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MaximeBICMTLMaximeBICMTL
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migrate orm to pathlib.Path
1 parent 685f4ae commit b6989c4

20 files changed

+112
-58
lines changed

‎python/lib/db/decorators/string_path.py‎

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@@ -0,0 +1,27 @@
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from pathlib import Path
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from sqlalchemy import String
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from sqlalchemy.engine import Dialect
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from sqlalchemy.types import TypeDecorator
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class StringPath(TypeDecorator[Path]):
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"""
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Decorator for a database path type.
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In SQL, the type will appear as a string.
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In Python, the type will appear as a path object.
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"""
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impl = String
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def process_bind_param(self, value: Path | None, dialect: Dialect) -> str | None:
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if value is None:
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return None
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return str(value)
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def process_result_value(self, value: str | None, dialect: Dialect) -> Path | None:
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if value is None:
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return None
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return Path(value)

‎python/lib/db/models/dicom_archive.py‎

Lines changed: 4 additions & 2 deletions
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@@ -1,4 +1,5 @@
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from datetime import date, datetime
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from pathlib import Path
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from typing import Optional
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from sqlalchemy import ForeignKey
@@ -12,6 +13,7 @@
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import lib.db.models.session as db_session
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from lib.db.base import Base
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from lib.db.decorators.int_bool import IntBool
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from lib.db.decorators.string_path import StringPath
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class DbDicomArchive(Base):
@@ -37,8 +39,8 @@ class DbDicomArchive(Base):
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creating_user : Mapped[str] = mapped_column('CreatingUser')
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sum_type_version : Mapped[int] = mapped_column('sumTypeVersion')
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tar_type_version : Mapped[int | None] = mapped_column('tarTypeVersion')
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source_location : Mapped[str] = mapped_column('SourceLocation')
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archive_location : Mapped[str | None] = mapped_column('ArchiveLocation')
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source_path : Mapped[Path] = mapped_column('SourceLocation', StringPath)
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archive_path : Mapped[Path | None] = mapped_column('ArchiveLocation', StringPath)
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scanner_manufacturer : Mapped[str] = mapped_column('ScannerManufacturer')
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scanner_model : Mapped[str] = mapped_column('ScannerModel')
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scanner_serial_number : Mapped[str] = mapped_column('ScannerSerialNumber')

‎python/lib/db/models/file.py‎

Lines changed: 3 additions & 1 deletion
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@@ -1,4 +1,5 @@
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from datetime import date, datetime
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from pathlib import Path
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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -8,14 +9,15 @@
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from lib.db.base import Base
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from lib.db.decorators.int_bool import IntBool
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from lib.db.decorators.int_datetime import IntDatetime
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from lib.db.decorators.string_path import StringPath
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class DbFile(Base):
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__tablename__ = 'files'
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id : Mapped[int] = mapped_column('FileID', primary_key=True)
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session_id : Mapped[int] = mapped_column('SessionID', ForeignKey('session.ID'))
18-
rel_path : Mapped[str] = mapped_column('File')
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path : Mapped[Path] = mapped_column('File', StringPath)
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series_uid : Mapped[str | None] = mapped_column('SeriesUID')
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echo_time : Mapped[float | None] = mapped_column('EchoTime')
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phase_encoding_direction : Mapped[str | None] = mapped_column('PhaseEncodingDirection')

‎python/lib/db/models/mri_protocol_violated_scan.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
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from datetime import datetime
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from pathlib import Path
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from typing import Optional
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from sqlalchemy import ForeignKey
@@ -8,6 +9,7 @@
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import lib.db.models.dicom_archive as db_dicom_archive
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import lib.db.models.mri_protocol_group as db_mri_protocol_group
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from lib.db.base import Base
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from lib.db.decorators.string_path import StringPath
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class DbMriProtocolViolatedScan(Base):
@@ -19,7 +21,7 @@ class DbMriProtocolViolatedScan(Base):
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dicom_archive_id : Mapped[int | None] = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
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time_run : Mapped[datetime | None] = mapped_column('time_run')
2123
series_description : Mapped[str | None] = mapped_column('series_description')
22-
file_rel_path : Mapped[str | None] = mapped_column('minc_location')
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file_path : Mapped[Path | None] = mapped_column('minc_location', StringPath)
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patient_name : Mapped[str | None] = mapped_column('PatientName')
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tr_range : Mapped[str | None] = mapped_column('TR_range')
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te_range : Mapped[str | None] = mapped_column('TE_range')

