#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018 Piero Dalle Pezze
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
import argparse
import glob
import os
import errno
import shutil
from os.path import basename
from sbpipe.utils.io import replace_str_in_file
[docs]def get_index(name='', output_path='.'):
"""
Get the largest index of the reports in output_path
:param name: the name of the report
:param output_path: the output path storing reports
:return: the largest index or -1 if no file was found
"""
files = glob.glob(os.path.join(output_path, name) + '_' + '*')
print('Existing files in `' + output_path + '` : ' + str(len(files)))
# print(files)
# +1 is because the dataset include an underscore between the name and the sequence number
name_length = len(name) + 1
numbers = [-1]
for my_file in files:
# get the base name without extension
f = basename(my_file).split('.')[0]
numbers.append(int(f[name_length:]))
return max(numbers)
[docs]def move_dataset(name='', input_path='', output_path=''):
"""
Move data sets from one path to another and update the sequence number.
:param name: the model name without extension
:param input_path: the path containing the input files
:param output_path: the path to store the output files
"""
try:
os.makedirs(output_path)
print('Created missing output directory `' + output_path + '`')
except OSError as e:
if e.errno != errno.EEXIST:
raise
# get the last index
index = get_index(name, output_path)
# update the index
index += 1
files = glob.glob(os.path.join(input_path, name) + '_' + '*')
print('Files to copy from `' + input_path + '` to `' + output_path + '` : ' + str(len(files)))
for filein in files:
# get the base name extension
ext = basename(filein).split('.')[1]
fileout = os.path.join(output_path, name + '_' + str(index) + '.' + ext)
shutil.move(filein, fileout)
replace_str_in_file(fileout, basename(filein).split('.')[0], basename(fileout).split('.')[0])
index += 1
[docs]def main(argv=None):
"""
Move data sets from one Path to another and update the sequence number.
"""
parser = argparse.ArgumentParser(prog='sbpipe_move_datasets',
description='SBpipe script to move data sets from one path to another '
'and update the sequence number.',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog='''
Report bugs to sbpipe@googlegroups.com
SBpipe home page: <https://github.com/pdp10/sbpipe>
For complete documentation, see http://sbpipe.readthedocs.io .
''')
parser.add_argument('-n', '--model-name',
help='the model name without extension',
metavar='NAME',
required=True,
nargs=1)
parser.add_argument('-i', '--input-path',
help='the path containing the input files',
metavar='PATH',
required=True,
nargs=1)
parser.add_argument('-o', '--output-path',
help='the path to store the output files',
metavar='PATH',
required=True,
nargs=1)
args = parser.parse_args()
name = args.model_name[0]
input_path = args.input_path[0]
output_path = args.output_path[0]
move_dataset(name=name, input_path=input_path, output_path=output_path)
if __name__ == "__main__":
main()