samply / golang-fhir-models Goto Github PK

In the docs for Extensibility it reads

The value[x] element has an actual name of "value" and then the TitleCased name of one of these defined types, and its contents are those as defined for that type:
valueBase64Binary: base64Binary
valueBoolean: boolean
valueCanonical: canonical
...

The Extension type does not provide for the values, which is the useful part of the extension

What happened:
Marshalling an IssueType leads to partially wrong codes within the result. This makes it impossible to unmarshall an IssueType if it has previously been marshalled using this package.

What you expected to happen:
Being able to marshall an IssueType and unmarshall it right back.

Example for reproduction:

issueType := fm.IssueTypeTooLong
issueTypeRawJSON, _ := json.Marshal(issueType)
		
var parsedIssueType fm.IssueType
err := json.Unmarshal(issueTypeRawJSON, &parsedIssueType)
if err != nil {
    fmt.Println(err)
}

This will fail with the following error message: unknown IssueType code Content Too Long

Additional Info:

The problem has to be in IssueType's Code function. It seems to be mimicking the Display function at several places instead of ensuring it is doing the opposite of what the switch statement in the Unmarshalling function does.

Environment:
golang-fhir-models version: 0.2.0

Hello,

Thanks for this nice package.
I was wondering why is there pointer on each generated resources' properties?

My objective here is to read fhir data from a bigquery. But the type mapping is not possible because of properties generated with pointer
I know this is not the purpose of this package to let us map fhir data from bigquery.

For example :

func (r Request) EncounteredPatients(practitionerId string) ([]fhir.Patient, error) {
	it, err := r.Raw(fmt.Sprintf(`SELECT * 
		FROM <gcp_project_id>.<bigquery_datasets>.Patient patient 
		INNER  JOIN (
			SELECT DISTINCT subject.patientId  
			FROM bios-innov.metamedical.Encounter as encounter, UNNEST(encounter.participant) as participant  
			WHERE participant.individual.practitionerId = '%v') encounters  
		ON patient.id = encounters.PatientId`, practitionerId))
	if err != nil {
		return []fhir.Patient{}, fmt.Errorf("EncounteredPatients failed for %v: %w", practitionerId, err)
	}
	patients := make([]fhir.Patient, 0, 0)
	for {
		var patient fhir.Patient

		err := it.Next(&patient)
		if err == iterator.Done {
			break
		}
		if err != nil {
			return patients, fmt.Errorf("Failed to read result : %w", err) // TODO: Handle error.
		}
		// fmt.Println(row)
		patients = append(patients, patient)
	}
	return patients, nil
}

Will lead to an error bigquery: schema field active of type BOOLEAN is not assignable to struct field Active of type *bool

But doing this

func (r Request) EncounteredPatients(practitionerId string) ([]fhir.Patient, error) {
	it, err := r.Raw(fmt.Sprintf(`SELECT * 
		FROM <gcp_project_id>.<bigquery_datasets>.Patient patient 
		INNER  JOIN (
			SELECT DISTINCT subject.patientId  
			FROM bios-innov.metamedical.Encounter as encounter, UNNEST(encounter.participant) as participant  
			WHERE participant.individual.practitionerId = '%v') encounters  
		ON patient.id = encounters.PatientId`, practitionerId))
	if err != nil {
		return []fhir.Patient{}, fmt.Errorf("EncounteredPatients failed for %v: %w", practitionerId, err)
	}
	patients := make([]fhir.Patient, 0, 0)
	for {
		var patient fhir.Patient
		var row map[string]bigquery.Value
		err := it.Next(&row)
		if err == iterator.Done {
			break
		}
		if err != nil {
			return patients, fmt.Errorf("Failed to read result : %w", err) // TODO: Handle error.
		}
		jsonRaw, errJson := json.Marshal(row)
		if errJson != nil {
			return patients, fmt.Errorf("Failed to marshal result : %w", errJson)
		}
		errReDecode := json.Unmarshal(jsonRaw, &patient)
		if errReDecode != nil {
			return patients, fmt.Errorf("Failed to Unmarshal result : %w", errReDecode)
		}
		// fmt.Println(row)
		patients = append(patients, patient)
	}
	return patients, nil
}

