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
56
57
|
import optparse
import os
import numpy as np
from ase.db import connect
from ase.db.sqlite import index_statements
from ase.utils import basestring
def convert(name, opts):
con1 = connect(name, use_lock_file=False)
con1._allow_reading_old_format = True
newname = name[:-2] + 'new.db'
with connect(newname, create_indices=False, use_lock_file=False) as con2:
row = None
for row in con1.select():
kvp = row.get('key_value_pairs', {})
if opts.convert_strings_to_numbers:
for key, value in kvp.items():
if isinstance(value, basestring):
try:
value = float(value)
except ValueError:
pass
else:
kvp[key] = value
if opts.convert_minus_to_not_a_number:
for key, value in kvp.items():
if value == '-':
kvp[key] = np.nan
con2.write(row, data=row.get('data'), **kvp)
assert row is not None, 'Your database is empty!'
c = con2._connect()
for statement in index_statements:
c.execute(statement)
c.commit()
os.rename(name, name[:-2] + 'old.db')
os.rename(newname, name)
def main():
parser = optparse.OptionParser()
parser.add_option('-S', '--convert-strings-to-numbers', action='store_true')
parser.add_option('-N', '--convert-minus-to-not-a-number',
action='store_true')
opts, args = parser.parse_args()
for name in args:
convert(name, opts)
if __name__ == '__main__':
main()
|
