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Merge pull request #831 from NHSDigital/feature/made14-NRL-1279-supplier-data-tests
[NRL-1279] Add supplier samples test data and automated validation tests
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‎layer/nrlf/core/tests/test_sample_pointers.py‎

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

‎scripts/redact_live_pointers.py‎

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

‎tests/data/samples/11X_ADVANCE_CARE_PLAN_Feb25.json‎

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

‎tests/data/samples/11X_PERSONALISED_CARE_AND_SUPPORT_PLAN_Feb25.json‎

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

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