git-annex/Annex/Ingest.hs

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{- git-annex content ingestion
-
- Copyright 2010-2016 Joey Hess <id@joeyh.name>
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-
- Licensed under the GNU GPL version 3 or higher.
-}
module Annex.Ingest (
LockedDown(..),
LockDownConfig(..),
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lockDown,
ingestAdd,
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ingest,
ingest',
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finishIngestDirect,
finishIngestUnlocked,
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cleanOldKeys,
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addLink,
makeLink,
addUnlocked,
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restoreFile,
forceParams,
addAnnexedFile,
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) where
import Annex.Common
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import Types.KeySource
import Backend
import Annex.Content
import Annex.Content.Direct
import Annex.Perms
import Annex.Link
import Annex.MetaData
import Annex.Version
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import Logs.Location
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import qualified Annex
import qualified Annex.Queue
import qualified Database.Keys
import qualified Git
import qualified Git.Branch
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import Config
import Utility.InodeCache
import Annex.ReplaceFile
import Utility.Tmp
import Utility.CopyFile
import Utility.Touch
import Git.FilePath
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import Annex.InodeSentinal
import Annex.AdjustedBranch
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import Control.Exception (IOException)
data LockedDown = LockedDown
{ lockDownConfig :: LockDownConfig
, keySource :: KeySource
}
deriving (Show)
data LockDownConfig = LockDownConfig
{ lockingFile :: Bool -- ^ write bit removed during lock down
, hardlinkFileTmp :: Bool -- ^ hard link to temp directory
}
deriving (Show)
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{- The file that's being ingested is locked down before a key is generated,
- to prevent it from being modified in between. This lock down is not
- perfect at best (and pretty weak at worst). For example, it does not
- guard against files that are already opened for write by another process.
- So, the InodeCache can be used to detect any changes that might be made
- to the file after it was locked down.
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-
- When possible, the file is hard linked to a temp directory. This guards
- against some changes, like deletion or overwrite of the file, and
- allows lsof checks to be done more efficiently when adding a lot of files.
-
- Lockdown can fail if a file gets deleted, and Nothing will be returned.
-}
lockDown :: LockDownConfig -> FilePath -> Annex (Maybe LockedDown)
lockDown cfg file = either
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(\e -> warning (show e) >> return Nothing)
(return . Just)
=<< lockDown' cfg file
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lockDown' :: LockDownConfig -> FilePath -> Annex (Either IOException LockedDown)
lockDown' cfg file = ifM (pure (not (hardlinkFileTmp cfg)) <||> crippledFileSystem)
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( withTSDelta $ liftIO . tryIO . nohardlink
, tryIO $ do
tmp <- fromRepo gitAnnexTmpMiscDir
createAnnexDirectory tmp
when (lockingFile cfg) $
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freezeContent file
withTSDelta $ \delta -> liftIO $ do
(tmpfile, h) <- openTempFile tmp $
relatedTemplate $ takeFileName file
hClose h
nukeFile tmpfile
withhardlink delta tmpfile `catchIO` const (nohardlink delta)
)
where
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nohardlink delta = do
cache <- genInodeCache file delta
return $ LockedDown cfg $ KeySource
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{ keyFilename = file
, contentLocation = file
, inodeCache = cache
}
withhardlink delta tmpfile = do
createLink file tmpfile
cache <- genInodeCache tmpfile delta
return $ LockedDown cfg $ KeySource
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{ keyFilename = file
, contentLocation = tmpfile
, inodeCache = cache
}
{- Ingests a locked down file into the annex. Updates the work tree and
- index. -}
ingestAdd :: Maybe LockedDown -> Annex (Maybe Key)
ingestAdd Nothing = return Nothing
ingestAdd ld@(Just (LockedDown cfg source)) = do
(mk, mic) <- ingest ld
case mk of
Nothing -> return Nothing
Just k -> do
let f = keyFilename source
if lockingFile cfg
then do
liftIO $ nukeFile f
addLink f k mic
else ifM isDirect
( do
l <- calcRepo $ gitAnnexLink f k
stageSymlink f =<< hashSymlink l
, do
mode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus (contentLocation source)
stagePointerFile f mode =<< hashPointerFile k
)
return (Just k)
{- Ingests a locked down file into the annex. Does not update the working
- tree or the index.
