git-annex/Command/Fsck.hs
Joey Hess b7c8bf5274
Preserve execute bits of unlocked files in v6 mode.
When annex.thin is set, adding an object will add the execute bits to the
work tree file, and this does mean that the annex object file ends up
executable.

This doesn't add any complexity that wasn't already present, because git
annex add of an executable file has always ingested it so that the annex
object ends up executable.

But, since an annex object file can be executable or not, when populating
an unlocked file from one, the executable bit is always added or removed
to match the mode of the pointer file.
2016-04-14 14:47:08 -04:00

638 lines
20 KiB
Haskell

{- git-annex command
-
- Copyright 2010-2016 Joey Hess <id@joeyh.name>
-
- Licensed under the GNU GPL version 3 or higher.
-}
{-# LANGUAGE CPP #-}
module Command.Fsck where
import Command
import qualified Annex
import qualified Remote
import qualified Types.Backend
import qualified Backend
import Annex.Content
import qualified Annex.Content.Direct as Direct
import Annex.Direct
import Annex.Perms
import Annex.Link
import Logs.Location
import Logs.Trust
import Logs.Activity
import Logs.TimeStamp
import Annex.NumCopies
import Annex.UUID
import Annex.ReplaceFile
import Utility.DataUnits
import Config
import Utility.HumanTime
import Utility.CopyFile
import Git.FilePath
import Utility.PID
import qualified Database.Keys
import qualified Database.Fsck as FsckDb
import Types.CleanupActions
import Data.Time.Clock.POSIX
import System.Posix.Types (EpochTime)
cmd :: Command
cmd = withGlobalOptions (jobsOption : annexedMatchingOptions) $
command "fsck" SectionMaintenance
"find and fix problems"
paramPaths (seek <$$> optParser)
data FsckOptions = FsckOptions
{ fsckFiles :: CmdParams
, fsckFromOption :: Maybe (DeferredParse Remote)
, incrementalOpt :: Maybe IncrementalOpt
, keyOptions :: Maybe KeyOptions
}
data IncrementalOpt
= StartIncrementalO
| MoreIncrementalO
| ScheduleIncrementalO Duration
optParser :: CmdParamsDesc -> Parser FsckOptions
optParser desc = FsckOptions
<$> cmdParams desc
<*> optional (parseRemoteOption $ strOption
( long "from" <> short 'f' <> metavar paramRemote
<> help "check remote"
<> completeRemotes
))
<*> optional parseincremental
<*> optional (parseKeyOptions False)
where
parseincremental =
flag' StartIncrementalO
( long "incremental" <> short 'S'
<> help "start an incremental fsck"
)
<|> flag' MoreIncrementalO
( long "more" <> short 'm'
<> help "continue an incremental fsck"
)
<|> (ScheduleIncrementalO <$> option (str >>= parseDuration)
( long "incremental-schedule" <> metavar paramTime
<> help "schedule incremental fscking"
))
seek :: FsckOptions -> CommandSeek
seek o = allowConcurrentOutput $ do
from <- maybe (pure Nothing) (Just <$$> getParsed) (fsckFromOption o)
u <- maybe getUUID (pure . Remote.uuid) from
checkDeadRepo u
i <- prepIncremental u (incrementalOpt o)
withKeyOptions (keyOptions o) False
(\k -> startKey i k =<< getNumCopies)
(withFilesInGit $ whenAnnexed $ start from i)
(fsckFiles o)
cleanupIncremental i
void $ tryIO $ recordActivity Fsck u
checkDeadRepo :: UUID -> Annex ()
checkDeadRepo u =
whenM ((==) DeadTrusted <$> lookupTrust u) $
earlyWarning "Warning: Fscking a repository that is currently marked as dead."
