add annex.dbdir (WIP)

WIP: This is mostly complete, but there is a problem: createDirectoryUnder
throws an error when annex.dbdir is set to outside the git repo.

annex.dbdir is a workaround for filesystems where sqlite does not work,
due to eg, the filesystem not properly supporting locking.

It's intended to be set before initializing the repository. Changing it
in an existing repository can be done, but would be the same as making a
new repository and moving all the annexed objects into it. While the
databases get recreated from the git-annex branch in that situation, any
information that is in the databases but not stored in the branch gets
lost. It may be that no information ever gets stored in the databases
that cannot be reconstructed from the branch, but I have not verified
that.

Sponsored-by: Dartmouth College's Datalad project

Annex.hs

@@ -27,6 +27,7 @@ module Annex (
 	inRepo,
 	fromRepo,
 	calcRepo,
+	calcRepo',
 	getGitConfig,
 	overrideGitConfig,
 	changeGitRepo,
@@ -361,6 +362,11 @@ calcRepo a = do
 	s <- getState id
 	liftIO $ a (repo s) (gitconfig s)
 
+calcRepo' :: (Git.Repo -> GitConfig -> a) -> Annex a
+calcRepo' f = do
+	s <- getState id
+	pure $ f (repo s) (gitconfig s)
+
 {- Gets the GitConfig settings. -}
 getGitConfig :: Annex GitConfig
 getGitConfig = getState gitconfig

Annex/Common.hs

@@ -6,7 +6,7 @@ import Common as X
 import Types as X
 import Key as X
 import Types.UUID as X
-import Annex as X (gitRepo, inRepo, fromRepo, calcRepo)
+import Annex as X (gitRepo, inRepo, fromRepo, calcRepo, calcRepo')
 import Annex.Locations as X
 import Annex.Debug as X (fastDebug, debug)
 import Messages as X

Annex/Content/Presence.hs

@@ -137,7 +137,7 @@ withContentLockFile :: Key -> (Maybe RawFilePath -> Annex a) -> Annex a
 withContentLockFile k a = do
 	v <- getVersion
 	if versionNeedsWritableContentFiles v
-		then withSharedLock gitAnnexContentLockLock $ do
+		then fromRepo gitAnnexContentLockLock >>= \lck -> withSharedLock lck $ do
 			{- While the lock is held, check to see if the git
 			 - config has changed, and reload it if so. This
 			 - updates the annex.version after the v10 upgrade,
@@ -156,7 +156,7 @@ withContentLockFile k a = do
 					reloadConfig
 					getVersion
 			go (v')
-		else (go v)
+		else go v
   where
 	go v = contentLockFile k v >>= a
 

Annex/Import.hs

@@ -412,8 +412,10 @@ importKeys remote importtreeconfig importcontent thirdpartypopulated importablec
 		| importcontent = a
 		| otherwise = reuseVectorClockWhile a
 
-	withciddb = withExclusiveLock gitAnnexContentIdentifierLock .
-		bracket CIDDb.openDb CIDDb.closeDb
+	withciddb a = do
+		cidlck <- calcRepo' gitAnnexContentIdentifierLock
+		withExclusiveLock cidlck $
+			bracket CIDDb.openDb CIDDb.closeDb a
 
 	run cidmap importing db = do
 		largematcher <- largeFilesMatcher

Annex/Journal.hs

@@ -281,4 +281,6 @@ data JournalLocked = ProduceJournalLocked
 {- Runs an action that modifies the journal, using locking to avoid
  - contention with other git-annex processes. -}
 lockJournal :: (JournalLocked -> Annex a) -> Annex a
-lockJournal a = withExclusiveLock gitAnnexJournalLock $ a ProduceJournalLocked
+lockJournal a = do
+	lck <- fromRepo gitAnnexJournalLock
+	withExclusiveLock lck $ a ProduceJournalLocked

Annex/Locations.hs

@@ -37,7 +37,7 @@ module Annex.Locations (
 	gitAnnexBadDir,
 	gitAnnexBadLocation,
 	gitAnnexUnusedLog,
-	gitAnnexKeysDb,
+	gitAnnexKeysDbDir,
 	gitAnnexKeysDbLock,
 	gitAnnexKeysDbIndexCache,
 	gitAnnexFsckState,
@@ -321,38 +321,42 @@ gitAnnexUnusedLog :: RawFilePath -> Git.Repo -> RawFilePath
 gitAnnexUnusedLog prefix r = gitAnnexDir r P.</> (prefix <> "unused")
 
