Timezone linter

pyproject.toml

@@ -69,7 +69,7 @@ preview = true
 
 [tool.ruff.lint]
 ignore = ["E202", "E203", "E221", "E241", "E251", "E272"]
-select = ["E", "EXE", "F", "I", "N", "RUF", "UP", "W"]
+select = ["DTZ", "E", "EXE", "F", "I", "N", "RUF", "UP", "W"]
 
 [tool.ruff.lint.pycodestyle]
 max-doc-length = 100

python/lib/database_lib/mri_scanner.py

@@ -1,6 +1,6 @@
 """This class performs database queries for the mri_scanner table"""
 
-import datetime
+from datetime import UTC, datetime
 
 from typing_extensions import deprecated
 
@@ -77,7 +77,7 @@
         if results:
             return results[0]['ScannerID']
 
         # if could not find a scanner ID, register a new scanner in mri_scanner
         scanner_id = self.register_new_scanner(
             manufacturer, software_version, serial_number, scanner_model, center_id, project_id
         )
@@ -114,8 +114,8 @@
             'UserID', 'Entity_type', 'RegistrationProjectID', 'Date_registered',
         )
         values = (
-            new_cand_id,  'scanner', center_id,  datetime.datetime.now(),
-            'imaging.py', 'Scanner', project_id, datetime.datetime.now()
+            new_cand_id,  'scanner', center_id,  datetime.now(UTC),
+            'imaging.py', 'Scanner', project_id, datetime.now(UTC),
         )
 
         candidate_id = self.db.insert(

python/lib/database_lib/notification.py

@@ -1,6 +1,6 @@
 """This class performs database queries for the notification_spool table"""
 
-import datetime
+from datetime import UTC, datetime
 
 from typing_extensions import deprecated
 
@@ -76,7 +76,7 @@ def write_to_notification_spool(self, message, is_error, is_verbose, center_id=N
             'ProcessID',          'Error',       'Verbose'
         )
         values = (
-            type_id,         datetime.datetime.now(),  message,   self.notification_origin,
+            type_id,         datetime.now(UTC),  message,   self.notification_origin,
             self.process_id, is_error,                 is_verbose
         )
 

python/lib/db/decorators/int_datetime.py

@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import UTC, datetime
 
 from sqlalchemy import Integer
 from sqlalchemy.engine import Dialect
@@ -24,4 +24,4 @@ def process_result_value(self, value: int | None | None, dialect: Dialect) -> da
         if value is None:
             return None
 
-        return datetime.fromtimestamp(value)
+        return datetime.fromtimestamp(value, tz=UTC)

python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py

@@ -1,11 +1,12 @@
-import datetime
 import json
 import os
 import re
 import subprocess
 import sys
+from datetime import UTC, datetime
 from pathlib import Path
 
+import dateutil
 from loris_bids_importer.file_type import get_check_bids_imaging_file_type_from_extension
 from loris_bids_importer.mri.sidecar import add_bids_mri_sidecar_file_parameters, get_bids_mri_sidecar_session_info
 from loris_bids_utils.mri.sidecar import BidsMriSidecarJsonFile
@@ -635,7 +636,7 @@ def _register_violations_log(self, violations_list, file_rel_path):
         scan_param = self.json_file_dict
         phase_enc_dir = scan_param['PhaseEncodingDirection'] if 'PhaseEncodingDirection' in scan_param.keys() else None
         base_info_dict = {
-            'TimeRun': datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'),
+            'TimeRun': datetime.now(UTC).strftime('%Y-%m-%d %H:%M:%S'),
             'SeriesUID': scan_param['SeriesInstanceUID'] if 'SeriesInstanceUID' in scan_param.keys() else None,
             'TarchiveID': self.dicom_archive.id,
             'MincFile': file_rel_path,
@@ -666,9 +667,7 @@ def _register_into_files_and_parameter_file(self, nifti_rel_path):
         scan_param = self.json_file_dict
         acquisition_date = None
         if "AcquisitionDateTime" in scan_param.keys():
-            acquisition_date = datetime.datetime.strptime(
-                scan_param['AcquisitionDateTime'], '%Y-%m-%dT%H:%M:%S.%f'
-            ).date()
+            acquisition_date = dateutil.parser.parse(scan_param['AcquisitionDateTime']).date()
         file_type = get_check_bids_imaging_file_type_from_extension(self.env, Path(nifti_rel_path))
 
         file = register_mri_file(

python/lib/imaging.py

@@ -1,10 +1,10 @@
 """This class performs database queries and common imaging checks (MRI...)"""
 
