NRL-1705 find and identify duplicates for a set of custodians

Author: katebobyn-nhs

reports/find_duplicate_pointers.py

@@ -0,0 +1,111 @@
+from datetime import datetime, timedelta, timezone
+from typing import Any
+
+import boto3
+import fire
+
+from nrlf.core.logger import logger
+
+dynamodb = boto3.client("dynamodb")
+paginator = dynamodb.get_paginator("scan")
+
+logger.setLevel("ERROR")
+
+REQUIRED_ATTRIBUTES = [
+    "nhs_number",
+    "custodian",
+    "id",
+    "master_identifier",
+    "type_id",
+    "created_on",
+]
+
+
+def _get_duplicates(table_name: str, custodians: str | tuple[str]) -> Any:
+    """
+    Get masterids for duplicate pointers in the given table for a list of custodians.
+    Parameters:
+    - table_name: The name of the pointers table to use.
+    """
+    custodian_list = (
+        custodians.split(",") if isinstance(custodians, str) else list(custodians)
+    )
+
+    print(  # noqa
+        f"Finding duplicate pointers for custodians {custodian_list} in table {table_name}...."
+    )
+
+    required_attributes = REQUIRED_ATTRIBUTES
+
+    expression_names_str = ",".join(
+        [f":param{custodian}" for custodian in custodian_list]
+    )
+    expression_values_list = {
+        f":param{custodian}": {"S": custodian} for custodian in custodian_list
+    }
+
+    params: dict[str, Any] = {
+        "TableName": table_name,
+        "PaginationConfig": {"PageSize": 50},
+        "FilterExpression": f"custodian IN ({expression_names_str})",
+        "ExpressionAttributeValues": expression_values_list,
+        "ProjectionExpression": ",".join(required_attributes),
+    }
+    pointers_by_key = dict()
+    total_scanned_count = 0
+    duplicate_count = 0
+    duplicates_set = set()
+
+    start_time = datetime.now(tz=timezone.utc)
+
+    for page in paginator.paginate(**params):
+        for item in page["Items"]:
+            pointer_id = item.get("id", {}).get("S", "no-id")
+            pointer_type = item.get("type_id", {}).get("S", "no-type")
+            master_id = item.get("master_identifier", {}).get("S", "no-master-id")
+            custodian = item.get("custodian", {}).get("S", "no-custodian")
+            patient_id = item.get("nhs_number", {}).get("S", "no-patient-id")
+            created_on = item.get("created_on", {}).get("S", "no-creation-datetime")
+
+            pointer_data = {
+                "id": pointer_id,
+                "master_id": master_id,
+                "datetime": created_on,
+            }
+
+            px_type_ods_key = f"{patient_id}-{custodian}-{pointer_type}"
+
+            if px_type_ods_key not in pointers_by_key:
+                pointers_by_key[px_type_ods_key] = [pointer_data]
+            else:
+                pointers_by_key[px_type_ods_key].append(pointer_data)
+                duplicate_count += 1
+                duplicates_set.add(px_type_ods_key)
+
+        total_scanned_count += page["ScannedCount"]
+
+        if total_scanned_count % 1000 == 0:
+            print(".", end="", flush=True)  # noqa
+
+        if total_scanned_count % 100000 == 0:
+            print(  # noqa
+                f"scanned={total_scanned_count} found={duplicate_count} potential duplicates "
+            )
+
+    end_time = datetime.now(tz=timezone.utc)
+
+    print(" Table scan completed")  # noqa
+
+    for key in duplicates_set:
+        print(f"Duplicates for {key}:")  # noqa
+        print(pointers_by_key[key])  # noqa
+
+    return {
+        "duplicates-found": duplicate_count,
+        "scanned-count": total_scanned_count,
+        "took-secs": timedelta.total_seconds(end_time - start_time),
+    }
+
+
+if __name__ == "__main__":
+    fire.Fire(_get_duplicates)