NRL-1509 add devOps script to identify pointers with malformed URLs

reports/find_malformed_urls.py

@@ -0,0 +1,101 @@
+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
+
+dynamodb = boto3.client("dynamodb")
+paginator = dynamodb.get_paginator("scan")
+
+logger.setLevel("ERROR")
+
+
+def _validate_url(document: str):
+    """
+    Per NRL-1509 improperly truncated pointer URLs end with '/Binary/[ODSCODE]/'
+    Properly formed full pointer URLs from these custodians end with '/Binary/[ODSCODE]/[unique-id-string]'
+    """
+    docref = DocumentReference.model_validate_json(document)
+
+    for content in docref.content:
+        if content.attachment.contentType == "application/pdf":
+            url = content.attachment.url
+            if url[-1] == "/":
+                raise RuntimeError("Malformed URL found: " + str(url))
+
+    validator = DocumentReferenceValidator()
+    result = validator.validate(data=docref)
+    if not result.is_valid:
+        raise RuntimeError("Failed to validate document: " + str(result.issues))
+
+
+def _find_malformed_urls(
+    table_name: str, custodian_ods_codes: set[str]
+) -> dict[str, float | int]:
+    """
+    Find pointers in the given table that have malformed URLs.
+    This is required for NRL-1509 because some suppliers suspect their pointer retrieval URLs may have been improperly truncated.
+    Parameters:
+    - table_name: The name of the pointers table to use.
+    - custodian_ods_codes: Set of ODS codes whose pointers may have malformed URLs.
+    """
+
+    print(f"Finding invalid URLs in table {table_name}....")  # noqa
+
+    params: dict[str, Any] = {
+        "TableName": table_name,
+        "PaginationConfig": {"PageSize": 50},
+    }
+
+    malformed_pointers: list[dict[str, Any]] = []
+    total_scanned_count = 0
+
+    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", "")
+            custodian, _ = pointer_id.split("-", 1)
+            # only need to check pointers created by the specified custodians
+            if custodian in custodian_ods_codes:
+                patient_number = item.get("nhs_number", {}).get("S", "")
+                document = item.get("document", {}).get("S", "")
+                try:
+                    _validate_url(document)
+                except Exception as exc:
+                    malformed_pointers.append(
+                        {"id": pointer_id, "patient_number": patient_number, "err": exc}
+                    )
+
+        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} invalid={len(malformed_pointers)}"
+            )
+
+    end_time = datetime.now(tz=timezone.utc)
+
+    print(" Done")  # noqa
+
+    print("Writing malformed_pointers to file ./malformed_pointers.txt ...")  # noqa
+    with open("malformed_pointers.txt", "w") as f:
+        for malformed_pointer_info in malformed_pointers:
+            f.write(f"{malformed_pointer_info}\n")
+
+    return {
+        "malformed_pointers": len(malformed_pointers),
+        "scanned_count": total_scanned_count,
+        "took-secs": timedelta.total_seconds(end_time - start_time),
+    }
+
+
+if __name__ == "__main__":
+    fire.Fire(_find_malformed_urls)