Merge pull request #771 from NHSDigital/feature/eema1-NRL-1076-IdentifyLinkedStudiesAndReports

eesa456 · web-flow · commit 32d461f24ad9 · 2024-12-13T15:51:08.000Z
NRL-1076 add integration and unit tests for accession number
diff --git a/api/consumer/searchDocumentReference/search_document_reference.py b/api/consumer/searchDocumentReference/search_document_reference.py
@@ -53,7 +53,7 @@ def handler(
             pointer_types=metadata.pointer_types,
         )
         return SpineErrorResponse.INVALID_CODE_SYSTEM(
-            diagnostics="Invalid query parameter (The provided type system does not match the allowed types for this organisation)",
+            diagnostics="Invalid query parameter (The provided type does not match the allowed types for this organisation)",
             expression="type",
         )
 
diff --git a/api/consumer/searchDocumentReference/tests/test_search_document_reference_consumer.py b/api/consumer/searchDocumentReference/tests/test_search_document_reference_consumer.py
@@ -59,6 +59,56 @@ def test_search_document_reference_happy_path(repository: DocumentPointerReposit
     }
 
 
+@mock_aws
+@mock_repository
+def test_search_document_reference_accession_number_in_pointer(
+    repository: DocumentPointerRepository,
+):
+    doc_ref = load_document_reference("Y05868-736253002-Valid")
+    doc_ref.identifier = [
+        {"type": {"text": "Accession-Number"}, "value": "Y05868.123456789"}
+    ]
+    doc_pointer = DocumentPointer.from_document_reference(doc_ref)
+    repository.create(doc_pointer)
+
+    event = create_test_api_gateway_event(
+        headers=create_headers(),
+        query_string_parameters={
+            "subject:identifier": "https://fhir.nhs.uk/Id/nhs-number|6700028191",
+        },
+    )
+
+    result = handler(event, create_mock_context())
+    body = result.pop("body")
+
+    assert result == {
+        "statusCode": "200",
+        "headers": default_response_headers(),
+        "isBase64Encoded": False,
+    }
+
+    parsed_body = json.loads(body)
+    assert parsed_body == {
+        "resourceType": "Bundle",
+        "type": "searchset",
+        "total": 1,
+        "link": [
+            {
+                "relation": "self",
+                "url": "https://pytest.api.service.nhs.uk/record-locator/consumer/FHIR/R4/DocumentReference?subject:identifier=https://fhir.nhs.uk/Id/nhs-number|6700028191",
+            }
+        ],
+        "entry": [{"resource": doc_ref.model_dump(exclude_none=True)}],
+    }
+
+    created_doc_pointer = repository.get_by_id("Y05868-99999-99999-999999")
+
+    assert created_doc_pointer is not None
+    assert json.loads(created_doc_pointer.document)["identifier"] == [
+        {"type": {"text": "Accession-Number"}, "value": "Y05868.123456789"}
+    ]
+
+
 @mock_aws
 @mock_repository
 def test_search_document_reference_happy_path_with_custodian(
@@ -451,7 +501,7 @@ def test_search_document_reference_invalid_type(repository: DocumentPointerRepos
                         }
                     ]
                 },
-                "diagnostics": "Invalid query parameter (The provided type system does not match the allowed types for this organisation)",
+                "diagnostics": "Invalid query parameter (The provided type does not match the allowed types for this organisation)",
                 "expression": ["type"],
             }
         ],
diff --git a/api/consumer/searchPostDocumentReference/search_post_document_reference.py b/api/consumer/searchPostDocumentReference/search_post_document_reference.py
@@ -57,7 +57,7 @@ def handler(
             pointer_types=metadata.pointer_types,
         )
         return SpineErrorResponse.INVALID_CODE_SYSTEM(
-            diagnostics="Invalid type (The provided type system does not match the allowed types for this organisation)",
+            diagnostics="The provided type does not match the allowed types for this organisation",
             expression="type",
         )
 