 {- .git/annex/keysdb/ contains a database of information about keys. -}
-gitAnnexKeysDb :: Git.Repo -> RawFilePath
-gitAnnexKeysDb r = gitAnnexDir r P.</> "keysdb"
+gitAnnexKeysDbDir :: Git.Repo -> GitConfig -> RawFilePath
+gitAnnexKeysDbDir r c = fromMaybe (gitAnnexDir r) (annexDbDir c) P.</> "keysdb"
 
 {- Lock file for the keys database. -}
-gitAnnexKeysDbLock :: Git.Repo -> RawFilePath
-gitAnnexKeysDbLock r = gitAnnexKeysDb r <> ".lck"
+gitAnnexKeysDbLock :: Git.Repo -> GitConfig -> RawFilePath
+gitAnnexKeysDbLock r c = gitAnnexKeysDbDir r c <> ".lck"
 
 {- Contains the stat of the last index file that was
  - reconciled with the keys database. -}
-gitAnnexKeysDbIndexCache :: Git.Repo -> RawFilePath
-gitAnnexKeysDbIndexCache r = gitAnnexKeysDb r <> ".cache"
+gitAnnexKeysDbIndexCache :: Git.Repo -> GitConfig -> RawFilePath
+gitAnnexKeysDbIndexCache r c = gitAnnexKeysDbDir r c <> ".cache"
 
 {- .git/annex/fsck/uuid/ is used to store information about incremental
  - fscks. -}
-gitAnnexFsckDir :: UUID -> Git.Repo -> RawFilePath
-gitAnnexFsckDir u r = gitAnnexDir r P.</> "fsck" P.</> fromUUID u
+gitAnnexFsckDir :: UUID -> Git.Repo -> Maybe GitConfig -> RawFilePath
+gitAnnexFsckDir u r mc = case annexDbDir =<< mc of
+	Nothing -> go (gitAnnexDir r)
+	Just d -> go d
+  where
+	go d = d P.</> "fsck" P.</> fromUUID u
 
 {- used to store information about incremental fscks. -}
 gitAnnexFsckState :: UUID -> Git.Repo -> RawFilePath
-gitAnnexFsckState u r = gitAnnexFsckDir u r P.</> "state"
+gitAnnexFsckState u r = gitAnnexFsckDir u r Nothing P.</> "state"
 
 {- Directory containing database used to record fsck info. -}
-gitAnnexFsckDbDir :: UUID -> Git.Repo -> RawFilePath
-gitAnnexFsckDbDir u r = gitAnnexFsckDir u r P.</> "fsckdb"
+gitAnnexFsckDbDir :: UUID -> Git.Repo -> GitConfig -> RawFilePath
+gitAnnexFsckDbDir u r c = gitAnnexFsckDir u r (Just c) P.</> "fsckdb"
 
 {- Directory containing old database used to record fsck info. -}
-gitAnnexFsckDbDirOld :: UUID -> Git.Repo -> RawFilePath
-gitAnnexFsckDbDirOld u r = gitAnnexFsckDir u r P.</> "db"
+gitAnnexFsckDbDirOld :: UUID -> Git.Repo -> GitConfig -> RawFilePath
+gitAnnexFsckDbDirOld u r c = gitAnnexFsckDir u r (Just c) P.</> "db"
 
 {- Lock file for the fsck database. -}
-gitAnnexFsckDbLock :: UUID -> Git.Repo -> RawFilePath
-gitAnnexFsckDbLock u r = gitAnnexFsckDir u r P.</> "fsck.lck"
+gitAnnexFsckDbLock :: UUID -> Git.Repo -> GitConfig -> RawFilePath
+gitAnnexFsckDbLock u r c = gitAnnexFsckDir u r (Just c) P.</> "fsck.lck"
 
 {- .git/annex/fsckresults/uuid is used to store results of git fscks -}
 gitAnnexFsckResultsLog :: UUID -> Git.Repo -> RawFilePath
@@ -384,20 +388,22 @@ gitAnnexMoveLock r = gitAnnexDir r P.</> "move.lck"
 
 {- .git/annex/export/ is used to store information about
  - exports to special remotes. -}
-gitAnnexExportDir :: Git.Repo -> RawFilePath
-gitAnnexExportDir r = gitAnnexDir r P.</> "export"
+gitAnnexExportDir :: Git.Repo -> GitConfig -> RawFilePath
+gitAnnexExportDir r c = fromMaybe (gitAnnexDir r) (annexDbDir c) P.</> "export"
 
 {- Directory containing database used to record export info. -}
-gitAnnexExportDbDir :: UUID -> Git.Repo -> RawFilePath
-gitAnnexExportDbDir u r = gitAnnexExportDir r P.</> fromUUID u P.</> "exportdb"
+gitAnnexExportDbDir :: UUID -> Git.Repo -> GitConfig -> RawFilePath
+gitAnnexExportDbDir u r c = 
+	gitAnnexExportDir r c P.</> fromUUID u P.</> "exportdb"
 