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-}
ingest :: Maybe LockedDown -> Annex (Maybe Key, Maybe InodeCache)
ingest = ingest' Nothing
ingest' :: Maybe Backend -> Maybe LockedDown -> Annex (Maybe Key, Maybe InodeCache)
ingest' _ Nothing = return (Nothing, Nothing)
ingest' preferredbackend (Just (LockedDown cfg source)) = withTSDelta $ \delta -> do
backend <- maybe (chooseBackend $ keyFilename source) (return . Just) preferredbackend
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k <- genKey source backend
let src = contentLocation source
ms <- liftIO $ catchMaybeIO $ getFileStatus src
mcache <- maybe (pure Nothing) (liftIO . toInodeCache delta src) ms
case (mcache, inodeCache source) of
(_, Nothing) -> go k mcache ms
(Just newc, Just c) | compareStrong c newc -> go k mcache ms
_ -> failure "changed while it was being added"
where
go (Just (key, _)) mcache (Just s)
| lockingFile cfg = golocked key mcache s
| otherwise = ifM isDirect
( godirect key mcache s
, gounlocked key mcache s
)
go _ _ _ = failure "failed to generate a key"
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golocked key mcache s = do
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catchNonAsync (moveAnnex key $ contentLocation source)
(restoreFile (keyFilename source) key)
populateAssociatedFiles key source
success key mcache s
gounlocked key (Just cache) s = do
-- Remove temp directory hard link first because
-- linkToAnnex falls back to copying if a file
-- already has a hard link.
cleanCruft source
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cleanOldKeys (keyFilename source) key
r <- linkToAnnex key (keyFilename source) (Just cache)
case r of
LinkAnnexFailed -> failure "failed to link to annex"
_ -> do
finishIngestUnlocked' key source
success key (Just cache) s
gounlocked _ _ _ = failure "failed statting file"
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godirect key (Just cache) s = do
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addInodeCache key cache
finishIngestDirect key source
success key (Just cache) s
godirect _ _ _ = failure "failed statting file"
success k mcache s = do
genMetaData k (keyFilename source) s
return (Just k, mcache)
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failure msg = do
warning $ keyFilename source ++ " " ++ msg
cleanCruft source
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return (Nothing, Nothing)
finishIngestDirect :: Key -> KeySource -> Annex ()
finishIngestDirect key source = do
void $ addAssociatedFile key $ keyFilename source
cleanCruft source
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{- Copy to any other locations using the same key. -}
otherfs <- filter (/= keyFilename source) <$> associatedFiles key
forM_ otherfs $
addContentWhenNotPresent key (keyFilename source)
finishIngestUnlocked :: Key -> KeySource -> Annex ()
finishIngestUnlocked key source = do
cleanCruft source
finishIngestUnlocked' key source
finishIngestUnlocked' :: Key -> KeySource -> Annex ()
finishIngestUnlocked' key source = do
Database.Keys.addAssociatedFile key =<< inRepo (toTopFilePath (keyFilename source))
populateAssociatedFiles key source
{- Copy to any other locations using the same key. -}
populateAssociatedFiles :: Key -> KeySource -> Annex ()
populateAssociatedFiles key source = do
obj <- calcRepo (gitAnnexLocation key)
g <- Annex.gitRepo
ingestedf <- flip fromTopFilePath g
<$> inRepo (toTopFilePath (keyFilename source))
afs <- map (`fromTopFilePath` g) <$> Database.Keys.getAssociatedFiles key
forM_ (filter (/= ingestedf) afs) $
populatePointerFile key obj
cleanCruft :: KeySource -> Annex ()
cleanCruft source = when (contentLocation source /= keyFilename source) $
liftIO $ nukeFile $ contentLocation source
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-- If a worktree file was was hard linked to an annex object before,
-- modifying the file would have caused the object to have the wrong
-- content. Clean up from that.
cleanOldKeys :: FilePath -> Key -> Annex ()
cleanOldKeys file newkey = do
g <- Annex.gitRepo
ingestedf <- flip fromTopFilePath g <$> inRepo (toTopFilePath file)
topf <- inRepo (toTopFilePath file)
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oldkeys <- filter (/= newkey)
<$> Database.Keys.getAssociatedKey topf
lock: Fix edge cases where data loss could occur in v6 mode. In the case where the pointer file is in place, and not the content of the object, lock's performNew was called with filemodified=True, which caused it to try to repopulate the object from an unmodified associated file, of which there were none. So, the content of the object got thrown away incorrectly. This was the cause (although not the root cause) of data loss in https://github.com/datalad/datalad/issues/1020 The same problem could also occur when the work tree file is modified, but the object is not, and lock is called with --force. Added a test case for this, since it's excercising the same code path and is easier to set up than the problem above. Note that this only occurred when the keys database did not have an inode cache recorded for the annex object. Normally, the annex object would be in there, but there are of course circumstances where the inode cache is out of sync with reality, since it's only a cache. Fixed by checking if the object is unmodified; if so we don't need to try to repopulate it. This does add an additional checksum to the unlock path, but it's already checksumming the worktree file in another case, so it doesn't slow it down overall. Further investigation found a similar problem occurred when smudge --clean is called on a file and the inode cache is not populated. cleanOldKeys deleted the unmodified old object file in this case. This was also fixed by checking if the object is unmodified. In general, use of getInodeCaches and sameInodeCache is potentially dangerous if the inode cache has not gotten populated for some reason. Better to use isUnmodified. I breifly auited other places that check the inode cache, and did not see any immediate problems, but it would be easy to miss this kind of problem.
