Stricter linter configuration

pyproject.toml

@@ -1,13 +1,13 @@
 [tool.ruff]
+src = ["python"]
 include = ["python/**/*.py"]
 exclude = ["python/react-series-data-viewer"]
 line-length = 120
 preview = true
 
 [tool.ruff.lint]
 ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
-# TODO: Select "F", "I", "N", "UP" and format the codebase accordingly.
-select = ["E", "W"]
+select = ["E", "F", "I", "N", "UP", "W"]
 
 # The strict type checking configuration is used to type check only the modern (typed) modules. An
 # additional basic type checking configuration to type check legacy modules can be found in the

python/bids_import.py

@@ -2,21 +2,22 @@
 
 """Script to import BIDS structure into LORIS."""
 
-import os
-import sys
 import getopt
-import re
 import json
+import os
+import re
+import sys
+
 import lib.exitcode
-import lib.utilities
 import lib.physiological
-from lib.database   import Database
-from lib.candidate  import Candidate
+import lib.utilities
 from lib.bidsreader import BidsReader
-from lib.session    import Session
-from lib.eeg        import Eeg
-from lib.mri        import Mri
+from lib.candidate import Candidate
+from lib.database import Database
 from lib.database_lib.config import Config
+from lib.eeg import Eeg
+from lib.mri import Mri
+from lib.session import Session
 
 __license__ = "GPLv3"
 
@@ -63,7 +64,7 @@ def main():
     )
 
     try:
-        opts, args = getopt.getopt(sys.argv[1:], 'hp:d:csinat:v', long_options)
+        opts, _ = getopt.getopt(sys.argv[1:], 'hp:d:csinat:v', long_options)
     except getopt.GetoptError:
         print(usage)
         sys.exit(lib.exitcode.GETOPT_FAILURE)
@@ -321,7 +322,7 @@ def read_and_insert_bids(
             event_metadata = json.load(metadata_file)
         blake2 = lib.utilities.compute_blake2b_hash(root_event_metadata_file.path)
         physio = lib.physiological.Physiological(db, verbose)
-        file_id, dataset_tag_dict = physio.insert_event_metadata(
+        _, dataset_tag_dict = physio.insert_event_metadata(
             event_metadata=event_metadata,
             event_metadata_file=event_metadata_path,
             physiological_file_id=None,

python/extract_eeg_bids_archive.py

@@ -3,15 +3,16 @@
 """Script that extract EEG archives"""
 
 import os
-import sys
 import re
-from lib.lorisgetopt import LorisGetOpt
-from lib.imaging_io import ImagingIO
+import sys
+
+import lib.utilities as utilities
 from lib.database import Database
 from lib.database_lib.config import Config
-from lib.exitcode import SUCCESS, BAD_CONFIG_SETTING
+from lib.exitcode import BAD_CONFIG_SETTING, SUCCESS
+from lib.imaging_io import ImagingIO
 from lib.log import Log
-import lib.utilities as utilities
+from lib.lorisgetopt import LorisGetOpt
 
 __license__ = "GPLv3"
 

python/ingest_eeg_bids_datasets.py

@@ -3,12 +3,13 @@
 """Script that ingests EEG BIDS datasets"""
 
 import os
+import subprocess
 import sys
-from lib.lorisgetopt import LorisGetOpt
+
 from lib.database import Database
 from lib.database_lib.config import Config
-from lib.exitcode import SUCCESS, INVALID_ARG
-import subprocess
+from lib.exitcode import INVALID_ARG, SUCCESS
+from lib.lorisgetopt import LorisGetOpt
 
 __license__ = "GPLv3"
 

python/lib/aws_s3.py

@@ -1,10 +1,12 @@
 """This class interacts with S3 Buckets"""
 
-import boto3
-import lib.utilities
 import os
+
+import boto3
 from botocore.exceptions import ClientError, EndpointConnectionError
 
+import lib.utilities
+
 __license__ = "GPLv3"
 
 
@@ -214,7 +216,7 @@ def delete_file(self, s3_object_name):
         print(f"Deleting {s3_object_name}")
 
         try:
-            (s3_bucket_name, s3_bucket, s3_file_name) = self.get_s3_object_path_part(s3_object_name)
+            (_, s3_bucket, s3_file_name) = self.get_s3_object_path_part(s3_object_name)
             objects_to_delete = [{'Key': obj.key} for obj in s3_bucket.objects.filter(Prefix=s3_file_name)]
             s3_bucket.delete_objects(
                 Delete={
@@ -239,8 +241,8 @@ def copy_file(self, src_s3_object_name, dst_s3_object_name, delete = False):
         print(f"Copying {src_s3_object_name} to {dst_s3_object_name}")
 