-{- Lock file for export state for a special remote. -}
-gitAnnexExportLock :: UUID -> Git.Repo -> RawFilePath
-gitAnnexExportLock u r = gitAnnexExportDbDir u r <> ".lck"
+{- Lock file for export database. -}
+gitAnnexExportLock :: UUID -> Git.Repo -> GitConfig -> RawFilePath
+gitAnnexExportLock u r c = gitAnnexExportDbDir u r c <> ".lck"
 
-{- Lock file for updating the export state for a special remote. -}
-gitAnnexExportUpdateLock :: UUID -> Git.Repo -> RawFilePath
-gitAnnexExportUpdateLock u r = gitAnnexExportDbDir u r <> ".upl"
+{- Lock file for updating the export database with information from the
+ - repository. -}
+gitAnnexExportUpdateLock :: UUID -> Git.Repo -> GitConfig -> RawFilePath
+gitAnnexExportUpdateLock u r c = gitAnnexExportDbDir u r c <> ".upl"
 
 {- Log file used to keep track of files that were in the tree exported to a
  - remote, but were excluded by its preferred content settings. -}
@@ -409,12 +415,13 @@ gitAnnexExportExcludeLog u r = gitAnnexDir r P.</> "export.ex" P.</> fromUUID u
  - (This used to be "cid", but a problem with the database caused it to
  - need to be rebuilt with a new name.)
  -}
-gitAnnexContentIdentifierDbDir :: Git.Repo -> RawFilePath
-gitAnnexContentIdentifierDbDir r = gitAnnexDir r P.</> "cidsdb"
+gitAnnexContentIdentifierDbDir :: Git.Repo -> GitConfig -> RawFilePath
+gitAnnexContentIdentifierDbDir r c =
+	fromMaybe (gitAnnexDir r) (annexDbDir c) P.</> "cidsdb"
 
 {- Lock file for writing to the content id database. -}
-gitAnnexContentIdentifierLock :: Git.Repo -> RawFilePath
-gitAnnexContentIdentifierLock r = gitAnnexContentIdentifierDbDir r <> ".lck"
+gitAnnexContentIdentifierLock :: Git.Repo -> GitConfig -> RawFilePath
+gitAnnexContentIdentifierLock r c = gitAnnexContentIdentifierDbDir r c <> ".lck"
 
 {- .git/annex/schedulestate is used to store information about when
  - scheduled jobs were last run. -}

Annex/LockFile.hs

@@ -21,7 +21,6 @@ module Annex.LockFile (
 import Annex.Common
 import Annex
 import Types.LockCache
-import qualified Git
 import Annex.Perms
 import Annex.LockPool
 
@@ -63,9 +62,8 @@ changeLockCache a = do
 
 {- Runs an action with a shared lock held. If an exclusive lock is held,
  - blocks until it becomes free. -}
-withSharedLock :: (Git.Repo -> RawFilePath) -> Annex a -> Annex a
-withSharedLock getlockfile a = debugLocks $ do
-	lockfile <- fromRepo getlockfile
+withSharedLock :: RawFilePath -> Annex a -> Annex a
+withSharedLock lockfile a = debugLocks $ do
 	createAnnexDirectory $ P.takeDirectory lockfile
 	mode <- annexFileMode
 	bracket (lock mode lockfile) (liftIO . dropLock) (const a)
@@ -78,16 +76,15 @@ withSharedLock getlockfile a = debugLocks $ do
 
 {- Runs an action with an exclusive lock held. If the lock is already
  - held, blocks until it becomes free. -}
-withExclusiveLock :: (Git.Repo -> RawFilePath) -> Annex a -> Annex a
-withExclusiveLock getlockfile a = bracket
-	(takeExclusiveLock getlockfile)
+withExclusiveLock :: RawFilePath -> Annex a -> Annex a
+withExclusiveLock lockfile a = bracket
+	(takeExclusiveLock lockfile)
 	(liftIO . dropLock)
 	(const a)
 
 {- Takes an exclusive lock, blocking until it's free. -}
-takeExclusiveLock :: (Git.Repo -> RawFilePath) -> Annex LockHandle
-takeExclusiveLock getlockfile = debugLocks $ do
-	lockfile <- fromRepo getlockfile
+takeExclusiveLock :: RawFilePath -> Annex LockHandle
+takeExclusiveLock lockfile = debugLocks $ do
 	createAnnexDirectory $ P.takeDirectory lockfile
 	mode <- annexFileMode
 	lock mode lockfile
@@ -100,9 +97,8 @@ takeExclusiveLock getlockfile = debugLocks $ do
 