-import datetime
 import json
 import os
 import re
 import tarfile
+from datetime import UTC, datetime
 
 import nibabel as nib
 from loris_utils.crypto import compute_file_blake2b_hash
@@ -184,7 +184,7 @@ def insert_parameter_file(self, file_id, parameter_name, value):
             'ParameterTypeID': param_type_id,
             'FileID': file_id,
             'Value': value,
-            'InsertTime': datetime.datetime.now().timestamp()
+            'InsertTime': datetime.now(UTC).timestamp()
         }
 
         pf_entry = self.param_file_db_obj.get_parameter_file_for_file_id_param_type_id(file_id, param_type_id)
@@ -222,7 +222,7 @@ def insert_mri_candidate_errors(self, patient_name, tarchive_id, scan_param, fil
                 return
 
         info_to_insert_dict = {
-            "TimeRun": datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'),
+            "TimeRun": datetime.now(UTC).strftime('%Y-%m-%d %H:%M:%S'),
             "SeriesUID": series_uid,
             "TarchiveID": tarchive_id,
             "MincFile": file_rel_path,
@@ -277,7 +277,7 @@ def insert_protocol_violated_scan(self, patient_name, cand_id, psc_id, tarchive_
             "CandidateID": candidate_id,
             "PSCID": psc_id,
             "TarchiveID": tarchive_id,
-            "time_run": datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S'),
+            "time_run": datetime.now(UTC).strftime('%Y-%m-%d %H:%M:%S'),
             "series_description": scan_param["SeriesDescription"] if "SeriesDescription" in scan_param.keys() else None,
             "minc_location": file_rel_path,
             "PatientName": patient_name,

python/lib/imaging_io.py

@@ -1,9 +1,9 @@
-import datetime
 import os
 import shutil
 import sys
 import tarfile
 import tempfile
+from datetime import UTC, datetime
 
 from typing_extensions import deprecated
 
@@ -27,7 +27,7 @@ def extract_archive(self, location, prefix, tmp_dir):
             :rtype: str
         """
 
-        now = datetime.datetime.now()
+        now = datetime.now(UTC)
         upload_prefix = f'{prefix}_DIR_{now.strftime("%Y-%m-%d_%Hh%Mm%Ss")}_'
         extract_location = tempfile.mkdtemp(prefix=upload_prefix, dir=tmp_dir)
         tar_file = tarfile.open(location)

python/lib/imaging_lib/file.py

@@ -1,5 +1,5 @@
 import getpass
-from datetime import date, datetime
+from datetime import UTC, date, datetime
 from pathlib import Path
 
 from lib.db.models.dicom_archive import DbDicomArchive
@@ -31,7 +31,7 @@ def register_mri_file(
     """
 
     user = getpass.getuser()
-    time = datetime.now()
+    time = datetime.now(UTC)
 
     file = DbFile(
         path                     = file_path,

python/lib/imaging_lib/file_parameter.py

@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import UTC, datetime
 from typing import Any
 
 from lib.db.models.file import DbFile
@@ -31,7 +31,7 @@ def register_mri_file_parameter(env: Env, file: DbFile, parameter_name: str, par
 
     parameter = try_get_file_parameter_with_file_id_type_id(env.db, file.id, parameter_type.id)
     if parameter is None:
-        time = datetime.now()
+        time = datetime.now(UTC)
 
         parameter = DbFileParameter(
             type_id     = parameter_type.id,

python/lib/imaging_lib/mri_scanner.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass
-from datetime import datetime
+from datetime import UTC, datetime
 
