NRL-746 add extension to model

Author: eesa456

layer/nrlf/consumer/fhir/r4/model.py

@@ -424,42 +424,60 @@ class RequestHeaderCorrelationId(BaseModel):
     __root__: Annotated[str, Field(example="11C46F5F-CDEF-4865-94B2-0EE0EDCC26DA")]
 
 
-class DocumentReferenceContent(BaseModel):
+class CodeableConcept(BaseModel):
     id: Annotated[
         str | None,
         Field(
             description="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
             regex="[A-Za-z0-9\\-\\.]{1,64}",
         ),
     ] = None
-    attachment: Annotated[
-        Attachment,
+    coding: list[Coding] | None = None
+    text: Annotated[
+        str | None,
         Field(
-            description="The document or URL of the document along with critical metadata to prove content has integrity."
+            description="A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.",
+            regex="[ \\r\\n\\t\\S]+",
         ),
-    ]
-    format: Annotated[
-        Coding | None,
+    ] = None
+
+
+class Extension(BaseModel):
+    valueCodeableConcept: Annotated[
+        CodeableConcept,
         Field(
-            description="An identifier of the document encoding, structure, and template that the document conforms to beyond the base format indicated in the mimeType."
+            description="Details about the extension.",
         ),
-    ] = None
+    ]
+    url: Annotated[
+        str, Field(description="The reference link for the details.", regex="\\S*")
+    ]
 
 
-class CodeableConcept(BaseModel):
+class DocumentReferenceContent(BaseModel):
     id: Annotated[
         str | None,
         Field(
             description="Unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces.",
             regex="[A-Za-z0-9\\-\\.]{1,64}",
         ),
     ] = None
-    coding: list[Coding] | None = None
-    text: Annotated[
-        str | None,
+    attachment: Annotated[
+        Attachment,
         Field(
-            description="A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user.",
-            regex="[ \\r\\n\\t\\S]+",
+            description="The document or URL of the document along with critical metadata to prove content has integrity."
+        ),
+    ]
+    format: Annotated[
+        Coding | None,
+        Field(
+            description="An identifier of the document encoding, structure, and template that the document conforms to beyond the base format indicated in the mimeType."
+        ),
+    ] = None
+    extension: Annotated[
+        list[Extension] | None,
+        Field(
+            description="Additional code system information for the document content."
         ),
     ] = None
 

