Error creating resource object

[julsas]

• fhir.resources version: 6.0.0
• Python version: 3.6.9
• Operating System: ubuntu

Description

Creation of resource objects fails for some data types when parsing and creating resource objects from json data. This is the case for decimal within e.g. Quantity and for datetime. Calling .dict() on the object does not return a valid python dict.

What I Did

with open('./Medication-example.json') as json_file:
    json_data = json.load(json_file)

med = Medication.parse_obj(json_data)
med = med.dict()
print(med)

{'id': 'demo-medication-3', 'code': {'coding': [{'code': '116602009', 'display': 'Prednisone (substance)', 'system': 'http://snomed.info/sct'}, {'code': 'H02AB07', 'display': 'prednisone', 'system': 'http://www.whocc.no/atc'}], 'text': 'Deltacortene tablet 25 mg'}, 'form': {'coding': [{'code': '10219000', 'display': 'Tablet', 'system': 'urn:oid:0.4.0.127.0.16.1.1.2.1'}]}, 'ingredient': [{'itemCodeableConcept': {'coding': [{'code': '116602009', 'display': 'Prednisone (substance)', 'system': 'http://snomed.info/sct'}]}, 'strength': {'denominator': {'code': '1', 'system': 'http://unitsofmeasure.org', 'unit': 'tablet', 'value': Decimal('1')}, 'numerator': {'code': 'mg', 'system': 'http://unitsofmeasure.org', 'value': Decimal('25')}}}], 'resourceType': 'Medication'}

med == dict
False

print(json.dumps(med, indent=4))
TypeError: Object of type 'Decimal' is not JSON serializable

---

with open('./Observation-example.json') as json_file:
    json_data = json.load(json_file)

obs = Observation(**json_data)
obs = obs.dict()
print(obs)

{'code': {'coding': [{'code': '718-7', 'display': 'Hemoglobin [Mass/volume] in Blood', 'system': 'http://loinc.org'}], 'text': 'Hemoglobin'}, 'effectiveDateTime': datetime.datetime(2021, 1, 18, 11, 5, 52, tzinfo=datetime.timezone(datetime.timedelta(0, 3600))), 'status': 'final', 'subject': {'reference': 'Patient/156ff0c4-5122-41ca-8bf5-32faf8d3f3a1'}, 'valueQuantity': {'code': 'g/dL', 'system': 'http://unitsofmeasure.org', 'unit': 'g/dL', 'value': Decimal('9.3')}, 'resourceType': 'Observation'}

print(json.dumps(obs, indent=4))
TypeError: Object of type 'datetime' is not JSON serializable

[nazrulworld]

It is always recommended that use the built-in method json. For example in your case

obs = Observation(**json_data)
print(obs.json(indent=2))

If you really want to use json.dumps (python built-in), then you have to do a little bit of extra

import json
from pydantic.json import pydantic_encoder
obs = Observation(**json_data)
obs = obs.dict()
print(json.dumps(obs,indent=2, default=pydantic_encoder))

[julsas]

Thanks for the clarification! I hadn't figured out that I needed the pydantic_encoder.