         try:
-            (src_s3_bucket_name, src_s3_bucket, src_s3_file_name) = self.get_s3_object_path_part(src_s3_object_name)
-            (dst_s3_bucket_name, dst_s3_bucket, dst_s3_file_name) = self.get_s3_object_path_part(dst_s3_object_name)
+            (_, src_s3_bucket, src_s3_file_name) = self.get_s3_object_path_part(src_s3_object_name)
+            (_, dst_s3_bucket, dst_s3_file_name) = self.get_s3_object_path_part(dst_s3_object_name)
             for obj in src_s3_bucket.objects.filter(Prefix=src_s3_file_name):
                 subcontent = obj.key.replace(src_s3_file_name, "")
                 dst_s3_bucket.Object(

python/lib/bidsreader.py

@@ -1,14 +1,14 @@
 """Reads a BIDS structure into a data dictionary using bids.grabbids."""
 
+import json
 import re
 import sys
-import json
+
+from bids import BIDSLayout
 
 import lib.exitcode
 import lib.utilities as utilities
 
-from bids import BIDSLayout
-
 # import bids
 # BIDSLayoutIndexer is required for PyBIDS >= 0.12.1
 # bids_pack_version = list(map(int, bids.__version__.split('.')))

python/lib/candidate.py

@@ -1,9 +1,11 @@
 """This class gather functions for candidate handling."""
 
 import random
+import sys
+
 from dateutil.parser import parse
+
 import lib.exitcode
-import sys
 
 __license__ = "GPLv3"
 

python/lib/database.py

@@ -1,9 +1,10 @@
 """Allows LORIS database connectivity for LORIS-MRI python code base"""
 
-import MySQLdb
 import sys
-import lib.exitcode
 
+import MySQLdb
+
+import lib.exitcode
 
 __license__ = "GPLv3"
 
@@ -166,9 +167,7 @@ def insert(self, table_name, column_names, values, get_last_id=False):
 
         placeholders = ','.join(map(lambda x: '%s', column_names))
 
-        query = "INSERT INTO %s (%s) VALUES (%s)" % (
-            table_name, ', '.join(column_names), placeholders
-        )
+        query = f"INSERT INTO {table_name} ({', '.join(column_names)}) VALUES ({placeholders})"
 
         if self.verbose:
             print("\nExecuting query:\n\t" + query + "\n"

python/lib/database_lib/candidate_db.py

@@ -2,7 +2,6 @@
 
 from typing_extensions import deprecated
 
-
 __license__ = "GPLv3"
 
 

python/lib/database_lib/mri_scanner.py

@@ -1,6 +1,7 @@
 """This class performs database queries for the mri_scanner table"""
 
 import datetime
+
 from lib.candidate import Candidate
 
 __license__ = "GPLv3"

python/lib/database_lib/physiological_coord_system.py

@@ -9,6 +9,7 @@
 """
 
 from typing import Dict, List
+
 # from lib.point_3d import Point3D
 # from lib.database_lib.point_3d import Point3DDB
 

python/lib/database_lib/visit_windows.py

@@ -3,7 +3,6 @@
 
 from typing_extensions import deprecated
 
-
 __license__ = "GPLv3"
 
 

python/lib/db/connect.py

@@ -1,8 +1,8 @@
 from typing import Any
+
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session
 
-
 default_port = 3306
 
 

python/lib/db/model/candidate.py

@@ -1,6 +1,8 @@
 from datetime import date
 from typing import Optional
+
 from sqlalchemy.orm import Mapped, mapped_column
+
 from lib.db.base import Base
 
 

python/lib/db/model/dicom_archive.py

@@ -1,11 +1,13 @@
 from datetime import date, datetime
 from typing import List, Optional
+
 from sqlalchemy import String
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from lib.db.base import Base
+
 import lib.db.model.dicom_archive_file as db_dicom_archive_file
 import lib.db.model.dicom_archive_series as db_dicom_archive_series
 import lib.db.model.mri_upload as db_mri_upload
+from lib.db.base import Base
 
 
 class DbDicomArchive(Base):

python/lib/db/model/dicom_archive_file.py

@@ -1,9 +1,11 @@
 from typing import Optional
-from sqlalchemy.orm import Mapped, mapped_column, relationship
+
 from sqlalchemy import ForeignKey
-from lib.db.base import Base
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
 import lib.db.model.dicom_archive as db_dicom_archive
 import lib.db.model.dicom_archive_series as db_dicom_archive_series
+from lib.db.base import Base
 
 
 class DbDicomArchiveFile(Base):

python/lib/db/model/dicom_archive_series.py

@@ -1,9 +1,11 @@
 from typing import List, Optional
-from sqlalchemy.orm import Mapped, mapped_column, relationship
+
 from sqlalchemy import ForeignKey
-from lib.db.base import Base
+from sqlalchemy.orm import Mapped, mapped_column, relationship
+
 import lib.db.model.dicom_archive as db_dicom_archive
 import lib.db.model.dicom_archive_file as db_dicom_archive_file
+from lib.db.base import Base
 
