[NRL-1279] Add supplier samples test data and automated validation tests #831

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Merged

mattdean3-nhs merged 4 commits into develop from feature/made14-NRL-1279-supplier-data-tests

Feb 11, 2025

layer/nrlf/core/tests/test_sample_pointers.py

-Original file line number
+Diff line change
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+    import os
+    import pytest
+    from nrlf.consumer.fhir.r4.model import DocumentReference as ConsumerDocumentReference
+    from nrlf.core.validators import DocumentReferenceValidator
+    from nrlf.producer.fhir.r4.model import DocumentReference as ProducerDocumentReference
+    def sample_pointer_files() -> list[str]:
+        return [f for f in os.listdir("./tests/data/samples") if f.endswith(".json")]
+    def load_sample_pointer_data(pointer_file: str) -> str:
+        with open(f"./tests/data/samples/{pointer_file}", "r") as f:
+            return f.read()
+    @pytest.mark.parametrize("sample_pointer_file", sample_pointer_files())
+    def test_sample_pointer_as_consumer(sample_pointer_file: str):
+        sample_pointer_data = load_sample_pointer_data(sample_pointer_file)
+        docref = ConsumerDocumentReference.model_validate_json(sample_pointer_data)
+        result = DocumentReferenceValidator().validate(data=docref)
+        assert result.is_valid
+    @pytest.mark.parametrize("sample_pointer_file", sample_pointer_files())
+    def test_sample_pointer_as_producer(sample_pointer_file: str):
+        sample_pointer_data = load_sample_pointer_data(sample_pointer_file)
+        docref = ProducerDocumentReference.model_validate_json(sample_pointer_data)
+        result = DocumentReferenceValidator().validate(data=docref)
+        assert result.is_valid

scripts/redact_live_pointers.py

-Original file line number
+Diff line change
@@ -0,0 +1,99 @@
+    import json
+    import os
+    from datetime import datetime, timedelta, timezone
+    from typing import Any
+    import boto3
+    import fire
+    from nrlf.consumer.fhir.r4.model import DocumentReference
+    from nrlf.core.constants import PointerTypes
+    from nrlf.core.logger import logger
+    from nrlf.core.utils import create_fhir_instant
+    from nrlf.core.validators import DocumentReferenceValidator
+    dynamodb = boto3.client("dynamodb")
+    paginator = dynamodb.get_paginator("scan")
+    logger.setLevel("ERROR")
+    type_to_name = {pointer_type.value: pointer_type.name for pointer_type in PointerTypes}
+    def _redact_timestamps(docref: DocumentReference) -> None:
+        mock_timestamp = create_fhir_instant()
+        docref.meta.lastUpdated = mock_timestamp
+        docref.date = mock_timestamp
+    def _redact_ids(docref: DocumentReference) -> None:
+        ods_code = docref.custodian.identifier.value
+        mock_id = "c2a99222-eb50-4451-ad6e-1e951627800e"
+        docref.subject.identifier.value = "9999999999"
+        docref.id = f"{ods_code}-{mock_id}"
+        if docref.masterIdentifier:
+            docref.masterIdentifier.value = f"mid_{mock_id}"
+        if docref.relatesTo:
+            for relates_to in docref.relatesTo:
+                relates_to.target.identifier.value = f"rel_{mock_id}"
+    def _redact_content(docref: DocumentReference) -> None:
+        mock_timestamp = create_fhir_instant()
+        for content in docref.content:
+            if content.attachment.url.startswith("ssp://"):
+                content.attachment.url = "ssp://content.test.local/content"
+            else:
+                content.attachment.url = "https://content.test.local/content"
+            content.attachment.creation = mock_timestamp
+    def _redact_context(docref: DocumentReference) -> None:
+        if docref.context.related:
+            for related in docref.context.related:
+                related.identifier.value = "012345678910"
+        mock_timestamp = create_fhir_instant()
+        if docref.context.period:
+            if docref.context.period.start:
+                docref.context.period.start = mock_timestamp
+            if docref.context.period.end:
+                docref.context.period.end = mock_timestamp
+    def _redact_pointers(src_path: str, dest_path: str) -> None:
+        """
+        Redact pointers in .json files in from the source path and write the redacted pointer to the destination path.
+        Parameters:
+        - src_path: The path to the source directory containing the pointers.
+        - dest_path: The path to the destination directory to write the redacted pointers.
+        """
+        src_pointer_files = [f for f in os.listdir(src_path) if f.endswith(".json")]
+        for src_pointer_file in src_pointer_files:
+            print("Reading", src_pointer_file)
+            with open(f"{src_path}/{src_pointer_file}", "r") as f:
+                pointer_data = f.read()
+            docref = DocumentReference.model_validate_json(pointer_data)
+            ods_code = docref.custodian.identifier.value
+            type_coding = docref.type.coding[0]
+            pointer_type = type_to_name[f"{type_coding.system}|{type_coding.code}"]
+            _redact_ids(docref)
+            _redact_timestamps(docref)
+            _redact_content(docref)
+            _redact_context(docref)
+            month_year = datetime.now().strftime("%b%y")
+            filename = f"{dest_path}/{ods_code}_{pointer_type}_{month_year}.json"
+            print("Writing", filename)
+            with open(filename, "w") as f:
+                f.write(docref.model_dump_json(indent=2, exclude_unset=True))
+    if __name__ == "__main__":
+        fire.Fire(_redact_pointers)

