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Add db components from ispyb for processing outputs #706

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@stephen-riggs stephen-riggs commented Dec 1, 2025 •
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Current issues:

  • How to set up murfey with/without processing DB
  • Ways to insert processing results
  • GridSquare, FoilHole, Movie tables are duplicate names
  • Do we want cascade delete on tables?

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src/murfey/util/db.py

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.
src/murfey/util/db.py
if TYPE_CHECKING:
from murfey.util.processing_db import (
CTF,
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.
src/murfey/util/db.py
from murfey.util.processing_db import (
CTF,
MotionCorrection,
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.
src/murfey/util/db.py
CTF,
MotionCorrection,
ParticleClassificationGroup,
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.
src/murfey/util/db.py
MotionCorrection,
ParticleClassificationGroup,
ParticlePicker,
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.
src/murfey/util/db.py
ParticlePicker,
RelativeIceThickness,
TiltImageAlignment,
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.
src/murfey/util/processing_db.py
from sqlmodel import Enum, Field, Relationship, SQLModel

if TYPE_CHECKING:
from murfey.util.db import AutoProcProgram, DataCollection, Movie, SearchMap

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'AutoProcProgram' may not be defined if module
murfey.util.db
Loading
is imported before module
murfey.util.processing_db
Loading
, as the
definition
Loading
of AutoProcProgram occurs after the cyclic
import
Loading
of murfey.util.processing_db.
src/murfey/util/processing_db.py
from sqlmodel import Enum, Field, Relationship, SQLModel

if TYPE_CHECKING:
from murfey.util.db import AutoProcProgram, DataCollection, Movie, SearchMap

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'DataCollection' may not be defined if module
murfey.util.db
Loading
is imported before module
murfey.util.processing_db
Loading
, as the
definition
Loading
of DataCollection occurs after the cyclic
import
Loading
of murfey.util.processing_db.
src/murfey/util/processing_db.py
from sqlmodel import Enum, Field, Relationship, SQLModel

if TYPE_CHECKING:
from murfey.util.db import AutoProcProgram, DataCollection, Movie, SearchMap

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

'Movie' may not be defined if module
murfey.util.db
Loading
is imported before module
murfey.util.processing_db
Loading
, as the
definition
Loading
of Movie occurs after the cyclic
import
Loading
of murfey.util.processing_db.
src/murfey/util/processing_db.py
from sqlmodel import Enum, Field, Relationship, SQLModel

if TYPE_CHECKING:
from murfey.util.db import AutoProcProgram, DataCollection, Movie, SearchMap

Check failure

Code scanning / CodeQL

Module-level cyclic import Error

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

@stephen-riggs