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Add column defaults to ORM models and tests #1204

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Add column defaults to ORM models and tests #1204

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e91efc1
add defaults check
maximemulder Oct 20, 2024
d88e2a5
add decorators
maximemulder Oct 20, 2024
370072c
add orm defaults
maximemulder Oct 20, 2024
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4 changes: 2 additions & 2 deletions python/lib/db/base.py
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@@ -1,7 +1,7 @@
from sqlalchemy.orm import DeclarativeBase
from sqlalchemy.orm import DeclarativeBase, MappedAsDataclass


class Base(DeclarativeBase):
class Base(DeclarativeBase, MappedAsDataclass):
"""
Base SQLAlchemy class that must be inherited by all the ORM model classes.
"""
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33 changes: 33 additions & 0 deletions python/lib/db/decorator/true_false_bool.py
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@@ -0,0 +1,33 @@
from typing import Literal

from sqlalchemy import Enum
from sqlalchemy.engine import Dialect
from sqlalchemy.types import TypeDecorator


class TrueFalseBool(TypeDecorator[bool]):
"""
Decorator for a database yes/no type.
In SQL, the type will appear as 'true' | 'false'.
In Python, the type will appear as a boolean.
"""

impl = Enum('true', 'false')

def process_bind_param(self, value: bool | None, dialect: Dialect):
match value:
case True:
return 'true'
case False:
return 'false'
case None:
return None

def process_result_value(self, value: Literal['true', 'false'] | None, dialect: Dialect):
match value:
case 'true':
return True
case 'false':
return False
case None:
return None
60 changes: 33 additions & 27 deletions python/lib/db/model/candidate.py
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Expand Up @@ -3,46 +3,52 @@

from sqlalchemy import ForeignKey
from sqlalchemy.orm import Mapped, mapped_column, relationship
from sqlalchemy.sql.functions import current_timestamp

import lib.db.model.project as db_project
import lib.db.model.session as db_session
import lib.db.model.site as db_site
from lib.db.base import Base
from lib.db.decorator.true_false_bool import TrueFalseBool
from lib.db.decorator.y_n_bool import YNBool


class DbCandidate(Base):
__tablename__ = 'candidate'

id : Mapped[int] = mapped_column('ID', primary_key=True)
id : Mapped[int] = mapped_column('ID',
primary_key=True, autoincrement=True, init=False)
cand_id : Mapped[int] = mapped_column('CandID')
psc_id : Mapped[str] = mapped_column('PSCID')
external_id : Mapped[Optional[str]] = mapped_column('ExternalID')
date_of_birth : Mapped[Optional[date]] = mapped_column('DoB')
dete_of_death : Mapped[Optional[date]] = mapped_column('DoD')
edc : Mapped[Optional[date]] = mapped_column('EDC')
sex : Mapped[Optional[str]] = mapped_column('Sex')
registration_site_id : Mapped[int] = mapped_column('RegistrationCenterID', ForeignKey('psc.CenterID'))
registration_project_id : Mapped[int] \
= mapped_column('RegistrationProjectID', ForeignKey('Project.ProjectID'))
ethnicity : Mapped[Optional[str]] = mapped_column('Ethnicity')
active : Mapped[bool] = mapped_column('Active', YNBool)
date_active : Mapped[Optional[date]] = mapped_column('Date_active')
registered_by : Mapped[Optional[str]] = mapped_column('RegisteredBy')
user_id : Mapped[str] = mapped_column('UserID')
date_registered : Mapped[Optional[date]] = mapped_column('Date_registered')
flagged_caveatemptor : Mapped[Optional[str]] = mapped_column('flagged_caveatemptor')
flagged_reason : Mapped[Optional[int]] = mapped_column('flagged_reason')
flagged_other : Mapped[Optional[str]] = mapped_column('flagged_other')
flagged_other_status : Mapped[Optional[str]] = mapped_column('flagged_other_status')
test_date : Mapped[datetime] = mapped_column('Testdate')
entity_type : Mapped[str] = mapped_column('Entity_type')
proband_sex : Mapped[Optional[str]] = mapped_column('ProbandSex')
proband_sate_of_birth : Mapped[Optional[date]] = mapped_column('ProbandDoB')
registration_site_id : Mapped[int] = mapped_column('RegistrationCenterID',
ForeignKey('psc.CenterID'))
registration_project_id : Mapped[int] = mapped_column('RegistrationProjectID',
ForeignKey('Project.ProjectID'))
psc_id : Mapped[str] = mapped_column('PSCID', default='')
external_id : Mapped[Optional[str]] = mapped_column('ExternalID', default=None)
date_of_birth : Mapped[Optional[date]] = mapped_column('DoB', default=None)
dete_of_death : Mapped[Optional[date]] = mapped_column('DoD', default=None)
edc : Mapped[Optional[date]] = mapped_column('EDC', default=None)
sex : Mapped[Optional[str]] = mapped_column('Sex', default=None)
ethnicity : Mapped[Optional[str]] = mapped_column('Ethnicity', default=None)
active : Mapped[bool] = mapped_column('Active', YNBool, default=True)
date_active : Mapped[Optional[date]] = mapped_column('Date_active', default=None)
registered_by : Mapped[Optional[str]] = mapped_column('RegisteredBy', default=None)
user_id : Mapped[str] = mapped_column('UserID', default='')
date_registered : Mapped[Optional[date]] = mapped_column('Date_registered', default=None)
flagged_caveatemptor : Mapped[Optional[str]] = mapped_column('flagged_caveatemptor',
TrueFalseBool, default=False)
flagged_reason : Mapped[Optional[int]] = mapped_column('flagged_reason', default=None)
flagged_other : Mapped[Optional[str]] = mapped_column('flagged_other', default=None)
flagged_other_status : Mapped[Optional[str]] = mapped_column('flagged_other_status', default=None)
test_date : Mapped[datetime] = mapped_column('Testdate',
default=current_timestamp(), onupdate=current_timestamp())
entity_type : Mapped[str] = mapped_column('Entity_type', default='Human')
proband_sex : Mapped[Optional[str]] = mapped_column('ProbandSex', default=None)
proband_sate_of_birth : Mapped[Optional[date]] = mapped_column('ProbandDoB', default=None)

