1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
|
"""
Validate NIX files for missing or inconsistent objects and annotations.
"""
import os
import nixio as nix
def format_obj(obj):
return "{} '{}' (ID: {})".format(type(obj).__name__, obj.name, obj.id)
def print_header(text):
print(" {}".format(text))
print(" " + "-"*len(text))
def validate(filename):
nf = nix.File(filename, mode=nix.FileMode.ReadOnly)
results = nf.validate()
print("Results for '{}'".format(filename))
errors = results["errors"]
if errors:
plural = "s" if len(errors) > 1 else ""
print_header("{} object{} with errors".format(len(errors), plural))
for idx, (obj, messages) in enumerate(errors.items()):
print(" [{}] {}".format(idx+1, format_obj(obj)))
for msg in messages:
print(" {}".format(msg))
warnings = results["warnings"]
if warnings:
plural = "s" if len(warnings) > 1 else ""
print_header("{} object{} with warnings".format(len(warnings), plural))
for idx, (obj, messages) in enumerate(warnings.items()):
print(" [{}] {}".format(idx+1, format_obj(obj)))
for msg in messages:
print(" {}".format(msg))
print()
def create_subcmd_parser(parser):
parser.add_argument("file", type=str, nargs="+",
help="path to file to validate (at least one)")
return parser
def main(args):
filenames = args.file
for nixfn in filenames:
if os.path.exists(nixfn):
validate(nixfn)
else:
print("error: No such file '{}'".format(nixfn))
|