diff --git a/api/consumer/searchPostDocumentReference/tests/test_search_post_document_reference_consumer.py b/api/consumer/searchPostDocumentReference/tests/test_search_post_document_reference_consumer.py
@@ -424,7 +424,7 @@ def test_search_post_document_reference_invalid_type(
                         }
                     ]
                 },
-                "diagnostics": "Invalid type (The provided type system does not match the allowed types for this organisation)",
+                "diagnostics": "The provided type does not match the allowed types for this organisation",
                 "expression": ["type"],
             }
         ],
diff --git a/api/producer/searchDocumentReference/search_document_reference.py b/api/producer/searchDocumentReference/search_document_reference.py
@@ -55,7 +55,7 @@ def handler(
             pointer_types=metadata.pointer_types,
         )
         return SpineErrorResponse.INVALID_CODE_SYSTEM(
-            diagnostics="Invalid query parameter (The provided type system does not match the allowed types for this organisation)",
+            diagnostics="Invalid query parameter (The provided type does not match the allowed types for this organisation)",
             expression="type",
         )
 
diff --git a/api/producer/searchDocumentReference/tests/test_search_document_reference_producer.py b/api/producer/searchDocumentReference/tests/test_search_document_reference_producer.py
@@ -201,7 +201,7 @@ def test_search_document_reference_invalid_type(repository: DocumentPointerRepos
                         }
                     ]
                 },
-                "diagnostics": "Invalid query parameter (The provided type system does not match the allowed types for this organisation)",
+                "diagnostics": "Invalid query parameter (The provided type does not match the allowed types for this organisation)",
                 "expression": ["type"],
             }
         ],
diff --git a/api/producer/searchPostDocumentReference/search_post_document_reference.py b/api/producer/searchPostDocumentReference/search_post_document_reference.py
@@ -49,7 +49,7 @@ def handler(
             pointer_types=metadata.pointer_types,
         )
         return SpineErrorResponse.INVALID_CODE_SYSTEM(
-            diagnostics="The provided type system does not match the allowed types for this organisation",
+            diagnostics="The provided type does not match the allowed types for this organisation",
             expression="type",
         )
 
diff --git a/api/producer/searchPostDocumentReference/tests/test_search_post_document_reference_producer.py b/api/producer/searchPostDocumentReference/tests/test_search_post_document_reference_producer.py
@@ -206,7 +206,7 @@ def test_search_document_reference_invalid_type(repository: DocumentPointerRepos
                         }
                     ]
                 },
-                "diagnostics": "The provided type system does not match the allowed types for this organisation",
+                "diagnostics": "The provided type does not match the allowed types for this organisation",
                 "expression": ["type"],
             }
         ],
diff --git a/layer/nrlf/core/validators.py b/layer/nrlf/core/validators.py
@@ -26,7 +26,7 @@
 
 def validate_type(type_: Optional[RequestQueryType], pointer_types: List[str]) -> bool:
     """
-    Validates if the given type system is present in the list of pointer types.
+    Validates if the given type is present in the list of pointer types.
     """
     if not type_:
         return True
diff --git a/tests/features/consumer/searchDocumentReference-failure.feature b/tests/features/consumer/searchDocumentReference-failure.feature
@@ -77,7 +77,35 @@ Feature: Consumer - searchDocumentReference - Failure Scenarios
             "display": "Invalid code system"
           }]
         },
-        "diagnostics": "Invalid query parameter (The provided type system does not match the allowed types for this organisation)",
+        "diagnostics": "Invalid query parameter (The provided type does not match the allowed types for this organisation)",
+        "expression": ["type"]
+      }
+      """
+
+  Scenario: Search rejects request with type they are not allowed to use
+    Given the application 'DataShare' (ID 'z00z-y11y-x22x') is registered to access the API
+    And the organisation 'RX898' is authorised to access pointer types:
+      | system                 | value     |
+      | http://snomed.info/sct | 736253002 |
+    When consumer 'RX898' searches for DocumentReferences with parameters:
+      | parameter | value                                   |
+      | subject   | 9278693472                              |
+      | type      | http://snomed.info/sct\|887701000000100 |
+    Then the response status code is 400
+    And the response is an OperationOutcome with 1 issue
+    And the OperationOutcome contains the issue:
+      """
+      {
+        "severity": "error",
+        "code": "code-invalid",
+        "details": {
+          "coding": [{
+            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+            "code": "INVALID_CODE_SYSTEM",
+            "display": "Invalid code system"
+          }]
+        },
+        "diagnostics": "Invalid query parameter (The provided type does not match the allowed types for this organisation)",
         "expression": ["type"]
       }
       """
diff --git a/tests/features/consumer/searchDocumentReference-success.feature b/tests/features/consumer/searchDocumentReference-success.feature
@@ -36,6 +36,44 @@ Feature: Consumer - searchDocumentReference - Success Scenarios
       | custodian   | 02V                             |
       | author      | 02V                             |
 