 {- Tries to take an exclusive lock and run an action. If the lock is
  - already held, returns Nothing. -}
-tryExclusiveLock :: (Git.Repo -> RawFilePath) -> Annex a -> Annex (Maybe a)
-tryExclusiveLock getlockfile a = debugLocks $ do
-	lockfile <- fromRepo getlockfile
+tryExclusiveLock :: RawFilePath -> Annex a -> Annex (Maybe a)
+tryExclusiveLock lockfile a = debugLocks $ do
 	createAnnexDirectory $ P.takeDirectory lockfile
 	mode <- annexFileMode
 	bracket (lock mode lockfile) (liftIO . unlock) go

Annex/Queue.hs

@@ -65,9 +65,11 @@ flush = do
  - git locking files. So, only one queue is allowed to flush at a time.
  -}
 flush' :: Git.Queue.Queue Annex -> Annex (Git.Queue.Queue Annex)
-flush' q = withExclusiveLock gitAnnexGitQueueLock $ do
-	showStoringStateAction
-	Git.Queue.flush q =<< gitRepo
+flush' q = do
+	lck <- fromRepo gitAnnexGitQueueLock
+	withExclusiveLock lck $ do
+		showStoringStateAction
+		Git.Queue.flush q =<< gitRepo
 
 {- Gets the size of the queue. -}
 size :: Annex Int

Annex/Tmp.hs

@@ -27,7 +27,7 @@ withOtherTmp a = do
 	Annex.addCleanupAction OtherTmpCleanup cleanupOtherTmp
 	tmpdir <- fromRepo gitAnnexTmpOtherDir
 	tmplck <- fromRepo gitAnnexTmpOtherLock
-	withSharedLock (const tmplck) $ do
+	withSharedLock tmplck $ do
 		void $ createAnnexDirectory tmpdir
 		a tmpdir
 
@@ -56,7 +56,7 @@ withEventuallyCleanedOtherTmp = bracket setup cleanup
 cleanupOtherTmp :: Annex ()
 cleanupOtherTmp = do
 	tmplck <- fromRepo gitAnnexTmpOtherLock
-	void $ tryIO $ tryExclusiveLock (const tmplck) $ do
+	void $ tryIO $ tryExclusiveLock tmplck $ do
 		tmpdir <- fromRawFilePath <$> fromRepo gitAnnexTmpOtherDir
 		void $ liftIO $ tryIO $ removeDirectoryRecursive tmpdir
 		oldtmp <- fromRawFilePath <$> fromRepo gitAnnexTmpOtherDirOld

CHANGELOG

@@ -17,6 +17,9 @@ git-annex (10.20220725) UNRELEASED; urgency=medium
   * When bup split fails, display its stderr.
   * Avoid running multiple bup split processes concurrently, since
     bup is not concurrency safe.
+  * Added annex.dbdir config which can be used to move sqlite databases
+    to a different filesystem than the git-annex repo, when the repo is on
+    a filesystem that sqlite does not work well in.
 
  -- Joey Hess <id@joeyh.name>  Mon, 25 Jul 2022 15:35:45 -0400
 

Command/Move.hs

@@ -375,12 +375,14 @@ logMove srcuuid destuuid deststartedwithcopy key a = go =<< setup
 
 	setup = do
 		logf <- fromRepo gitAnnexMoveLog
+		lckf <- fromRepo gitAnnexMoveLock
 		-- Only log when there was no copy.
 		unless deststartedwithcopy $
-			appendLogFile logf gitAnnexMoveLock logline
+			appendLogFile logf lckf logline
 		return logf
 
 	cleanup logf = do
+		lck <- fromRepo gitAnnexMoveLock
 		-- This buffers the log file content in memory.
 		-- The log file length is limited to the number of
 		-- concurrent jobs, times the number of times a move
@@ -388,13 +390,14 @@ logMove srcuuid destuuid deststartedwithcopy key a = go =<< setup
 		-- That could grow without bounds given enough time,
 		-- so the log is also truncated to the most recent
 		-- 100 items.
-		modifyLogFile logf gitAnnexMoveLock
+		modifyLogFile logf lck
 			(filter (/= logline) . reverse . take 100 . reverse)
 
 	go logf
 		-- Only need to check log when there is a copy.
 		| deststartedwithcopy = do
-			wasnocopy <- checkLogFile (fromRawFilePath logf) gitAnnexMoveLock
+			lck <- fromRepo gitAnnexMoveLock
+			wasnocopy <- checkLogFile (fromRawFilePath logf) lck
 				(== logline)
 			if wasnocopy
 				then go' logf False

Database/ContentIdentifier.hs

@@ -78,7 +78,7 @@ AnnexBranch
  -}
 openDb :: Annex ContentIdentifierHandle
 openDb = do
-	dbdir <- fromRepo gitAnnexContentIdentifierDbDir
+	dbdir <- calcRepo' gitAnnexContentIdentifierDbDir
 	let db = dbdir P.</> "db"
 	ifM (liftIO $ not <$> R.doesPathExist db)
 		( initDb db $ void $ 

