diff --git a/src/murfey/client/contexts/atlas.py b/src/murfey/client/contexts/atlas.py index 04869e89e..f3fdb8a47 100644 --- a/src/murfey/client/contexts/atlas.py +++ b/src/murfey/client/contexts/atlas.py @@ -75,6 +75,30 @@ def post_transfer_serialem( session_id=environment.murfey_session, data=dcg_data, ) + capture_post( + base_url=str(environment.url.geturl()), + router_name="session_control.spa_router", + function_name="register_atlas", + token=self._token, + instrument_name=environment.instrument_name, + session_id=environment.murfey_session, + data={ + "name": f"{environment.visit}-slot-{sample}", + "acquisition_uuid": environment.acquisition_uuid, + "register_grid": False, + "tag": str(transferred_file.parent / transferred_file.stem), + "storage_folder": str( + _atlas_destination( + environment, + source, + Path(self._machine_config.get("rsync_basepath", "")), + ) + / "atlas" + if source + else "" + ), + }, + ) logger.info( f"Registered data collection group for atlas {str(transferred_file.stem)!r}" ) diff --git a/src/murfey/util/db.py b/src/murfey/util/db.py index a6a59bf74..f49fed38b 100644 --- a/src/murfey/util/db.py +++ b/src/murfey/util/db.py @@ -7,7 +7,7 @@ from typing import List, Optional import sqlalchemy -from sqlmodel import Enum, Field, Relationship, SQLModel, create_engine +from sqlmodel import DateTime, Enum, Field, Relationship, SQLModel, create_engine """ ======================================================================================= @@ -52,7 +52,9 @@ class Session(SQLModel, table=True): # type: ignore current_gain_ref: str = Field(default="") instrument_name: str = Field(default="") process: bool = Field(default=True) - visit_end_time: Optional[datetime] = Field(default=None) + visit_end_time: Optional[datetime] = Field( + default=None, sa_type=DateTime(timezone=False) + ) smartem_acquisition_uuid: str | None = Field(default=None) # Image sites associated with this session @@ -672,6 +674,7 @@ class Movie(SQLModel, table=True): # type: ignore creation_time: datetime = Field( alias="createdTimeStamp", sa_column_kwargs={"name": "createdTimeStamp"}, + sa_type=DateTime(timezone=False), default_factory=datetime.now, ) tag: str @@ -987,7 +990,9 @@ class Tomogram(SQLModel, table=True): # type: ignore xyShiftPlot: Optional[str] = None projXY: Optional[str] = None projXZ: Optional[str] = None - recordTimeStamp: Optional[datetime] = None + recordTimeStamp: Optional[datetime] = Field( + sa_type=DateTime(timezone=False), default_factory=datetime.now + ) globalAlignmentQuality: Optional[float] = None gridSquareId: Optional[int] = Field(foreign_key="searchmap.id") pixelLocationX: Optional[int] = None