Python.oshelper.file_operation.is_file_name_unique() - Code Metrics - Inspection of "Merge pull request #2 from CNBP/DICOMAnonimization" - CNBP/DICOMTransit - Measure and Improve Code Quality continuously with Scrutinizer

Passed

Push — master ( 9e6838...cf264a )

by Yang

created 2018-08-01 16:42 UTC

is_file_name_unique() A

↳ Parent: Python.oshelper.file_operation

Complexity

Conditions

Size

Total Lines	13
Code Lines	7

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
eloc	7
dl	0
loc	13
rs	10
c	0
b	0
f	0
cc	2
nop	1

import os
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
import logging
from DICOM.validate import DICOM_validator

from DICOM.decompress import DICOM_RequireDecompression, DICOM_TransferSyntax



def recursive_list_files(root_dicom_path):
    """
    load all the files, validate and then pass to decompress or anonimize.
    :param path:
    :return:
    """
    global file_list

    file_list = []

    for root, directories, filenames in os.walk(root_dicom_path):

        #for directory in directories:
            #file_list.append(os.path.join(root, directory))
        for filename in filenames:
            file_list.append(os.path.join(root,filename))

    return file_list


def decompress_folder(file_list):
param = 5

class Foo:
    def __init__(self, param):   # "param" would be flagged here
        self.param = param
    """
    Decompress all compressed file within the lsit.
    :param file_list:
    :return:
    """

    for file in file_list:
        logger = logging.getLogger("Compression checking file: " + file)

        # find if the file is DICOM, if not, skip this file.
        is_DICOM_file, _ = DICOM_validator(file)

        if not is_DICOM_file:
            continue

        # check if the file is compressed.
        TransferSyntax = DICOM_TransferSyntax(file)

        try:
            RequireDecompression = DICOM_RequireDecompression(TransferSyntax)

            # if RequireDecompression:
                # DecompressFile

        except ValueError:
            logger.info("Unknwonw DICOM syntax. You sure it is DICOM?")
            continue



def copy_files_to_flat_folder(file_list, destination_path):
param = 5

class Foo:
    def __init__(self, param):   # "param" would be flagged here
        self.param = param
    """
    Takes in a list of files and flatten them to the desintation path while ensure they are guarnteed to be unique files.

    :param file_list: the list of files from different path.
    :param destination_path:
    """
    logger = logging.getLogger(__name__)
    logger.info("Copying checking and checking files to destination: " + destination_path)

    from shutil import copyfile

    for file in file_list:

        # find if the file is DICOM, if not, skip this file.
        is_DICOM_file, _ = DICOM_validator(file)

        if not is_DICOM_file:
            continue

        # get the final path name.
        file_name = os.path.basename(file)
        destination_path_name = os.path.join(destination_path, file_name)

        # check if the final path is unique.
        unique, new_name = is_file_name_unique(destination_path_name)

        # append date time microsecond string if the file is not unique.
        if not unique:
            destination_path_name = new_name

        copyfile(file, destination_path_name)

def is_file_name_unique(path):
    """
    Determine if the proposed file exist and suggest alternative name.
    :param path:
    :return:
    """
    import datetime
    timestamp = datetime.datetime.now().isoformat()
    timestamp = timestamp.replace(':','') # string : which are incompatible with path

    if os.path.exists(path):

        return False, path + "_" + timestamp
    else:
        return True, path

def zip_with_name(path, name):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    return