sessions : Mapped[list['db_session.DbSession']] \
= relationship('DbSession', back_populates='candidate')
= relationship('DbSession', back_populates='candidate', init=False)
registration_site : Mapped['db_site.DbSite'] \
= relationship('DbSite')
= relationship('DbSite', init=False)
registration_project : Mapped['db_project.DbProject'] \
= relationship('DbProject')
= relationship('DbProject', init=False)
4 changes: 2 additions & 2 deletions python/lib/db/model/config.py
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class DbConfig(Base):
__tablename__ = 'Config'

id : Mapped[int] = mapped_column('ID', primary_key=True)
id : Mapped[int] = mapped_column('ID', primary_key=True, autoincrement=True, init=False)
setting_id : Mapped[int] = mapped_column('ConfigID', ForeignKey('ConfigSettings.ID'))
value : Mapped[Optional[str]] = mapped_column('Value')

setting : Mapped['db_config_setting.DbConfigSetting'] = relationship('DbConfigSetting')
setting : Mapped['db_config_setting.DbConfigSetting'] = relationship('DbConfigSetting', init=False)
16 changes: 8 additions & 8 deletions python/lib/db/model/config_setting.py
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Expand Up @@ -8,12 +8,12 @@
class DbConfigSetting(Base):
__tablename__ = 'ConfigSettings'

id : Mapped[int] = mapped_column('ID', primary_key=True)
id : Mapped[int] = mapped_column('ID', primary_key=True, autoincrement=True, init=False)
name : Mapped[str] = mapped_column('Name')
description : Mapped[Optional[str]] = mapped_column('Description')
visible : Mapped[Optional[bool]] = mapped_column('Visible')
allow_multiple : Mapped[Optional[bool]] = mapped_column('AllowMultiple')
data_type : Mapped[Optional[str]] = mapped_column('DataType')
parent_id : Mapped[Optional[int]] = mapped_column('Parent')
label : Mapped[Optional[str]] = mapped_column('Label')
order_number : Mapped[Optional[int]] = mapped_column('OrderNumber')
description : Mapped[Optional[str]] = mapped_column('Description', default=None)
visible : Mapped[Optional[bool]] = mapped_column('Visible', default=False)
allow_multiple : Mapped[Optional[bool]] = mapped_column('AllowMultiple', default=False)
data_type : Mapped[Optional[str]] = mapped_column('DataType', default=None)
parent_id : Mapped[Optional[int]] = mapped_column('Parent', default=None)
label : Mapped[Optional[str]] = mapped_column('Label', default=None)
order_number : Mapped[Optional[int]] = mapped_column('OrderNumber', default=None)
70 changes: 36 additions & 34 deletions python/lib/db/model/dicom_archive.py
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Expand Up @@ -14,44 +14,46 @@
class DbDicomArchive(Base):
__tablename__ = 'tarchive'

