update for utcnow deprecation (#418)

* update for  deprecation

* typo

* fix call

* black formatting

* fixing import

* fixing datetime call

* fix import

* fix imports

* datetime.now

* type fix

* revert to utc now tmeporarily

* try setting tz=None to avoid utc offset

* Use UTC timezone use datetime instead of localdatetime

---------

Co-authored-by: Ian Kenney <ianmichaelkenney@gmail.com>

Author: atravitz

alchemiscale/compute/api.py

@@ -5,7 +5,8 @@
 """
 
 import json
-from datetime import datetime, timedelta
+import datetime
+from datetime import timedelta
 import random
 
 from fastapi import FastAPI, APIRouter, Body, Depends, Request
@@ -103,7 +104,7 @@ def register_computeservice(
     compute_service_id,
     n4js: Neo4jStore = Depends(get_n4js_depends),
 ):
-    now = datetime.utcnow()
+    now = datetime.datetime.now(tz=datetime.UTC)
     csreg = ComputeServiceRegistration(
         identifier=ComputeServiceID(compute_service_id),
         registered=now,
@@ -134,7 +135,7 @@ def heartbeat_computeservice(
     n4js: Neo4jStore = Depends(get_n4js_depends),
     settings: ComputeAPISettings = Depends(get_base_api_settings),
 ):
-    now = datetime.utcnow()
+    now = datetime.datetime.now(tz=datetime.UTC)
 
     # expire any stale registrations, along with their claims
     expire_delta = timedelta(
@@ -215,7 +216,7 @@ def claim_tasks(
 
     """
     # check if the compute service can claim tasks
-    now = datetime.now()
+    now = datetime.datetime.now(tz=datetime.UTC)
     if not n4js.compute_service_can_claim(
         compute_service_id,
         now - timedelta(seconds=settings.ALCHEMISCALE_COMPUTE_API_FORGIVE_TIME_SECONDS),
@@ -384,7 +385,7 @@ async def set_task_result(
         n4js.set_task_error(tasks=[task_sk])
 
         # report that the compute service experienced a failure
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         n4js.log_failure_compute_service(compute_service_id, now)
         n4js.resolve_task_restarts(task_scoped_keys=[task_sk])
 

alchemiscale/security/auth.py

@@ -5,7 +5,8 @@
 """
 
 import secrets
-from datetime import datetime, timedelta
+import datetime
+from datetime import timedelta
 
 import bcrypt
 from fastapi import HTTPException, status
@@ -112,7 +113,7 @@ def create_access_token(
 ) -> str:
     to_encode = data.copy()
 
-    expire = datetime.utcnow() + timedelta(seconds=expires_seconds)
+    expire = datetime.datetime.now(tz=datetime.UTC) + timedelta(seconds=expires_seconds)
     to_encode.update({"exp": expire})
 
     encoded_jwt = jwt.encode(to_encode, secret_key, algorithm=jwt_algorithm)

alchemiscale/security/models.py

@@ -4,7 +4,7 @@
 
 """
 
-from datetime import datetime
+import datetime
 
 from pydantic import BaseModel, field_validator
 
@@ -23,7 +23,7 @@ class TokenData(BaseModel):
 
 class CredentialedEntity(BaseModel):
     hashed_key: str
-    expires: datetime | None = None
+    expires: datetime.datetime | None = None
 
 
 class ScopedIdentity(BaseModel):

alchemiscale/storage/models.py

@@ -6,7 +6,7 @@
 
 from abc import abstractmethod
 from copy import copy
-from datetime import datetime
+import datetime
 from enum import Enum
 from uuid import uuid4
 import hashlib
@@ -39,7 +39,7 @@ def __str__(self):
 
     @classmethod
     def from_now(cls, identifier: ComputeServiceID):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         return cls(
             identifier=identifier, registered=now, heartbeat=now, failure_times=[]
         )
@@ -96,7 +96,7 @@ class Task(GufeTokenizable):
     status: TaskStatusEnum
     priority: int
     claim: str | None
-    datetime_created: datetime | None
+    datetime_created: datetime.datetime | None
     creator: str | None
     extends: str | None
 
