Parsing error for StructureDefinitions with type slicing in R4B

[cybernop]

• fhir.resources version: 7.1.0
• Python version: 3.12.3
• Operating System: Ubuntu

Description

I was trying to read a structure definition that contains type slicing. The definition has the canonical http://fhir.de/StructureDefinition/observation-de-vitalsign.

What I Did

Then I tried to read the the resource from a JSON file

from fhir.resources.R4B.structuredefinition import StructureDefinition

file_path = pathlib.Path("profile.json")
StructureDefinition.parse_file(file_path)

which gave the errors

pydantic.v1.error_wrappers.ValidationError: 36 validation errors for StructureDefinition
differential -> element -> 2 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 4 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 5 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 7 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 8 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 9 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 10 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 11 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 12 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 14 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 15 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 16 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 17 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 18 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
differential -> element -> 19 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 14 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 19 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 20 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 25 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 28 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 29 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 30 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 31 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 32 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 33 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 34 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 35 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 60 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 61 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 62 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 63 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 64 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 65 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 66 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 67 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
snapshot -> element -> 68 -> id
  string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
def test_fhir_profile_from_json():
        file = Path(PROFILE_FILE)
    
        assert file.exists()
    
>       result = FhirProfile.from_json(file)

service/tests/data/test_fhir_profile.py:13: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
service/src/structure_comparer/data/fhir_profile.py:27: in from_json
    data = StructureDefinition.parse_file(file_path)
.venv/lib/python3.12/site-packages/fhir/resources/core/fhirabstractmodel.py:243: in parse_file
    return cls.parse_obj(obj)
.venv/lib/python3.12/site-packages/pydantic/v1/main.py:526: in parse_obj
    return cls(**obj)
.venv/lib/python3.12/site-packages/fhir/resources/core/fhirabstractmodel.py:105: in __init__
    BaseModel.__init__(__pydantic_self__, **data)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

__pydantic_self__ = StructureDefinition()
data = {'abstract': False, 'baseDefinition': 'http://hl7.org/fhir/StructureDefinition/Observation', 'contact': [{'telecom': [{'system': 'url', 'value': 'http://hl7.de/technische-komitees/fhir/'}]}], 'date': '2023-11-30', ...}
values = {'abstract': False, 'abstract__ext': None, 'baseDefinition': 'http://hl7.org/fhir/StructureDefinition/Observation', 'baseDefinition__ext': None, ...}
fields_set = {'abstract', 'baseDefinition', 'contact', 'date', 'derivation', 'description', ...}
validation_error = ValidationError(model='StructureDefinition', errors=[{'loc': ('differential', 'element', 2, 'id'), 'msg': 'string does...oes not match regex "^[A-Za-z0-9\\-.]+$"', 'type': 'value_error.str.regex', 'ctx': {'pattern': '^[A-Za-z0-9\\-.]+$'}}])

    def __init__(__pydantic_self__, **data: Any) -> None:
        """
        Create a new model by parsing and validating input data from keyword arguments.
    
        Raises ValidationError if the input data cannot be parsed to form a valid model.
        """
        # Uses something other than `self` the first arg to allow "self" as a settable attribute
        values, fields_set, validation_error = validate_model(__pydantic_self__.__class__, data)
        if validation_error:
>           raise validation_error
E           pydantic.v1.error_wrappers.ValidationError: 36 validation errors for StructureDefinition
E           differential -> element -> 2 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 4 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 5 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 7 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 8 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 9 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 10 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 11 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 12 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 14 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 15 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 16 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 17 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 18 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           differential -> element -> 19 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 14 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 19 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 20 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 25 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 28 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 29 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 30 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 31 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 32 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 33 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 34 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 35 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 60 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 61 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 62 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 63 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 64 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$)
E           snapshot -> element -> 65 -> id
E             string does not match regex "^[A-Za-z0-9\-.]+$" (type=value_error.str.regex; pattern=^[A-Za-z0-9\-.]+$

Expectation

It is expected to parse this definition correctly. The issue here is that a regex for id is used on Element.id which is an string and therefore does allow other symbols.

[cybernop]

This issue will be solved by PR #160

[cybernop]

Bump. This is still not solved and prevents usage of this library any StructureDefinition in Germany as we only use R4(B).

In my opinion the current state of the support for R4B is broken and there appears to be no interest in fixing it.