forked from rucio/rucio
-
Notifications
You must be signed in to change notification settings - Fork 0
/
consistency.py
449 lines (368 loc) · 15.7 KB
/
consistency.py
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
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
# -*- coding: utf-8 -*-
# Copyright European Organization for Nuclear Research (CERN) since 2012
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import datetime
import logging
import os
import re
import subprocess
import tempfile
from rucio.common import dumper
from rucio.common.dumper import DUMPS_CACHE_DIR, data_models, error, path_parsing
subcommands = ['consistency', 'consistency-manual']
class Consistency(data_models.DataModel):
SCHEMA = (
('apparent_status', str),
('path', str),
)
@classmethod
def dump(cls, subcommand, ddm_endpoint, storage_dump, prev_date_fname=None, next_date_fname=None,
prev_date=None, next_date=None, sort_rucio_replica_dumps=True, date=None,
cache_dir=DUMPS_CACHE_DIR):
logger = logging.getLogger('auditor.consistency')
if subcommand == 'consistency':
prev_date_fname = data_models.Replica.download(
ddm_endpoint, prev_date, cache_dir=cache_dir)
next_date_fname = data_models.Replica.download(
ddm_endpoint, next_date, cache_dir=cache_dir)
assert prev_date_fname is not None
assert next_date_fname is not None
else:
assert subcommand == 'consistency-manual'
prefix_components = path_parsing.components(dumper.ddmendpoint_url(ddm_endpoint))
def parser(line):
'''
Simple parser for Rucio replica dumps.
:param line: String with one line of a dump.
:returns: A tuple with the path and status of the replica.
'''
fields = line.split('\t')
path = fields[6].strip().lstrip('/')
status = fields[8].strip()
return ','.join((path, status))
def strip_storage_dump(line):
'''
Parser to have consistent paths in storage dumps.
:param line: String with one line of a dump.
:returns: Path formated as in the Rucio Replica Dumps.
'''
relative = path_parsing.remove_prefix(
prefix_components,
path_parsing.components(line),
)
if relative[0] == 'rucio':
relative = relative[1:]
return '/'.join(relative)
if sort_rucio_replica_dumps:
prev_date_fname_sorted = gnu_sort(
parse_and_filter_file(prev_date_fname, parser=parser, cache_dir=cache_dir),
delimiter=',',
fieldspec='1',
cache_dir=cache_dir,
)
next_date_fname_sorted = gnu_sort(
parse_and_filter_file(next_date_fname, parser=parser, cache_dir=cache_dir),
delimiter=',',
fieldspec='1',
cache_dir=cache_dir,
)
else:
prev_date_fname_sorted = parse_and_filter_file(
prev_date_fname,
parser=parser,
cache_dir=cache_dir,
)
next_date_fname_sorted = parse_and_filter_file(
next_date_fname,
parser=parser,
cache_dir=cache_dir,
)
standard_name_re = r'(ddmendpoint_{0}_\d{{2}}-\d{{2}}-\d{{4}}_[0-9a-f]{{40}})$'.format(ddm_endpoint)
standard_name_match = re.search(standard_name_re, storage_dump)
if standard_name_match is not None:
# If the original filename was generated using the expected format,
# just use the name as prefix for the parsed file.
sd_prefix = standard_name_match.group(0)
elif date is not None:
# Otherwise try to use the date information and DDMEndpoint name to
# have a meaningful filename.
sd_prefix = 'ddmendpoint_{0}_{1}'.format(
ddm_endpoint,
date.strftime('%d-%m-%Y'),
)
else:
# As last resort use only the DDMEndpoint name, but this is error
# prone as old dumps may interfere with the checks.
sd_prefix = 'ddmendpoint_{0}_unknown_date'.format(
ddm_endpoint,
)
logger.warning(
'Using basic and error prune naming for RSE dump as no date '
'information was provided, %s dump will be named %s',
ddm_endpoint,
sd_prefix,
)
storage_dump_fname_sorted = gnu_sort(
parse_and_filter_file(
storage_dump,
parser=strip_storage_dump,
prefix=sd_prefix,
cache_dir=cache_dir,
),
prefix=sd_prefix,
cache_dir=cache_dir,
)
with open(prev_date_fname_sorted) as prevf:
with open(next_date_fname_sorted) as nextf:
with open(storage_dump_fname_sorted) as sdump:
for path, where, status in compare3(prevf, sdump, nextf):
prevstatus, nextstatus = status
if where[0] and not where[1] and where[2]:
if prevstatus == 'A' and nextstatus == 'A':
yield cls('LOST', path)
if not where[0] and where[1] and not where[2]:
yield cls('DARK', path)
def _try_to_advance(it, default=None):
try:
el = next(it)
except StopIteration:
return default
return el.strip()
def min3(*values):
'''
Minimum between the 3 values ignoring None
'''
values = [value for value in values if value is not None]
assert len(values) > 0
return min(values)
def split_if_not_none(value, sep=',', fields=2):
return value.split(sep) if value is not None else ([None] * fields)
def compare3(it0, it1, it2):
'''
Generator to compare 3 sorted iterables, in each
iteration it yields a tuple of the form (current, (bool, bool, bool))
where current is the current element checked and the
second element of the tuple is a triplet whose elements take
a true value if current is contained in the it0, it1 or it2
respectively.