@@ -105,7 +105,7 @@ def __init__(
         *,
         status: str | TaskStatusEnum = TaskStatusEnum.waiting,
         priority: int = 10,
-        datetime_created: datetime | None = None,
+        datetime_created: datetime.datetime | None = None,
         creator: str | None = None,
         extends: str | None = None,
         claim: str | None = None,
@@ -118,7 +118,9 @@ def __init__(
         self.priority = priority
 
         self.datetime_created = (
-            datetime_created if datetime_created is not None else datetime.utcnow()
+            datetime_created
+            if datetime_created is not None
+            else datetime.datetime.now(tz=datetime.UTC)
         )
 
         self.creator = creator
@@ -422,7 +424,7 @@ def __init__(
         obj_key: GufeKey,
         scope: Scope,
         ok: bool,
-        datetime_created: datetime | None = None,
+        datetime_created: datetime.datetime | None = None,
         creator: str | None = None,
     ):
         self.location = location
@@ -450,7 +452,7 @@ def _to_dict(self):
     def _from_dict(cls, d):
         d_ = copy(d)
         d_["datetime_created"] = (
-            datetime.fromisoformat(d["datetime_created"])
+            datetime.datetime.fromisoformat(d["datetime_created"])
             if d.get("received") is not None
             else None
         )

alchemiscale/storage/objectstore.py

@@ -5,7 +5,7 @@
 """
 
 import os
-from datetime import datetime
+import datetime
 from boto3.session import Session
 from functools import lru_cache
 
@@ -237,7 +237,7 @@ def push_protocoldagresult(
             obj_key=protocoldagresult_gufekey,
             scope=transformation.scope,
             ok=ok,
-            datetime_created=datetime.utcnow(),
+            datetime_created=datetime.datetime.now(tz=datetime.UTC),
             creator=creator,
         )
 

alchemiscale/storage/statestore.py

@@ -6,7 +6,7 @@
 
 import abc
 import bisect
-from datetime import datetime
+import datetime
 from contextlib import contextmanager
 import json
 import re
@@ -115,7 +115,7 @@ def _select_tasks_from_taskpool(taskpool: list[tuple[str, float]], count) -> lis
 
     // create CLAIMS relationship with given compute service
     MATCH (csreg:ComputeServiceRegistration {{identifier: $compute_service_id}})
-    CREATE (t)<-[cl:CLAIMS {{claimed: localdatetime($datetimestr)}}]-(csreg)
+    CREATE (t)<-[cl:CLAIMS {{claimed: datetime($datetimestr)}}]-(csreg)
 
     SET t.status = '{TaskStatusEnum.running.value}'
 
@@ -1255,25 +1255,25 @@ def deregister_computeservice(self, compute_service_id: ComputeServiceID):
         return ComputeServiceID(identifier)
 
     def heartbeat_computeservice(
-        self, compute_service_id: ComputeServiceID, heartbeat: datetime
+        self, compute_service_id: ComputeServiceID, heartbeat: datetime.datetime
     ):
         """Update the heartbeat for the given ComputeServiceID."""
 
         q = f"""
         MATCH (n:ComputeServiceRegistration {{identifier: $compute_service_id}})
-        SET n.heartbeat = localdatetime('{heartbeat.isoformat()}')
+        SET n.heartbeat = datetime('{heartbeat.isoformat()}')
 
         """
         with self.transaction() as tx:
             tx.run(q, compute_service_id=str(compute_service_id))
 
         return compute_service_id
 
-    def expire_registrations(self, expire_time: datetime):
+    def expire_registrations(self, expire_time: datetime.datetime):
         """Remove all registrations with last heartbeat prior to the given `expire_time`."""
         q = f"""
         MATCH (n:ComputeServiceRegistration)
-        WHERE n.heartbeat < localdatetime('{expire_time.isoformat()}')
+        WHERE n.heartbeat < datetime('{expire_time.isoformat()}')
 
         WITH n
 
@@ -1298,7 +1298,7 @@ def expire_registrations(self, expire_time: datetime):
     def log_failure_compute_service(
         self,
         compute_service_id: ComputeServiceID,
-        failure_time: datetime,
+        failure_time: datetime.datetime,
     ) -> ComputeServiceID:
         """Add a reported compute service failure to the database.
 
@@ -1311,7 +1311,7 @@ def log_failure_compute_service(
         """
         q = """
         MATCH (n:ComputeServiceRegistration {identifier: $compute_service_id})
-        SET n.failure_times = [localdatetime($failure_time)] + n.failure_times
+        SET n.failure_times = [datetime($failure_time)] + n.failure_times
         """
 
