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Add atlas registration for serialem #894

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Merged
stephen-riggs merged 3 commits into from
Sep 22, 2026
Merged

Add atlas registration for serialem #894

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e8465bf
Add atlas registration for serialem
stephen-riggs Sep 21, 2026
d249349
Try and fix timestamp issue
stephen-riggs Sep 22, 2026
6a63d6c
Another datetime
stephen-riggs Sep 22, 2026
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24 changes: 24 additions & 0 deletions src/murfey/client/contexts/atlas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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}"
)
Expand Down
11 changes: 8 additions & 3 deletions src/murfey/util/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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

"""
=======================================================================================
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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