fix(persistence): address review feedback on PR #1851

- Fix naive datetime.now() → datetime.now(UTC) in all ORM models
- Fix seq race condition in DbRunEventStore.put() with FOR UPDATE
  and UNIQUE(thread_id, seq) constraint
- Encapsulate _store access in RunManager.update_run_completion()
- Deduplicate _store.put() logic in RunManager via _persist_to_store()
- Add update_run_completion to RunStore ABC + MemoryRunStore
- Wire follow_up_to_run_id through the full create path
- Add error recovery to RunJournal._flush_sync() lost-event scenario
- Add migration note for search_threads breaking change
- Fix test_checkpointer_none_fix mock to set database=None

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

backend/packages/harness/deerflow/persistence/models/feedback.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from datetime import datetime
+from datetime import UTC, datetime
 
 from sqlalchemy import DateTime, String, Text
 from sqlalchemy.orm import Mapped, mapped_column
@@ -27,4 +27,4 @@ class FeedbackRow(Base):
     comment: Mapped[str | None] = mapped_column(Text)
     # Optional text feedback from the user
 
-    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now())
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))

backend/packages/harness/deerflow/persistence/models/run.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from datetime import datetime
+from datetime import UTC, datetime
 
 from sqlalchemy import JSON, DateTime, Index, String, Text
 from sqlalchemy.orm import Mapped, mapped_column
@@ -43,7 +43,7 @@ class RunRow(Base):
     # Follow-up association
     follow_up_to_run_id: Mapped[str | None] = mapped_column(String(64))
 
-    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now())
-    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(), onupdate=lambda: datetime.now())
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
+    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC), onupdate=lambda: datetime.now(UTC))
 
     __table_args__ = (Index("ix_runs_thread_status", "thread_id", "status"),)

backend/packages/harness/deerflow/persistence/models/run_event.py

@@ -2,9 +2,9 @@
 
 from __future__ import annotations
 
-from datetime import datetime
+from datetime import UTC, datetime
 
-from sqlalchemy import JSON, DateTime, Index, String, Text
+from sqlalchemy import JSON, DateTime, Index, String, Text, UniqueConstraint
 from sqlalchemy.orm import Mapped, mapped_column
 
 from deerflow.persistence.base import Base
@@ -22,9 +22,10 @@ class RunEventRow(Base):
     content: Mapped[str] = mapped_column(Text, default="")
     event_metadata: Mapped[dict] = mapped_column(JSON, default=dict)
     seq: Mapped[int] = mapped_column(nullable=False)
-    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now())
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
 
     __table_args__ = (
+        UniqueConstraint("thread_id", "seq", name="uq_events_thread_seq"),
         Index("ix_events_thread_cat_seq", "thread_id", "category", "seq"),
         Index("ix_events_run", "thread_id", "run_id", "seq"),
     )

backend/packages/harness/deerflow/persistence/models/thread_meta.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from datetime import datetime
+from datetime import UTC, datetime
 
 from sqlalchemy import JSON, DateTime, String
 from sqlalchemy.orm import Mapped, mapped_column
@@ -19,5 +19,5 @@ class ThreadMetaRow(Base):
     display_name: Mapped[str | None] = mapped_column(String(256))
     status: Mapped[str] = mapped_column(String(20), default="idle")
     metadata_json: Mapped[dict] = mapped_column(JSON, default=dict)
-    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now())
-    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(), onupdate=lambda: datetime.now())
+    created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC))
+    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=lambda: datetime.now(UTC), onupdate=lambda: datetime.now(UTC))

backend/packages/harness/deerflow/persistence/repositories/run_repo.py

@@ -78,6 +78,7 @@ class RunRepository(RunStore):
         kwargs=None,
         error=None,
         created_at=None,
+        follow_up_to_run_id=None,
     ):
         now = datetime.now(UTC)
         row = RunRow(
@@ -90,6 +91,7 @@ class RunRepository(RunStore):
             metadata_json=self._safe_json(metadata) or {},
             kwargs_json=self._safe_json(kwargs) or {},
             error=error,
+            follow_up_to_run_id=follow_up_to_run_id,
             created_at=datetime.fromisoformat(created_at) if created_at else now,
             updated_at=now,
         )