         with self.transaction() as tx:
@@ -1326,7 +1326,7 @@ def log_failure_compute_service(
     def compute_service_can_claim(
         self,
         compute_service_id: ComputeServiceID,
-        forgive_time: datetime,
+        forgive_time: datetime.datetime,
         max_failures: int,
     ) -> bool:
         """Check if a compute service is able to claim a ``Task``.
@@ -1345,7 +1345,7 @@ def compute_service_can_claim(
         # get the number of failures that occured after `forgive_time`
         query = """
         MATCH (cs:ComputeServiceRegistration {identifier: $compute_service_id})
-        SET cs.failure_times = [entry IN cs.failure_times WHERE entry > localdatetime($forgive_time)]
+        SET cs.failure_times = [entry IN cs.failure_times WHERE entry > datetime($forgive_time)]
         RETURN size(cs.failure_times) as n_failures
         """
         results = self.execute_query(
@@ -2074,7 +2074,7 @@ def task_count(task_dict: dict):
                 tx.run(
                     CLAIM_QUERY,
                     tasks_list=[str(task) for task in tasks if task is not None],
-                    datetimestr=str(datetime.utcnow().isoformat()),
+                    datetimestr=str(datetime.datetime.now(tz=datetime.UTC).isoformat()),
                     compute_service_id=str(compute_service_id),
                 )
 

alchemiscale/tests/integration/compute/client/test_compute_client.py

@@ -1,7 +1,7 @@
 import pytest
 import json
 import os
-from datetime import datetime
+import datetime
 from time import sleep
 
 from gufe.tokenization import JSON_HANDLER
@@ -378,7 +378,7 @@ def test_set_task_result_legacy(
             obj_key=protocoldagresult.key,
             scope=tf_sk.scope,
             ok=protocoldagresult.ok(),
-            datetime_created=datetime.utcnow(),
+            datetime_created=datetime.datetime.now(tz=datetime.UTC),
             creator=None,
         )
 

alchemiscale/tests/integration/compute/client/test_compute_service.py

@@ -171,7 +171,7 @@ def test_cycle_max_failures(self, n4js_preloaded, s3os_server_fresh, service):
         # create blocking failures
         query = """
         MATCH (cs:ComputeServiceRegistration {identifier: $compute_service_id})
-        SET cs.failure_times = [localdatetime()] + cs.failure_times
+        SET cs.failure_times = [datetime()] + cs.failure_times
         """
 
         for _ in range(4):

alchemiscale/tests/integration/interface/client/test_client.py

@@ -1,5 +1,5 @@
 import pytest
-from datetime import datetime
+import datetime
 from time import sleep
 import os
 from pathlib import Path
@@ -2212,7 +2212,7 @@ def _push_result_legacy(task_scoped_key, protocoldagresult, n4js, s3os_server):
             obj_key=protocoldagresult.key,
             scope=transformation_sk.scope,
             ok=ok,
-            datetime_created=datetime.utcnow(),
+            datetime_created=datetime.datetime.now(tz=datetime.UTC),
             creator=None,
         )
         n4js.set_task_result(

alchemiscale/tests/integration/storage/test_statestore.py

@@ -1,4 +1,5 @@
-from datetime import datetime, timedelta
+import datetime
+from datetime import timedelta
 import random
 from pathlib import Path
 from functools import reduce
@@ -573,7 +574,7 @@ def test_get_transformation_failures(
     ### compute
 
     def test_register_computeservice(self, n4js, compute_service_id):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         registration = ComputeServiceRegistration(
             identifier=compute_service_id,
             registered=now,
@@ -599,7 +600,7 @@ def test_register_computeservice(self, n4js, compute_service_id):
         assert int(csreg["heartbeat"].to_native().timestamp()) == int(now.timestamp())
 
     def test_deregister_computeservice(self, n4js, compute_service_id):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         registration = ComputeServiceRegistration(
             identifier=compute_service_id,
             registered=now,
@@ -622,7 +623,7 @@ def test_deregister_computeservice(self, n4js, compute_service_id):
         assert not csreg.records
 
     def test_heartbeat_computeservice(self, n4js, compute_service_id):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         registration = ComputeServiceRegistration(
             identifier=compute_service_id,
             registered=now,
@@ -651,7 +652,7 @@ def test_heartbeat_computeservice(self, n4js, compute_service_id):
         )
 
     def test_expire_registrations(self, n4js, compute_service_id):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         yesterday = now - timedelta(days=1)
         an_hour_ago = now - timedelta(hours=1)
         registration = ComputeServiceRegistration(
@@ -678,7 +679,7 @@ def test_expire_registrations(self, n4js, compute_service_id):
         assert compute_service_id in identities
 
     def test_log_failure_computeservice(self, n4js, compute_service_id):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         registration = ComputeServiceRegistration(
             identifier=compute_service_id,
             registered=now,
@@ -706,7 +707,7 @@ def test_log_failure_computeservice(self, n4js, compute_service_id):
         assert 6 == results.records[0]["n_failures"]
 
     def test_compute_service_can_claim(self, n4js, compute_service_id):
-        now = datetime.utcnow()
+        now = datetime.datetime.now(tz=datetime.UTC)
         registration = ComputeServiceRegistration(
             identifier=compute_service_id,
             registered=now,