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forM_ oldkeys $ \key ->
unlessM (isUnmodified key =<< calcRepo (gitAnnexLocation key)) $ do
caches <- Database.Keys.getInodeCaches key
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unlinkAnnex key
fs <- filter (/= ingestedf)
. map (`fromTopFilePath` g)
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<$> Database.Keys.getAssociatedFiles key
fs' <- filterM (`sameInodeCache` caches) fs
case fs' of
-- If linkToAnnex fails, the associated
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-- file with the content is still present,
-- so no need for any recovery.
(f:_) -> do
ic <- withTSDelta (liftIO . genInodeCache f)
void $ linkToAnnex key f ic
_ -> logStatus key InfoMissing
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{- On error, put the file back so it doesn't seem to have vanished.
- This can be called before or after the symlink is in place. -}
restoreFile :: FilePath -> Key -> SomeException -> Annex a
restoreFile file key e = do
whenM (inAnnex key) $ do
liftIO $ nukeFile file
-- The key could be used by other files too, so leave the
-- content in the annex, and make a copy back to the file.
obj <- calcRepo $ gitAnnexLocation key
unlessM (liftIO $ copyFileExternal CopyTimeStamps obj file) $
warning $ "Unable to restore content of " ++ file ++ "; it should be located in " ++ obj
thawContent file
throwM e
{- Creates the symlink to the annexed content, returns the link target. -}
makeLink :: FilePath -> Key -> Maybe InodeCache -> Annex String
makeLink file key mcache = flip catchNonAsync (restoreFile file key) $ do
l <- calcRepo $ gitAnnexLink file key
replaceFile file $ makeAnnexLink l
-- touch symlink to have same time as the original file,
-- as provided in the InodeCache
case mcache of
Just c -> liftIO $ touch file (TimeSpec $ inodeCacheToMtime c) False
Nothing -> noop
return l
{- Creates the symlink to the annexed content, and stages it in git.
-
- As long as the filesystem supports symlinks, we use
- git add, rather than directly staging the symlink to git.
- Using git add is best because it allows the queuing to work
- and is faster (staging the symlink runs hash-object commands each time).
- Also, using git add allows it to skip gitignored files, unless forced
- to include them.
-}
addLink :: FilePath -> Key -> Maybe InodeCache -> Annex ()
addLink file key mcache = ifM (coreSymlinks <$> Annex.getGitConfig)
( do
_ <- makeLink file key mcache
ps <- forceParams
Annex.Queue.addCommand "add" (ps++[Param "--"]) [file]
, do
l <- makeLink file key mcache
addAnnexLink l file
)
{- Parameters to pass to git add, forcing addition of ignored files. -}
forceParams :: Annex [CommandParam]
forceParams = ifM (Annex.getState Annex.force)
( return [Param "-f"]
, return []
)
{- Whether a file should be added unlocked or not. Default is to not,
- unless symlinks are not supported. annex.addunlocked can override that.
- Also, when in an adjusted unlocked branch, always add files unlocked.
-}
addUnlocked :: Annex Bool
addUnlocked = isDirect <||>
(versionSupportsUnlockedPointers <&&>
((not . coreSymlinks <$> Annex.getGitConfig) <||>
(annexAddUnlocked <$> Annex.getGitConfig) <||>
(maybe False (\b -> getAdjustment b == Just UnlockAdjustment) <$> cachedCurrentBranch)
)
)
cachedCurrentBranch :: Annex (Maybe Git.Branch)
cachedCurrentBranch = maybe cache (return . Just)
=<< Annex.getState Annex.cachedcurrentbranch
where
cache :: Annex (Maybe Git.Branch)
cache = do
mb <- inRepo Git.Branch.currentUnsafe
case mb of
Nothing -> return Nothing
Just b -> do
Annex.changeState $ \s ->
s { Annex.cachedcurrentbranch = Just b }
return (Just b)
{- Adds a file to the work tree for the key, and stages it in the index.
- The content of the key may be provided in a temp file, which will be
- moved into place. -}
addAnnexedFile :: FilePath -> Key -> Maybe FilePath -> Annex ()
addAnnexedFile file key mtmp = ifM (addUnlocked <&&> not <$> isDirect)
( do
mode <- maybe
(pure Nothing)
(\tmp -> liftIO $ catchMaybeIO $ fileMode <$> getFileStatus tmp)
mtmp
stagePointerFile file mode =<< hashPointerFile key
Database.Keys.addAssociatedFile key =<< inRepo (toTopFilePath file)
case mtmp of
Just tmp -> do
moveAnnex key tmp
linkunlocked mode
Nothing -> ifM (inAnnex key)
( linkunlocked mode
, liftIO $ writePointerFile file key mode
)
, do
addLink file key Nothing
whenM isDirect $ do
void $ addAssociatedFile key file
case mtmp of
Just tmp -> do
{- For moveAnnex to work in direct mode, the
- symlink must already exist, so flush the queue. -}
whenM isDirect $
Annex.Queue.flush
moveAnnex key tmp
Nothing -> return ()
)
where
linkunlocked mode = do
r <- linkFromAnnex key file mode
case r of
LinkAnnexFailed -> liftIO $
writePointerFile file key mode
_ -> return ()