ORM improvements again

python/lib/db/models/file.py

@@ -3,7 +3,7 @@
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-import lib.db.models.parameter_file as db_parameter_file
+import lib.db.models.file_parameter as db_file_parameter
 import lib.db.models.session as db_session
 from lib.db.base import Base
 
@@ -13,7 +13,7 @@ class DbFile(Base):
 
     id                             : Mapped[int]          = mapped_column('FileID', primary_key=True)
     session_id                     : Mapped[int]          = mapped_column('SessionID', ForeignKey('session.ID'))
-    file_name                      : Mapped[str]          = mapped_column('File')
+    rel_path                       : Mapped[str]          = mapped_column('File')
     series_uid                     : Mapped[str | None]   = mapped_column('SeriesUID')
     echo_time                      : Mapped[float | None] = mapped_column('EchoTime')
     phase_encoding_direction       : Mapped[str | None]   = mapped_column('PhaseEncodingDirection')
@@ -37,5 +37,5 @@ class DbFile(Base):
 
     session    : Mapped['db_session.DbSession'] \
         = relationship('DbSession', back_populates='files')
-    parameters : Mapped[list['db_parameter_file.DbParameterFile']] \
-        = relationship('DbParameterFile', back_populates='file')
+    parameters : Mapped[list['db_file_parameter.DbFileParameter']] \
+        = relationship('DbFileParameter', back_populates='file')

python/lib/db/models/parameter_file.py → python/lib/db/models/file_parameter.py

@@ -6,7 +6,7 @@
 from lib.db.base import Base
 
 
-class DbParameterFile(Base):
+class DbFileParameter(Base):
     __tablename__ = 'parameter_file'
 
     id          : Mapped[int]        = mapped_column('ParameterFileID', primary_key=True)
@@ -18,4 +18,4 @@ class DbParameterFile(Base):
     file: Mapped['db_file.DbFile'] \
         = relationship('DbFile', back_populates='parameters')
     type: Mapped['db_parameter_type.DbParameterType'] \
-        = relationship('DbParameterType', back_populates='parameter_files')
+        = relationship('DbParameterType', back_populates='file_parameters')

python/lib/db/models/parameter_type.py

@@ -1,6 +1,6 @@
 from sqlalchemy.orm import Mapped, mapped_column, relationship
 
-import lib.db.models.parameter_file as db_parameter_file
+import lib.db.models.file_parameter as db_file_parameter
 from lib.db.base import Base
 
 
@@ -20,5 +20,5 @@ class DbParameterType(Base):
     queryable        : Mapped[bool | None]  = mapped_column('Queryable')
     is_file          : Mapped[bool | None]  = mapped_column('IsFile')
 
-    parameter_files: Mapped[list['db_parameter_file.DbParameterFile']] \
-        = relationship('DbParameterFile', back_populates='type')
+    file_parameters: Mapped[list['db_file_parameter.DbFileParameter']] \
+        = relationship('DbFileParameter', back_populates='type')

python/lib/db/queries/file.py

@@ -2,7 +2,7 @@
 from sqlalchemy.orm import Session as Database
 
 from lib.db.models.file import DbFile
-from lib.db.models.parameter_file import DbParameterFile
+from lib.db.models.file_parameter import DbFileParameter
 from lib.db.models.parameter_type import DbParameterType
 
 
@@ -30,15 +30,15 @@ def try_get_parameter_value_with_file_id_parameter_name(
     db: Database,
     file_id: int,
     parameter_name: str
-) -> DbParameterFile | None:
+) -> DbFileParameter | None:
     """
     Get parameter value from file ID and parameter name, or return `None` if no entry was found
     """
 
-    return db.execute(select(DbParameterFile)
-        .join(DbParameterFile.type)
+    return db.execute(select(DbFileParameter)
+        .join(DbFileParameter.type)
         .where(DbParameterType.name == parameter_name)
-        .where(DbParameterFile.file_id == file_id)
+        .where(DbFileParameter.file_id == file_id)
     ).scalar_one_or_none()
 
 
@@ -50,7 +50,7 @@ def try_get_file_with_hash(db: Database, file_hash: str) -> DbFile | None:
 
     return db.execute(select(DbFile)
         .join(DbFile.parameters)
-        .join(DbParameterFile.type)
+        .join(DbFileParameter.type)
         .where(DbParameterType.name.in_(['file_blake2b_hash', 'md5hash']))
-        .where(DbParameterFile.value == file_hash)
+        .where(DbFileParameter.value == file_hash)
     ).scalar_one_or_none()

python/tests/integration/scripts/test_run_nifti_insertion.py

@@ -334,12 +334,12 @@ def test_nifti_mri_protocol_violated_scans_features():
     violated_scan_entry = violated_scans[0]
 