Database/Export.hs

@@ -99,7 +99,7 @@ ExportTreeCurrent
  -}
 openDb :: UUID -> Annex ExportHandle
 openDb u = do
-	dbdir <- fromRepo (gitAnnexExportDbDir u)
+	dbdir <- calcRepo' (gitAnnexExportDbDir u)
 	let db = dbdir P.</> "db"
 	unlessM (liftIO $ R.doesPathExist db) $ do
 		initDb db $ void $
@@ -263,8 +263,9 @@ updateExportDb = runExportDiffUpdater $ mkExportDiffUpdater removeold addnew
  -}
 writeLockDbWhile :: ExportHandle -> Annex a -> Annex a
 writeLockDbWhile db@(ExportHandle _ u) a = do
-	updatelck <- takeExclusiveLock (gitAnnexExportUpdateLock u)
-	withExclusiveLock (gitAnnexExportLock u) $ do
+	updatelck <- takeExclusiveLock =<< calcRepo' (gitAnnexExportUpdateLock u)
+	exlck <- calcRepo' (gitAnnexExportLock u)
+	withExclusiveLock exlck $ do
 		bracket_ (setup updatelck) cleanup a
   where
 	setup updatelck = do
@@ -285,15 +286,17 @@ data ExportUpdateResult = ExportUpdateSuccess | ExportUpdateConflict
  - not. Either way, it will block until the update is complete.
  -}
 updateExportTreeFromLog :: ExportHandle -> Annex ExportUpdateResult
-updateExportTreeFromLog db@(ExportHandle _ u) =
+updateExportTreeFromLog db@(ExportHandle _ u) = do
 	-- If another process or thread is performing the update,
 	-- this will block until it's done.
-	withExclusiveLock (gitAnnexExportUpdateLock u) $ do
+	exlck <- calcRepo' (gitAnnexExportUpdateLock u)
+	withExclusiveLock exlck $ do
+		lck <- calcRepo' (gitAnnexExportLock u)
 		-- If the database is locked by something else,
 		-- this will not run the update. But, in that case,
 		-- writeLockDbWhile is running, and has already
 		-- completed the update, so we don't need to do anything.
-		mr <- tryExclusiveLock (gitAnnexExportLock u) $
+		mr <- tryExclusiveLock lck $
 			updateExportTreeFromLog' db
 		case mr of
 			Just r -> return r

Database/Fsck.hs

@@ -60,29 +60,31 @@ Fscked
  - or unknown behavior.
  -}
 newPass :: UUID -> Annex Bool
-newPass u = isJust <$> tryExclusiveLock (gitAnnexFsckDbLock u) go
+newPass u = do
+	lck <- calcRepo' (gitAnnexFsckDbLock u)
+	isJust <$> tryExclusiveLock lck go
   where
 	go = do
-		removedb =<< fromRepo (gitAnnexFsckDbDir u)
-		removedb =<< fromRepo (gitAnnexFsckDbDirOld u)
+		removedb =<< calcRepo' (gitAnnexFsckDbDir u)
+		removedb =<< calcRepo' (gitAnnexFsckDbDirOld u)
 	removedb = liftIO . void . tryIO . removeDirectoryRecursive . fromRawFilePath
 
 {- Opens the database, creating it if it doesn't exist yet. -}
 openDb :: UUID -> Annex FsckHandle
 openDb u = do
-	dbdir <- fromRepo (gitAnnexFsckDbDir u)
+	dbdir <- calcRepo' (gitAnnexFsckDbDir u)
 	let db = dbdir P.</> "db"
 	unlessM (liftIO $ R.doesPathExist db) $ do
 		initDb db $ void $
 			runMigrationSilent migrateFsck
-	lockFileCached =<< fromRepo (gitAnnexFsckDbLock u)
+	lockFileCached =<< calcRepo' (gitAnnexFsckDbLock u)
 	h <- liftIO $ H.openDbQueue db "fscked"
 	return $ FsckHandle h u
 
 closeDb :: FsckHandle -> Annex ()
 closeDb (FsckHandle h u) = do
 	liftIO $ H.closeDbQueue h
-	unlockFile =<< fromRepo (gitAnnexFsckDbLock u)
+	unlockFile =<< calcRepo' (gitAnnexFsckDbLock u)
 
 addDb :: FsckHandle -> Key -> IO ()
 addDb (FsckHandle h _) k = H.queueDb h checkcommit $