start :: Maybe Remote -> Incremental -> FilePath -> Key -> CommandStart
start from inc file key = do
v <- Backend.getBackend file key
case v of
Nothing -> stop
Just backend -> do
numcopies <- getFileNumCopies file
case from of
Nothing -> go $ perform key file backend numcopies
Just r -> go $ performRemote key file backend numcopies r
where
go = runFsck inc file key
perform :: Key -> FilePath -> Backend -> NumCopies -> Annex Bool
perform key file backend numcopies = do
keystatus <- getKeyFileStatus key file
check
-- order matters
[ fixLink key file
, verifyLocationLog key keystatus file
, verifyAssociatedFiles key keystatus file
, verifyWorkTree key file
, checkKeySize key keystatus
, checkBackend backend key keystatus (Just file)
, checkKeyNumCopies key (Just file) numcopies
]
{- To fsck a remote, the content is retrieved to a tmp file,
- and checked locally. -}
performRemote :: Key -> FilePath -> Backend -> NumCopies -> Remote -> Annex Bool
performRemote key file backend numcopies remote =
dispatch =<< Remote.hasKey remote key
where
dispatch (Left err) = do
showNote err
return False
dispatch (Right True) = withtmp $ \tmpfile -> do
r <- getfile tmpfile
case r of
Nothing -> go True Nothing
Just True -> go True (Just tmpfile)
Just False -> do
warning "failed to download file from remote"
void $ go True Nothing
return False
dispatch (Right False) = go False Nothing
go present localcopy = check
[ verifyLocationLogRemote key file remote present
, checkKeySizeRemote key remote localcopy
, checkBackendRemote backend key remote localcopy
, checkKeyNumCopies key (Just file) numcopies
]
withtmp a = do
pid <- liftIO getPID
t <- fromRepo gitAnnexTmpObjectDir
createAnnexDirectory t
let tmp = t </> "fsck" ++ show pid ++ "." ++ keyFile key
let cleanup = liftIO $ catchIO (removeFile tmp) (const noop)
cleanup
cleanup `after` a tmp
getfile tmp = ifM (checkDiskSpace (Just (takeDirectory tmp)) key 0 True)
( ifM (Remote.retrieveKeyFileCheap remote key (Just file) tmp)
( return (Just True)
, ifM (Annex.getState Annex.fast)
( return Nothing
, Just . fst <$>
Remote.retrieveKeyFile remote key Nothing tmp dummymeter
)
)
, return (Just False)
)
dummymeter _ = noop
startKey :: Incremental -> Key -> NumCopies -> CommandStart
startKey inc key numcopies =
case Backend.maybeLookupBackendName (keyBackendName key) of
Nothing -> stop
Just backend -> runFsck inc (key2file key) key $
performKey key backend numcopies
performKey :: Key -> Backend -> NumCopies -> Annex Bool
performKey key backend numcopies = do
keystatus <- getKeyStatus key
check
[ verifyLocationLog key keystatus (key2file key)
, checkKeySize key keystatus
, checkBackend backend key keystatus Nothing
, checkKeyNumCopies key Nothing numcopies
]
check :: [Annex Bool] -> Annex Bool
check cs = and <$> sequence cs
{- Checks that symlinks points correctly to the annexed content.
-}
fixLink :: Key -> FilePath -> Annex Bool
fixLink key file = do
want <- calcRepo $ gitAnnexLink file key
have <- getAnnexLinkTarget file
maybe noop (go want) have
return True
where
go want have
| want /= fromInternalGitPath have = do
showNote "fixing link"
liftIO $ createDirectoryIfMissing True (parentDir file)
liftIO $ removeFile file
addAnnexLink want file
| otherwise = noop
{- Checks that the location log reflects the current status of the key,
- in this repository only. -}
verifyLocationLog :: Key -> KeyStatus -> String -> Annex Bool
verifyLocationLog key keystatus desc = do
obj <- calcRepo $ gitAnnexLocation key
present <- if isKeyUnlocked keystatus
then liftIO (doesFileExist obj)
else inAnnex key
direct <- isDirect
u <- getUUID
{- Since we're checking that a key's object file is present, throw
- in a permission fixup here too. -}
when (present && not direct) $ void $ tryIO $
if isKeyUnlocked keystatus
then thawContent obj
else freezeContent obj
whenM (liftIO $ doesDirectoryExist $ parentDir obj) $
freezeContentDir obj
{- In direct mode, modified files will show up as not present,
- but that is expected and not something to do anything about. -}
if direct && not present
then return True
else verifyLocationLog' key desc present u (logChange key u)
verifyLocationLogRemote :: Key -> String -> Remote -> Bool -> Annex Bool
verifyLocationLogRemote key desc remote present =
verifyLocationLog' key desc present (Remote.uuid remote)
(Remote.logStatus remote key)
verifyLocationLog' :: Key -> String -> Bool -> UUID -> (LogStatus -> Annex ()) -> Annex Bool
verifyLocationLog' key desc present u updatestatus = do
uuids <- loggedLocations key
case (present, u `elem` uuids) of
(True, False) -> do
fix InfoPresent
-- There is no data loss, so do not fail.
return True
(False, True) -> do
fix InfoMissing
warning $
"** Based on the location log, " ++ desc
++ "\n** was expected to be present, " ++
"but its content is missing."