This function can't compare the iterators properly if None is
a valid value.
'''
it0 = iter(it0)
it1 = iter(it1)
it2 = iter(it2)
v0 = _try_to_advance(it0)
v1 = _try_to_advance(it1)
v2 = _try_to_advance(it2)
while v0 is not None or v1 is not None or v2 is not None:
path0, status0 = split_if_not_none(v0)
path2, status2 = split_if_not_none(v2)
vmin = min3(path0, v1, path2)
in0 = in1 = in2 = False
in0_status = in2_status = None
# Detect in which iterables the value is present
# inN is True if the value is present on the N iterable.
# sN is the status of the path in the rucio replica
# dumps (N is either 0 or 2).
if path0 is not None and path0 == vmin:
in0 = True
in0_status = status0
if v1 is not None and v1 == vmin:
in1 = True
if path2 is not None and path2 == vmin:
in2 = True
in2_status = status2
# yield the value, in which iterables is present, and the status
# in each rucio replica dumps (if it is present there, else None).
yield (vmin, (in0, in1, in2), (in0_status, in2_status))
# Discard duplicate entries (it shouldn't be duplicate entries
# anyways) and
# advance the iterators, if the iterator N is depleted vN is set
# to None.
while v0 is not None and path0 == vmin:
v0 = _try_to_advance(it0)
path0, status0 = split_if_not_none(v0)
while v1 is not None and v1 == vmin:
v1 = _try_to_advance(it1)
while v2 is not None and path2 == vmin:
v2 = _try_to_advance(it2)
path2, status2 = split_if_not_none(v2)
def parse_and_filter_file(filepath, parser=lambda s: s, filter_=lambda s: s, prefix=None, postfix='parsed', cache_dir=DUMPS_CACHE_DIR):
'''
Opens `filepath` as a read-only file, and for each line of the file
for which the `filter_` function returns True, it writes a version
parsed with the `parser` function.
The name of the output file is generated appending '_' + `postfix` to
the filename in `filepath`. If `prefix` is given it is used instead
of `filepath`.
The output file (and temporary files while processing are stored in
`cache_dir`.
Default values for the arguments:
- `parser`: returns the same string.
- `filter_`: returns True for any argument.
- `prefix`: None (the name of the input file is used as prefix).
- `postfix`: 'parsed'.
- `cache_dir`: DUMPS_CACHE_DIR.
The output file is created with a random name and renamed atomically
when it is complete.
'\n' is appended to each line, therefore if the input is 'a\nb\n' and `parser`
is not especified the output will be 'a\n\nb\n\n'
'''
prefix = os.path.basename(filepath) if prefix is None else prefix
output_name = '_'.join((prefix, postfix))
output_path = os.path.join(cache_dir, output_name)
if os.path.exists(output_path):
return output_path
with dumper.temp_file(cache_dir, final_name=output_name) as (output, _):
input_ = dumper.smart_open(filepath)
if input_ is not None:
for line in input_:
if filter_(line):
output.write(parser(line) + '\n')
input_.close()
return output_path
def gnu_sort(file_path, prefix=None, delimiter=None, fieldspec=None, cache_dir=DUMPS_CACHE_DIR):
'''
Sort the file with path `file_path` using the GNU sort command, the
original file is unchanged, the output file is saved with path
<cache_dir>/<prefix>_sorted.
:param prefix: If given the output file will be named <prefix>_sorted.
Otherwise the prefix is the name of the input file.
:param delimiter: Delimiter character if the data is formated in
columns (argument of -t in the sort command).
:param fieldspec: String with the specification of column or columns
to be used to sort (argument -k in the sort command).
:param cachedir: Working dir where the output file will be placed.
Note: Using GNU sort to sort large files is convenient as it has low
memory and it is relatively fast if used with the environment variable
LC_ALL set to C as in this function.