Database/Init.hs

@@ -10,6 +10,7 @@
 module Database.Init where
 
 import Annex.Common
+import qualified Annex
 import Annex.Perms
 import Utility.FileMode
 import Utility.Directory.Create
@@ -34,7 +35,10 @@ initDb db migration = do
 	let tmpdbdir = dbdir <> ".tmp"
 	let tmpdb = tmpdbdir P.</> "db"
 	let tdb = T.pack (fromRawFilePath tmpdb)
-	top <- parentDir <$> fromRepo gitAnnexDir
+	gc <- Annex.getGitConfig
+	top <- case annexDbDir gc of
+		Just topdbdir -> pure $ parentDir $ topdbdir
+		Nothing -> parentDir <$> fromRepo gitAnnexDir
 	liftIO $ do
 		createDirectoryUnder top tmpdbdir
 		runSqliteInfo (enableWAL tdb) migration

Database/Keys.hs

@@ -118,15 +118,17 @@ runWriterIO a = runWriter (liftIO . a)
 openDb :: Bool -> DbState -> Annex DbState
 openDb _ st@(DbOpen _) = return st
 openDb False DbUnavailable = return DbUnavailable
-openDb forwrite _ = catchPermissionDenied permerr $ withExclusiveLock gitAnnexKeysDbLock $ do
-	dbdir <- fromRepo gitAnnexKeysDb
-	let db = dbdir P.</> "db"
-	dbexists <- liftIO $ R.doesPathExist db
-	case dbexists of
-		True -> open db
-		False -> do
-			initDb db SQL.createTables
-			open db
+openDb forwrite _ = do
+	lck <- calcRepo' gitAnnexKeysDbLock
+	catchPermissionDenied permerr $ withExclusiveLock lck $ do
+		dbdir <- calcRepo' gitAnnexKeysDbDir
+		let db = dbdir P.</> "db"
+		dbexists <- liftIO $ R.doesPathExist db
+		case dbexists of
+			True -> open db
+			False -> do
+				initDb db SQL.createTables
+				open db
   where
 	-- If permissions don't allow opening the database, and it's being
 	-- opened for read, treat it as if it does not exist.
@@ -248,7 +250,7 @@ isInodeKnown i s = or <$> runReaderIO ((:[]) <$$> SQL.isInodeKnown i s)
 reconcileStaged :: H.DbQueue -> Annex ()
 reconcileStaged qh = unlessM (Git.Config.isBare <$> gitRepo) $ do
 	gitindex <- inRepo currentIndexFile
-	indexcache <- fromRawFilePath <$> fromRepo gitAnnexKeysDbIndexCache
+	indexcache <- fromRawFilePath <$> calcRepo' gitAnnexKeysDbIndexCache
 	withTSDelta (liftIO . genInodeCache gitindex) >>= \case
 		Just cur -> readindexcache indexcache >>= \case
 			Nothing -> go cur indexcache =<< getindextree

Logs/File.hs

@@ -1,6 +1,6 @@
 {- git-annex log files
  -
- - Copyright 2018-2020 Joey Hess <id@joeyh.name>
+ - Copyright 2018-2022 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -20,7 +20,6 @@ import Annex.Common
 import Annex.Perms
 import Annex.LockFile
 import Annex.ReplaceFile
-import qualified Git
 import Utility.Tmp
 
 import qualified Data.ByteString.Lazy as L
@@ -51,7 +50,7 @@ withLogHandle f a = do
 
 -- | Appends a line to a log file, first locking it to prevent
 -- concurrent writers.
-appendLogFile :: RawFilePath -> (Git.Repo -> RawFilePath) -> L.ByteString -> Annex ()
+appendLogFile :: RawFilePath -> RawFilePath -> L.ByteString -> Annex ()
 appendLogFile f lck c = 
 	createDirWhenNeeded f $
 		withExclusiveLock lck $ do
@@ -69,7 +68,7 @@ appendLogFile f lck c =
 --
 -- The file is locked to prevent concurrent writers, and it is written
 -- atomically.
-modifyLogFile :: RawFilePath -> (Git.Repo -> RawFilePath) -> ([L.ByteString] -> [L.ByteString]) -> Annex ()
+modifyLogFile :: RawFilePath -> RawFilePath -> ([L.ByteString] -> [L.ByteString]) -> Annex ()
 modifyLogFile f lck modf = withExclusiveLock lck $ do
 	ls <- liftIO $ fromMaybe []
 		<$> tryWhenExists (L8.lines <$> L.readFile f')
@@ -89,7 +88,7 @@ modifyLogFile f lck modf = withExclusiveLock lck $ do
 -- action is concurrently modifying the file. It does not lock the file,
 -- for speed, but instead relies on the fact that a log file usually
 -- ends in a newline.
-checkLogFile :: FilePath -> (Git.Repo -> RawFilePath) -> (L.ByteString -> Bool) -> Annex Bool
+checkLogFile :: FilePath -> RawFilePath -> (L.ByteString -> Bool) -> Annex Bool
 checkLogFile f lck matchf = withExclusiveLock lck $ bracket setup cleanup go
   where
 	setup = liftIO $ tryWhenExists $ openFile f ReadMode
@@ -123,7 +122,7 @@ fullLines = go []
 -- 
 -- Locking is used to prevent writes to to the log file while this
 -- is running.
-streamLogFile :: FilePath -> (Git.Repo -> RawFilePath) -> (String -> Annex ()) -> Annex ()
+streamLogFile :: FilePath -> RawFilePath -> (String -> Annex ()) -> Annex ()
 streamLogFile f lck a = withExclusiveLock lck $ bracketOnError setup cleanup go
   where
 	setup = liftIO $ tryWhenExists $ openFile f ReadMode 