+  Scenario: Search for a DocumentReference and Accession Number is in response
+    Given the application 'DataShare' (ID 'z00z-y11y-x22x') is registered to access the API
+    And the organisation 'RX898' is authorised to access pointer types:
+      | system                 | value     |
+      | http://snomed.info/sct | 736253002 |
+    And a DocumentReference resource exists with values:
+      | property    | value                           |
+      | id          | 02V-1111111111-SearchDocRefTest |
+      | subject     | 9278693472                      |
+      | status      | current                         |
+      | type        | 736253002                       |
+      | category    | 734163000                       |
+      | contentType | application/pdf                 |
+      | url         | https://example.org/my-doc.pdf  |
+      | custodian   | 02V                             |
+      | author      | 02V                             |
+      | identifier  | 02V.123456789                   |
+    When consumer 'RX898' searches for DocumentReferences with parameters:
+      | parameter | value      |
+      | subject   | 9278693472 |
+    Then the response status code is 200
+    And the response is a searchset Bundle
+    And the Bundle has a self link matching 'DocumentReference?subject:identifier=https://fhir.nhs.uk/Id/nhs-number|9278693472'
+    And the Bundle has a total of 1
+    And the Bundle has 1 entry
+    And the Bundle contains an DocumentReference with values
+      | property    | value                           |
+      | id          | 02V-1111111111-SearchDocRefTest |
+      | subject     | 9278693472                      |
+      | status      | current                         |
+      | type        | 736253002                       |
+      | category    | 734163000                       |
+      | contentType | application/pdf                 |
+      | url         | https://example.org/my-doc.pdf  |
+      | custodian   | 02V                             |
+      | author      | 02V                             |
+      | identifier  | 02V.123456789                   |
+
   Scenario: Search for a DocumentReference by NHS Number and Custodian where both search parameters match
     Given the application 'DataShare' (ID 'z00z-y11y-x22x') is registered to access the API
     And the organisation 'RX898' is authorised to access pointer types:
diff --git a/tests/features/consumer/searchPostDocumentReference-failure.feature b/tests/features/consumer/searchPostDocumentReference-failure.feature
@@ -77,7 +77,35 @@ Feature: Consumer - searchDocumentReference - Failure Scenarios
             "display": "Invalid code system"
           }]
         },
-        "diagnostics": "Invalid type (The provided type system does not match the allowed types for this organisation)",
+        "diagnostics": "The provided type does not match the allowed types for this organisation",
+        "expression": ["type"]
+      }
+      """
+
+  Scenario: Search rejects request with type they are not allowed to use
+    Given the application 'DataShare' (ID 'z00z-y11y-x22x') is registered to access the API
+    And the organisation 'RX898' is authorised to access pointer types:
+      | system                 | value     |
+      | http://snomed.info/sct | 736253002 |
+    When consumer 'RX898' searches for DocumentReferences using POST with request body:
+      | key     | value                                   |
+      | subject | 9278693472                              |
+      | type    | http://snomed.info/sct\|887701000000100 |
+    Then the response status code is 400
+    And the response is an OperationOutcome with 1 issue
+    And the OperationOutcome contains the issue:
+      """
+      {
+        "severity": "error",
+        "code": "code-invalid",
+        "details": {
+          "coding": [{
+            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+            "code": "INVALID_CODE_SYSTEM",
+            "display": "Invalid code system"
+          }]
+        },
+        "diagnostics": "The provided type does not match the allowed types for this organisation",
         "expression": ["type"]
       }
       """
diff --git a/tests/features/steps/3_assert.py b/tests/features/steps/3_assert.py
@@ -218,6 +218,14 @@ def assert_document_reference_matches_value(
             context.response.json(),
         )
 
+    if identifier := items.get("identifier"):
+        assert doc_ref.identifier[0].value == identifier, format_error(
+            "DocumentReference Identifier does not match",
+            identifier,
+            doc_ref.identifier[0].value,
+            context.response.json(),
+        )
+
 
