]',
        resourceId: 'UKCore-Patient-RichardSmith-Example',
        severity: 'warning',
        message: 'Code "Personal" (https://fhir.hl7.org.uk/CodeSystem/UKCore-AdditionalPersonRelationshipRole) not found in value set'
      },
      {
        location: 'Patient.communication[0].language',
        resourceId: 'UKCore-Patient-RichardSmith-Example',
        severity: 'warning',
        message: 'Code "en" (https://fhir.hl7.org.uk/CodeSystem/UKCore-HumanLanguage) not found in value set'
      }

I wonder if this is related to the UK Core StructureDefinitions, as they don't contain a snapshot field. I am trying to create it using the fhir.generateSnapshot() function on the bundle. However, when doing this, I get the following error: Cannot find base definition "http://hl7.org/fhir/StructureDefinition/Extension" in bundle or core FHIR specification.

Could you please help me identifying why I am still getting the warnings on the validation of the resource? This is code I came up with:

// Generate bundles
const fhirValueSetBundle = SnapshotGenerator.createBundle.apply(this, fhirValueSets);
const fhirStructureDefinitionBundle = SnapshotGenerator.createBundle.apply(
  this,
  fhirStructureDefinitions,
);
const ukCoreValueSetBundle = SnapshotGenerator.createBundle.apply(this, ukCoreValueSets);
const ukCoreStructureDefinitionBundle = SnapshotGenerator.createBundle.apply(
  this,
  ukCoreStructureDefinitions,
);

// Parse all bundles into the conformance checker
const parser = new ParseConformance(false, Versions.R4);
parser.parseBundle(fhirValueSetBundle);
parser.parseBundle(ukCoreValueSetBundle);
parser.parseBundle(fhirStructureDefinitionBundle);
parser.parseBundle(ukCoreStructureDefinitionBundle);

const fhir = new Fhir(parser);
// fhir.generateSnapshot(ukCoreStructureDefinitionBundle);

const results = fhir.validate(ukCorePatientExample);
console.log(results);
expect(results.valid).toBe(true);

PS: Additionally, I believe there is an issue with the package exports, as I had to manually expose the SnapShotGenerator in the index.js file.

Many thanks.

[mintusah25]

Hi, I am also getting the same issue as mentioned by @jorgealarco
I tried to validate Observation resource[https://build.fhir.org/observation-example-f001-glucose.json.html] as below. I used valuesets.json and other json files from: https://build.fhir.org/downloads.html as mentioned in readme.

// Read the content of the 'observation.json' file which contains json from above mentioned url
var observation = fs.readFileSync('./observation.json').toString();

async function main() {
    // Get the data for new value sets, types, and resources from definitions.json
    let newValueSets = JSON.parse(
        fs
            .readFileSync('/definitions.json/valuesets.json')
            .toString()
    );
    let newTypes = JSON.parse(
        fs
            .readFileSync('/definitions.json/profiles-types.json')
            .toString()
    );
    let newResources = JSON.parse(
        fs
            .readFileSync('/definitions.json/profiles-resources.json')
            .toString()
    );

    // Create a parser instance with R4 FHIR version and load new definitions
    let parser = new ParseConformance(true, FhirVersions.R4);
    parser.parseBundle(newValueSets);
    parser.parseBundle(newTypes);
    parser.parseBundle(newResources);

    // Create a Fhir instance using the parser
    const v = new Fhir(parser);

    // Validate the observation data using the Fhir instance
    const result = v.validate(JSON.parse(observation));

    // Output the validation result to the console
    console.log('result', result);
}

// Call the main function to execute the logic
main();

Output:

result {
  valid: true,
  messages: [
    {
      location: 'Observation.code',
      resourceId: 'f001',
      severity: 'info',
      message: 'Value set "http://hl7.org/fhir/ValueSet/observation-codes" could not be found.'
    },
    {
      location: 'Observation.code',
      resourceId: 'f001',
      severity: 'warning',
      message: 'Code "15074-8" (http://loinc.org) not found in value set'
    },
    {
      location: 'Observation.interpretation[0]',
      resourceId: 'f001',
      severity: 'info',
      message: 'Value set "http://hl7.org/fhir/ValueSet/observation-interpretation" could not be found.'
    },
    {
      location: 'Observation.interpretation[0]',
      resourceId: 'f001',
      severity: 'warning',
      message: 'Code "H" (http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation) not found in value set'
    }
  ]
}

Since http://hl7.org/fhir/ValueSet/observation-codes is present in valuesets.json file downloaded from FHIR, I am getting this issue.
On some investigation, found that this valueset has some dependent valuesets present in: compose>include of object(refer valuesets.json file), and these valuesets are not present as provided by FHIR.

Is this logic actually required? As I am getting this issue for multiple number of valuesets and each having multiple dependencies.

Also any idea why getting error: message: 'Code "15074-8" (http://loinc.org) not found in value set' ? As this is a valid code, refer: https://loinc.org/15074-8#:~:text=LOINC%2015074%2D8%20Glucose%20%5BMoles%2Fvolume%5D%20in%20Blood