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[NRL-1311] Add script to set pointer supersede info. Add script to put pointers from JSON files #856

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Merged
mattdean3-nhs merged 4 commits into from
Mar 12, 2025
Merged

[NRL-1311] Add script to set pointer supersede info. Add script to put pointers from JSON files #856

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1836d7a
[NRL-1311] Add script to set pointer supersede info. Add script to pu…
mattdean3-nhs Mar 7, 2025
a576ed4
Merge branch 'develop' into feature/made14-NRL-1311-supersede-fixup-s…
mattdean3-nhs Mar 10, 2025
18aab26
[NRL-1311] Add prod env warn to new scripts. Fix supersede typo
mattdean3-nhs Mar 11, 2025
ca426b5
[NRL-1311] Fix typo dev->prod
mattdean3-nhs Mar 11, 2025
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53 changes: 53 additions & 0 deletions scripts/put_pointers_from_files.py
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#!/usr/bin/env python
# Put pointers from the provided files into the pointers table
# This will overwrite the pointer if it already exists in the table
import json
import os

import fire
from aws_session_assume import get_boto_session

from nrlf.core.dynamodb.model import DocumentPointer
from nrlf.core.logger import logger
from nrlf.producer.fhir.r4.model import DocumentReference

logger.setLevel("ERROR")

SKIP_PROD_WARNING = os.getenv("SKIP_PROD_WARNING", "false")


def _put_pointers_from_files(
*filenames, env: str = "dev", table_name: str | None = None
):
if env == "prod" and SKIP_PROD_WARNING != "true":
confirmation = input(
"\nWARNING - This command will modify the PROD environment. Continue? [y/n] "
)
if confirmation != "y":
return "Exiting at user request"

docrefs: list[DocumentReference] = []
print("Reading docrefs from files...")
for filename in filenames:
with open(filename) as f:
docref_json = json.load(f)
docref = DocumentReference.model_validate(docref_json)
docrefs.append(docref)

session = get_boto_session(env)
dynamodb = session.resource("dynamodb")
if not table_name:
table_name = f"nhsd-nrlf--{env}-pointers-table"
table = dynamodb.Table(table_name)

for docref in docrefs:
try:
print(f"Putting {docref.id}....")
pointer = DocumentPointer.from_document_reference(docref)
table.put_item(Item=pointer.model_dump())
except Exception as e:
print(f"Unable to put pointer for {docref.id}. Error: {e}")


if __name__ == "__main__":
fire.Fire(_put_pointers_from_files)
107 changes: 107 additions & 0 deletions scripts/set_pointer_supersede.py
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#!/usr/bin/env python
# Set supersede info on a pointer
import json
import os

import aws_session_assume
import fire

from nrlf.core.dynamodb.model import DocumentPointer
from nrlf.core.logger import logger
from nrlf.producer.fhir.r4.model import (
DocumentReference,
DocumentReferenceRelatesTo,
Identifier,
Reference,
)

logger.setLevel("ERROR")

SKIP_PROD_WARNING = os.getenv("SKIP_PROD_WARNING", "false")


def _set_pointer_supersede_info(
pointer_id: str,
supersede_pointer_id: str,
delete_superseded: bool = False,
env: str = "dev",
table_name: str | None = None,
):
if env == "prod" and SKIP_PROD_WARNING != "true":
confirmation = input(
"\nWARNING - This command will modify the PROD environment. Continue? [y/n] "
)
if confirmation != "y":
return "Exiting at user request"

session = aws_session_assume.get_boto_session(env)
dynamodb = session.resource("dynamodb")

if not table_name:
table_name = f"nhsd-nrlf--{env}-pointers-table"
table = dynamodb.Table(table_name)

print(
f"Setting pointer {pointer_id} in {table_name} to supersede {supersede_pointer_id}...."
)

try:
doc_key = f"D#{pointer_id}"
print(f"Getting {pointer_id}...")
result = table.get_item(
Key={"pk": doc_key, "sk": doc_key},
)
except Exception as e:
print(f"Unable to get pointer. Error: {e}")
return

if "Item" not in result:
print(f"Unable to set superseded info. Pointer {pointer_id} not found.")
return

item = result["Item"]

try:
pointer = DocumentPointer.model_validate({"_from_dynamo": True, **item})
doc_ref = DocumentReference.model_validate_json(pointer.document)
except Exception as e:
print(f"Could not validate pointer from table. Error: {e}")
return

if not doc_ref.relatesTo:
doc_ref.relatesTo = []

existing_supersedes = [
relates_to for relates_to in doc_ref.relatesTo if relates_to.code == "replaces"
]
if existing_supersedes:
print(
f"Unable to add supersede info as pointer is already superseding a pointer: {existing_supersedes}"
)
return

doc_ref.relatesTo.append(
DocumentReferenceRelatesTo(
code="replaces",
target=Reference(
type="DocumentReference",
identifier=Identifier(value=supersede_pointer_id),
),
)
)

print(f"Adding supersede info to {pointer_id}...")
updated_pointer = DocumentPointer.from_document_reference(doc_ref)
table.put_item(
Item=updated_pointer.dict(exclude_none=True, exclude={"_from_dynamo"})
)

if delete_superseded:
print(f"Deleting superseded {supersede_pointer_id}...")
table.delete_item(
Key={"pk": f"D#{supersede_pointer_id}", "sk": f"D#{supersede_pointer_id}"}
)


if __name__ == "__main__":
fire.Fire(_set_pointer_supersede_info)
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