Draft attempt at ingestion using mapping file

fhirflat/flat2fhir.py

@@ -17,7 +17,7 @@ def create_codeable_concept(
     """Re-creates a codeableConcept structure from the FHIRflat representation."""
 
     # for reading in from ingestion pipeline
-    if (name + ".code" and name + ".system") in old_dict:
+    if name + ".code" in old_dict and name + ".system" in old_dict:
         code = old_dict[name + ".code"]
         if isinstance(code, list) and len(code) > 1:
             new_dict = {"coding": []}

fhirflat/resources/extension_types.py

@@ -51,5 +51,9 @@ class birthSexType(AbstractType):
     __resource_type__ = "birthSex"
 
 
+class raceType(AbstractType):
+    __resource_type__ = "Race"
+
+
 class dateTimeExtensionType(AbstractType):
     __resource_type__ = "dateTimeExtension"

fhirflat/resources/extension_validators.py

@@ -65,6 +65,7 @@ def __init__(self):
             "Duration": (None, ".extensions"),
             "Age": (None, ".extensions"),
             "birthSex": (None, ".extensions"),
+            "Race": (None, ".extensions"),
             "dateTimeExtension": (None, ".extensions"),
         }
 
@@ -230,5 +231,9 @@ def birthsex_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
     return Validators().fhir_model_validator("birthSex", v)
 
 
+def race_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
+    return Validators().fhir_model_validator("Race", v)
+
+
 def datetimeextension_validator(v: Union[StrBytes, dict, Path, FHIRAbstractModel]):
     return Validators().fhir_model_validator("dateTimeExtension", v)

fhirflat/resources/extensions.py

@@ -417,6 +417,42 @@ def elements_sequence(cls):
         ]
 
 
+class Race(_DataType):
+    """
+    An ISARIC extension collecting data on the race of a patient.
+    """
+
+    resource_type = Field("Race", const=True)
+
+    url = Field("race", const=True, alias="url")
+
+    valueCodeableConcept: fhirtypes.CodeableConceptType = Field(
+        None,
+        alias="valueCodeableConcept",
+        title="Value of extension",
+        description=(
+            "Value of extension - must be one of a constrained set of the data "
+            "types (see [Extensibility](extensibility.html) for a list)."
+        ),
+        # if property is element of this resource.
+        element_property=True,
+        element_required=True,
+    )
+
+    @classmethod
+    def elements_sequence(cls):
+        """returning all elements names from
+        ``Extension`` according specification,
+        with preserving original sequence order.
+        """
+        return [
+            "id",
+            "extension",
+            "url",
+            "valueCodeableConcept",
+        ]
+
+
 # ------------------- extension types ------------------------------
 
 

fhirflat/resources/patient.py

@@ -1,10 +1,7 @@
 from fhir.resources.patient import Patient
 from .base import FHIRFlatBase
-from .extension_types import (
-    ageType,
-    birthSexType,
-)
-from .extensions import Age, birthSex
+from .extension_types import ageType, birthSexType, raceType
+from .extensions import Age, birthSex, Race
 import orjson
 
 from ..flat2fhir import expand_concepts
@@ -16,18 +13,20 @@
 
 
 class Patient(Patient, FHIRFlatBase):
-    extension: list[Union[ageType, birthSexType, fhirtypes.ExtensionType]] = Field(
-        None,
-        alias="extension",
-        title="Additional content defined by implementations",
-        description=(
-            """
+    extension: list[Union[ageType, birthSexType, raceType, fhirtypes.ExtensionType]] = (
+        Field(
+            None,
+            alias="extension",
+            title="Additional content defined by implementations",
+            description=(
+                """
             Contains the G.H 'age' and 'birthSex' extensions,
             and allows extensions from other implementations to be included."""
-        ),
-        # if property is element of this resource.
-        element_property=True,
-        union_mode="smart",
+            ),
+            # if property is element of this resource.
+            element_property=True,
+            union_mode="smart",
+        )
     )
 
     # attributes to exclude from the flat representation
@@ -47,9 +46,10 @@ class Patient(Patient, FHIRFlatBase):
     def validate_extension_contents(cls, extensions):
         age_count = sum(isinstance(item, Age) for item in extensions)
         birthsex_count = sum(isinstance(item, birthSex) for item in extensions)
+        race_count = sum(isinstance(item, Race) for item in extensions)
 
-        if age_count > 1 or birthsex_count > 1:
-            raise ValueError("Age and birthSex can only appear once.")
+        if age_count > 1 or birthsex_count > 1 or race_count > 1:
+            raise ValueError("Age, birthSex and Race can only appear once.")
 
         return extensions