‎python/lib/db/models/mri_upload.py‎

Lines changed: 4 additions & 2 deletions
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@@ -1,4 +1,5 @@
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from datetime import datetime
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from pathlib import Path
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from typing import Optional
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from sqlalchemy import ForeignKey
@@ -8,6 +9,7 @@
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import lib.db.models.session as db_session
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from lib.db.base import Base
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from lib.db.decorators.int_bool import IntBool
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from lib.db.decorators.string_path import StringPath
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from lib.db.decorators.y_n_bool import YNBool
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1315

@@ -17,8 +19,8 @@ class DbMriUpload(Base):
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id : Mapped[int] = mapped_column('UploadID', primary_key=True)
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uploaded_by : Mapped[str] = mapped_column('UploadedBy')
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upload_date : Mapped[datetime | None] = mapped_column('UploadDate')
20-
upload_location : Mapped[str] = mapped_column('UploadLocation')
21-
decompressed_location : Mapped[str] = mapped_column('DecompressedLocation')
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upload_path : Mapped[Path] = mapped_column('UploadLocation', StringPath)
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decompressed_path : Mapped[Path] = mapped_column('DecompressedLocation', StringPath)
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insertion_complete : Mapped[bool] = mapped_column('InsertionComplete', IntBool)
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inserting : Mapped[bool | None] = mapped_column('Inserting', IntBool)
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patient_name : Mapped[str] = mapped_column('PatientName')

‎python/lib/db/models/mri_violation_log.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
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from datetime import datetime
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from pathlib import Path
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from typing import Optional
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from sqlalchemy import ForeignKey
@@ -9,6 +10,7 @@
910
import lib.db.models.mri_protocol_check_group as db_mri_protocol_check_group
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import lib.db.models.mri_scan_type as db_mri_scan_type
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from lib.db.base import Base
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from lib.db.decorators.string_path import StringPath
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class DbMriViolationLog(Base):
@@ -19,7 +21,7 @@ class DbMriViolationLog(Base):
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series_uid : Mapped[str | None] = mapped_column('SeriesUID')
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dicom_archive_id : Mapped[int | None] \
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= mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
22-
file_rel_path : Mapped[str | None] = mapped_column('MincFile')
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file_path : Mapped[Path | None] = mapped_column('MincFile', StringPath)
2325
patient_name : Mapped[str | None] = mapped_column('PatientName')
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candidate_id : Mapped[int | None] = mapped_column('CandidateID', ForeignKey('candidate.ID'))
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visit_label : Mapped[str | None] = mapped_column('Visit_label')

‎python/lib/db/models/physio_channel.py‎

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@@ -1,5 +1,6 @@
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from datetime import datetime
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from decimal import Decimal
3+
from pathlib import Path
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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -8,6 +9,7 @@
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import lib.db.models.physio_file as db_physio_file
910
import lib.db.models.physio_status_type as db_physio_status_type
1011
from lib.db.base import Base
12+
from lib.db.decorators.string_path import StringPath
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1315
class DbPhysioChannel(Base):
@@ -28,7 +30,7 @@ class DbPhysioChannel(Base):
2830
reference : Mapped[str | None] = mapped_column('Reference')
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status_description : Mapped[str | None] = mapped_column('StatusDescription')
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unit : Mapped[str | None] = mapped_column('Unit')
31-
file_path : Mapped[str | None] = mapped_column('FilePath')
33+
file_path : Mapped[Path | None] = mapped_column('FilePath', StringPath)
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physio_file : Mapped['db_physio_file.DbPhysioFile'] = relationship('DbPhysioFile', back_populates='channels')
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channel_type : Mapped['db_physio_channel_type.DbPhysioChannelType'] = relationship('DbPhysioChannelType')

