Fix StructureDefinition Version-Specific Validation and Data Loss Issues

docs/user-guide/resources-construction.md

@@ -37,23 +37,27 @@ snapshot_structure_def = {
     "type": "Resource",
     "url": "http://example.org/fhir/StructureDefinition/LegacyPatient",
     "fhirVersion": "4.0.1",
-    "kind": "resource",
+    "kind": "logical",
     "status": "draft",
-    "abstract": False,
+    "abstract": True,
     "snapshot": {
         "element": [
             {
                 "id": "LegacyPatient",
                 "path": "LegacyPatient",
                 "min": 0,
-                "max": "*"
+                "max": "*",
+                "definition": "A legacy patient",
+                "base": {"path": "Resource", "min": 0, "max": "*"},
             },
             {
                 "id": "LegacyPatient.fullName",
                 "path": "LegacyPatient.fullName",
                 "min": 1,
                 "max": "1",
-                "type": [{"code": "string"}]
+                "type": [{"code": "string"}],
+                "definition": "A legacy patient's full name",
+                "base": {"path": "Resource", "min": 0, "max": "*"},
             }
         ]
     }

fhircraft/fhir/mapper/__init__.py

@@ -20,7 +20,10 @@
 from fhircraft.fhir.mapper.parser import FhirMappingLanguageParser
 from fhircraft.fhir.resources.datatypes.R5.core.concept_map import ConceptMap
 from fhircraft.fhir.resources.datatypes.R5.core.structure_map import StructureMap
-from fhircraft.fhir.resources.repository import CompositeStructureDefinitionRepository
+from fhircraft.fhir.resources.repository import (
+    CompositeStructureDefinitionRepository,
+    validate_structure_definition,
+)
 
 from .parser import FhirMappingLanguageParser
 
@@ -273,14 +276,8 @@ def add_structure_definition(
         Raises:
             ValueError: If structure definition is invalid or already exists
         """
-        from fhircraft.fhir.resources.definitions import StructureDefinition
-
-        if isinstance(structure_definition, dict):
-            struct_def = StructureDefinition(**structure_definition)
-        else:
-            struct_def = structure_definition
-
-        self.repository.add(struct_def, fail_if_exists=fail_if_exists)
+        structure_definition = validate_structure_definition(structure_definition)
+        self.repository.add(structure_definition, fail_if_exists=fail_if_exists)
 
     def add_structure_definitions_from_file(
         self, file_path: Union[str, Path], fail_if_exists: bool = False
@@ -299,7 +296,6 @@ def add_structure_definitions_from_file(
             FileNotFoundError: If file doesn't exist
             ValueError: If file format is invalid
         """
-        from fhircraft.fhir.resources.definitions import StructureDefinition
 
         path = Path(file_path)
         if not path.exists():
@@ -314,16 +310,18 @@ def add_structure_definitions_from_file(
         if isinstance(data, dict):
             if data.get("resourceType") == "StructureDefinition":
                 # Single StructureDefinition
-                struct_def = StructureDefinition(**data)
-                self.repository.add(struct_def, fail_if_exists=fail_if_exists)
+                structure_definition = validate_structure_definition(data)
+                self.repository.add(structure_definition, fail_if_exists=fail_if_exists)
                 count = 1
             elif data.get("resourceType") == "Bundle" and data.get("entry"):
                 # Bundle containing StructureDefinitions
                 for entry in data["entry"]:
                     resource = entry.get("resource", {})
                     if resource.get("resourceType") == "StructureDefinition":
-                        struct_def = StructureDefinition(**resource)
-                        self.repository.add(struct_def, fail_if_exists=fail_if_exists)
+                        structure_definition = validate_structure_definition(resource)
+                        self.repository.add(
+                            structure_definition, fail_if_exists=fail_if_exists
+                        )
                         count += 1
             else:
                 raise ValueError(

fhircraft/fhir/resources/__init__.py

@@ -13,7 +13,6 @@
 """
 
