Fix LGTM alerts (#186)

* LGTM warning: Unguarded next in generator

Call to next() in a generator

Additionnlly, dicom_file cannot be None:
• os.path.splitext(dicom_file) would raise TypeException
• In the case of a ZIP file, which I believe is the one the existing
  code was trying to address, we continue on StopIteration if the ZIP
  file is empty.

* LGTM recommendation: Unused import

Import of 'Sequence' is not used.
Import of 'remove_sequences' is not used.
Import of 'os' is not used.
Import of 'read_json' is not used.
Import of 'DeidRecipe' is not used.
Import of 'get_private' is not used.
Import of 'remove_sequences' is not used.
Import of 'extract_fields_list' is not used.
Import of 'extract_values_list' is not used.
Import of 'get_fields' is not used.
Import of 'DataElement' is not used.
Import of 'operator' is not used.
Import of 'get_installdir' is not used.
Import of 'os' is not used.
mport of 'read_file' is not used.
Import of 'os' is not used.

* LGTM recommendation: Except block handles 'BaseException'

Except block directly handles BaseException.

Function dateutil.parser.parse() raises the following exceptions:
• ParserError – Raised for invalid or unknown string formats, if the provided tzinfo is not in a valid format, or if an invalid date would be created.
• OverflowError – Raised if the parsed date exceeds the largest valid C integer on your system.

deid/dicom/filter.py

@@ -23,7 +23,6 @@
 """
 
 from pydicom.dataset import Dataset
-from pydicom.sequence import Sequence
 from deid.logger import bot
 import re
 

deid/dicom/groups.py

@@ -26,12 +26,9 @@
 
 
 from deid.logger import bot
-from .tags import remove_sequences
 from .fields import get_fields, expand_field_expression
 from pydicom.multival import MultiValue
 
-import os
-
 
 def extract_values_list(dicom, actions, fields=None):
     """Given a list of actions for a named group (a list) extract values from

deid/dicom/header.py

@@ -26,16 +26,11 @@
 
 
 from deid.logger import bot
-from deid.utils import read_json
-
-from deid.config import DeidRecipe
 
 from pydicom import read_file
 
 from deid.dicom.utils import save_dicom
-from deid.dicom.tags import remove_sequences, get_private
-from deid.dicom.groups import extract_values_list, extract_fields_list
-from deid.dicom.fields import get_fields
+from deid.dicom.tags import remove_sequences
 from deid.dicom.parser import DicomParser
 
 import os

deid/dicom/tags.py

@@ -25,7 +25,6 @@
 from deid.logger import bot
 from pydicom.tag import tag_in_exception
 from pydicom.sequence import Sequence
-from pydicom.dataelem import DataElement
 from pydicom._dicom_dict import DicomDictionary, RepeatersDictionary
 from pydicom.tag import Tag
 import re

deid/dicom/utils.py

@@ -64,21 +64,23 @@ def get_files(contenders, check=True, pattern=None, force=False, tempdir=None):
             if dextension == ".zip":
                 with zipfile.ZipFile(dicom_file, "r") as compressedFile:
                     compressedFile.extractall(tempdir)
-                    dicom_file = next(
-                        os.path.join(tempdir, f)
-                        for f in os.listdir(tempdir)
-                        if os.path.isfile(os.path.join(tempdir, f))
-                    )
-
-            if dicom_file is not None:
-                if check:
-                    validated_files = validate_dicoms(dicom_file, force=force)
-                else:
-                    validated_files = [dicom_file]
-
-                for validated_file in validated_files:
-                    bot.debug("Found contender file %s" % (validated_file))
-                    yield validated_file
+                    try:
+                        dicom_file = next(
+                            os.path.join(tempdir, f)
+                            for f in os.listdir(tempdir)
+                            if os.path.isfile(os.path.join(tempdir, f))
+                        )
+                    except StopIteration:
+                        continue  # ZIP file does not contain any file
+
+            if check:
+                validated_files = validate_dicoms(dicom_file, force=force)
+            else:
+                validated_files = [dicom_file]
+
+            for validated_file in validated_files:
+                bot.debug("Found contender file %s" % (validated_file))
+                yield validated_file
 
 
 def save_dicom(dicom, dicom_file, output_folder=None, overwrite=False):

deid/utils/actions.py

@@ -98,7 +98,7 @@ def get_timestamp(item_date, item_time=None, jitter_days=None, format=None):
 
     try:
         timestamp = dateutil.parser.parse("%s%s" % (item_date, item_time))
-    except:
+    except (dateutil.parser.ParserError, OverflowError):
         timestamp = datetime.strptime("%s%s" % (item_date, item_time), format)
 
     if jitter_days is not None:

examples/dicom/dicom-extract/create-dicom-csv.py

@@ -3,7 +3,6 @@
 import os
 import platform
 import csv
-import operator
 from collections.abc import Sequence
 from collections import OrderedDict
 

examples/dicom/header-manipulation/func-replacement.py

@@ -1,9 +1,7 @@
 #!/usr/bin/env python3
 
 from deid.dicom import get_files, replace_identifiers
-from deid.utils import get_installdir
 from deid.data import get_dataset
-import os
 
 # This is an example of replacing fields in dicom headers,
 # but via a function instead of a preset identifier.

examples/dicom/pixels/run-inspect-pixels.py

@@ -7,10 +7,8 @@
 
 # This will get a set of example cookie dicoms
 from deid.dicom import get_files, has_burned_pixels
-from pydicom import read_file
 from deid.data import get_dataset
 from deid.logger import bot
-import os
 
 bot.level = 3