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Add db components from ispyb for processing outputs #706

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1b1cf5f
Add db components from ispyb
stephen-riggs Dec 1, 2025
ce045b6
Merge together all similar tables
stephen-riggs Dec 1, 2025
e966b2a
Register movies on the murfey side
stephen-riggs Dec 2, 2025
7dad07e
Wrong naming
stephen-riggs Dec 2, 2025
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12 changes: 12 additions & 0 deletions src/murfey/server/api/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -443,6 +443,7 @@ async def request_spa_preprocessing(
db.add(feedback_params)
movie = Movie(
murfey_id=murfey_ids[0],
data_collection_id=detached_ids[1],
path=proc_file.path,
image_number=proc_file.image_number,
tag=proc_file.tag,
Expand Down Expand Up @@ -695,6 +696,17 @@ async def request_tomography_preprocessing(
0
].eer_fractionation_file

movie = Movie(
murfey_id=murfey_ids[0],
data_collection_id=dcid,
path=proc_file.path,
image_number=proc_file.image_number,
tag=proc_file.tag,
)
db.add(movie)
db.commit()
db.close()

zocalo_message: dict = {
"recipes": [recipe_name],
"parameters": {
Expand Down
1 change: 1 addition & 0 deletions src/murfey/server/feedback.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1488,6 +1488,7 @@ def _flush_tomography_preprocessing(message: dict, _db):
p.parent.mkdir(parents=True)
movie = db.Movie(
murfey_id=murfey_ids[0],
data_collection_id=detached_ids[1],
path=f.file_path,
image_number=f.image_number,
tag=f.tag,
Expand Down
76 changes: 75 additions & 1 deletion src/murfey/util/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,22 @@
"""

from datetime import datetime
from typing import List, Optional
from typing import TYPE_CHECKING, List, Optional

import sqlalchemy
from sqlmodel import Field, Relationship, SQLModel, create_engine

if TYPE_CHECKING:
from murfey.util.processing_db import (
CTF,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'CTF' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of CTF occurs after the cyclic
import
Loading
of murfey.util.db.
MotionCorrection,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'MotionCorrection' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of MotionCorrection occurs after the cyclic
import
Loading
of murfey.util.db.
ParticleClassificationGroup,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'ParticleClassificationGroup' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of ParticleClassificationGroup occurs after the cyclic
import
Loading
of murfey.util.db.
ParticlePicker,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'ParticlePicker' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of ParticlePicker occurs after the cyclic
import
Loading
of murfey.util.db.
RelativeIceThickness,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'RelativeIceThickness' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of RelativeIceThickness occurs after the cyclic
import
Loading
of murfey.util.db.
TiltImageAlignment,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'TiltImageAlignment' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of TiltImageAlignment occurs after the cyclic
import
Loading
of murfey.util.db.
Tomogram,

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'Tomogram' may not be defined if module
murfey.util.processing_db
Loading
is imported before module
murfey.util.db
Loading
, as the
definition
Loading
of Tomogram occurs after the cyclic
import
Loading
of murfey.util.db.
)

"""
GENERAL
"""
Expand Down Expand Up @@ -429,6 +440,14 @@
sa_relationship_kwargs={"cascade": "delete"},
)
)
grid_squares: List["GridSquare"] = Relationship(
back_populates="data_collection_group",
sa_relationship_kwargs={"cascade": "delete"},
)
search_maps: List["SearchMap"] = Relationship(
back_populates="data_collection_group",
sa_relationship_kwargs={"cascade": "delete"},
)


class NotificationParameter(SQLModel, table=True): # type: ignore
Expand Down Expand Up @@ -468,6 +487,13 @@
processing_jobs: List["ProcessingJob"] = Relationship(
back_populates="data_collection", sa_relationship_kwargs={"cascade": "delete"}
)
movies: List["Movie"] = Relationship(
back_populates="data_collection", sa_relationship_kwargs={"cascade": "delete"}
)
MotionCorrection: List["MotionCorrection"] = Relationship(
back_populates="DataCollection"
)
Tomogram: List["Tomogram"] = Relationship(back_populates="DataCollection")


class ProcessingJob(SQLModel, table=True): # type: ignore
Expand Down Expand Up @@ -569,6 +595,20 @@
murfey_ids: List["MurfeyLedger"] = Relationship(
back_populates="auto_proc_program", sa_relationship_kwargs={"cascade": "delete"}
)
MotionCorrection: List["MotionCorrection"] = Relationship(
back_populates="DataCollection"
)
Tomogram: List["Tomogram"] = Relationship(back_populates="AutoProcProgram")
CTF: List["CTF"] = Relationship(back_populates="AutoProcProgram")
ParticlePicker: List["ParticlePicker"] = Relationship(
back_populates="AutoProcProgram"
)
RelativeIceThickness: List["RelativeIceThickness"] = Relationship(
back_populates="AutoProcProgram"
)
ParticleClassificationGroup: List["ParticleClassificationGroup"] = Relationship(
back_populates="AutoProcProgram"
)


