More fsck tools, including fixes
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parent
71cd7ed9b7
commit
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4
Makefile
4
Makefile
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@ -1,5 +1,5 @@
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# By default, run the tests.
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all: test
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all: fscktest
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version:
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python setup.py version
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@ -25,7 +25,7 @@ lint:
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fscktest:
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# python -c "import nilmdb.fsck; nilmdb.fsck.Fsck('/home/jim/wsgi/db').check()"
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python -c "import nilmdb.fsck; nilmdb.fsck.Fsck('/home/jim/mnt/bucket/mnt/sharon/data/db').check()"
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python -c "import nilmdb.fsck; nilmdb.fsck.Fsck('/home/jim/mnt/bucket/mnt/sharon/data/db', True).check()"
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test:
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ifeq ($(INSIDE_EMACS), t)
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@ -1 +0,0 @@
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jim@pilot.lees.18066:1373305995
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@ -12,13 +12,25 @@ from nilmdb.utils.time import timestamp_to_string
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from collections import defaultdict
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import sqlite3
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import os
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import sys
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import progressbar
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import re
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import time
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import shutil
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import cPickle as pickle
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class FsckError(Exception):
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def __init__(self, format, *args):
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Exception.__init__(self, sprintf(format, *args))
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def __init__(self, msg = "", *args):
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if args:
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msg = sprintf(msg, *args)
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Exception.__init__(self, msg)
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class FixableFsckError(FsckError):
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def __init__(self, msg = "", *args):
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if args:
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msg = sprintf(msg, *args)
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FsckError.__init__(self, "%s\nThis may be fixable with \"-y\".", msg)
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class RetryFsck(FsckError):
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pass
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def log(format, *args):
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printf(format, *args)
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@ -26,6 +38,19 @@ def log(format, *args):
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def err(format, *args):
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fprintf(sys.stderr, format, *args)
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# Decorator that retries a function if it returns a specific value
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def retry_if_raised(exc, message = None):
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def f1(func):
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def f2(*args, **kwargs):
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while True:
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try:
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return func(*args, **kwargs)
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except exc as e:
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if message:
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log("%s\n\n", message)
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return f2
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return f1
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class Progress(object):
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def __init__(self, maxval):
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self.bar = progressbar.ProgressBar(maxval = maxval)
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@ -42,31 +67,30 @@ class Progress(object):
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printf("\n")
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def update(self, val):
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self.bar.update(val)
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#now = time.time()
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#if now - self.last_update < 0.005:
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# time.sleep(0.005)
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#self.last_update = now
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class Fsck(object):
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def __init__(self, path):
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def __init__(self, path, fix = False):
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self.basepath = path
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self.sqlpath = os.path.join(path, "data.sql")
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self.bulkpath = os.path.join(path, "data")
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self.bulklock = os.path.join(path, "data.lock")
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self.fix = fix
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@retry_if_raised(RetryFsck, "Something was fixed: restarting fsck")
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def check(self):
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self.check_paths()
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self.check_sql()
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self.check_streams()
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self.check_intervals()
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log("ok\n")
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def check_paths(self):
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log("checking paths\n")
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if not os.path.isfile(self.sqlpath):
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raise FsckError("SQL database missing")
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raise FsckError("SQL database missing (%s)", self.sqlpath)
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if not os.path.isdir(self.bulkpath):
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raise FsckError("Bulk data directory missing")
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raise FsckError("Bulk data directory missing (%s)", self.bulkpath)
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with open(self.bulklock, "w") as lockfile:
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if not nilmdb.utils.lock.exclusive_lock(lockfile):
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raise FsckError('database already locked by another process')
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@ -116,8 +140,8 @@ class Fsck(object):
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self.stream_meta[r[0]][r[1]] = r[2]
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def check_streams(self):
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log("checking streams\n")
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ids = self.stream_path.keys()
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log("checking %d streams\n", len(ids))
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with Progress(len(ids)) as pbar:
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for i, sid in enumerate(ids):
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pbar.update(i)
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@ -152,7 +176,7 @@ class Fsck(object):
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timeiset += new
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except IntervalError:
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raise FsckError("%s: overlap in intervals:\n"
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"set: %s\nnew: %s\n",
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"set: %s\nnew: %s",
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path, str(timeiset), str(new))
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if spos != epos:
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new = Interval(spos, epos)
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@ -160,14 +184,13 @@ class Fsck(object):
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posiset += new
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except IntervalError:
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raise FsckError("%s: overlap in file offsets:\n"
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"set: %s\nnew: %s\n",
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"set: %s\nnew: %s",
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path, str(posiset), str(new))
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# check bulkdata
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self.check_bulkdata(sid, path, bulk)
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continue
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# verify we can can open it with bulkdata
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# Check that we can open bulkdata
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try:
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tab = None
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try:
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@ -175,11 +198,43 @@ class Fsck(object):
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except Exception as e:
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raise FsckError("%s: can't open bulkdata: %s",
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path, str(e))
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self.check_bulkdata(path, tab)
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finally:
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if tab:
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tab.close()
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def fix_empty_subdir(self, subpath):
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msg = sprintf("bulkdata path %s is missing data files", subpath)
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if not self.fix:
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raise FixableFsckError(msg)
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# Try to fix it by just deleting whatever is present,
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# as long as it's only ".removed" files.
