Mercurial > repos > brenninc > xdirectory_reader_limited_by_data_table

comparison directory_copier.py @ 8:288a172e95aa draft default tip

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author brenninc
date Mon, 09 May 2016 02:25:23 -0400
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7:1d1b8eb0e6b7 8:288a172e95aa
1 import gzip
2 import optparse # using optparse as hydra still python 2.6
3 import os.path
4 import shutil
5 import sys
6
7 def report_error(*args):
8 sys.stderr.write(' '.join(map(str,args)) + '\n')
9 sys.stderr.flush()
10 sys.exit(1)
11
12
13 def check_pattern_get_new_name(a_file, ending, options):
14 if options.start:
15 if not(a_file.startswith(options.start)):
16 return None
17 if options.last:
18 if ending[0] == ".":
19 last = options.last + ending
20 else:
21 if options.last[-1] == ".":
22 last = options.last + ending
23 else:
24 last = options.last + "." + ending
25 if not(a_file.endswith(last)):
26 return None
27 if options.new_ending:
28 name = a_file[:-len(ending)]
29 if options.new_ending[0] ==".":
30 if name[-1] == ".":
31 name = name[:-1]
32 return name + options.new_ending
33 if options.decompress:
34 if a_file.endswith(".gz"):
35 return a_file[:-3]
36 return a_file
37
38
39 def check_and_get_new_name(a_file, options):
40 for ending in options.endings:
41 if a_file.endswith(ending):
42 return check_pattern_get_new_name (a_file, ending, options)
43 return None
44
45
46 def link(a_file, new_name, path):
47 file_path = os.path.join(os.path.realpath(path), a_file)
48 sym_path = os.path.join(os.path.realpath("output"), new_name)
49 #if not(os.path.exists(sym_path)):
50 os.link(file_path, sym_path)
51
52
53 def decompress(a_file, new_name, path):
54 file_path = os.path.join(os.path.realpath(path), a_file)
55 target_path = os.path.join(os.path.realpath("output"), new_name)
56 with gzip.open(file_path, 'rb') as f_in, open(target_path, 'wb') as f_out:
57 shutil.copyfileobj(f_in, f_out)
58
59
60 def copy_and_link(path, options):
61 os.mkdir("output")
62 with open(options.list, 'w') as list_file:
63 files = os.listdir(path)
64 files.sort()
65 for a_file in files:
66 new_name = check_and_get_new_name(a_file, options)
67 if new_name:
68 list_file.write(new_name)
69 list_file.write("\n")
70 if options.decompress:
71 if a_file.endswith(".gz"):
72 decompress(a_file, new_name,path)
73 else:
74 link(a_file, new_name, path)
75 elif options.link:
76 link(a_file, new_name, path)
77
78
79 if __name__ == '__main__':
80 parser = optparse.OptionParser()
81 parser.add_option("--path", action="store", type="string",
82 help="Path of directory to check. ")
83 parser.add_option("--ending", action="append", type="string", dest="endings",
84 help="Ending that can be listed and if requested linked or decompressed. ")
85 parser.add_option("--start", action="store", type="string",
86 help="String that must be at the start of the file name ")
87 parser.add_option("--last", action="store", type="string",
88 help="String that must be the last bit of the file name before the endings")
89 parser.add_option("--new_ending", action="store", type="string",
90 help="New ending to replace any previous ending in list and if required links or decompressions. Note: If not set decompression will auto remove the compressioned part of the ending")
91 #parser.add_option("--regex", action="store", type="string",
92 # help="Regex pattern the file name (less . ending) must match before the endings")
93 parser.add_option("--list", action="store", type="string",
94 help="Path to where all files should be listed. ")
95 parser.add_option("--link", action="store_true", default=False,
96 help="If set will cause links to be added in output directory. ")
97 parser.add_option("--decompress", action="store_true", default=False,
98 help="If set will cause gz files to be decompressed or if not a supported decompression ending linked.")
99 (options, args) = parser.parse_args()
100
101
102 path = options.path.strip()
103 if path[-1] != '/':
104 path = path + "/"
105 copy_and_link(path, options)
106