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Database corruption with the shelve module #91228Description
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assignee = None
closed_at = None
created_at = <Date 2022-03-20.17:29:23.398>
labels = ['type-bug', '3.8', '3.10']
title = 'Database corruption with the shelve module'
updated_at = <Date 2022-03-27.12:01:09.272>
user = 'https://github.com/HubTou' bugs.python.org fields:
activity = <Date 2022-03-27.12:01:09.272>
actor = 'Leilei'
assignee = 'none'
closed = False
closed_date = None
closer = None
components = ['Demos and Tools']
creation = <Date 2022-03-20.17:29:23.398>
creator = 'HubTou'
dependencies = []
files = ['50693', '50703', '50704']
hgrepos = []
issue_num = 47072
keywords = []
message_count = 7.0
messages = ['415625', '416036', '416045', '416063', '416108', '416110', '416119']
nosy_count = 4.0
nosy_names = ['lemburg', 'terry.reedy', 'koobs', 'HubTou']
pr_nums = []
priority = 'normal'
resolution = None
stage = None
status = 'open'
superseder = None
type = 'behavior'
url = 'https://bugs.python.org/issue47072'
versions = ['Python 3.8', 'Python 3.10'] ActivityHubTou commented on Mar 20, 2022 MannequinAuthor More actions After adding a few records, the shelve module corrupts the database keys (the database is still readable if an element key is known, but no more iterable):
Traceback (most recent call last):
File "./shelve-test.py", line 81, in <module>
_verify_whois_cache()
File "./shelve-test.py", line 61, in _verify_whois_cache
for key in db.keys():
File "/usr/local/lib/python3.8/_collections_abc.py", line 720, in __iter__
yield from self._mapping
File "/usr/local/lib/python3.8/shelve.py", line 95, in __iter__
for k in self.dict.keys():
SystemError: Negative size passed to PyBytes_FromStringAndSizeI provide a short test program and data that systematically reproduces the bug. I added the a script showing execution messages, the resulting database in DB and text formats.
Tested with Python 3.8.12 on FreeBSD 13.0-RELEASE-p8.
I suppose Python is using my system package db5-5.3.28_8 (Oracle Berkeley DB, revision 5.3).
See also similar issues:
https://bugs.python.org/issue33074
https://bugs.python.org/issue30388 terryjreedy commented on Mar 26, 2022 3.8 only gets security patches. If you can, please test with a newer version. HubTou commented on Mar 26, 2022 MannequinAuthor More actions Hello,
Same results with Python 3.10.4:
[...]
Adding 185.220.102.6
Database has 62 records for 442368 bytes. Last record was 640 bytes long
Traceback (most recent call last):
File "./shelve-test.py", line 84, in <module>
_verify_whois_cache()
File "./shelve-test.py", line 63, in _verify_whois_cache
for key in db.keys():
File "/usr/local/lib/python3.10/_collections_abc.py", line 881, in __iter__
yield from self._mapping
File "/usr/local/lib/python3.10/shelve.py", line 95, in __iter__
for k in self.dict.keys():
SystemError: Negative size passed to PyBytes_FromStringAndSize
# freebsd-version -uk
13.0-RELEASE-p8
13.0-RELEASE-p10
# python3.10 --version
Python 3.10.4The point at which the database breaks depends (from 50 to 500+ records), the size of the database doesn't seem to be relevant (from 400K to 1800K).
The size of the record *apparently* doesn't seem to be relevant (but I'm not 100% sure it's the right figure), though I've had other shelve module uses without issues with many more records but much smaller and less complex. HubTou commented on Mar 26, 2022 MannequinAuthor More actions I modified the test program to better reflect the size of the data structures stored in shelve (sys.getsizeof() which I used was far off the real size).
I saw that the database was corrupted with big records, though even bigger previous records had not corrupted it. Records larger than 1K (mentioned in one of the other problem report) were routinely OK. Records larger than 4K (also mentioned on another PR) were sometimes OK.
When I took a problematic record and used it single alone or with few other records, no corruption occurred.
Any idea? HubTou commented on Mar 27, 2022 MannequinAuthor More actions Additional note: the test code WORKS under Windows 8.1 / Python 3.9.1 (though the data file is suffixed .dat instead of .db) resulting in a 4 MB database with 1065 records, some of them > 11 KB.
So maybe the bug is system dependent. HubTou commented on Mar 27, 2022 MannequinAuthor More actions The storage format used under Windows is completely different from the one used under Unix (or *BSD).
Apart from the .dat datafile, there is a .dir index file with CSV lines such as "'key', (offset, length)".
Whereas under Unix (or *BSD), I have:
# file whois_cache.db
whois_cache.db: Berkeley DB 1.85 (Hash, version 2, native byte-order)
I'll make a test on a Linux Raspberry Pi, to see if the issue is *BSD specific... malemburg commented on Mar 27, 2022 ronaldoussoren commented on Apr 11, 2022 #74573 might be related, this is an older similar issue on macOS.
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