Drop stale _runtime.tmp.linked_instances.* collections

nmdc_runtime/api/core/util.py

@@ -52,9 +52,14 @@ def raise404_if_none(doc, detail="Not found"):
     return doc
 
 
-def now(as_str=False):
-    dt = datetime.now(timezone.utc)
-    return dt.isoformat() if as_str else dt
+def now() -> datetime:
+    """Get a `datetime` representing the current time in UTC."""
+    return datetime.now(timezone.utc)
+
+
+def now_str() -> str:
+    """Get an ISO string representing the current time in UTC."""
+    return now().isoformat()
 
 
 def expiry_dt_from_now(days=0, hours=0, minutes=0, seconds=0):

nmdc_runtime/api/endpoints/lib/linked_instances.py

@@ -6,14 +6,16 @@
 
 """
 
+from datetime import timedelta
 from typing import Literal, Any
 
 from bson import ObjectId
 from pymongo.collection import Collection as MongoCollection
 from pymongo.database import Database as MongoDatabase
 from toolz import merge
 
-from nmdc_runtime.api.core.util import hash_from_str
+from nmdc_runtime.api.core.util import hash_from_str, now
+from nmdc_runtime.api.db.mongo import get_mongo_db
 from nmdc_runtime.util import get_class_name_to_collection_names_map, nmdc_schema_view
 
 
@@ -35,6 +37,17 @@ def temp_linked_instances_collection_name(ids: list[str], types: list[str]) -> s
     return f"_runtime.tmp.linked_instances.{hash_from_ids_and_types(ids=ids,types=types)}.{ObjectId()}"
 
 
+def drop_stale_temp_linked_instances_collections() -> None:
+    """Drop any temporary linked-instances collections that were generated earlier than one day ago."""
+    mdb = get_mongo_db()
+    one_day_ago = now() - timedelta(days=1)
+    for collection_name in mdb.list_collection_names(
+        filter={"name": {"$regex": r"^_runtime.tmp.linked_instances\..*"}}
+    ):
+        if ObjectId(collection_name.split(".")[-1]).generation_time < one_day_ago:
+            mdb.drop_collection(collection_name)
+
+
 def gather_linked_instances(
     alldocs_collection: MongoCollection,
     ids: list[str],

nmdc_runtime/api/endpoints/nmdcschema.py

@@ -3,7 +3,7 @@
 from typing import List, Dict, Annotated
 
 import pymongo
-from fastapi import APIRouter, Depends, HTTPException, Path, Query
+from fastapi import APIRouter, BackgroundTasks, Depends, HTTPException, Path, Query
 from pydantic import AfterValidator
 from refscan.lib.helpers import (
     get_collection_names_from_schema,
@@ -13,6 +13,7 @@
 from nmdc_runtime.api.endpoints.lib.linked_instances import (
     gather_linked_instances,
     hydrated,
+    drop_stale_temp_linked_instances_collections,
 )
 from nmdc_runtime.config import IS_LINKED_INSTANCES_ENDPOINT_ENABLED
 from nmdc_runtime.minter.config import typecodes
@@ -122,7 +123,11 @@ def get_nmdc_database_collection_stats(
 @decorate_if(condition=IS_LINKED_INSTANCES_ENDPOINT_ENABLED)(
     router.get(
         "/nmdcschema/linked_instances",
-        response_model=ListResponse[Doc],
+        responses={
+            status.HTTP_200_OK: {
+                "model": ListResponse[Doc],
+            }
+        },
         response_model_exclude_unset=True,
     )
 )
@@ -179,6 +184,12 @@ def get_linked_instances(
         ),
     ] = 20,
     mdb: MongoDatabase = Depends(get_mongo_db),
+    # FastAPI will inject this `background_tasks` argument, to which we can add background tasks
+    # for FastAPI to run after it returns the HTTP response.
+    # References:
+    # - https://fastapi.tiangolo.com/tutorial/background-tasks/ (RE: `BackgroundTasks`)
+    # - https://stackoverflow.com/a/68807219 (RE: how to specify it after some optional parameters)
+    background_tasks: BackgroundTasks = BackgroundTasks(),
 ):
     """
     Retrieves database instances that are both (a) linked to any of `ids`, and (b) of a type in `types`.
@@ -222,6 +233,7 @@ class definition ([linkml:ClassDefinition](https://w3id.org/linkml/ClassDefiniti
     [nmdc:Sample](https://w3id.org/nmdc/Sample), etc. -- may be given.
     If no value for `types` is given, then all [nmdc:NamedThing](https://w3id.org/nmdc/NamedThing)s are returned.
     """
+    background_tasks.add_task(drop_stale_temp_linked_instances_collections)
     if page_token is not None:
         rv = list_resources(
             req=ListRequest(page_token=page_token, max_page_size=max_page_size), mdb=mdb
@@ -237,6 +249,7 @@ class definition ([linkml:ClassDefinition](https://w3id.org/linkml/ClassDefiniti
             status_code=status.HTTP_404_NOT_FOUND,
             detail=f"Some IDs not found: {ids_not_found}.",
         )
+
     types = types or ["nmdc:NamedThing"]
     types_possible = set([f"nmdc:{name}" for name in nmdc_schema_view().all_classes()])
     types_not_found = list(set(types) - types_possible)

nmdc_runtime/api/models/run.py

@@ -9,7 +9,7 @@
 from toolz import merge
 
 from nmdc_runtime.api.core.idgen import generate_one_id
-from nmdc_runtime.api.core.util import now, raise404_if_none, pick
+from nmdc_runtime.api.core.util import now, now_str, raise404_if_none, pick
 from nmdc_runtime.api.models.user import User
 
 PRODUCER_URL_BASE_DEFAULT = (
@@ -90,7 +90,7 @@ def _add_run_requested_event(run_spec: RunUserSpec, mdb: MongoDatabase, user: Us
             {"producer": PRODUCER_URL, "schemaURL": SCHEMA_URL},
         ),
         type=RunEventType.REQUESTED,
-        time=now(as_str=True),
+        time=now_str(),
         inputs=run_spec.inputs,
     )
     mdb.run_events.insert_one(event.model_dump())
@@ -112,7 +112,7 @@ def _add_run_started_event(run_id: str, mdb: MongoDatabase):
             run=requested.run,
             job=requested.job,
             type=RunEventType.STARTED,
-            time=now(as_str=True),
+            time=now_str(),
         ).model_dump()
     )
     return run_id
@@ -133,7 +133,7 @@ def _add_run_fail_event(run_id: str, mdb: MongoDatabase):
             run=requested.run,
             job=requested.job,
             type=RunEventType.FAIL,
-            time=now(as_str=True),
+            time=now_str(),
         ).model_dump()
     )
     return run_id
@@ -154,7 +154,7 @@ def _add_run_complete_event(run_id: str, mdb: MongoDatabase, outputs: List[str])
             run=started.run,
             job=started.job,
             type=RunEventType.COMPLETE,
-            time=now(as_str=True),
+            time=now_str(),
             outputs=outputs,
         ).model_dump()
     )