# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need to download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2023, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# 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,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program. If not, see <http://www.gnu.org/licenses/>.
#
#
# CITATION:
# When using The Virtual Brain for scientific publications, please cite it as explained here:
# https://www.thevirtualbrain.org/tvb/zwei/neuroscience-publications
#
#
"""
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""
import os
import json
from datetime import datetime
import uuid
import urllib.request, urllib.parse, urllib.error
from hashlib import md5
import numpy
import six
from tvb.basic.profile import TvbProfile
CHAR_SEPARATOR = "__"
CHAR_SPACE = "--"
CHAR_DRIVE = "-DriVe-"
DRIVE_SEP = ":"
COMPLEX_TIME_FORMAT = '%Y-%m-%d,%H-%M-%S.%f'
# LESS_COMPLEX_TIME_FORMAT is also compatible with data exported from TVB 1.0.
# This is only used as a fallback in the string to date conversion.
LESS_COMPLEX_TIME_FORMAT = '%Y-%m-%d,%H-%M-%S'
SIMPLE_TIME_FORMAT = "%m-%d-%Y"
################## PATH related methods start here ###############
[docs]def path2url_part(file_path):
"""
Prepare a File System Path for passing into an URL.
"""
if not os.path.isabs(file_path):
file_path = os.path.join(TvbProfile.current.TVB_STORAGE, file_path)
result = file_path.replace(os.sep, CHAR_SEPARATOR).replace(" ", CHAR_SPACE).replace(DRIVE_SEP, CHAR_DRIVE)
return urllib.parse.quote(result)
[docs]def url2path(encoded_path):
"""
Retrieve File System Path from encoded URL (inverse of path2url_part).
"""
return encoded_path.replace(CHAR_SEPARATOR, os.sep).replace(CHAR_SPACE, " ").replace(CHAR_DRIVE, DRIVE_SEP)
[docs]def get_unique_file_name(storage_folder, file_name, try_number=0):
"""
Compute non-existent file name, in storage_folder.
Try file_name, and if already exists, try adding a number.
"""
# TODO this method should be re-tought
name, ext = os.path.splitext(file_name)
date = str(datetime.now())
date = date.replace(' ', '').replace(':', '').replace('.', '').replace('-', '')
if try_number > 0:
file_ = '%s-%s%s' % (name, date, ext)
else:
file_ = file_name
full_path = os.path.join(storage_folder, file_)
if os.path.exists(full_path):
# Try another name, by appending the consecutive try_number
return get_unique_file_name(storage_folder, file_name, try_number + 1)
return full_path, file_
################## PATH related methods end here ###############
################## CONVERT related methods start here ###############
[docs]def string2date(string_input, complex_format=True, date_format=None):
"""Read date from string, after internal format"""
if string_input == 'None':
return None
if date_format is not None:
return datetime.strptime(string_input, date_format)
if complex_format:
try:
return datetime.strptime(string_input, COMPLEX_TIME_FORMAT)
except ValueError:
# For backwards compatibility with TVB 1.0
return datetime.strptime(string_input, LESS_COMPLEX_TIME_FORMAT)
return datetime.strptime(string_input, SIMPLE_TIME_FORMAT)
[docs]def date2string(date_input, complex_format=True, date_format=None):
"""Convert date into string, after internal format"""
if date_input is None:
return "None"
if date_format is not None:
return date_input.strftime(date_format)
if complex_format:
return date_input.strftime(COMPLEX_TIME_FORMAT)
return date_input.strftime(SIMPLE_TIME_FORMAT)
[docs]def string2bool(string_input):
""" Convert given string into boolean value."""
string_input = str(string_input).lower()
return string_input in ("yes", "true", "t", "1")
[docs]def parse_json_parameters(parameters):
"""
From JSON with Unicodes, return a dictionary having strings as keys.
Loading from DB a JSON will return instead of string keys, unicodes.
"""
params = json.loads(parameters)
new_params = {}
for key, value in six.iteritems(params):
new_params[str(key)] = value
return new_params
[docs]class TVBJSONEncoder(json.JSONEncoder):
"""
Custom encoder class. Referring towards "to_json" method, when found, or default behaviour otherwise.
"""
[docs] def default(self, obj):
if hasattr(obj, "to_json"):
return obj.to_json()
if isinstance(obj, bytes):
return obj.decode('utf-8')
try:
# TVB-2565 numpy int serialization
if numpy.issubdtype(obj, numpy.integer):
return int(obj)
except TypeError:
pass
return json.JSONEncoder.default(self, obj)
################## CONVERT related methods end here ###############
################## GENERIC methods start here ###############
[docs]def generate_guid():
"""
Generate new Global Unique Identifier.
This identifier should be unique per each station,
and unique for different machines.
"""
return str(uuid.uuid1())
[docs]def prepare_time_slice(total_time_length, max_length=10 ** 4):
"""
Limit the time dimension when retrieving from TS.
If total time length is greater than MAX, then retrieve only the last part of the TS
:param total_time_length: TS time dimension
:param max_length: limiting number of TS steps
:return: python slice
"""
if total_time_length < max_length:
return slice(total_time_length)
return slice(total_time_length - max_length, total_time_length)
[docs]def hash_password(pass_string):
return md5(pass_string.encode('utf-8')).hexdigest()