return False
_ -> return True
where
fix s = do
showNote "fixing location log"
updatestatus s
{- Verifies the associated file records. -}
verifyAssociatedFiles :: Key -> KeyStatus -> FilePath -> Annex Bool
verifyAssociatedFiles key keystatus file = do
ifM isDirect (godirect, goindirect)
return True
where
godirect = do
fs <- Direct.addAssociatedFile key file
forM_ fs $ \f ->
unlessM (liftIO $ doesFileExist f) $
void $ Direct.removeAssociatedFile key f
goindirect = case keystatus of
KeyUnlocked -> do
f <- inRepo $ toTopFilePath file
afs <- Database.Keys.getAssociatedFiles key
unless (getTopFilePath f `elem` map getTopFilePath afs) $
Database.Keys.addAssociatedFile key f
_ -> return ()
verifyWorkTree :: Key -> FilePath -> Annex Bool
verifyWorkTree key file = do
ifM isDirect ( godirect, goindirect )
return True
where
{- Ensures that files whose content is available are in direct mode. -}
godirect = whenM (isJust <$> isAnnexLink file) $ do
v <- toDirectGen key file
case v of
Nothing -> noop
Just a -> do
showNote "fixing direct mode"
a
{- Make sure that a pointer file is replaced with its content,
- when the content is available. -}
goindirect = do
mk <- liftIO $ isPointerFile file
case mk of
Just k | k == key -> whenM (inAnnex key) $ do
showNote "fixing worktree content"
replaceFile file $ \tmp -> do
mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus file
ifM (annexThin <$> Annex.getGitConfig)
( void $ linkFromAnnex key tmp mode
, do
obj <- calcRepo $ gitAnnexLocation key
void $ checkedCopyFile key obj tmp mode
thawContent tmp
)
Database.Keys.storeInodeCaches key [file]
_ -> return ()
{- The size of the data for a key is checked against the size encoded in
- the key's metadata, if available.
-
- Not checked when a file is unlocked, or in direct mode.
-}
checkKeySize :: Key -> KeyStatus -> Annex Bool
checkKeySize _ KeyUnlocked = return True
checkKeySize key _ = do
file <- calcRepo $ gitAnnexLocation key
ifM (liftIO $ doesFileExist file)
( checkKeySizeOr badContent key file
, return True
)
checkKeySizeRemote :: Key -> Remote -> Maybe FilePath -> Annex Bool
checkKeySizeRemote _ _ Nothing = return True
checkKeySizeRemote key remote (Just file) =
checkKeySizeOr (badContentRemote remote file) key file
checkKeySizeOr :: (Key -> Annex String) -> Key -> FilePath -> Annex Bool
checkKeySizeOr bad key file = case keySize key of
Nothing -> return True
Just size -> do
size' <- liftIO $ getFileSize file
comparesizes size size'
where
comparesizes a b = do
let same = a == b
unless same $ badsize a b
return same
badsize a b = do
msg <- bad key
warning $ concat
[ "Bad file size ("
, compareSizes storageUnits True a b
, "); "
, msg
]
{- Runs the backend specific check on a key's content object.
-
- When a file is unlocked, it may be a hard link to the object,
- thus when the user modifies the file, the object will be modified and
- not pass the check, and we don't want to find an error in this case.
- So, skip the check if the key is unlocked and modified.
-
- In direct mode this is not done if the file has clearly been modified,
- because modification of direct mode files is allowed. It's still done
- if the file does not appear modified, to catch disk corruption, etc.
-}
checkBackend :: Backend -> Key -> KeyStatus -> Maybe FilePath -> Annex Bool
checkBackend backend key keystatus mfile = go =<< isDirect
where
go False = do
content <- calcRepo $ gitAnnexLocation key
ifM (pure (isKeyUnlocked keystatus) <&&> (not <$> isUnmodified key content))
( nocheck
, checkBackendOr badContent backend key content
)
go True = maybe nocheck checkdirect mfile
checkdirect file = ifM (Direct.goodContent key file)
( checkBackendOr' (badContentDirect file) backend key file
(Direct.goodContent key file)
, nocheck
)
nocheck = return True
checkBackendRemote :: Backend -> Key -> Remote -> Maybe FilePath -> Annex Bool
checkBackendRemote backend key remote = maybe (return True) go
where
go file = checkBackendOr (badContentRemote remote file) backend key file
checkBackendOr :: (Key -> Annex String) -> Backend -> Key -> FilePath -> Annex Bool
checkBackendOr bad backend key file =
checkBackendOr' bad backend key file (return True)
-- The postcheck action is run after the content is verified,
-- in order to detect situations where the file is changed while being
-- verified (particularly in direct mode).