 
 class DbDicomArchiveSeries(Base):

python/lib/db/model/mri_upload.py

@@ -1,9 +1,11 @@
 from datetime import datetime
 from typing import Optional
+
 from sqlalchemy import ForeignKey
 from sqlalchemy.orm import Mapped, mapped_column, relationship
-from lib.db.base import Base
+
 import lib.db.model.dicom_archive as db_dicom_archive
+from lib.db.base import Base
 
 
 class DbMriUpload(Base):

python/lib/db/model/session.py

@@ -1,6 +1,8 @@
 from datetime import date, datetime
 from typing import Optional
+
 from sqlalchemy.orm import Mapped, mapped_column
+
 from lib.db.base import Base
 
 

python/lib/db/model/visit_window.py

@@ -1,5 +1,7 @@
 from typing import Optional
+
 from sqlalchemy.orm import Mapped, mapped_column
+
 from lib.db.base import Base
 
 

python/lib/db/query/candidate.py

@@ -1,5 +1,6 @@
 from sqlalchemy import select
 from sqlalchemy.orm import Session as Database
+
 from lib.db.model.candidate import DbCandidate
 
 

python/lib/db/query/visit.py

@@ -1,5 +1,6 @@
 from sqlalchemy import select
 from sqlalchemy.orm import Session as Database
+
 from lib.db.model.visit_window import DbVisitWindow
 
 

python/lib/dcm2bids_imaging_pipeline_lib/base_pipeline.py

@@ -3,20 +3,19 @@
 import shutil
 import sys
 
-from lib.exception.determine_subject_exception import DetermineSubjectException
-from lib.exception.validate_subject_exception import ValidateSubjectException
 import lib.exitcode
 import lib.utilities
-
-from lib.database_lib.config import Config
 from lib.database import Database
+from lib.database_lib.config import Config
+from lib.db.connect import connect_to_db
 from lib.dicom_archive import DicomArchive
+from lib.exception.determine_subject_info_error import DetermineSubjectInfoError
+from lib.exception.validate_subject_info_error import ValidateSubjectInfoError
 from lib.imaging import Imaging
-from lib.log import Log
 from lib.imaging_upload import ImagingUpload
+from lib.log import Log
 from lib.session import Session
 from lib.validate_subject_ids import validate_subject_ids
-from lib.db.connect import connect_to_db
 
 
 class BasePipeline:
@@ -111,9 +110,9 @@ def __init__(self, loris_getopt_obj, script_name):
         if self.dicom_archive_obj.tarchive_info_dict.keys():
             try:
                 self.subject_id_dict = self.imaging_obj.determine_subject_ids(self.dicom_archive_obj.tarchive_info_dict)
-            except DetermineSubjectException as exception:
+            except DetermineSubjectInfoError as error:
                 self.log_error_and_exit(
-                    exception.message,
+                    error.message,
                     lib.exitcode.PROJECT_CUSTOMIZATION_FAILURE,
                     is_error="Y",
                     is_verbose="N"
@@ -259,8 +258,8 @@ def validate_subject_ids(self):
             self.imaging_upload_obj.update_mri_upload(
                 upload_id=self.upload_id, fields=('IsCandidateInfoValidated',), values=('1',)
             )
-        except ValidateSubjectException as exception:
-            self.log_info(exception.message, is_error='Y', is_verbose='N')
+        except ValidateSubjectInfoError as error:
+            self.log_info(error.message, is_error='Y', is_verbose='N')
             self.imaging_upload_obj.update_mri_upload(
                 upload_id=self.upload_id, fields=('IsCandidateInfoValidated',), values=('0',)
             )

python/lib/dcm2bids_imaging_pipeline_lib/dicom_archive_loader_pipeline.py

@@ -160,7 +160,7 @@ def _run_dcm2niix_conversion(self):
             stdout=subprocess.PIPE,
             stderr=subprocess.STDOUT
         )
-        stdout, stderr = dcm2niix_process.communicate()
+        stdout, _ = dcm2niix_process.communicate()
         self.log_info(stdout, is_error="N", is_verbose="Y")
 
         return nifti_tmp_dir
@@ -302,7 +302,7 @@ def _run_nifti_insertion(self, nifti_file_path, json_file_path, bval_file_path=N
             nifti_insertion_command.append("-v")
 
         insertion_process = subprocess.Popen(nifti_insertion_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
-        stdout, stderr = insertion_process.communicate()
+        stdout, _ = insertion_process.communicate()
 
         if insertion_process.returncode == 0:
             message = f"run_nifti_insertion.py successfully executed for file {nifti_file_path}"