Imaging branch

README.md

@@ -511,3 +511,26 @@ Once you have a new release version ready, you can deploy it through our environ
 2. If any issues arise in the deployment, fix the issues, create a new release version and start this process again.
 3. Once the deployments are complete, use the "Persistent Environment Deploy" Github Action workflow to deploy the release version to `ref`.
 4. Once that is complete, use the "Persistent Environment Deploy" workflow to deploy the release version to `prod`.
+
+## Reports
+
+Reports are provided as scripts in the `reports/` directory. To run a report:
+
+1. Login to your AWS account on the command line, choosing the account that contains the resources you want to report on.
+2. Run your chosen report script, giving the script the resource names and parameters it requires. See each report script for details.
+
+For example, to count the number of pointers from X26 in the pointers table in the dev environment:
+
+```
+$ poetry run python ./scripts/count_pointers_for_custodian.py \
+   nhsd-nrlf--dev-pointers-table \
+   X26
+```
+
+### Running reports in the prod environment
+
+The reports scripts may require resources that could affect the performance of the live production system. Because of this, it is recommended that you take steps to minimise this impact before running reports.
+
+If you are running a report against the DynamoDB pointers table in prod, you should create a copy (or restore a PITR backup) of the table and run your report against the copy.
+
+Please ensure any duplicated resource/data is deleted from the prod environment once you have finished using it.

api/producer/createDocumentReference/tests/test_create_document_reference.py

@@ -238,6 +238,21 @@ def test_create_document_reference_invalid_body():
                 "diagnostics": "Request body could not be parsed (status: Field required)",
                 "expression": ["status"],
             },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (author: Field required)",
+                "expression": ["author"],
+            },
             {
                 "severity": "error",
                 "code": "invalid",

api/producer/swagger.yaml

@@ -1383,6 +1383,7 @@ components:
         - resourceType
         - status
         - content
+        - author
     Bundle:
       type: object
       properties:

api/producer/updateDocumentReference/tests/test_update_document_reference.py

@@ -246,6 +246,21 @@ def test_create_document_reference_invalid_body():
                 "diagnostics": "Request body could not be parsed (status: Field required)",
                 "expression": ["status"],
             },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (author: Field required)",
+                "expression": ["author"],
+            },
             {
                 "severity": "error",
                 "code": "invalid",

api/producer/upsertDocumentReference/tests/test_upsert_document_reference.py

@@ -323,6 +323,21 @@ def test_upsert_document_reference_invalid_body():
                 "diagnostics": "Request body could not be parsed (status: Field required)",
                 "expression": ["status"],
             },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (author: Field required)",
+                "expression": ["author"],
+            },
             {
                 "severity": "error",
                 "code": "invalid",

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

@@ -1,6 +1,6 @@
 # generated by datamodel-codegen:
 #   filename:  swagger.yaml
-#   timestamp: 2024-10-28T10:30:48+00:00
+#   timestamp: 2024-11-04T11:43:16+00:00
 
 from __future__ import annotations
 

layer/nrlf/core/constants.py

@@ -8,7 +8,15 @@ class Source(Enum):
 
 VALID_SOURCES = frozenset(item.value for item in Source.__members__.values())
 EMPTY_VALUES = ("", None, [], {})
-REQUIRED_CREATE_FIELDS = ["custodian", "id", "type", "status", "subject", "category"]
+REQUIRED_CREATE_FIELDS = [
+    "custodian",
+    "id",
+    "type",
+    "status",
+    "subject",
+    "category",
+    "author",
+]
 JSON_TYPES = {dict, list}
 NHS_NUMBER_INDEX = "idx_nhs_number_by_id"
 ID_SEPARATOR = "-"

layer/nrlf/core/errors.py

@@ -1,13 +1,25 @@
 from typing import List, Optional
 
 from pydantic import ValidationError
+from pydantic_core import ErrorDetails
 
 from nrlf.core.response import Response
 from nrlf.core.types import CodeableConcept
 from nrlf.producer.fhir.r4 import model as producer_model
 from nrlf.producer.fhir.r4.model import OperationOutcome, OperationOutcomeIssue
 