 from lib.candidate import generate_new_cand_id
 from lib.db.models.candidate import DbCandidate
@@ -43,7 +43,7 @@ def get_or_create_scanner(
         return mri_scanner
 
     cand_id = generate_new_cand_id(env)
-    now = datetime.now()
+    now = datetime.now(UTC)
 
     candidate = DbCandidate(
         cand_id                 = cand_id,

python/lib/logging.py

@@ -1,5 +1,5 @@
 import sys
-from datetime import datetime
+from datetime import UTC, datetime
 from typing import Never
 
 from lib.db.models.notification_spool import DbNotificationSpool
@@ -80,7 +80,7 @@ def register_notification(env: Env, message: str, is_error: bool, is_verbose: bo
 
     notification = DbNotificationSpool(
         type_id      = env.notifier.type_id,
-        time_spooled = datetime.now(),
+        time_spooled = datetime.now(UTC),
         message      = message,
         origin       = env.notifier.origin,
         process_id   = env.notifier.process_id,

python/lib/make_env.py

@@ -1,6 +1,6 @@
 import sys
 import tempfile
-from datetime import datetime
+from datetime import UTC, datetime
 from pathlib import Path
 from typing import Any, cast
 
@@ -104,7 +104,7 @@ def create_script_tmp_dir(script_name: str) -> Path:
     env_tmp_dir = tempfile.gettempdir()
 
     # Create a recognizable temporary directory name for this pipeline.
-    date_string = datetime.now().strftime('%Y-%m-%d_%Hh%Mm%Ss_')
+    date_string = datetime.now(UTC).strftime('%Y-%m-%d_%Hh%Mm%Ss_')
     tmp_dir_prefix = f'{script_name}_{date_string}'
 
     # Create and return the pipeline temporary directory.

python/lib/physio/channels.py

@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import UTC, datetime
 from decimal import Decimal
 from pathlib import Path
 
@@ -36,7 +36,7 @@ def insert_physio_channel(
         file_path          = file_path,
         channel_type_id    = channel_type.id,
         status_type_id     = status_type.id if status_type is not None else None,
-        insert_time        = datetime.now(),
+        insert_time        = datetime.now(UTC),
         name               = name,
         description        = description,
         sampling_frequency = sampling_frequency,

python/lib/physio/events.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass
-from datetime import datetime
+from datetime import UTC, datetime
 from decimal import Decimal
 from pathlib import Path
 from typing import Any
@@ -239,7 +239,7 @@ def insert_physio_task_event(
     event_task_file = DbPhysioTaskEvent(
         physio_file_id = physio_file.id,
         event_file_id  = events_file.id,
-        insert_time    = datetime.now(),
+        insert_time    = datetime.now(UTC),
         onset          = onset,
         duration       = duration,
         event_code     = event_code,

python/lib/utilities.py

@@ -7,7 +7,7 @@
 import sys
 import tarfile
 import tempfile
-from datetime import datetime
+from datetime import UTC, datetime
 
 import loris_utils.crypto
 import mat73
@@ -250,7 +250,7 @@ def create_processing_tmp_dir(template_prefix):
     env_tmp_dir = os.environ.get("TMPDIR")
 
     # append date and time information to the prefix name for the tmp dir
-    now = datetime.now()
+    now = datetime.now(UTC)
     template_prefix += f"_{now.strftime('%Y-%m-%d_%Hh%Mm%Ss_')}"
 
     # create the temporary directory and return it

python/loris_bids_importer/src/loris_bids_importer/validation/subjects.py

@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import UTC, datetime
 
 from lib.candidate import generate_new_cand_id
 from lib.db.models.candidate import DbCandidate
@@ -103,7 +103,7 @@ def create_bids_candidate(env: Env, participant: BidsParticipantTsvRow) -> DbCan
         )
     )
 
-    now = datetime.now()
+    now = datetime.now(UTC)
 
     candidate = DbCandidate(
         cand_id                 = cand_id,

python/loris_dicom_importer/src/loris_dicom_importer/dicom_database.py

@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import UTC, datetime
 from functools import cmp_to_key
 from pathlib import Path
 
