Add IntBool ORM decorator (ORM PR 2)

python/lib/db/decorators/int_bool.py

@@ -0,0 +1,33 @@
+from typing import Literal
+
+from sqlalchemy import Integer
+from sqlalchemy.engine import Dialect
+from sqlalchemy.types import TypeDecorator
+
+
+class IntBool(TypeDecorator[bool]):
+    """
+    Decorator for a database boolean integer type.
+    In SQL, the type will appear as 'int'.
+    In Python, the type will appear as a boolean.
+    """
+
+    impl = Integer
+
+    def process_bind_param(self, value: bool | None, dialect: Dialect) -> Literal[0, 1] | None:
+        match value:
+            case True:
+                return 1
+            case False:
+                return 0
+            case None:
+                return None
+
+    def process_result_value(self, value: Literal[0, 1] | None, dialect: Dialect) -> bool | None:
+        match value:
+            case 1:
+                return True
+            case 0:
+                return False
+            case None:
+                return None

python/lib/db/models/cohort.py

@@ -1,13 +1,14 @@
 from sqlalchemy.orm import Mapped, mapped_column
 
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 
 
 class DbCohort(Base):
     __tablename__ = 'cohort'
 
     id                 : Mapped[int]         = mapped_column('CohortID', primary_key=True)
     name               : Mapped[str]         = mapped_column('title')
-    use_edc            : Mapped[bool | None] = mapped_column('useEDC')
+    use_edc            : Mapped[bool | None] = mapped_column('useEDC', IntBool)
     window_difference  : Mapped[str | None]  = mapped_column('WindowDifference')
     recruitment_target : Mapped[int | None]  = mapped_column('RecruitmentTarget')

python/lib/db/models/config_setting.py

@@ -1,6 +1,7 @@
 from sqlalchemy.orm import Mapped, mapped_column
 
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 
 
 class DbConfigSetting(Base):
@@ -9,8 +10,8 @@ class DbConfigSetting(Base):
     id             : Mapped[int]         = mapped_column('ID', primary_key=True)
     name           : Mapped[str]         = mapped_column('Name')
     description    : Mapped[str | None]  = mapped_column('Description')
-    visible        : Mapped[bool | None] = mapped_column('Visible')
-    allow_multiple : Mapped[bool | None] = mapped_column('AllowMultiple')
+    visible        : Mapped[bool | None] = mapped_column('Visible', IntBool)
+    allow_multiple : Mapped[bool | None] = mapped_column('AllowMultiple', IntBool)
     data_type      : Mapped[str | None]  = mapped_column('DataType')
     parent_id      : Mapped[int | None]  = mapped_column('Parent')
     label          : Mapped[str | None]  = mapped_column('Label')

python/lib/db/models/dicom_archive.py

@@ -11,6 +11,7 @@
 import lib.db.models.mri_violation_log as db_mri_violation_log
 import lib.db.models.session as db_session
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 
 
 class DbDicomArchive(Base):
@@ -47,7 +48,7 @@ class DbDicomArchive(Base):
     create_info              : Mapped[str | None]      = mapped_column('CreateInfo')
     acquisition_metadata     : Mapped[str]             = mapped_column('AcquisitionMetadata')
     date_sent                : Mapped[datetime | None] = mapped_column('DateSent')
-    pending_transfer         : Mapped[bool]            = mapped_column('PendingTransfer')
+    pending_transfer         : Mapped[bool]            = mapped_column('PendingTransfer', IntBool)
 
     series      : Mapped[list['db_dicom_archive_series.DbDicomArchiveSeries']] \
         = relationship('DbDicomArchiveSeries', back_populates='archive')

python/lib/db/models/file.py

@@ -6,6 +6,7 @@
 import lib.db.models.file_parameter as db_file_parameter
 import lib.db.models.session as db_session
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 from lib.db.decorators.int_datetime import IntDatetime
 
 
@@ -29,7 +30,7 @@ class DbFile(Base):
     pipeline_date                  : Mapped[date | None]  = mapped_column('PipelineDate')
     source_file_id                 : Mapped[int | None]   = mapped_column('SourceFileID')
     process_protocol_id            : Mapped[int | None]   = mapped_column('ProcessProtocolID')
-    caveat                         : Mapped[bool | None]  = mapped_column('Caveat')
+    caveat                         : Mapped[bool | None]  = mapped_column('Caveat', IntBool)
     dicom_archive_id               : Mapped[int | None]   = mapped_column('TarchiveSource')
     hrrt_archive_id                : Mapped[int | None]   = mapped_column('HrrtArchiveID')
     scanner_id                     : Mapped[int | None]   = mapped_column('ScannerID')

python/lib/db/models/mri_upload.py

@@ -7,6 +7,7 @@
 import lib.db.models.dicom_archive as db_dicom_archive
 import lib.db.models.session as db_session
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 from lib.db.decorators.y_n_bool import YNBool
 
