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
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
|
'''
scilo - A scientific workflow and efficiency library
Copyright (C) 2012 Joseph Hunkeler <jhunkeler@gmail.com>
This file is part of scilo.
scilo 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.
scilo 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 scilo. If not, see <http://www.gnu.org/licenses/>.
'''
import numpy as np
import sqlite3
import os
import glob
class scilo:
def __init__(self, path):
self.database_mtime = None
self.database_mtime_cursor = None
self.path = os.path.abspath(path)
#self.subdirs = ['data', 'result', 'npz']
self.subdirs = {
'data':False,
'result':False,
'npy':False
}
print("Dataset '%s'..." % (path)),
if not os.path.exists(path):
print("not found")
os.mkdir(os.path.abspath(self.path))
print("Generating structure...")
for key in self.subdirs.iterkeys():
d = os.path.join(self.path, key)
self.subdirs[key] = d
print("Creating directory: '%s'" % (self.subdirs[key]))
os.mkdir(self.subdirs[key])
else:
print("found")
for key in self.subdirs.iterkeys():
d = os.path.join(self.path, key)
self.subdirs[key] = d
def __getitem__(self, key):
return self.subdirs[key]
def aggregate(self, globular):
sources = glob.glob(globular)
if not sources:
return False
for src in sources:
dest = os.path.join(self.subdirs['data'], os.path.basename(src))
src = os.path.abspath(src)
if os.rename(src, dest) == False:
continue
return True
def _npy_mtime_populate(self):
database = os.path.join(self.subdirs['npy'], 'npy_mtime.db')
if not os.path.exists(database):
print("Creating modification tracking database...")
connection = sqlite3.connect(database)
c = connection.cursor()
self.database_mtime = sqlite3.connect(database)
self.database_mtime_cursor = c
c.execute("CREATE TABLE npy(file, mtime)")
for f in glob.glob(os.path.join(self.subdirs['data'], "*.*")):
print("\tFile: %s\tmtime: %f" % (os.path.basename(f), os.path.getmtime(f)))
self._npy_mtime_insert(f, os.path.getmtime(f))
connection.commit()
else:
connection = sqlite3.connect(database)
c = connection.cursor()
self.database_mtime = connection
self.database_mtime_cursor = c
return
def _npy_mtime_insert(self, path, mtime):
connection = self.database_mtime
c = self.database_mtime_cursor
values = (path, mtime,)
c.execute("INSERT INTO npy VALUES (?,?)", values)
connection.commit()
def _npy_mtime_update(self, path, stored, current):
connection = self.database_mtime
c = self.database_mtime_cursor
values = (path, current, path, stored)
c.execute("UPDATE npy SET file=?, mtime=? WHERE file==? AND mtime==?", values)
connection.commit()
print("'%s' updated mtime: %f" % (path, current))
def _npy_mtime_delete(self, path):
connection = self.database_mtime
c = self.database_mtime_cursor
values = (path,)
c.execute("DELETE FROM npy WHERE file==?", (values))
connection.commit()
print("'%s' removed from mtime database" % path)
return
def _npy_mtime_check(self):
mtime_stored = []
mtime_current = []
c = self.database_mtime_cursor
c.execute("SELECT file, mtime FROM npy")
files = glob.glob(os.path.join(self.subdirs['data'], '*.*'))
for f in files:
mtime_current.append([f, os.path.getmtime(f)])
for f, mtime in c.fetchall():
mtime_stored.append([str(f), mtime])
for stored_file, stored_mtime in mtime_stored:
for current_file, current_mtime in mtime_current:
if not os.path.exists(stored_file) or not os.path.exists(current_file):
print("Missing data file: '%s'" % stored_file)
self._npy_mtime_delete(stored_file)
self.npy_cache_drop(stored_file)
break
if current_file == stored_file:
if current_mtime != stored_mtime:
print("'%s' differs" % current_file)
self._npy_mtime_update(current_file, stored_mtime, current_mtime)
print("Rebuilding numpy cache for '%s'" % current_file)
self.npy_cache_build(current_file)
return
def npy_cache_build(self, path):
''' Generate 'path' npy file in npy directory'''
temp = np.loadtxt(path)
if np.save(os.path.join(self.subdirs['npy'], os.path.basename(path)), temp) == False:
return False
return True
def npy_cache_drop(self, path):
''' Remove 'path' from npy directory '''
# For security reasons, you are only allowed to unlink files in the 'npy' directory
if os.path.dirname(path) == 'npy':
print("Unlinking '%s'" % (path))
os.unlink(path)
def npy_cache_drop_all(self):
''' Remove all npy files '''
files = glob.glob(os.path.join(self.subdirs['npy'], '*.npy'))
if files:
[os.unlink(f) for f in files]
def npy_cache_populate(self):
files = glob.glob(os.path.join(self.subdirs['data'], '*.*'))
file_total = len(files)
file_current = 1
for f in files:
if os.path.exists(os.path.join(self.subdirs['npy'], os.path.basename(f) + '.npy')):
file_total -= 1
continue
print("Building cache %d of %d: '%s'..." % (file_current, file_total, os.path.basename(f))),
if not self.npy_cache_build(f):
print("failure")
print("success")
file_current += 1
self._npy_mtime_populate()
self._npy_mtime_check()
if __name__ == "__main__":
pass
|