‎python/lib/db/models/physio_coord_system.py‎

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,5 @@
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from pathlib import Path
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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column, relationship
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@@ -11,12 +13,12 @@
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class DbPhysioCoordSystem(Base):
1214
__tablename__ = 'physiological_coord_system'
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14-
id : Mapped[int] = mapped_column('PhysiologicalCoordSystemID', primary_key=True)
15-
name_id : Mapped[int] = mapped_column('NameID', ForeignKey('physiological_coord_system_name.PhysiologicalCoordSystemNameID'))
16-
type_id : Mapped[int] = mapped_column('TypeID', ForeignKey('physiological_coord_system_type.PhysiologicalCoordSystemTypeID'))
17-
unit_id : Mapped[int] = mapped_column('UnitID', ForeignKey('physiological_coord_system_unit.PhysiologicalCoordSystemUnitID'))
18-
modality_id : Mapped[int] = mapped_column('ModalityID', ForeignKey('physiological_modality.PhysiologicalModalityID'))
19-
file_path : Mapped[str | None] = mapped_column('FilePath')
16+
id : Mapped[int] = mapped_column('PhysiologicalCoordSystemID', primary_key=True)
17+
name_id : Mapped[int] = mapped_column('NameID', ForeignKey('physiological_coord_system_name.PhysiologicalCoordSystemNameID'))
18+
type_id : Mapped[int] = mapped_column('TypeID', ForeignKey('physiological_coord_system_type.PhysiologicalCoordSystemTypeID'))
19+
unit_id : Mapped[int] = mapped_column('UnitID', ForeignKey('physiological_coord_system_unit.PhysiologicalCoordSystemUnitID'))
20+
modality_id : Mapped[int] = mapped_column('ModalityID', ForeignKey('physiological_modality.PhysiologicalModalityID'))
21+
file_path : Mapped[Path | None] = mapped_column('FilePath')
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2123
name : Mapped['db_physio_coord_system_name.DbPhysioCoordSystemName'] = relationship('DbPhysioCoordSystemName')
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type : Mapped['db_physio_coord_system_type.DbPhysioCoordSystemType'] = relationship('DbPhysioCoordSystemType')

‎python/lib/db/models/physio_event_file.py‎

Lines changed: 9 additions & 7 deletions
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from datetime import datetime
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from pathlib import Path
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from sqlalchemy import ForeignKey
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from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -9,18 +10,19 @@
910
import lib.db.models.physio_task_event as db_physio_task_event
1011
import lib.db.models.project as db_project
1112
from lib.db.base import Base
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from lib.db.decorators.string_path import StringPath
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1416
class DbPhysioEventFile(Base):
1517
__tablename__ = 'physiological_event_file'
1618

17-
id : Mapped[int] = mapped_column('EventFileID', primary_key=True)
18-
physio_file_id : Mapped[int | None] = mapped_column('PhysiologicalFileID', ForeignKey('physiological_file.PhysiologicalFileID'))
19-
project_id : Mapped[int | None] = mapped_column('ProjectID', ForeignKey('Project.ProjectID'))
20-
file_type : Mapped[str] = mapped_column('FileType', ForeignKey('ImagingFileTypes.type'))
21-
file_path : Mapped[str | None] = mapped_column('FilePath')
22-
last_update : Mapped[datetime] = mapped_column('LastUpdate')
23-
last_written : Mapped[datetime] = mapped_column('LastWritten')
19+
id : Mapped[int] = mapped_column('EventFileID', primary_key=True)
20+
physio_file_id : Mapped[int | None] = mapped_column('PhysiologicalFileID', ForeignKey('physiological_file.PhysiologicalFileID'))
21+
project_id : Mapped[int | None] = mapped_column('ProjectID', ForeignKey('Project.ProjectID'))
22+
file_type : Mapped[str] = mapped_column('FileType', ForeignKey('ImagingFileTypes.type'))
23+
file_path : Mapped[Path | None] = mapped_column('FilePath', StringPath)
24+
last_update : Mapped[datetime] = mapped_column('LastUpdate')
25+
last_written : Mapped[datetime] = mapped_column('LastWritten')
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2527
physio_file : Mapped['db_physio_file.DbPhysioFile | None'] = relationship('PhysiologicalFile')
2628
project : Mapped['db_project.DbProject | None'] = relationship('Project')

‎python/lib/db/models/physio_file.py‎

Lines changed: 3 additions & 1 deletion
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from datetime import datetime
2+
from pathlib import Path
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34
from sqlalchemy import ForeignKey
45
from sqlalchemy.orm import Mapped, mapped_column, relationship
@@ -7,6 +8,7 @@
78
import lib.db.models.physio_modality as db_physio_modality
89
import lib.db.models.physio_output_type as db_physio_output_type
910
from lib.db.base import Base
11+
from lib.db.decorators.string_path import StringPath
1012

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1214
class DbPhysioFile(Base):
@@ -20,7 +22,7 @@ class DbPhysioFile(Base):
2022
file_type : Mapped[str | None] = mapped_column('FileType')
2123
acquisition_time : Mapped[datetime | None] = mapped_column('AcquisitionTime')
2224
inserted_by_user : Mapped[str] = mapped_column('InsertedByUser')
23-
path : Mapped[str] = mapped_column('FilePath')
25+
path : Mapped[Path] = mapped_column('FilePath', StringPath)
2426
index : Mapped[int | None] = mapped_column('Index')
2527
parent_id : Mapped[int | None] = mapped_column('ParentID')
2628

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