 
@@ -18,16 +19,16 @@ class DbMriUpload(Base):
     upload_date                 : Mapped[datetime | None] = mapped_column('UploadDate')
     upload_location             : Mapped[str]             = mapped_column('UploadLocation')
     decompressed_location       : Mapped[str]             = mapped_column('DecompressedLocation')
-    insertion_complete          : Mapped[bool]            = mapped_column('InsertionComplete')
-    inserting                   : Mapped[bool | None]     = mapped_column('Inserting')
+    insertion_complete          : Mapped[bool]            = mapped_column('InsertionComplete', IntBool)
+    inserting                   : Mapped[bool | None]     = mapped_column('Inserting', IntBool)
     patient_name                : Mapped[str]             = mapped_column('PatientName')
     number_of_minc_inserted     : Mapped[int | None]      = mapped_column('number_of_mincInserted')
     number_of_minc_created      : Mapped[int | None]      = mapped_column('number_of_mincCreated')
     dicom_archive_id            : Mapped[int | None] \
         = mapped_column('TarchiveID', ForeignKey('tarchive.TarchiveID'))
     session_id                  : Mapped[int | None]      = mapped_column('SessionID', ForeignKey('session.ID'))
-    is_candidate_info_validated : Mapped[bool | None]     = mapped_column('IsCandidateInfoValidated')
-    is_dicom_archive_validated  : Mapped[bool]            = mapped_column('IsTarchiveValidated')
+    is_candidate_info_validated : Mapped[bool | None]     = mapped_column('IsCandidateInfoValidated', IntBool)
+    is_dicom_archive_validated  : Mapped[bool]            = mapped_column('IsTarchiveValidated', IntBool)
     is_phantom                  : Mapped[bool]            = mapped_column('IsPhantom', YNBool)
 
     dicom_archive : Mapped[Optional['db_dicom_archive.DbDicomArchive']] \

python/lib/db/models/notification_type.py

@@ -1,12 +1,13 @@
 from sqlalchemy.orm import Mapped, mapped_column
 
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 
 
 class DbNotificationType(Base):
     __tablename__ = 'notification_types'
 
     id         : Mapped[int]         = mapped_column('NotificationTypeID', primary_key=True)
     name       : Mapped[str]         = mapped_column('Type')
-    private    : Mapped[bool | None] = mapped_column('private')
+    private    : Mapped[bool | None] = mapped_column('private', IntBool)
     description: Mapped[str | None]  = mapped_column('Description')

python/lib/db/models/parameter_type.py

@@ -2,6 +2,7 @@
 
 import lib.db.models.file_parameter as db_file_parameter
 from lib.db.base import Base
+from lib.db.decorators.int_bool import IntBool
 
 
 class DbParameterType(Base):
@@ -17,8 +18,8 @@ class DbParameterType(Base):
     source_field     : Mapped[str | None]   = mapped_column('SourceField')
     source_from      : Mapped[str | None]   = mapped_column('SourceFrom')
     source_condition : Mapped[str | None]   = mapped_column('SourceCondition')
-    queryable        : Mapped[bool | None]  = mapped_column('Queryable')
-    is_file          : Mapped[bool | None]  = mapped_column('IsFile')
+    queryable        : Mapped[bool | None]  = mapped_column('Queryable', IntBool)
+    is_file          : Mapped[bool | None]  = mapped_column('IsFile', IntBool)
 
     file_parameters: Mapped[list['db_file_parameter.DbFileParameter']] \
         = relationship('DbFileParameter', back_populates='type')

python/tests/integration/test_orm_sql_sync.py

@@ -3,7 +3,7 @@
 from typing import Any
 
 from sqlalchemy import MetaData
-from sqlalchemy.dialects.mysql.types import DOUBLE, TINYINT
+from sqlalchemy.dialects.mysql.types import DOUBLE
 from sqlalchemy.types import TypeDecorator, TypeEngine
 
 from lib.db.base import Base
@@ -59,9 +59,6 @@ def get_orm_python_type(orm_type: TypeEngine[Any]):
 
 
 def get_sql_python_type(sql_type: TypeEngine[Any]):
-    if isinstance(sql_type, TINYINT) and sql_type.display_width == 1:  # type: ignore
-        return bool
-
     if isinstance(sql_type, DOUBLE):
         return float