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err("\n%s\n", msg)
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for fn in os.listdir(subpath):
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if not fn.endswith(".removed"):
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raise FsckError("can't fix automatically: please manually "
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"remove the file %s and try again",
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os.path.join(subpath, fn))
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# Remove the whole thing
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err("Removing empty subpath\n")
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shutil.rmtree(subpath)
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raise RetryFsck
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def fix_bad_filesize(self, path, filepath, offset, row_size):
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extra = offset % row_size
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msg = sprintf("%s: size of file %s (%d) is not a multiple" +
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" of row size (%d): %d extra bytes present",
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path, filepath, offset, row_size, extra)
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if not self.fix:
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raise FixableFsckError(msg)
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# Try to fix it by just truncating the file
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err("\n%s\n", msg)
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newsize = offset - extra
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err("Truncating file to %d bytes and retrying\n", newsize)
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with open(filepath, "r+b") as f:
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f.truncate(newsize)
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raise RetryFsck
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@retry_if_raised(RetryFsck)
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def check_bulkdata(self, sid, path, bulk):
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with open(os.path.join(bulk, "_format"), "rb") as f:
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fmt = pickle.load(f)
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@ -192,3 +247,61 @@ class Fsck(object):
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if layout != self.stream_layout[sid]:
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raise FsckError("%s: layout mismatch %s != %s", path,
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layout, self.stream_layout[sid])
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# Every file should have a size that's the multiple of the row size
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rkt = nilmdb.server.rocket.Rocket(layout, None)
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row_size = rkt.binary_size
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rkt.close()
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# Find all directories
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regex = re.compile("^[0-9a-f]{4,}$")
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subdirs = sorted(filter(regex.search, os.listdir(bulk)),
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key = lambda x: int(x, 16), reverse = True)
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for subdir in subdirs:
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# Find all files in that dir
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subpath = os.path.join(bulk, subdir)
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files = filter(regex.search, os.listdir(subpath))
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if not files:
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self.fix_empty_subdir(subpath)
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raise RetryFsck
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# Verify that their size is a multiple of the row size
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for filename in files:
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filepath = os.path.join(subpath, filename)
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offset = os.path.getsize(filepath)
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if offset % row_size:
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self.fix_bad_filesize(path, filepath, offset, row_size)
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def check_intervals(self):
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total_ints = sum(len(x) for x in self.stream_interval.values())
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log("checking %d intervals\n", total_ints)
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checked = 0
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with Progress(total_ints) as pbar:
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for sid in self.stream_interval:
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try:
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bulk = self.bulkpath + self.stream_path[sid]
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tab = nilmdb.server.bulkdata.Table(bulk)
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def update(x):
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pbar.update(checked + x)
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ints = self.stream_interval[sid]
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path = self.stream_path[sid]
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self.check_table_intervals(path, ints, tab, update)
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checked += len(ints)
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finally:
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tab.close()
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def check_table_intervals(self, path, ints, tab, update):
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# look in the table to make sure we can pick out the interval's
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# endpoints
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tab.file_open.cache_remove_all()
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for (i, intv) in enumerate(ints):
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(stime, etime, spos, epos) = intv
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update(i)
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if spos == epos:
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continue
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try:
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srow = tab[spos]
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erow = tab[epos-1]
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except Exception as e:
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msg = sprintf("%s: interval %s error accessing rows: %s",
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path, str(intv), str(e))
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raise FsckError(msg)
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@ -13,11 +13,12 @@ def main():
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formatter_class = argparse.ArgumentDefaultsHelpFormatter)
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parser.add_argument("-V", "--version", action="version",
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version = nilmdb.__version__)
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parser.add_argument('-d', '--database', help = 'Database directory',
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default = "./db")
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parser.add_argument('-y', dest="fix", action="store_true",
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default=False, help = 'Fix errors')
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parser.add_argument('database', help = 'Database directory')
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args = parser.parse_args()
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nilmdb.fsck.Fsck(args.database).check()
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nilmdb.fsck.Fsck(args.database).check(args.fix)
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if __name__ == "__main__":
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main()
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