checkBackendOr' :: (Key -> Annex String) -> Backend -> Key -> FilePath -> Annex Bool -> Annex Bool
checkBackendOr' bad backend key file postcheck =
case Types.Backend.verifyKeyContent backend of
Nothing -> return True
Just verifier -> do
ok <- verifier key file
ifM postcheck
( do
unless ok $ do
msg <- bad key
warning $ "Bad file content; " ++ msg
return ok
, return True
)
checkKeyNumCopies :: Key -> AssociatedFile -> NumCopies -> Annex Bool
checkKeyNumCopies key afile numcopies = do
let file = fromMaybe (key2file key) afile
locs <- loggedLocations key
(untrustedlocations, otherlocations) <- trustPartition UnTrusted locs
(deadlocations, safelocations) <- trustPartition DeadTrusted otherlocations
let present = NumCopies (length safelocations)
if present < numcopies
then ifM (pure (isNothing afile) <&&> checkDead key)
( do
showLongNote $ "This key is dead, skipping."
return True
, do
untrusted <- Remote.prettyPrintUUIDs "untrusted" untrustedlocations
dead <- Remote.prettyPrintUUIDs "dead" deadlocations
warning $ missingNote file present numcopies untrusted dead
when (fromNumCopies present == 0 && isNothing afile) $
showLongNote "(Avoid this check by running: git annex dead --key )"
return False
)
else return True
missingNote :: String -> NumCopies -> NumCopies -> String -> String -> String
missingNote file (NumCopies 0) _ [] dead =
"** No known copies exist of " ++ file ++ honorDead dead
missingNote file (NumCopies 0) _ untrusted dead =
"Only these untrusted locations may have copies of " ++ file ++
"\n" ++ untrusted ++
"Back it up to trusted locations with git-annex copy." ++ honorDead dead
missingNote file present needed [] _ =
"Only " ++ show (fromNumCopies present) ++ " of " ++ show (fromNumCopies needed) ++
" trustworthy copies exist of " ++ file ++
"\nBack it up with git-annex copy."
missingNote file present needed untrusted dead =
missingNote file present needed [] dead ++
"\nThe following untrusted locations may also have copies: " ++
"\n" ++ untrusted
honorDead :: String -> String
honorDead dead
| null dead = ""
| otherwise = "\nThese dead repositories used to have copies\n" ++ dead
{- Bad content is moved aside. -}
badContent :: Key -> Annex String
badContent key = do
dest <- moveBad key
return $ "moved to " ++ dest
{- Bad content is left where it is, but we touch the file, so it'll be
- committed to a new key. -}
badContentDirect :: FilePath -> Key -> Annex String
badContentDirect file key = do
void $ liftIO $ catchMaybeIO $ touchFile file
logStatus key InfoMissing
return "left in place for you to examine"
{- Bad content is dropped from the remote. We have downloaded a copy
- from the remote to a temp file already (in some cases, it's just a
- symlink to a file in the remote). To avoid any further data loss,
- that temp file is moved to the bad content directory unless
- the local annex has a copy of the content. -}
badContentRemote :: Remote -> FilePath -> Key -> Annex String
badContentRemote remote localcopy key = do
bad <- fromRepo gitAnnexBadDir
let destbad = bad </> key2file key
movedbad <- ifM (inAnnex key <||> liftIO (doesFileExist destbad))
( return False
, do
createAnnexDirectory (parentDir destbad)
liftIO $ catchDefaultIO False $
ifM (isSymbolicLink <$> getSymbolicLinkStatus localcopy)
( copyFileExternal CopyTimeStamps localcopy destbad
, do
moveFile localcopy destbad
return True
)
)
dropped <- Remote.removeKey remote key
when dropped $
Remote.logStatus remote key InfoMissing
return $ case (movedbad, dropped) of
(True, True) -> "moved from " ++ Remote.name remote ++
" to " ++ destbad
(False, True) -> "dropped from " ++ Remote.name remote
(_, False) -> "failed to drop from" ++ Remote.name remote
runFsck :: Incremental -> FilePath -> Key -> Annex Bool -> CommandStart
runFsck inc file key a = ifM (needFsck inc key)
( do
showStart "fsck" file
next $ do
ok <- a
when ok $
recordFsckTime inc key
next $ return ok
, stop
)
{- Check if a key needs to be fscked, with support for incremental fscks. -}
needFsck :: Incremental -> Key -> Annex Bool
needFsck (ScheduleIncremental _ _ i) k = needFsck i k
needFsck (ContIncremental h) key = liftIO $ not <$> FsckDb.inDb h key
needFsck _ _ = return True
recordFsckTime :: Incremental -> Key -> Annex ()
recordFsckTime inc key = withFsckDb inc $ \h -> liftIO $ FsckDb.addDb h key
{- Records the start time of an incremental fsck.