 
+def diag_for_error(error: ErrorDetails) -> str:
+    if error["loc"]:
+        return f"{error['loc'][0]}: {error['msg']}"
+    else:
+        return f"root: {error['msg']}"
+
+
+def expression_for_error(error: ErrorDetails) -> Optional[str]:
+    return str(error["loc"][0] if error["loc"] else "root")
+
+
 class OperationOutcomeError(Exception):
     """
     Will instantly trigger an OperationOutcome error response when raised
@@ -59,8 +71,8 @@ def from_validation_error(
                 severity="error",
                 code="invalid",
                 details=details,  # type: ignore
-                diagnostics=f"{msg} ({error['loc'][0]}: {error['msg']})",
-                expression=[str(error["loc"][0])],  # type: ignore
+                diagnostics=f"{msg} ({diag_for_error(error)})",
+                expression=[expression_for_error(error)],  # type: ignore
             )
             for error in exc.errors()
         ]

layer/nrlf/core/tests/test_request.py

@@ -2,8 +2,10 @@
 
 import pytest
 
-from nrlf.core.errors import OperationOutcomeError
-from nrlf.core.request import parse_headers
+from nrlf.core.errors import OperationOutcomeError, ParseError
+from nrlf.core.request import parse_body, parse_headers
+from nrlf.producer.fhir.r4.model import DocumentReference
+from nrlf.tests.data import load_document_reference_data
 
 
 def test_parse_headers_empty_headers():
@@ -129,3 +131,212 @@ def test_parse_headers_case_insensitive():
     assert metadata.client_rp_details.developer_app_name == "TestApp"
     assert metadata.client_rp_details.developer_app_id == "12345"
     assert metadata.ods_code_parts == ("X26", "001")
+
+
+def test_parse_body_no_model_no_body():
+    body = None
+    model = None
+
+    result = parse_body(model, body)
+
+    assert result is None
+
+
+def test_parse_body_valid_docref():
+    model = DocumentReference
+    docref_body = load_document_reference_data("Y05868-736253002-Valid")
+
+    result = parse_body(model, docref_body)
+
+    assert isinstance(result, DocumentReference)
+
+
+def test_parse_body_no_body():
+    model = DocumentReference
+    body = None
+
+    with pytest.raises(OperationOutcomeError) as error:
+        parse_body(model, body)
+
+    exc = error.value
+
+    assert exc.status_code == "400"
+    assert exc.operation_outcome.model_dump(exclude_none=True) == {
+        "resourceType": "OperationOutcome",
+        "issue": [
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "BAD_REQUEST",
+                            "display": "Bad request",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body is required",
+            }
+        ],
+    }
+
+
+def test_parse_body_invalid_docref_json():
+    model = DocumentReference
+    docref_body = load_document_reference_data("Y05868-736253002-Valid")
+
+    docref_body = docref_body.replace('unstructured"', "unstructured")
+
+    with pytest.raises(ParseError) as error:
+        parse_body(model, docref_body)
+
+    response = error.value.response.model_dump()
+
+    assert response["statusCode"] == "400"
+    assert json.loads(response["body"]) == {
+        "resourceType": "OperationOutcome",
+        "issue": [
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                        }
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (root: Invalid JSON: control character (\\u0000-\\u001F) found while parsing a string at line 72 column 0)",
+                "expression": ["root"],
+            }
+        ],
+    }
+
+
+def test_parse_body_invalid_json():
+    model = DocumentReference
+    body = '{ "type": "is-not-a-docref" }'
+
+    with pytest.raises(ParseError) as error:
+        parse_body(model, body)
+
+    response = error.value.response.model_dump()
+
+    assert response["statusCode"] == "400"
+    assert json.loads(response["body"]) == {
+        "resourceType": "OperationOutcome",
+        "issue": [
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                        }
+                    ]
+                },
+                "diagnostics": "Request body could not be parsed (resourceType: Field required)",
+                "expression": ["resourceType"],
+            },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                        }
+                    ]
+                },
+                "diagnostics": "Request body could not be parsed (status: Field required)",
+                "expression": ["status"],
+            },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                        }
+                    ]
+                },
+                "diagnostics": "Request body could not be parsed (type: Input should be an object)",
+                "expression": ["type"],
+            },
+            {
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                        },
+                    ],
+                },
+                "diagnostics": "Request body could not be parsed (author: Field required)",
+                "expression": [
+                    "author",
+                ],
+                "severity": "error",
+            },
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                        }
+                    ]
+                },
+                "diagnostics": "Request body could not be parsed (content: Field required)",
+                "expression": ["content"],
+            },
+        ],
+    }
+
+
+def test_parse_body_not_json():
+    model = DocumentReference
+    body = "is not json"
+
+    with pytest.raises(ParseError) as error:
+        parse_body(model, body)
+
+    response = error.value.response
+
+    assert response.statusCode == "400"
+    assert json.loads(response.body) == {
+        "resourceType": "OperationOutcome",
+        "issue": [
+            {
+                "severity": "error",
+                "code": "invalid",
+                "details": {
+                    "coding": [
+                        {
+                            "system": "https://fhir.nhs.uk/ValueSet/Spine-ErrorOrWarningCode-1",
+                            "code": "MESSAGE_NOT_WELL_FORMED",
+                            "display": "Message not well formed",
+                        }
+                    ]
+                },
+                "diagnostics": "Request body could not be parsed (root: Invalid JSON: expected value at line 1 column 1)",
+                "expression": ["root"],
+            }
+        ],
+    }