Make Age and Duration extensions lower case for urls (#29)

* Change 'age' and 'extension' urls to be lower case, keep Uppercase for python class names

* Update .gitignore

* Increase test coverage

.gitignore

@@ -66,4 +66,6 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
-cover/
+cover/
+
+.DS_Store

fhirflat/resources/extensions.py

@@ -316,7 +316,7 @@ class Duration(_DataType):
 
     resource_type = Field("Duration", const=True)
 
-    url = Field("Duration", const=True, alias="url")
+    url = Field("duration", const=True, alias="url")
 
     valueQuantity: fhirtypes.QuantityType = Field(
         None,
@@ -352,7 +352,7 @@ class Age(_DataType):
 
     resource_type = Field("Age", const=True)
 
-    url = Field("Age", const=True, alias="url")
+    url = Field("age", const=True, alias="url")
 
     valueQuantity: fhirtypes.QuantityType = Field(
         None,

fhirflat/resources/patient.py

@@ -22,7 +22,7 @@ class Patient(Patient, FHIRFlatBase):
         title="Additional content defined by implementations",
         description=(
             """
-            Contains the G.H 'Age' and 'birthSex' extensions,
+            Contains the G.H 'age' and 'birthSex' extensions,
             and allows extensions from other implementations to be included."""
         ),
         # if property is element of this resource.

fhirflat/resources/procedure.py

@@ -33,7 +33,7 @@ class Procedure(_Procedure, FHIRFlatBase):
         title="Additional content defined by implementations",
         description=(
             """
-            Contains the G.H 'timingPhase', 'relativePeriod' and 'Duration' extensions,
+            Contains the G.H 'timingPhase', 'relativePeriod' and 'duration' extensions,
             and allows extensions from other implementations to be included."""
         ),
         # if property is element of this resource.
@@ -75,7 +75,7 @@ def validate_extension_contents(cls, extensions):
 
         if duration_count > 1 or tim_phase_count > 1 or rel_phase_count > 1:
             raise ValueError(
-                "Duration, timingPhase and relativePeriod can only appear once."
+                "duration, timingPhase and relativePeriod can only appear once."
             )
 
         return extensions

fhirflat/util.py

@@ -32,7 +32,7 @@ def get_fhirtype(t: str | list[str]):
     if isinstance(t, list):
         return [get_fhirtype(x) for x in t]
 
-    if not hasattr(extensions, t):
+    if not (hasattr(extensions, t) or hasattr(extensions, t.capitalize())):
         try:
             return getattr(getattr(fhir.resources, t.lower()), t)
         except AttributeError:
@@ -61,4 +61,7 @@ def get_local_extension_type(t: str):
     try:
         return getattr(extensions, t)
     except AttributeError:
-        raise AttributeError(f"Could not find {t} in fhirflat extensions")
+        try:
+            return getattr(extensions, t.capitalize())
+        except AttributeError:
+            raise AttributeError(f"Could not find {t} in fhirflat extensions")

tests/test_extensions.py

@@ -107,15 +107,15 @@ def test_approximateDate(data, expected_type_date, expected_type_str):
     assert type(approximate_date.valueString) is expected_type_str
 
 
-dur = {"url": "Duration", "valueQuantity": {"value": 3, "unit": "days"}}
+dur = {"url": "duration", "valueQuantity": {"value": 3, "unit": "days"}}
 
 
-def test_Duration():
-    duration = Duration(**dur)
-    assert isinstance(duration, DataType)
-    assert duration.resource_type == "Duration"
-    assert duration.url == "Duration"
-    assert type(duration.valueQuantity) is _Quantity
+def test_duration():
+    duration_inst = Duration(**dur)
+    assert isinstance(duration_inst, DataType)
+    assert duration_inst.resource_type == "Duration"
+    assert duration_inst.url == "duration"
+    assert type(duration_inst.valueQuantity) is _Quantity
 
 
 dte = {"extension": [{"url": "approximateDate", "valueDate": "2021-01-01"}, rel_day]}

tests/test_patient_resource.py

@@ -90,7 +90,7 @@ def test_bulk_fhir_to_flat_patient():
     "id": "f001",
     "active": True,
     "extension": [
-        {"url": "Age", "valueQuantity": {"value": 25, "unit": "years"}},
+        {"url": "age", "valueQuantity": {"value": 25, "unit": "years"}},
         {
             "url": "birthSex",
             "valueCodeableConcept": {
@@ -112,8 +112,8 @@ def test_bulk_fhir_to_flat_patient():
 PATIENT_EXT_FLAT = {
     "resourceType": "Patient",
     "id": "f001",
-    "extension.Age.value": 25,
-    "extension.Age.unit": "years",
+    "extension.age.value": 25,
+    "extension.age.unit": "years",
     "extension.birthSex.code": "http://snomed.info/sct|248152002",
     "extension.birthSex.text": "Female (finding)",
     "gender": "female",
@@ -123,7 +123,7 @@ def test_bulk_fhir_to_flat_patient():
 PATIENT_EXT_DICT_OUT = {
     "id": "f001",
     "extension": [
-        {"url": "Age", "valueQuantity": {"value": 25, "unit": "years"}},
+        {"url": "age", "valueQuantity": {"value": 25, "unit": "years"}},
         {
             "url": "birthSex",
             "valueCodeableConcept": {

tests/test_procedure_resource.py

@@ -10,7 +10,7 @@
     "instantiatesCanonical": ["http://example.org/fhir/PlanDefinition/KDN5"],
     "status": "completed",
     "extension": [
-        {"url": "Duration", "valueQuantity": {"value": 1, "unit": "d"}},
+        {"url": "duration", "valueQuantity": {"value": 1, "unit": "d"}},
         {
             "url": "timingPhase",
             "valueCodeableConcept": {
@@ -73,8 +73,8 @@
 
 PROCEDURE_FLAT = {
     "resourceType": "Procedure",
-    "extension.Duration.value": 1,
-    "extension.Duration.unit": "d",
+    "extension.duration.value": 1,
+    "extension.duration.unit": "d",
     "extension.timingPhase.code": "timing.com|1234",
     "extension.timingPhase.text": None,
     "extension.relativePeriod.relativeStart": 2,
@@ -97,7 +97,7 @@
     "resourceType": "Procedure",
     "status": "completed",
     "extension": [
-        {"url": "Duration", "valueQuantity": {"value": 1.0, "unit": "d"}},
+        {"url": "duration", "valueQuantity": {"value": 1.0, "unit": "d"}},
         {
             "url": "relativePeriod",
             "extension": [

tests/test_utils.py

@@ -5,7 +5,7 @@
 from fhir.resources.codeableconcept import CodeableConcept
 from fhir.resources.medicationstatement import MedicationStatementAdherence
 
-from fhirflat.resources.extensions import dateTimeExtension
+from fhirflat.resources.extensions import dateTimeExtension, Duration
 
 
 def test_group_keys():
@@ -42,6 +42,7 @@ def test_group_keys():
         ("CodeableConcept", CodeableConcept),
         ("MedicationStatementAdherence", MedicationStatementAdherence),
         ("dateTimeExtension", dateTimeExtension),
+        ("duration", Duration),
     ],
 )
 def test_get_fhirtype(input, expected):