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Source code for tvb.contrib.scripts.utils.file_utils

# -*- coding: utf-8 -*-
#
#
#  TheVirtualBrain-Contributors Package. This package holds simulator extensions.
#  See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, Baycrest Centre for Geriatric Care ("Baycrest") and others
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# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
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# You should have received a copy of the GNU General Public License along with this
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#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
File writing/reading and manipulations

.. moduleauthor:: Dionysios Perdikis <Denis@tvb.invalid>
"""

import os
from datetime import datetime
import glob
import shutil


[docs]def ensure_unique_file(parent_folder, filename): final_path = os.path.join(parent_folder, filename) while os.path.exists(final_path): filename = input("\n\nFile %s already exists. Enter a different name: " % final_path) final_path = os.path.join(parent_folder, filename) return final_path
[docs]def change_filename_or_overwrite(path, overwrite=True): if overwrite: if os.path.exists(path): os.remove(path) return path parent_folder = os.path.dirname(path) while os.path.exists(path): filename = \ input("\n\nFile %s already exists. Enter a different name or press enter to overwrite file: " % path) if filename == "": overwrite = True break path = os.path.join(parent_folder, filename) if overwrite: os.remove(path) return path
[docs]def insensitive_glob(pattern): def either(c): return '[%s%s]' % (c.lower(), c.upper()) if c.isalpha() else c return glob.glob(''.join(map(either, pattern)))
[docs]def wildcardit(name, front=True, back=True): out = str(name) if front: out = "*" + out if back: out = out + "*" return out
[docs]def delete_all_files_in_folder(folderpath): if os.path.isdir(folderpath): for filename in os.listdir(folderpath): file_path = os.path.join(folderpath, filename) try: if os.path.isfile(file_path) or os.path.islink(file_path): os.unlink(file_path) elif os.path.isdir(file_path): shutil.rmtree(file_path) except Exception as e: print('Failed to delete %s. Reason: %s' % (file_path, e))
[docs]def delete_folder_safely(folderpath): if os.path.isdir(folderpath): try: shutil.rmtree(folderpath) except Exception as e: print('Failed to delete %s.\nReason: %s' % (folderpath, e))
[docs]def change_filename_or_overwrite_with_wildcard(path, overwrite=True): wild_path = path + "*" existing_files = glob.glob(path + "*") if len(existing_files) > 0: if overwrite: for file in existing_files: if os.path.exists(file): os.remove(file) return path else: print("The following files already exist for base paths " + wild_path + " !: ") for file in existing_files: print(file) filename = input("\n\nEnter a different name or press enter to overwrite files: ") if filename == "": return change_filename_or_overwrite_with_wildcard(path, overwrite=True) else: parent_folder = os.path.dirname(path) path = os.path.join(parent_folder, filename) return change_filename_or_overwrite_with_wildcard(path, overwrite) else: return path
[docs]def move_overwrite_files_to_folder_with_wildcard(folder, path_wildcard): if not os.path.isdir(folder): os.makedirs(folder) for file in glob.glob(path_wildcard): if os.path.isfile(file): filepath = os.path.join(folder, os.path.basename(file)) shutil.move(file, filepath)
[docs]def write_metadata_in_xml(meta_dict, h5_file, key_date, key_version, path="/"): root = h5_file[path].attrs root[key_date] = str(datetime.now()) root[key_version] = 2 for key, val in meta_dict.items(): root[key] = val
[docs]def safe_makedirs(folder): # solution based on https://stackoverflow.com/questions/600268/mkdir-p-functionality-in-python if not os.path.isdir(folder): try: # This should work for Python >= 3.2 os.makedirs(folder, exist_ok=True) except OSError as exc: # Python ≥ 2.5 try: os.makedirs(folder) except: try: # just in case errno cannot be imported... import errno if exc.errno == errno.EEXIST and os.path.isdir(folder): pass else: raise except: pass