 @then("the Bundle contains an DocumentReference with values")
 def assert_bundle_contains_documentreference_values_step(context: Context):
diff --git a/tests/features/utils/data.py b/tests/features/utils/data.py
@@ -160,6 +160,12 @@ def create_test_document_reference(items: dict) -> DocumentReference:
                 ),
             )
         ]
+    if items.get("identifier"):
+        base_doc_ref.identifier = [
+            Identifier(
+                type=CodeableConcept(text="Accession-Number"), value=items["identifier"]
+            )
+        ]
 
     return base_doc_ref
 

Original file line number	Diff line number	Diff line change
`@@ -53,7 +53,7 @@ def handler(`
`53`	`53`	`pointer_types=metadata.pointer_types,`
`54`	`54`	`)`
`55`	`55`	`return SpineErrorResponse.INVALID_CODE_SYSTEM(`
`56`		`- diagnostics="Invalid query parameter (The provided type system does not match the allowed types for this organisation)",`
	`56`	`+ diagnostics="Invalid query parameter (The provided type does not match the allowed types for this organisation)",`
`57`	`57`	`expression="type",`
`58`	`58`	`)`
`59`	`59`
Original file line number	Diff line number	Diff line change
`@@ -57,7 +57,7 @@ def handler(`
`57`	`57`	`pointer_types=metadata.pointer_types,`
`58`	`58`	`)`
`59`	`59`	`return SpineErrorResponse.INVALID_CODE_SYSTEM(`
`60`		`- diagnostics="Invalid type (The provided type system does not match the allowed types for this organisation)",`
	`60`	`+ diagnostics="The provided type does not match the allowed types for this organisation",`
`61`	`61`	`expression="type",`
`62`	`62`	`)`
`63`	`63`
Original file line number	Diff line number	Diff line change
`@@ -424,7 +424,7 @@ def test_search_post_document_reference_invalid_type(`
`424`	`424`	`}`
`425`	`425`	`]`
`426`	`426`	`},`
`427`		`- "diagnostics": "Invalid type (The provided type system does not match the allowed types for this organisation)",`
	`427`	`+ "diagnostics": "The provided type does not match the allowed types for this organisation",`
`428`	`428`	`"expression": ["type"],`
`429`	`429`	`}`
`430`	`430`	`],`
Original file line number	Diff line number	Diff line change
`@@ -55,7 +55,7 @@ def handler(`
`55`	`55`	`pointer_types=metadata.pointer_types,`
`56`	`56`	`)`
`57`	`57`	`return SpineErrorResponse.INVALID_CODE_SYSTEM(`
`58`		`- diagnostics="Invalid query parameter (The provided type system does not match the allowed types for this organisation)",`
	`58`	`+ diagnostics="Invalid query parameter (The provided type does not match the allowed types for this organisation)",`
`59`	`59`	`expression="type",`
`60`	`60`	`)`
`61`	`61`
Original file line number	Diff line number	Diff line change
`@@ -201,7 +201,7 @@ def test_search_document_reference_invalid_type(repository: DocumentPointerRepos`
`201`	`201`	`}`
`202`	`202`	`]`
`203`	`203`	`},`
`204`		`- "diagnostics": "Invalid query parameter (The provided type system does not match the allowed types for this organisation)",`
	`204`	`+ "diagnostics": "Invalid query parameter (The provided type does not match the allowed types for this organisation)",`
`205`	`205`	`"expression": ["type"],`
`206`	`206`	`}`
`207`	`207`	`],`
Original file line number	Diff line number	Diff line change
`@@ -49,7 +49,7 @@ def handler(`
`49`	`49`	`pointer_types=metadata.pointer_types,`
`50`	`50`	`)`
`51`	`51`	`return SpineErrorResponse.INVALID_CODE_SYSTEM(`
`52`		`- diagnostics="The provided type system does not match the allowed types for this organisation",`
	`52`	`+ diagnostics="The provided type does not match the allowed types for this organisation",`
`53`	`53`	`expression="type",`
`54`	`54`	`)`
`55`	`55`
Original file line number	Diff line number	Diff line change
`@@ -206,7 +206,7 @@ def test_search_document_reference_invalid_type(repository: DocumentPointerRepos`
`206`	`206`	`}`
`207`	`207`	`]`
`208`	`208`	`},`
`209`		`- "diagnostics": "The provided type system does not match the allowed types for this organisation",`
	`209`	`+ "diagnostics": "The provided type does not match the allowed types for this organisation",`
`210`	`210`	`"expression": ["type"],`
`211`	`211`	`}`
`212`	`212`	`],`