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[NRL-1228] Fix advance care plan naming. Add report script to find invalid pointers #770
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katebobyn-nhs
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bugfix/made14-NRL-1228-advance-care-plans
Dec 12, 2024
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| 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.logger import logger | ||
| from nrlf.core.validators import DocumentReferenceValidator | ||
|
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| dynamodb = boto3.client("dynamodb") | ||
| paginator = dynamodb.get_paginator("scan") | ||
|
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| logger.setLevel("ERROR") | ||
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|
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| def _validate_document(document: str): | ||
| docref = DocumentReference.model_validate_json(document) | ||
|
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| validator = DocumentReferenceValidator() | ||
| result = validator.validate(data=docref) | ||
|
|
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| if not result.is_valid: | ||
| raise Exception("Failed to validate document: " + str(result.issues)) | ||
|
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| def _find_invalid_pointers(table_name: str) -> dict[str, float]: | ||
| """ | ||
| Find pointers in the given table that are invalid. | ||
| Parameters: | ||
| - table_name: The name of the pointers table to use. | ||
| """ | ||
|
|
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| print(f"Finding invalid pointers in table {table_name}....") # noqa | ||
|
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| params: dict[str, Any] = { | ||
| "TableName": table_name, | ||
| "PaginationConfig": {"PageSize": 50}, | ||
| } | ||
|
|
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| invalid_pointers = [] | ||
| total_scanned_count = 0 | ||
|
|
||
| start_time = datetime.now(tz=timezone.utc) | ||
|
|
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| for page in paginator.paginate(**params): | ||
| for item in page["Items"]: | ||
| id = item.get("id", {}).get("S") | ||
| document = item.get("document", {}).get("S", "") | ||
| try: | ||
| _validate_document(document) | ||
| except Exception as exc: | ||
| invalid_pointers.append((id, exc)) | ||
|
|
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| total_scanned_count += page["ScannedCount"] | ||
|
|
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| if total_scanned_count % 1000 == 0: | ||
| print(".", end="", flush=True) # noqa | ||
|
|
||
| if total_scanned_count % 100000 == 0: | ||
| print( # noqa | ||
| f"scanned={total_scanned_count} invalid={len(invalid_pointers)}" | ||
| ) | ||
|
|
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| end_time = datetime.now(tz=timezone.utc) | ||
|
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| print("Writing invalid_pointers to file ./invalid_pointers.txt ...") # noqa | ||
| with open("invalid_pointers.txt", "w") as f: | ||
| for id, err in invalid_pointers: | ||
| f.write(f"{id}: {err}\n") | ||
|
|
||
| print(" Done") # noqa | ||
| return { | ||
| "invalid_pointers": len(invalid_pointers), | ||
| "scanned_count": total_scanned_count, | ||
| "took-secs": timedelta.total_seconds(end_time - start_time), | ||
| } | ||
|
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||
|
|
||
| if __name__ == "__main__": | ||
| fire.Fire(_find_invalid_pointers) | ||
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nitpick