@@ -26,7 +26,7 @@ def insert_dicom_archive(
 
     dicom_archive = DbDicomArchive()
     populate_dicom_archive(dicom_archive, dicom_summary, dicom_import_log, archive_path)
-    dicom_archive.date_first_archived = datetime.now()
+    dicom_archive.date_first_archived = datetime.now(UTC)
     db.add(dicom_archive)
     db.commit()
     insert_files_series(db, dicom_archive, dicom_summary)
@@ -75,7 +75,7 @@ def populate_dicom_archive(
     dicom_archive.center_name              = dicom_summary.info.institution or ''
     dicom_archive.last_update              = None
     dicom_archive.date_acquired            = dicom_summary.info.scan_date
-    dicom_archive.date_last_archived       = datetime.now()
+    dicom_archive.date_last_archived       = datetime.now(UTC)
     dicom_archive.acquisition_count        = len(dicom_summary.dicom_series_files)
     dicom_archive.dicom_file_count         = count(flatten(dicom_summary.dicom_series_files.values()))
     dicom_archive.non_dicom_file_count     = len(dicom_summary.other_files)

python/loris_dicom_importer/src/loris_dicom_importer/import_log.py

@@ -2,7 +2,7 @@
 import os
 import socket
 from dataclasses import dataclass
-from datetime import datetime
+from datetime import UTC, datetime
 from pathlib import Path
 
 from loris_dicom_importer.text_dict import DictWriter
@@ -69,7 +69,7 @@ def make_dicom_study_import_log(source: Path, target: Path, tarball_md5_sum: str
         socket.gethostname(),
         os.uname().sysname,
         getpass.getuser(),
-        datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S"),
+        datetime.strftime(datetime.now(UTC), "%Y-%m-%d %H:%M:%S"),
         2,
         2,
         tarball_md5_sum,

python/loris_dicom_importer/src/loris_dicom_importer/text.py

@@ -42,14 +42,16 @@ def read_date_none(string: str | None):
     if string is None:
         return None
 
-    return datetime.strptime(string, '%Y-%m-%d').date()
+    # User-supplied date: no timezone.
+    return datetime.strptime(string, '%Y-%m-%d').date()  # noqa: DTZ007
 
 
 def read_dicom_date_none(string: str | None):
     if string is None:
         return None
 
-    return datetime.strptime(string, '%Y%m%d').date()
+    # User-supplied date: no timezone.
+    return datetime.strptime(string, '%Y%m%d').date()  # noqa: DTZ007
 
 
 def read_int_none(string: str | None):

python/loris_utils/src/loris_utils/fs.py

@@ -12,7 +12,8 @@ def extract_archive(tar_path: str, prefix: str, dir_path: str) -> str:
     the new directory location.
     """
 
-    date_string = datetime.now().strftime('%Y-%m-%d_%Hh%Mm%Ss')
+    # Use system timezone for log file name.
+    date_string = datetime.now().strftime('%Y-%m-%d_%Hh%Mm%Ss')  # noqa: DTZ005
     full_prefix = f'{prefix}_DIR_{date_string}_'
     extract_path = tempfile.mkdtemp(prefix=full_prefix, dir=dir_path)
     with tarfile.open(tar_path) as tar_file:

python/tests/integration/scripts/test_mass_nifti_pic.py

@@ -1,5 +1,5 @@
 import os
-from datetime import datetime
+from datetime import UTC, datetime
 from pathlib import Path
 
 from lib.db.models.file import DbFile
@@ -127,7 +127,7 @@ def test_running_on_a_text_file():
         file_type           = 'txt',
         session_id          = 564,
         output_type         = 'native',
-        insert_time         = datetime.now(),
+        insert_time         = datetime.now(UTC),
         inserted_by_user_id = 'test'
     )
 
@@ -175,7 +175,7 @@ def test_successful_run():
     file_pic_data = try_get_parameter_value_with_file_id_parameter_name(db, 2, 'check_pic_filename')
     assert file_pic_data is None
 
-    current_time = datetime.now()
+    current_time = datetime.now(UTC)
 
     process = run_integration_script([
         'mass_nifti_pic.py',