Logs/Smudge.hs

@@ -19,7 +19,8 @@ import qualified Data.ByteString.Lazy as L
 smudgeLog :: Key -> TopFilePath -> Annex ()
 smudgeLog k f = do
 	logf <- fromRepo gitAnnexSmudgeLog
-	appendLogFile logf gitAnnexSmudgeLock $ L.fromStrict $
+	lckf <- fromRepo gitAnnexSmudgeLock
+	appendLogFile logf lckf $ L.fromStrict $
 		serializeKey' k <> " " <> getTopFilePath f
 
 -- | Streams all smudged files, and then empties the log at the end.
@@ -32,7 +33,8 @@ smudgeLog k f = do
 streamSmudged :: (Key -> TopFilePath -> Annex ()) -> Annex ()
 streamSmudged a = do
 	logf <- fromRepo gitAnnexSmudgeLog
-	streamLogFile (fromRawFilePath logf) gitAnnexSmudgeLock $ \l -> 
+	lckf <- fromRepo gitAnnexSmudgeLock
+	streamLogFile (fromRawFilePath logf) lckf $ \l -> 
 		case parse l of
 			Nothing -> noop
 			Just (k, f) -> a k f

Logs/Upgrade.hs

@@ -24,8 +24,9 @@ import Data.Time.Clock.POSIX
 
 writeUpgradeLog :: RepoVersion -> POSIXTime-> Annex ()
 writeUpgradeLog v t = do
-	logfile <- fromRepo gitAnnexUpgradeLog
-	appendLogFile logfile gitAnnexUpgradeLock $ encodeBL $
+	logf <- fromRepo gitAnnexUpgradeLog
+	lckf <- fromRepo gitAnnexUpgradeLock
+	appendLogFile logf lckf $ encodeBL $
 		show (fromRepoVersion v) ++ " " ++ show t
 
 readUpgradeLog :: Annex [(RepoVersion, POSIXTime)]

Remote/Bup.hs

@@ -336,5 +336,5 @@ lockBup writer r a = do
 	let remoteid = fromUUID (uuid r)
 	let lck = dir P.</> remoteid <> ".lck"
 	if writer
-		then withExclusiveLock (const lck) a
-		else withSharedLock (const lck) a
+		then withExclusiveLock lck a
+		else withSharedLock lck a

Remote/Helper/ExportImport.hs

@@ -245,7 +245,8 @@ adjustExportImport' isexport isimport r rs = do
 			oldcids <- liftIO $ concat
 				<$> mapM (ContentIdentifier.getContentIdentifiers db rs) oldks
 			newcid <- storeExportWithContentIdentifier (importActions r) f k loc oldcids p
-			withExclusiveLock gitAnnexContentIdentifierLock $ do
+			cidlck <- calcRepo' gitAnnexContentIdentifierLock
+			withExclusiveLock cidlck $ do
 				liftIO $ ContentIdentifier.recordContentIdentifier db rs newcid k
 				liftIO $ ContentIdentifier.flushDbQueue db
 			recordContentIdentifier rs newcid k
@@ -280,8 +281,10 @@ adjustExportImport' isexport isimport r rs = do
 				( do
 					db <- ContentIdentifier.openDb
 					ContentIdentifier.needsUpdateFromLog db >>= \case
-						Just v -> withExclusiveLock gitAnnexContentIdentifierLock $
-							ContentIdentifier.updateFromLog db v
+						Just v -> do
+							cidlck <- calcRepo' gitAnnexContentIdentifierLock 
+							withExclusiveLock cidlck $
+								ContentIdentifier.updateFromLog db v
 						Nothing -> noop
 					liftIO $ atomically $ putTMVar dbtv db
 					return db