 from fhircraft.fhir.resources.base import FHIRBaseModel, FHIRSliceModel
-from fhircraft.fhir.resources.definitions import ElementDefinition, StructureDefinition
 from fhircraft.fhir.resources.factory import ResourceFactory, construct_resource_model
 from fhircraft.fhir.resources.repository import (
     CompositeStructureDefinitionRepository,
@@ -25,8 +24,6 @@
 __all__ = [
     "FHIRBaseModel",
     "FHIRSliceModel",
-    "StructureDefinition",
-    "ElementDefinition",
     "CompositeStructureDefinitionRepository",
     "HttpStructureDefinitionRepository",
     "PackageStructureDefinitionRepository",

fhircraft/fhir/resources/datatypes/R4/complex/__init__.py

@@ -51,9 +51,17 @@
 from .timing import Timing
 from .trigger_definition import TriggerDefinition
 from .usage_context import UsageContext
-
-
-from .element_definition import ElementDefinition
+from .element_definition import (
+    ElementDefinition,
+    ElementDefinitionType,
+    ElementDefinitionBase,
+    ElementDefinitionBinding,
+    ElementDefinitionConstraint,
+    ElementDefinitionSlicing,
+    ElementDefinitionSlicingDiscriminator,
+    ElementDefinitionExample,
+    ElementDefinitionMapping,
+)
 
 __all__ = [
     "Address",
@@ -73,6 +81,14 @@
     "Dosage",
     "Duration",
     "Element",
+    "ElementDefinitionType",
+    "ElementDefinitionBase",
+    "ElementDefinitionBinding",
+    "ElementDefinitionConstraint",
+    "ElementDefinitionSlicing",
+    "ElementDefinitionSlicingDiscriminator",
+    "ElementDefinitionExample",
+    "ElementDefinitionMapping",
     "ElementDefinition",
     "Expression",
     "Extension",
@@ -150,4 +166,12 @@
 TriggerDefinition.model_rebuild()
 UsageContext.model_rebuild()
 ElementDefinition.model_rebuild()
+ElementDefinitionType.model_rebuild()
+ElementDefinitionBase.model_rebuild()
+ElementDefinitionBinding.model_rebuild()
+ElementDefinitionConstraint.model_rebuild()
+ElementDefinitionSlicing.model_rebuild()
+ElementDefinitionSlicingDiscriminator.model_rebuild()
+ElementDefinitionExample.model_rebuild()
+ElementDefinitionMapping.model_rebuild()
 Extension.model_rebuild()

fhircraft/fhir/resources/datatypes/R4/complex/element_definition.py

@@ -2686,8 +2686,8 @@ def FHIR_eld_18_constraint_model_validator(self):
     def FHIR_eld_19_constraint_model_validator(self):
         return validate_model_constraint(
             self,
-            expression="path.matches('[^\\s\\.,:;\\\\'\"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\.[^\\s\\.,:;\\\\'\"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\[x\\])?(\\:[^\\s\\.]+)?)*')",
-            human="Element names cannot include some special characters",
+            expression="""path.matches('^[^\\s\\.,:;\\\'"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\.[^\\s\\.,:;\\\'"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\[x\\])?(\\:[^\\s\\.]+)?)*$')""",
+            human="Element path SHALL be expressed as a set of '.'-separated components with each component restricted to a maximum of 64 characters and with some limits on the allowed choice of characters",
             key="eld-19",
             severity="error",
         )
@@ -2696,8 +2696,8 @@ def FHIR_eld_19_constraint_model_validator(self):
     def FHIR_eld_20_constraint_model_validator(self):
         return validate_model_constraint(
             self,
-            expression="path.matches('[A-Za-z][A-Za-z0-9]*(\\.[a-z][A-Za-z0-9]*(\\[x])?)*')",
-            human="Element names should be simple alphanumerics with a max of 64 characters, or code generation tools may be broken",
+            expression="""path.matches('^[A-Za-z][A-Za-z0-9](\\.[a-z][A-Za-z0-9](\\[x])?)*$')""",
+            human="The first component of the path should be UpperCamelCase.  Additional components (following a '.') should be lowerCamelCase.  If this syntax is not adhered to, code generation tools may be broken. Logical models may be less concerned about this implication.",
             key="eld-20",
             severity="warning",
         )