id : Mapped[int] = mapped_column('TarchiveID', primary_key=True)
study_uid : Mapped[str] = mapped_column('DicomArchiveID')
patient_id : Mapped[str] = mapped_column('PatientID')
patient_name : Mapped[str] = mapped_column('PatientName')
patient_birthdate : Mapped[Optional[date]] = mapped_column('PatientDoB')
patient_sex : Mapped[Optional[str]] = mapped_column('PatientSex')
neuro_db_center_name : Mapped[Optional[str]] = mapped_column('neurodbCenterName')
center_name : Mapped[str] = mapped_column('CenterName')
last_update : Mapped[Optional[datetime]] = mapped_column('LastUpdate')
date_acquired : Mapped[Optional[date]] = mapped_column('DateAcquired')
date_first_archived : Mapped[Optional[datetime]] = mapped_column('DateFirstArchived')
date_last_archived : Mapped[Optional[datetime]] = mapped_column('DateLastArchived')
acquisition_count : Mapped[int] = mapped_column('AcquisitionCount')
dicom_file_count : Mapped[int] = mapped_column('DicomFileCount')
non_dicom_file_count : Mapped[int] = mapped_column('NonDicomFileCount')
md5_sum_dicom_only : Mapped[Optional[str]] = mapped_column('md5sumDicomOnly')
md5_sum_archive : Mapped[Optional[str]] = mapped_column('md5sumArchive')
creating_user : Mapped[str] = mapped_column('CreatingUser')
sum_type_version : Mapped[int] = mapped_column('sumTypeVersion')
tar_type_version : Mapped[Optional[int]] = mapped_column('tarTypeVersion')
source_location : Mapped[str] = mapped_column('SourceLocation')
archive_location : Mapped[Optional[str]] = mapped_column('ArchiveLocation')
scanner_manufacturer : Mapped[str] = mapped_column('ScannerManufacturer')
scanner_model : Mapped[str] = mapped_column('ScannerModel')
scanner_serial_number : Mapped[str] = mapped_column('ScannerSerialNumber')
scanner_software_version : Mapped[str] = mapped_column('ScannerSoftwareVersion')
session_id : Mapped[Optional[int]] = mapped_column('SessionID', ForeignKey('session.ID'))
upload_attempt : Mapped[int] = mapped_column('uploadAttempt')
create_info : Mapped[Optional[str]] = mapped_column('CreateInfo')
acquisition_metadata : Mapped[str] = mapped_column('AcquisitionMetadata')
date_sent : Mapped[Optional[datetime]] = mapped_column('DateSent')
pending_transfer : Mapped[bool] = mapped_column('PendingTransfer')
id : Mapped[int] = mapped_column('TarchiveID',
primary_key=True, autoincrement=True, init=False)
study_uid : Mapped[str] = mapped_column('DicomArchiveID', default='')
patient_id : Mapped[str] = mapped_column('PatientID', default='')
patient_name : Mapped[str] = mapped_column('PatientName', default='')
patient_birthdate : Mapped[Optional[date]] = mapped_column('PatientDoB', default=None)
patient_sex : Mapped[Optional[str]] = mapped_column('PatientSex', default=None)
neuro_db_center_name : Mapped[Optional[str]] = mapped_column('neurodbCenterName', default=None)
center_name : Mapped[str] = mapped_column('CenterName', default='')
last_update : Mapped[Optional[datetime]] = mapped_column('LastUpdate', default=None)
date_acquired : Mapped[Optional[date]] = mapped_column('DateAcquired', default=None)
date_first_archived : Mapped[Optional[datetime]] = mapped_column('DateFirstArchived', default=None)
date_last_archived : Mapped[Optional[datetime]] = mapped_column('DateLastArchived', default=None)
acquisition_count : Mapped[int] = mapped_column('AcquisitionCount', default=0)
dicom_file_count : Mapped[int] = mapped_column('DicomFileCount', default=0)
non_dicom_file_count : Mapped[int] = mapped_column('NonDicomFileCount', default=0)
md5_sum_dicom_only : Mapped[Optional[str]] = mapped_column('md5sumDicomOnly', default=None)
md5_sum_archive : Mapped[Optional[str]] = mapped_column('md5sumArchive', default=None)
creating_user : Mapped[str] = mapped_column('CreatingUser', default='')
sum_type_version : Mapped[int] = mapped_column('sumTypeVersion', default=0)
tar_type_version : Mapped[Optional[int]] = mapped_column('tarTypeVersion', default=None)
source_location : Mapped[str] = mapped_column('SourceLocation', default='')
archive_location : Mapped[Optional[str]] = mapped_column('ArchiveLocation', default=None)
scanner_manufacturer : Mapped[str] = mapped_column('ScannerManufacturer', default='')
scanner_model : Mapped[str] = mapped_column('ScannerModel', default='')
scanner_serial_number : Mapped[str] = mapped_column('ScannerSerialNumber', default='')
scanner_software_version : Mapped[str] = mapped_column('ScannerSoftwareVersion', default='')
session_id : Mapped[Optional[int]] = mapped_column('SessionID',
ForeignKey('session.ID'), default=None)
upload_attempt : Mapped[int] = mapped_column('uploadAttempt', default=0)
date_sent : Mapped[Optional[datetime]] = mapped_column('DateSent', default=None)
pending_transfer : Mapped[bool] = mapped_column('PendingTransfer', default=False)