'''
assert (delimiter is None and fieldspec is None) or (delimiter is not None and fieldspec is not None)
if delimiter is None:
cmd_line = 'LC_ALL=C sort {0} > {1}'
else:
cmd_line = 'LC_ALL=C sort -t {0} -k {1} {{0}} > {{1}}'.format(delimiter, fieldspec)
prefix = os.path.basename(file_path) if prefix is None else prefix
sorted_name = '_'.join((prefix, 'sorted'))
sorted_path = os.path.join(cache_dir, sorted_name)
if os.path.exists(sorted_path):
return sorted_path
# FIXME: mktemp() is an insecure function and this may be a security
# threat in some scenarios. Find another way to do it.
tfile = tempfile.mktemp(dir=cache_dir)
subprocess.check_call(
cmd_line.format(file_path, tfile),
shell=True,
)
os.link(tfile, sorted_path)
os.unlink(tfile)
return sorted_path
def populate_args(argparser):
# Option to download the rucio replica dumps automaticaly
parser = argparser.add_parser(
'consistency',
help='Consistency check to verify possible lost files and dark data '
'(replica dumps are downloaded automatically)'
)
parser.add_argument('ddm_endpoint')
parser.add_argument('storage_dump')
parser.add_argument(
'--delta',
help='Difference in days between the SE dump and the desired rucio '
'replica dumps (use either this argument or --prev-date and '
'--next-date)',
required=False
)
parser.add_argument(
'--prev-date',
help='Date of the older rucio replica dump to use',
required=False
)
parser.add_argument(
'--next-date',
help='Date of the newer rucio replica dump to use',
required=False
)
# Option to use already downloaded rucio replica dumps
parser_manual = argparser.add_parser(
'consistency-manual',
help='Consistency check to verify possible lost files and dark data '
'(replica dumps should be provided by the user)'
)
parser_manual.add_argument('ddm_endpoint')
parser_manual.add_argument('replicas_before')
parser_manual.add_argument('storage_dump')
parser_manual.add_argument('replicas_after')
for p in (parser, parser_manual):
p.add_argument(
'--sort-rucio-dumps',
help='Starting 18-08-2015 the Rucio Replica Dumps are sorted by '
'path. If you need to work with older dumps use this '
'argument.',
action='store_true'
)
_date_re = re.compile(r'dump_(\d{8})')
def _parse_args_consistency(args):
args_dict = {}
# Filename should contain the date
date_str = _date_re.match(os.path.basename(args.storage_dump))
if date_str is None:
error('The storage dump filename must be of the form '
'"dump_YYYYMMDD" where the date correspond to the date '
'of the newest files included')
date_str = date_str.group(1)
assert date_str is not None
try:
args_dict['date'] = date = datetime.datetime.strptime(date_str, '%Y%m%d')
except ValueError:
error('Invalid date {0}'.format(date_str))
if not os.path.exists(args.storage_dump):
error('File "{0}" does not exist'.format(args.storage_dump))
if (args.prev_date is not None or args.next_date is not None) and args.delta is not None:
error('Missing or conflicting arguments, specify either '
'"--delta" or "--prev-date" and "--next-date"')
if args.prev_date is not None and args.next_date is not None:
args_dict['prev_date'] = datetime.datetime.strptime(
args.prev_date, '%d-%m-%Y',
)
args_dict['next_date'] = datetime.datetime.strptime(
args.next_date, '%d-%m-%Y',
)
elif args.delta is not None:
delta = int(args.delta)
args_dict['prev_date'] = date - datetime.timedelta(days=delta)
args_dict['next_date'] = date + datetime.timedelta(days=delta)
else:
error('Missing arguments, specify either "--delta" or '
'"--prev-date" and "--next-date"')
return args_dict
def _parse_args_consistency_manual(args):
args_dict = {}
args_dict['prev_date_fname'] = args.replicas_before
args_dict['next_date_fname'] = args.replicas_after
for path in (args.storage_dump, args_dict['prev_date_fname'], args_dict['next_date_fname']):
if not os.path.exists(path):
error('File "{0}" does not exist'.format(path))
return args_dict
def parse_args(args):
args_dict = {}
args_dict['subcommand'] = args.subcommand
args_dict['ddm_endpoint'] = args.ddm_endpoint
args_dict['storage_dump'] = args.storage_dump
args_dict['sort_rucio_replica_dumps'] = args.sort_rucio_dumps
if args.subcommand == 'consistency':
args_dict.update(_parse_args_consistency(args))
else:
args_dict.update(_parse_args_consistency_manual(args))
return args_dict