layer/nrlf/core/tests/test_validators.py

@@ -599,6 +599,195 @@ def test_validate_category_coding_invalid_system():
     }
 
 
+def test_validate_content_extension_too_many_extensions():
+    validator = DocumentReferenceValidator()
+    document_ref_data = load_document_reference_json("Y05868-736253002-Valid")
+
+    document_ref_data["content"][0]["extension"].append(
+        {
+            "url": "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability",
+            "valueCodeableConcept": {
+                "coding": [
+                    {
+                        "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability",
+                        "code": "static",
+                        "display": "static",
+                    }
+                ]
+            },
+        }
+    )
+
+    result = validator.validate(document_ref_data)
+
+    assert result.is_valid is False
+    assert result.resource.id == "Y05868-99999-99999-999999"
+    assert len(result.issues) == 1
+    assert result.issues[0].dict(exclude_none=True) == {
+        "severity": "error",
+        "code": "invalid",
+        "details": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                    "code": "INVALID_RESOURCE",
+                    "display": "Invalid validation of resource",
+                }
+            ]
+        },
+        "diagnostics": "Invalid content extension length: 2 Extension must only contain a single value",
+        "expression": ["content[0].extension"],
+    }
+
+
+def test_validate_content_extension_invalid_code():
+    validator = DocumentReferenceValidator()
+    document_ref_data = load_document_reference_json("Y05868-736253002-Valid")
+
+    document_ref_data["content"][0]["extension"][0] = {
+        "url": "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability",
+        "valueCodeableConcept": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability",
+                    "code": "invalid",
+                    "display": "invalid",
+                }
+            ]
+        },
+    }
+
+    result = validator.validate(document_ref_data)
+
+    assert result.is_valid is False
+    assert result.resource.id == "Y05868-99999-99999-999999"
+    assert len(result.issues) == 1
+    assert result.issues[0].dict(exclude_none=True) == {
+        "severity": "error",
+        "code": "value",
+        "details": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                    "code": "INVALID_RESOURCE",
+                    "display": "Invalid validation of resource",
+                }
+            ]
+        },
+        "diagnostics": "Invalid content extension code: invalid Extension code must be 'static' or 'dynamic'",
+        "expression": ["content[0].extension[0].valueCodeableConcept.coding[0].code"],
+    }
+
+
+def test_validate_content_extension_invalid_system():
+    validator = DocumentReferenceValidator()
+    document_ref_data = load_document_reference_json("Y05868-736253002-Valid")
+
+    document_ref_data["content"][0]["extension"][0] = {
+        "url": "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability",
+        "valueCodeableConcept": {
+            "coding": [
+                {
+                    "system": "invalid",
+                    "code": "static",
+                    "display": "static",
+                }
+            ]
+        },
+    }
+
+    result = validator.validate(document_ref_data)
+
+    assert result.is_valid is False
+    assert result.resource.id == "Y05868-99999-99999-999999"
+    assert len(result.issues) == 1
+    assert result.issues[0].dict(exclude_none=True) == {
+        "severity": "error",
+        "code": "value",
+        "details": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                    "code": "INVALID_RESOURCE",
+                    "display": "Invalid validation of resource",
+                }
+            ]
+        },
+        "diagnostics": "Invalid content extension system: invalid Extension system must be 'https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability'",
+        "expression": ["content[0].extension[0].valueCodeableConcept.coding[0].system"],
+    }
+
+
+def test_validate_content_extension_invalid_url():
+    validator = DocumentReferenceValidator()
+    document_ref_data = load_document_reference_json("Y05868-736253002-Valid")
+
+    document_ref_data["content"][0]["extension"][0] = {
+        "url": "invalid",
+        "valueCodeableConcept": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability",
+                    "code": "static",
+                    "display": "static",
+                }
+            ]
+        },
+    }
+
+    result = validator.validate(document_ref_data)
+
+    assert result.is_valid is False
+    assert result.resource.id == "Y05868-99999-99999-999999"
+    assert len(result.issues) == 1
+    assert result.issues[0].dict(exclude_none=True) == {
+        "severity": "error",
+        "code": "value",
+        "details": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                    "code": "INVALID_RESOURCE",
+                    "display": "Invalid validation of resource",
+                }
+            ]
+        },
+        "diagnostics": "Invalid content extension url: invalid Extension url must be 'https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability'",
+        "expression": ["content[0].extension[0].url"],
+    }
+
+
+def test_validate_content_extension_missing_coding():
+    validator = DocumentReferenceValidator()
+    document_ref_data = load_document_reference_json("Y05868-736253002-Valid")
+
+    document_ref_data["content"][0]["extension"][0] = {
+        "url": "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability",
+        "valueCodeableConcept": {"coding": []},
+    }
+
+    result = validator.validate(document_ref_data)
+
+    assert result.is_valid is False
+    assert result.resource.id == "Y05868-99999-99999-999999"
+    assert len(result.issues) == 1
+    assert result.issues[0].dict(exclude_none=True) == {
+        "severity": "error",
+        "code": "required",
+        "details": {
+            "coding": [
+                {
+                    "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                    "code": "INVALID_RESOURCE",
+                    "display": "Invalid validation of resource",
+                }
+            ]
+        },
+        "diagnostics": "Missing content[0].extension[0].valueCodeableConcept.coding, extension must have at least one coding.",
+        "expression": ["content[0].extension.valueCodeableConcept.coding"],
+    }
+
+
 def test_validate_identifiers_invalid_systems():
     validator = DocumentReferenceValidator()
     document_ref_data = load_document_reference_json("Y05868-736253002-Valid")

