fixed typing

xnat_ingest/cli/stage.py

@@ -6,9 +6,8 @@
 from tqdm import tqdm
 from xnat_ingest.cli.base import cli
 from xnat_ingest.session import ImagingSession
-from frametree.xnat import Xnat
+from frametree.xnat import Xnat  # type: ignore[import-untyped]
 from xnat_ingest.utils import (
-    DicomField,
     AssociatedFiles,
     logger,
     LogFile,
@@ -39,7 +38,7 @@
     type=str,
     metavar="<mime-type>",
     multiple=True,
-    default="medimage/dicom-series",
+    default=["medimage/dicom-series"],
     envvar="XNAT_INGEST_STAGE_DATATYPE",
     help="The datatype of the primary files to to upload",
 )

xnat_ingest/session.py

@@ -5,15 +5,18 @@
 import os.path
 import subprocess as sp
 from functools import cached_property
-from typing_extensions import Self
 import shutil
+import random
+import string
+import platform
 from copy import deepcopy
-import yaml
-from tqdm import tqdm
-import attrs
 from itertools import chain
 from collections import defaultdict, Counter
 from pathlib import Path
+from typing_extensions import Self
+import attrs
+from tqdm import tqdm
+import yaml
 import pydicom
 from fileformats.generic import File
 from fileformats.application import Dicom
@@ -29,9 +32,6 @@
 from .exceptions import ImagingSessionParseError, StagingError
 from .utils import add_exc_note, transform_paths, AssociatedFiles
 from .dicom import dcmedit_path
-import random
-import string
-import platform
 
 logger = logging.getLogger("xnat-ingest")