     # Check that the NIfTI file can be found on the disk
-    assert violated_scan_entry.file_rel_path is not None \
-           and os.path.exists(os.path.join('/data/loris/', str(violated_scan_entry.file_rel_path)))
+    assert violated_scan_entry.file_rel_path is not None
+    assert os.path.exists(os.path.join('/data/loris/', violated_scan_entry.file_rel_path))
 
     # Rerun the script to test that it did not duplicate the entry in MRI protocol violated scans
     # Note: need to copy the violated file into incoming to rerun the script
-    new_nifti_path = os.path.join('/data/loris/', str(violated_scan_entry.file_rel_path))
+    new_nifti_path = os.path.join('/data/loris/', violated_scan_entry.file_rel_path)
     new_json_path = new_nifti_path.replace('.nii.gz', '.json')
     shutil.copyfile(new_nifti_path, nifti_path)
     shutil.copyfile(new_json_path, json_path)
@@ -398,7 +398,7 @@ def test_nifti_mri_protocol_violated_scans_features():
 
     # Check that all files related to that image have been properly linked in the database
     file_base_rel_path = 'assembly_bids/sub-400184/ses-V3/anat/sub-400184_ses-V3_run-1_T1w'
-    assert str(file.file_name) == f'{file_base_rel_path}.nii.gz'
+    assert file.rel_path == f'{file_base_rel_path}.nii.gz'
     file_json_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'bids_json_file')
     file_pic_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'check_pic_filename')
     assert file_json_data is not None and file_json_data.value == f'{file_base_rel_path}.json'
@@ -409,7 +409,7 @@ def test_nifti_mri_protocol_violated_scans_features():
             'sub-400184': {
                 'ses-V3': {
                     'anat': {
-                        basename(str(file.file_name)): None,
+                        basename(file.rel_path): None,
                         basename(str(file_json_data.value)): None,
                     }
                 }
@@ -486,10 +486,9 @@ def test_nifti_mri_violations_log_exclude_features():
     assert violation_entry.severity == 'exclude'
 
     # Check that the NIfTI file can be found in the filesystem
-    assert violation_entry.file_rel_path is not None \
-           and os.path.exists(os.path.join('/data/loris/', str(violation_entry.file_rel_path)))
+    assert os.path.exists(os.path.join('/data/loris/', violation_entry.file_rel_path))
     # Check that the rest of the expected files have been created
-    new_nifti_path = os.path.join('/data/loris/', str(violation_entry.file_rel_path))
+    new_nifti_path = os.path.join('/data/loris/', violation_entry.file_rel_path)
     new_json_path = new_nifti_path.replace('.nii.gz', '.json')
     new_bval_path = new_nifti_path.replace('.nii.gz', '.bval')
     new_bvec_path = new_nifti_path.replace('.nii.gz', '.bvec')
@@ -561,7 +560,7 @@ def test_nifti_mri_violations_log_exclude_features():
 
     # Check that all files related to that image have been properly linked in the database
     file_base_rel_path = 'assembly_bids/sub-400184/ses-V3/dwi/sub-400184_ses-V3_acq-65dir_run-1_dwi'
-    assert str(file.file_name) == f'{file_base_rel_path}.nii.gz'
+    assert file.rel_path == f'{file_base_rel_path}.nii.gz'
     file_json_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'bids_json_file')
     file_bval_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'check_bval_filename')
     file_bvec_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'check_bvec_filename')
@@ -576,7 +575,7 @@ def test_nifti_mri_violations_log_exclude_features():
             'sub-400184': {
                 'ses-V3': {
                     'dwi': {
-                        basename(str(file.file_name)): None,
+                        basename(file.rel_path): None,
                         basename(str(file_bval_data.value)): None,
                         basename(str(file_bvec_data.value)): None,
                         basename(str(file_json_data.value)): None,
@@ -645,8 +644,8 @@ def test_dwi_insertion_with_mri_violations_log_warning():
 
     # Check that all files related to that image have been properly linked in the database
     file_base_rel_path = 'assembly_bids/sub-400184/ses-V3/dwi/sub-400184_ses-V3_acq-25dir_run-1_dwi'
-    assert str(violation_entry.file_rel_path) \
-           == str(file.file_name) \
+    assert violation_entry.file_rel_path \
+           == file.rel_path \
            == f'{file_base_rel_path}.nii.gz'
     file_json_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'bids_json_file')
     file_bval_data = try_get_parameter_value_with_file_id_parameter_name(db, file.id, 'check_bval_filename')
@@ -662,7 +661,7 @@ def test_dwi_insertion_with_mri_violations_log_warning():
             'sub-400184': {
                 'ses-V3': {
                     'dwi': {
-                        basename(str(file.file_name)): None,
+                        basename(file.rel_path): None,
                         basename(str(file_bval_data.value)): None,
                         basename(str(file_bvec_data.value)): None,
                         basename(str(file_json_data.value)): None,