fhircraft/fhir/resources/datatypes/R4B/complex/__init__.py

@@ -52,7 +52,17 @@
 from .usage_context import UsageContext
 from .population import Population
 from .dosage import Dosage
-from .element_definition import ElementDefinition
+from .element_definition import (
+    ElementDefinition,
+    ElementDefinitionType,
+    ElementDefinitionBase,
+    ElementDefinitionBinding,
+    ElementDefinitionConstraint,
+    ElementDefinitionSlicing,
+    ElementDefinitionSlicingDiscriminator,
+    ElementDefinitionExample,
+    ElementDefinitionMapping,
+)
 
 __all__ = [
     "Address",
@@ -73,6 +83,14 @@
     "Dosage",
     "Duration",
     "Element",
+    "ElementDefinitionType",
+    "ElementDefinitionBase",
+    "ElementDefinitionBinding",
+    "ElementDefinitionConstraint",
+    "ElementDefinitionSlicing",
+    "ElementDefinitionSlicingDiscriminator",
+    "ElementDefinitionExample",
+    "ElementDefinitionMapping",
     "ElementDefinition",
     "Expression",
     "Extension",
@@ -151,4 +169,12 @@
 TriggerDefinition.model_rebuild()
 UsageContext.model_rebuild()
 ElementDefinition.model_rebuild()
+ElementDefinitionType.model_rebuild()
+ElementDefinitionBase.model_rebuild()
+ElementDefinitionBinding.model_rebuild()
+ElementDefinitionConstraint.model_rebuild()
+ElementDefinitionSlicing.model_rebuild()
+ElementDefinitionSlicingDiscriminator.model_rebuild()
+ElementDefinitionExample.model_rebuild()
+ElementDefinitionMapping.model_rebuild()
 Extension.model_rebuild()

fhircraft/fhir/resources/datatypes/R4B/complex/element_definition.py

@@ -2708,8 +2708,8 @@ def FHIR_eld_18_constraint_model_validator(self):
     def FHIR_eld_19_constraint_model_validator(self):
         return validate_model_constraint(
             self,
-            expression="path.matches('^[^\\s\\.,:;\\\\'\"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\.[^\\s\\.,:;\\\\'\"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\[x\\])?(\\:[^\\s\\.]+)?)*$')",
-            human="Element names cannot include some special characters",
+            expression="""path.matches('^[^\\s\\.,:;\\\'"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\.[^\\s\\.,:;\\\'"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\[x\\])?(\\:[^\\s\\.]+)?)*$')""",
+            human="Element path SHALL be expressed as a set of '.'-separated components with each component restricted to a maximum of 64 characters and with some limits on the allowed choice of characters",
             key="eld-19",
             severity="error",
         )
@@ -2718,8 +2718,8 @@ def FHIR_eld_19_constraint_model_validator(self):
     def FHIR_eld_20_constraint_model_validator(self):
         return validate_model_constraint(
             self,
-            expression="path.matches('^[A-Za-z][A-Za-z0-9]*(\\.[a-z][A-Za-z0-9]*(\\[x])?)*$')",
-            human="Element names should be simple alphanumerics with a max of 64 characters, or code generation tools may be broken",
+            expression="""path.matches('^[A-Za-z][A-Za-z0-9](\\.[a-z][A-Za-z0-9](\\[x])?)*$')""",
+            human="The first component of the path should be UpperCamelCase.  Additional components (following a '.') should be lowerCamelCase.  If this syntax is not adhered to, code generation tools may be broken. Logical models may be less concerned about this implication.",
             key="eld-20",
             severity="warning",
         )