Test.hs

@@ -817,7 +817,7 @@ test_lock_force = intmpclonerepo $ do
 		Database.Keys.removeInodeCaches k
 		Database.Keys.closeDb
 		liftIO . removeWhenExistsWith R.removeLink
-			=<< Annex.fromRepo Annex.Locations.gitAnnexKeysDbIndexCache
+			=<< Annex.calcRepo' Annex.Locations.gitAnnexKeysDbIndexCache
 	writecontent annexedfile "test_lock_force content"
 	git_annex_shouldfail "lock" [annexedfile] "lock of modified file should not be allowed"
 	git_annex "lock" ["--force", annexedfile] "lock --force of modified file"

Types/GitConfig.hs

@@ -119,6 +119,7 @@ data GitConfig = GitConfig
 	, annexVerify :: Bool
 	, annexPidLock :: Bool
 	, annexPidLockTimeout :: Seconds
+	, annexDbDir :: Maybe RawFilePath
 	, annexAddUnlocked :: GlobalConfigurable (Maybe String)
 	, annexSecureHashesOnly :: Bool
 	, annexRetry :: Maybe Integer
@@ -212,6 +213,7 @@ extractGitConfig configsource r = GitConfig
 	, annexPidLock = getbool (annexConfig "pidlock") False
 	, annexPidLockTimeout = Seconds $ fromMaybe 300 $
 		getmayberead (annexConfig "pidlocktimeout")
+	, annexDbDir = toRawFilePath <$> getmaybe (annexConfig "dbdir")
 	, annexAddUnlocked = configurable Nothing $
 		fmap Just $ getmaybe (annexConfig "addunlocked")
 	, annexSecureHashesOnly = getbool (annexConfig "securehashesonly") False

Upgrade/V7.hs

@@ -37,17 +37,17 @@ upgrade automatic = do
 	-- The old content identifier database is deleted here, but the
 	-- new database is not populated. It will be automatically
 	-- populated from the git-annex branch the next time it is used.
-	removeOldDb gitAnnexContentIdentifierDbDirOld
+	removeOldDb . fromRawFilePath =<< fromRepo gitAnnexContentIdentifierDbDirOld
 	liftIO . removeWhenExistsWith R.removeLink
 		=<< fromRepo gitAnnexContentIdentifierLockOld
 
 	-- The export databases are deleted here. The new databases
 	-- will be populated by the next thing that needs them, the same
 	-- way as they would be in a fresh clone.
-	removeOldDb gitAnnexExportDir
+	removeOldDb . fromRawFilePath =<< calcRepo' gitAnnexExportDir
 
 	populateKeysDb
-	removeOldDb gitAnnexKeysDbOld
+	removeOldDb . fromRawFilePath =<< fromRepo gitAnnexKeysDbOld
 	liftIO . removeWhenExistsWith R.removeLink
 		=<< fromRepo gitAnnexKeysDbIndexCacheOld
 	liftIO . removeWhenExistsWith R.removeLink
@@ -72,9 +72,8 @@ gitAnnexContentIdentifierDbDirOld r = gitAnnexDir r P.</> "cids"
 gitAnnexContentIdentifierLockOld :: Git.Repo -> RawFilePath
 gitAnnexContentIdentifierLockOld r = gitAnnexContentIdentifierDbDirOld r <> ".lck"
 
-removeOldDb :: (Git.Repo -> RawFilePath) -> Annex ()
-removeOldDb getdb = do
-	db <- fromRawFilePath <$> fromRepo getdb
+removeOldDb :: FilePath -> Annex ()
+removeOldDb db =
 	whenM (liftIO $ doesDirectoryExist db) $ do
 		v <- liftIO $ tryNonAsync $
 #if MIN_VERSION_directory(1,2,7)

Upgrade/V9.hs

@@ -71,7 +71,8 @@ performUpgrade automatic = do
 	
 	{- Take a lock to ensure that there are no other git-annex
 	 - processes running that are using the old content locking method. -}
-	withExclusiveLock gitAnnexContentLockLock $ do
+	lck <- fromRepo gitAnnexContentLockLock
+	withExclusiveLock lck $ do
 		{- When core.sharedRepository is set, object files
 		 - used to have their write bits set. That can now be
 		 - removed, if the user the upgrade is running as has

doc/git-annex.mdwn

@@ -1228,6 +1228,15 @@ repository, using [[git-annex-config]]. See its man page for a list.)
   file system. This timeout prevents git-annex waiting forever in such a
   situation.
 
+* `annex.dbdir`
+
+  Set to a directory where git-annex should store its sqlite databases.
+  The default location is inside `.git/annex/`. 
+
+  Certian filesystems, such as cifs, may not support locking operations
+  that sqlite needs, and setting this to a directory on another filesystem
+  can work around such a problem.
+
 * `annex.cachecreds`
 
   When "true" (the default), git-annex will cache credentials used to