layer/nrlf/core/validators.py

@@ -116,6 +116,8 @@ def validate(self, data: Dict[str, Any] | DocumentReference):
             self._validate_relates_to(resource)
             self._validate_ssp_asid(resource)
             self._validate_category(resource)
+            if resource.content[0].extension:
+                self._validate_content_extension(resource)
 
         except StopValidationError:
             logger.log(LogReference.VALIDATOR003)
@@ -388,3 +390,90 @@ def _validate_category(self, model: DocumentReference):
                 diagnostics=f"category code '{coding.code}' must have a display value of '{CATEGORIES.get(coding.code)}'",
                 field=f"category[0].coding[{0}].display",
             )
+
+    def _validate_content_extension(self, model: DocumentReference):
+        """
+        Validate the content.extension field contains an appropriate coding.
+        """
+        logger.log(LogReference.VALIDATOR001, step="content extension")
+
+        logger.debug("Validating extension")
+        for i, content in enumerate(model.content):
+            if len(content.extension) > 1:
+                logger.log(
+                    LogReference.VALIDATOR001,
+                    step=f"content[{i}].extension",
+                    reason="extension_too_long",
+                )
+                self.result.add_error(
+                    issue_code="invalid",
+                    error_code="INVALID_RESOURCE",
+                    diagnostics=f"Invalid content extension length: {len(content.extension)} Extension must only contain a single value",
+                    field=f"content[{i}].extension",
+                )
+                return
+
+            if len(content.extension[0].valueCodeableConcept.coding) < 1:
+                logger.log(
+                    LogReference.VALIDATOR001,
+                    step=f"content[{i}].extension.valueCodeableConcept.coding",
+                    reason="extension_coding_does_not_exist",
+                )
+                self.result.add_error(
+                    issue_code="required",
+                    error_code="INVALID_RESOURCE",
+                    diagnostics=f"Missing content[{i}].extension[0].valueCodeableConcept.coding, extension must have at least one coding.",
+                    field=f"content[{i}].extension.valueCodeableConcept.coding",
+                )
+                return
+
+            if (
+                content.extension[0].valueCodeableConcept.coding[0].system
+                != "https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability"
+            ):
+                logger.log(
+                    LogReference.VALIDATOR001,
+                    step=f"content[{i}].extension.valueCodeableConcept.coding[0].system",
+                    reason="extension_coding_system_invalid",
+                )
+                self.result.add_error(
+                    issue_code="value",
+                    error_code="INVALID_RESOURCE",
+                    diagnostics=f"Invalid content extension system: {content.extension[0].valueCodeableConcept.coding[0].system} Extension system must be 'https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability'",
+                    field=f"content[0].extension[0].valueCodeableConcept.coding[0].system",
+                )
+                return
+
+            if content.extension[0].valueCodeableConcept.coding[0].code not in [
+                "static",
+                "dynamic",
+            ]:
+                logger.log(
+                    LogReference.VALIDATOR001,
+                    step=f"content[{i}].extension.valueCodeableConcept.coding[0].code",
+                    reason="extension_coding_code_invalid",
+                )
+                self.result.add_error(
+                    issue_code="value",
+                    error_code="INVALID_RESOURCE",
+                    diagnostics=f"Invalid content extension code: {content.extension[0].valueCodeableConcept.coding[0].code} Extension code must be 'static' or 'dynamic'",
+                    field=f"content[{i}].extension[0].valueCodeableConcept.coding[0].code",
+                )
+                return
+
+            if (
+                content.extension[0].url
+                != "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability"
+            ):
+                logger.log(
+                    LogReference.VALIDATOR001,
+                    step=f"content[{i}].extension.url",
+                    reason="extension_url_invalid",
+                )
+                self.result.add_error(
+                    issue_code="value",
+                    error_code="INVALID_RESOURCE",
+                    diagnostics=f"Invalid content extension url: {content.extension[0].url} Extension url must be 'https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability'",
+                    field=f"content[{i}].extension[0].url",
+                )
+                return