series : Mapped[list['db_dicom_archive_series.DbDicomArchiveSeries']] \
= relationship('DbDicomArchiveSeries', back_populates='archive')
= relationship('DbDicomArchiveSeries', back_populates='archive', init=False)
files : Mapped[list['db_dicom_archive_file.DbDicomArchiveFile']] \
= relationship('DbDicomArchiveFile', back_populates='archive')
= relationship('DbDicomArchiveFile', back_populates='archive', init=False)
upload : Mapped[Optional['db_mri_upload.DbMriUpload']] \
= relationship('DbMriUpload', back_populates='dicom_archive')
= relationship('DbMriUpload', back_populates='dicom_archive', init=False)
session : Mapped[Optional['db_session.DbSession']] \
= relationship('DbSession')
= relationship('DbSession', init=False)
19 changes: 10 additions & 9 deletions python/lib/db/model/dicom_archive_file.py
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Expand Up @@ -11,18 +11,19 @@
class DbDicomArchiveFile(Base):
__tablename__ = 'tarchive_files'

id : Mapped[int] = mapped_column('TarchiveFileID', primary_key=True)
id : Mapped[int] = mapped_column('TarchiveFileID',
primary_key=True, autoincrement=True, init=False)
archive_id : Mapped[int] = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
series_id : Mapped[Optional[int]] \
= mapped_column('TarchiveSeriesID', ForeignKey('tarchive_series.TarchiveSeriesID'))
series_number : Mapped[Optional[int]] = mapped_column('SeriesNumber')
series_description : Mapped[Optional[str]] = mapped_column('SeriesDescription')
file_number : Mapped[Optional[int]] = mapped_column('FileNumber')
echo_number : Mapped[Optional[int]] = mapped_column('EchoNumber')
md5_sum : Mapped[str] = mapped_column('Md5Sum')
file_name : Mapped[str] = mapped_column('FileName')
series_id : Mapped[Optional[int]] \
= mapped_column('TarchiveSeriesID', ForeignKey('tarchive_series.TarchiveSeriesID'), default=None)
series_number : Mapped[Optional[int]] = mapped_column('SeriesNumber', default=None)
series_description : Mapped[Optional[str]] = mapped_column('SeriesDescription', default=None)
file_number : Mapped[Optional[int]] = mapped_column('FileNumber', default=None)
echo_number : Mapped[Optional[int]] = mapped_column('EchoNumber', default=None)

archive : Mapped['db_dicom_archive.DbDicomArchive'] \
= relationship('DbDicomArchive', back_populates='files')
= relationship('DbDicomArchive', back_populates='files', init=False)
series : Mapped[Optional['db_dicom_archive_series.DbDicomArchiveSeries']] \
= relationship('DbDicomArchiveSeries', back_populates='files')
= relationship('DbDicomArchiveSeries', back_populates='files', init=False)
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