Will succeed.

https://www.hl7.org/fhir/observation-definitions.html#Observation.value_x_
https://www.hl7.org/fhir/formats.html#choice

Thanks for the code

While using this library found that it is missing eventCoding in the message Header as per the standards in the hl7 URL. Felt like it would be nice to address and once it is updated it will be useful for parsing out that information in my code as well.

http://hl7.org/fhir/R4/messageheader.html.
{
"resourceType" : "MessageHeader",
// from Resource: id, meta, implicitRules, and language
// from DomainResource: text, contained, extension, and modifierExtension
// event[x]: Code for the event this message represents or link to event definition. One of these 2:
"eventCoding" : { Coding },
..................
//ignoring remaining fields
}
Any suggestions will be helpful

https://github.com/samply/golang-fhir-models/blob/master/fhir-models-gen/cmd/valueSet.go#L60 and https://github.com/samply/golang-fhir-models/blob/master/fhir-models-gen/cmd/genResources.go#L277 encode HTML characters deemed problematic (&, <, and >), because that is the default behaviour of json.Marshal. This behaviour can be turned off by using a custom encoder, see https://pkg.go.dev/encoding/json#Encoder.SetEscapeHTML.

There are certain fields in the FHIR models which contain those "problematic" characters, but they must not be escaped. For example, http://hl7.org/fhir/R4B/valueset-quantity-comparator.html and the div field of http://hl7.org/fhir/R4B/narrative.html.

I have a fix for this at michaelsauter@b45358a.

So far I've been working based on https://github.com/lifebox-healthcare/golang-fhir-models, as it contains PR #7, which I need for my work as well. @alexanderkiel I am wondering if the samply repo is still maintained? If not, can we somehow designate what the "main" fork is going forward so that all changes go in there? I detected a bunch of other issues and have fixes for them locally as well (wrong value decimal type, spelling of ID fields, gen script issues and FHIR v4.3.0 compatibility).

FYI @frankoid https://github.com/lifebox-healthcare/golang-fhir-models does not have issues enabled, otherwise I could open issues there as well (if the samply repo is not maintained). If your fork isn't maintained either, I'm going to open a new fork, enable issues there and push my fixes.

When marshaling then unmarshaling Observations we are encountering the following error

"unknown QuantityComparator code `\u003c`"

It appears that this is to do with how the UnmarshalJSON function is implemented for the QuantityComparator

Its seems that simply stringing the quantity comparator doesnt properly convert \u003c into < and instead the code would need to use json.Unmarshall?

https://github.com/samply/golang-fhir-models/blob/master/fhir-models/fhir/quantityComparator.go#L40

Example:

package observationtest

import (
	"encoding/json"
	"github.com/samply/golang-fhir-models/fhir-models/fhir"
	"testing"
)

func Test_observation_marshalling(t *testing.T) {
	id := "123"
	snomed := "snomed"
	code := "456"

	lessThan := fhir.QuantityComparatorLessThan

	o := fhir.Observation{
		Id:     &id,
		Status: fhir.ObservationStatusPreliminary,
		Code: fhir.CodeableConcept{
			Coding: []fhir.Coding{
				{
					System: &snomed,
					Code:   &code,
				},
			},
		},
		ValueQuantity: &fhir.Quantity{
			Comparator: &lessThan,
		},
	}

	b, err := json.Marshal(o)
	if err != nil {
		panic(err)
	}

	var observationUnmarshalled fhir.Observation

	err = json.Unmarshal(b, &observationUnmarshalled)
	if err != nil {
		panic(err)
	}
}