-
- To guard against time stamp damange (for example, if an annex directory
- is copied without -a), the fsckstate file contains a time that should
- be identical to its modification time.
- (This is not possible to do on Windows, and so the timestamp in
- the file will only be equal or greater than the modification time.)
-}
recordStartTime :: UUID -> Annex ()
recordStartTime u = do
f <- fromRepo (gitAnnexFsckState u)
createAnnexDirectory $ parentDir f
liftIO $ do
nukeFile f
withFile f WriteMode $ \h -> do
#ifndef mingw32_HOST_OS
t <- modificationTime <$> getFileStatus f
#else
t <- getPOSIXTime
#endif
hPutStr h $ showTime $ realToFrac t
where
showTime :: POSIXTime -> String
showTime = show
resetStartTime :: UUID -> Annex ()
resetStartTime u = liftIO . nukeFile =<< fromRepo (gitAnnexFsckState u)
{- Gets the incremental fsck start time. -}
getStartTime :: UUID -> Annex (Maybe EpochTime)
getStartTime u = do
f <- fromRepo (gitAnnexFsckState u)
liftIO $ catchDefaultIO Nothing $ do
timestamp <- modificationTime <$> getFileStatus f
let fromstatus = Just (realToFrac timestamp)
fromfile <- parsePOSIXTime <$> readFile f
return $ if matchingtimestamp fromfile fromstatus
then Just timestamp
else Nothing
where
matchingtimestamp fromfile fromstatus =
#ifndef mingw32_HOST_OS
fromfile == fromstatus
#else
fromfile >= fromstatus
#endif
data Incremental
= NonIncremental
| ScheduleIncremental Duration UUID Incremental
| StartIncremental FsckDb.FsckHandle
| ContIncremental FsckDb.FsckHandle
prepIncremental :: UUID -> Maybe IncrementalOpt -> Annex Incremental
prepIncremental _ Nothing = pure NonIncremental
prepIncremental u (Just StartIncrementalO) = do
recordStartTime u
ifM (FsckDb.newPass u)
( StartIncremental <$> openFsckDb u
, error "Cannot start a new --incremental fsck pass; another fsck process is already running."
)
prepIncremental u (Just MoreIncrementalO) =
ContIncremental <$> openFsckDb u
prepIncremental u (Just (ScheduleIncrementalO delta)) = do
started <- getStartTime u
i <- prepIncremental u $ Just $ case started of
Nothing -> StartIncrementalO
Just _ -> MoreIncrementalO
return (ScheduleIncremental delta u i)
cleanupIncremental :: Incremental -> Annex ()
cleanupIncremental (ScheduleIncremental delta u i) = do
v <- getStartTime u
case v of
Nothing -> noop
Just started -> do
now <- liftIO getPOSIXTime
when (now - realToFrac started >= durationToPOSIXTime delta) $
resetStartTime u
cleanupIncremental i
cleanupIncremental _ = return ()
openFsckDb :: UUID -> Annex FsckDb.FsckHandle
openFsckDb u = do
h <- FsckDb.openDb u
Annex.addCleanup FsckCleanup $
FsckDb.closeDb h
return h
withFsckDb :: Incremental -> (FsckDb.FsckHandle -> Annex ()) -> Annex ()
withFsckDb (ContIncremental h) a = a h
withFsckDb (StartIncremental h) a = a h
withFsckDb NonIncremental _ = noop
withFsckDb (ScheduleIncremental _ _ i) a = withFsckDb i a
data KeyStatus = KeyLocked | KeyUnlocked | KeyMissing
isKeyUnlocked :: KeyStatus -> Bool
isKeyUnlocked KeyUnlocked = True
isKeyUnlocked KeyLocked = False
isKeyUnlocked KeyMissing = False
getKeyStatus :: Key -> Annex KeyStatus
getKeyStatus key = ifM isDirect
( return KeyUnlocked
, catchDefaultIO KeyMissing $ do
unlocked <- not . null <$> Database.Keys.getAssociatedFiles key
return $ if unlocked then KeyUnlocked else KeyLocked
)
getKeyFileStatus :: Key -> FilePath -> Annex KeyStatus
getKeyFileStatus key file = do
s <- getKeyStatus key
case s of
KeyLocked -> catchDefaultIO KeyLocked $
ifM (isJust <$> isAnnexLink file)
( return KeyLocked
, return KeyUnlocked
)
_ -> return s