1			import os
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This module should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
2			import logging
3			from DICOM.validate import DICOM_validator
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.validate' Loading history...
4			from DICOM.decompress import DICOM_RequireDecompression, DICOM_TransferSyntax
			0 ignored issues – show introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unable to import 'DICOM.decompress' Loading history...
5
6
7			def recursive_list_files(root_dicom_path):
8			"""
9			load all the files, validate and then pass to decompress or anonimize.
10			:param path:
11			:return:
12			"""
13			global file_list
			0 ignored issues – show Bug introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Global variable 'file_list' undefined at the module level Loading history... Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `file_list` does not conform to the constant naming conventions (`(([A-Z_][A-Z0-9_])\|(__.__))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
14			file_list = []
15
16			for root, directories, filenames in os.walk(root_dicom_path):
			0 ignored issues – show Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The variable `directories` seems to be unused. Loading history...
17			#for directory in directories:
18			#file_list.append(os.path.join(root, directory))
19			for filename in filenames:
20			file_list.append(os.path.join(root,filename))
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Exactly one space required after comma Loading history...
21			return file_list
22
23
24			def decompress_folder(file_list):
			0 ignored issues – show Comprehensibility Bug introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report `file_list` is re-defining a name which is already available in the outer-scope (previously defined on line `14`). It is generally a bad practice to shadow variables from the outer-scope. In most cases, this is done unintentionally and might lead to unexpected behavior: param = 5 class Foo: def __init__(self, param): # "param" would be flagged here self.param = param Loading history...
25			"""
26			Decompress all compressed file within the lsit.
27			:param file_list:
28			:return:
29			"""
30
31			for file in file_list:
32			logger = logging.getLogger("Compression checking file: " + file)
33
34			# find if the file is DICOM, if not, skip this file.
35			is_DICOM_file, _ = DICOM_validator(file)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `is_DICOM_file` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
36			if not is_DICOM_file:
37			continue
38
39			# check if the file is compressed.
40			TransferSyntax = DICOM_TransferSyntax(file)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `TransferSyntax` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
41			try:
42			RequireDecompression = DICOM_RequireDecompression(TransferSyntax)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `RequireDecompression` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The variable `RequireDecompression` seems to be unused. Loading history...
43			# if RequireDecompression:
44			# DecompressFile
45
46			except ValueError:
47			logger.info("Unknwonw DICOM syntax. You sure it is DICOM?")
48			continue
49
50
51
52			def copy_files_to_flat_folder(file_list, destination_path):
			0 ignored issues – show Comprehensibility Bug introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report `file_list` is re-defining a name which is already available in the outer-scope (previously defined on line `14`). It is generally a bad practice to shadow variables from the outer-scope. In most cases, this is done unintentionally and might lead to unexpected behavior: param = 5 class Foo: def __init__(self, param): # "param" would be flagged here self.param = param Loading history...
53			"""
54			Takes in a list of files and flatten them to the desintation path while ensure they are guarnteed to be unique files.
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (121/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
55			:param file_list: the list of files from different path.
56			:param destination_path:
57			"""
58			logger = logging.getLogger(__name__)
59			logger.info("Copying checking and checking files to destination: " + destination_path)
60
61			from shutil import copyfile
62
63			for file in file_list:
64
65			# find if the file is DICOM, if not, skip this file.
66			is_DICOM_file, _ = DICOM_validator(file)
			0 ignored issues – show Coding Style Naming introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The name `is_DICOM_file` does not conform to the variable naming conventions (`(([a-z][a-z0-9_]{2,30})\|(_[a-z0-9_]*))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
67			if not is_DICOM_file:
68			continue
69
70			# get the final path name.
71			file_name = os.path.basename(file)
72			destination_path_name = os.path.join(destination_path, file_name)
73
74			# check if the final path is unique.
75			unique, new_name = is_file_name_unique(destination_path_name)
76
77			# append date time microsecond string if the file is not unique.
78			if not unique:
79			destination_path_name = new_name
80
81			copyfile(file, destination_path_name)
82
83			def is_file_name_unique(path):
84			"""
85			Determine if the proposed file exist and suggest alternative name.
86			:param path:
87			:return:
88			"""
89			import datetime
90			timestamp = datetime.datetime.now().isoformat()
91			timestamp = timestamp.replace(':','') # string : which are incompatible with path
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Exactly one space required after comma Loading history...
92			if os.path.exists(path):
			0 ignored issues – show unused-code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Unnecessary "else" after "return" Loading history...
93			return False, path + "_" + timestamp
94			else:
95			return True, path
96
97			def zip_with_name(path, name):
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report This function should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history... Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The argument `path` seems to be unused. Loading history... Unused Code introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report The argument `name` seems to be unused. Loading history...
98			return
			0 ignored issues – show Coding Style introduced 2018-07-31 12:18 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

CNBP / DICOMTransit

Push — master ( 9e6838...cf264a )

is_file_name_unique() A

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