fhircraft/fhir/resources/datatypes/R5/complex/__init__.py

@@ -58,7 +58,18 @@
 from .extended_contact_detail import ExtendedContactDetail
 from .virtual_service_detail import VirtualServiceDetail
 from .dosage import Dosage
-from .element_definition import ElementDefinition
+from .element_definition import (
+    ElementDefinition,
+    ElementDefinitionType,
+    ElementDefinitionBase,
+    ElementDefinitionBinding,
+    ElementDefinitionBindingAdditional,
+    ElementDefinitionConstraint,
+    ElementDefinitionSlicing,
+    ElementDefinitionSlicingDiscriminator,
+    ElementDefinitionExample,
+    ElementDefinitionMapping,
+)
 
 __all__ = [
     "Address",
@@ -83,6 +94,15 @@
     "Dosage",
     "Duration",
     "Element",
+    "ElementDefinitionType",
+    "ElementDefinitionBase",
+    "ElementDefinitionBinding",
+    "ElementDefinitionBindingAdditional",
+    "ElementDefinitionConstraint",
+    "ElementDefinitionMapping",
+    "ElementDefinitionSlicing",
+    "ElementDefinitionSlicingDiscriminator",
+    "ElementDefinitionExample",
     "ElementDefinition",
     "Expression",
     "ExtendedContactDetail",
@@ -169,4 +189,13 @@
 UsageContext.model_rebuild()
 VirtualServiceDetail.model_rebuild()
 ElementDefinition.model_rebuild()
+ElementDefinitionType.model_rebuild()
+ElementDefinitionBase.model_rebuild()
+ElementDefinitionBinding.model_rebuild()
+ElementDefinitionBindingAdditional.model_rebuild()
+ElementDefinitionConstraint.model_rebuild()
+ElementDefinitionSlicing.model_rebuild()
+ElementDefinitionSlicingDiscriminator.model_rebuild()
+ElementDefinitionExample.model_rebuild()
+ElementDefinitionMapping.model_rebuild()
 Extension.model_rebuild()

fhircraft/fhir/resources/datatypes/R5/complex/element_definition.py

@@ -2930,7 +2930,7 @@ def FHIR_eld_18_constraint_model_validator(self):
     def FHIR_eld_19_constraint_model_validator(self):
         return validate_model_constraint(
             self,
-            expression="path.matches('^[^\\s\\.,:;\\\\'\"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\.[^\\s\\.,:;\\\\'\"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\[x\\])?(\\:[^\\s\\.]+)?)*$')",
+            expression="""path.matches('^[^\\s\\.,:;\\\'"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\.[^\\s\\.,:;\\\'"\\/|?!@#$%&*()\\[\\]{}]{1,64}(\\[x\\])?(\\:[^\\s\\.]+)?)*$')""",
             human="Element path SHALL be expressed as a set of '.'-separated components with each component restricted to a maximum of 64 characters and with some limits on the allowed choice of characters",
             key="eld-19",
             severity="error",
@@ -2940,7 +2940,7 @@ def FHIR_eld_19_constraint_model_validator(self):
     def FHIR_eld_20_constraint_model_validator(self):
         return validate_model_constraint(
             self,
-            expression="path.matches('^[A-Za-z][A-Za-z0-9]{0,63}(\\.[a-z][A-Za-z0-9]{0,63}(\\[x])?)*$')",
+            expression="""path.matches('^[A-Za-z][A-Za-z0-9]{0,63}(\\.[a-z][A-Za-z0-9]{0,63}(\\[x])?)*$')""",
             human="The first component of the path should be UpperCamelCase.  Additional components (following a '.') should be lowerCamelCase.  If this syntax is not adhered to, code generation tools may be broken. Logical models may be less concerned about this implication.",
             key="eld-20",
             severity="warning",