class MurfeyLedger(SQLModel, table=True): # type: ignore
Expand Down Expand Up @@ -608,6 +648,7 @@
class GridSquare(SQLModel, table=True): # type: ignore
id: Optional[int] = Field(primary_key=True, default=None)
session_id: int = Field(foreign_key="session.id")
atlas_id: Optional[int] = Field(foreign_key="datacollectiongroup.id")
name: int
tag: str
x_location: Optional[float]
Expand All @@ -619,6 +660,13 @@
thumbnail_size_x: Optional[int]
thumbnail_size_y: Optional[int]
pixel_size: Optional[float] = None
scaled_pixel_size: Optional[float] = None
pixel_location_x: Optional[int] = None
pixel_location_y: Optional[int] = None
height: Optional[int] = None
width: Optional[int] = None
angle: Optional[float] = None
quality_indicator: Optional[float] = None
image: str = ""
session: Optional[Session] = Relationship(back_populates="grid_squares")
clem_image_series: List["CLEMImageSeries"] = Relationship(
Expand All @@ -627,6 +675,9 @@
foil_holes: List["FoilHole"] = Relationship(
back_populates="grid_square", sa_relationship_kwargs={"cascade": "delete"}
)
data_collection_group: Optional["DataCollectionGroup"] = Relationship(
back_populates="grid_squares"
)


class FoilHole(SQLModel, table=True): # type: ignore
Expand All @@ -643,6 +694,11 @@
thumbnail_size_x: Optional[int]
thumbnail_size_y: Optional[int]
pixel_size: Optional[float] = None
scaled_pixel_size: Optional[float] = None
pixel_location_x: Optional[int] = None
pixel_location_y: Optional[int] = None
diameter: Optional[int] = None
quality_indicator: Optional[float] = None
image: str = ""
grid_square: Optional[GridSquare] = Relationship(back_populates="foil_holes")
session: Optional[Session] = Relationship(back_populates="foil_holes")
Expand All @@ -657,13 +713,21 @@
class SearchMap(SQLModel, table=True): # type: ignore
id: Optional[int] = Field(primary_key=True, default=None)
session_id: int = Field(foreign_key="session.id")
atlas_id: Optional[int] = Field(foreign_key="datacollectiongroup.id")
name: str
tag: str
x_location: Optional[float] = None
y_location: Optional[float] = None
x_stage_position: Optional[float] = None
y_stage_position: Optional[float] = None
pixel_size: Optional[float] = None
scaled_pixel_size: Optional[float] = None
pixel_location_x: Optional[int] = None
pixel_location_y: Optional[int] = None
scaled_height: Optional[int] = None
scaled_width: Optional[int] = None
angle: Optional[float] = None
quality_indicator: Optional[float] = None
image: str = ""
binning: Optional[float] = None
reference_matrix_m11: Optional[float] = None
Expand All @@ -684,17 +748,27 @@
tilt_series: List["TiltSeries"] = Relationship(
back_populates="search_map", sa_relationship_kwargs={"cascade": "delete"}
)
data_collection_group: Optional["DataCollectionGroup"] = Relationship(
back_populates="search_maps"
)
Tomogram: List["Tomogram"] = Relationship(back_populates="SearchMap")


class Movie(SQLModel, table=True): # type: ignore
murfey_id: int = Field(primary_key=True, foreign_key="murfeyledger.id")
foil_hole_id: int = Field(foreign_key="foilhole.id", nullable=True, default=None)
data_collection_id: Optional[int] = Field(foreign_key="datacollection.id")
path: str
image_number: int
tag: str
preprocessed: bool = False
murfey_ledger: Optional[MurfeyLedger] = Relationship(back_populates="movies")
foil_hole: Optional[FoilHole] = Relationship(back_populates="movies")
data_collection: Optional["DataCollection"] = Relationship(back_populates="movies")
MotionCorrection: List["MotionCorrection"] = Relationship(back_populates="Movie")
TiltImageAlignment: List["TiltImageAlignment"] = Relationship(
back_populates="Movie"
)


class CtfParameters(SQLModel, table=True): # type: ignore
Expand Down
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