tests/data/samples/11X_ADVANCE_CARE_PLAN_Feb25.json

-Original file line number
+Diff line change
@@ -0,0 +1,103 @@
+    {
+      "resourceType": "DocumentReference",
+      "id": "11X-c2a99222-eb50-4451-ad6e-1e951627800e",
+      "meta": {
+        "lastUpdated": "2025-02-10T16:48:27.326Z"
+      },
+      "masterIdentifier": {
+        "system": "urn:ietf:rfc:3986",
+        "value": "mid_c2a99222-eb50-4451-ad6e-1e951627800e"
+      },
+      "status": "current",
+      "type": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "code": "736366004",
+            "display": "Advance care plan"
+          }
+        ]
+      },
+      "category": [
+        {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "734163000",
+              "display": "Care plan"
+            }
+          ]
+        }
+      ],
+      "subject": {
+        "identifier": {
+          "system": "https://fhir.nhs.uk/Id/nhs-number",
+          "value": "9999999999"
+        }
+      },
+      "date": "2025-02-10T16:48:27.326Z",
+      "author": [
+        {
+          "identifier": {
+            "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+            "value": "L85012"
+          }
+        }
+      ],
+      "custodian": {
+        "identifier": {
+          "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+          "value": "11X"
+        }
+      },
+      "content": [
+        {
+          "attachment": {
+            "contentType": "application/pdf",
+            "url": "ssp://content.test.local/content",
+            "creation": "2025-02-10T16:48:27.326Z"
+          },
+          "format": {
+            "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLFormatCode",
+            "code": "urn:nhs-ic:unstructured",
+            "display": "Unstructured Document"
+          },
+          "extension": [
+            {
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability",
+                    "code": "static",
+                    "display": "Static"
+                  }
+                ]
+              },
+              "url": "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability"
+            }
+          ]
+        }
+      ],
+      "context": {
+        "period": {
+          "start": "2025-02-10T16:48:27.326Z"
+        },
+        "practiceSetting": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "1060971000000108",
+              "display": "General practice service"
+            }
+          ]
+        },
+        "related": [
+          {
+            "identifier": {
+              "system": "https://fhir.nhs.uk/Id/nhsSpineASID",
+              "value": "012345678910"
+            }
+          }
+        ]
+      }
+    }

tests/data/samples/11X_PERSONALISED_CARE_AND_SUPPORT_PLAN_Feb25.json

-Original file line number
+Diff line change
@@ -0,0 +1,103 @@
+    {
+      "resourceType": "DocumentReference",
+      "id": "11X-c2a99222-eb50-4451-ad6e-1e951627800e",
+      "meta": {
+        "lastUpdated": "2025-02-10T16:48:27.327Z"
+      },
+      "masterIdentifier": {
+        "system": "urn:ietf:rfc:3986",
+        "value": "mid_c2a99222-eb50-4451-ad6e-1e951627800e"
+      },
+      "status": "current",
+      "type": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "code": "2181441000000107",
+            "display": "Personalised Care and Support Plan"
+          }
+        ]
+      },
+      "category": [
+        {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "734163000",
+              "display": "Care plan"
+            }
+          ]
+        }
+      ],
+      "subject": {
+        "identifier": {
+          "system": "https://fhir.nhs.uk/Id/nhs-number",
+          "value": "9999999999"
+        }
+      },
+      "date": "2025-02-10T16:48:27.327Z",
+      "author": [
+        {
+          "identifier": {
+            "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+            "value": "L85609"
+          }
+        }
+      ],
+      "custodian": {
+        "identifier": {
+          "system": "https://fhir.nhs.uk/Id/ods-organization-code",
+          "value": "11X"
+        }
+      },
+      "content": [
+        {
+          "attachment": {
+            "contentType": "application/pdf",
+            "url": "ssp://content.test.local/content",
+            "creation": "2025-02-10T16:48:27.327Z"
+          },
+          "format": {
+            "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLFormatCode",
+            "code": "urn:nhs-ic:unstructured",
+            "display": "Unstructured Document"
+          },
+          "extension": [
+            {
+              "valueCodeableConcept": {
+                "coding": [
+                  {
+                    "system": "https://fhir.nhs.uk/England/CodeSystem/England-NRLContentStability",
+                    "code": "static",
+                    "display": "Static"
+                  }
+                ]
+              },
+              "url": "https://fhir.nhs.uk/England/StructureDefinition/Extension-England-ContentStability"
+            }
+          ]
+        }
+      ],
+      "context": {
+        "period": {
+          "start": "2025-02-10T16:48:27.327Z"
+        },
+        "practiceSetting": {
+          "coding": [
+            {
+              "system": "http://snomed.info/sct",
+              "code": "1060971000000108",
+              "display": "General practice service"
+            }
+          ]
+        },
+        "related": [
+          {
+            "identifier": {
+              "system": "https://fhir.nhs.uk/Id/nhsSpineASID",
+              "value": "012345678910"
+            }
+          }
+        ]
+      }
+    }

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