optimise read and write for Keys database (untested)

Writes are optimised by queueing up multiple writes when possible.
The queue is flushed after the Annex monad action finishes. That makes it
happen on program termination, and also whenever a nested Annex monad action
finishes.

Reads are optimised by checking once (per AnnexState) if the database
exists. If the database doesn't exist yet, all reads return mempty.

Reads also cause queued writes to be flushed, so reads will always be
consistent with writes (as long as they're made inside the same Annex monad).
A future optimisation path would be to determine when that's not necessary,
which is probably most of the time, and avoid flushing unncessarily.

Design notes for this commit:

- separate reads from writes
- reuse a handle which is left open until program
  exit or until the MVar goes out of scope (and autoclosed then)
- writes are queued
  - queue is flushed periodically
  - immediate queue flush before any read
  - auto-flush queue when database handle is garbage collected
  - flush queue on exit from Annex monad
    (Note that this may happen repeatedly for a single database connection;
    or a connection may be reused for multiple Annex monad actions,
    possibly even concurrent ones.)
- if database does not exist (or is empty) the handle
  is not opened by reads; reads instead return empty results
- writes open the handle if it was not open previously

10 files changed, 213 insertions, 91 deletions

diff --git a/Annex.hs b/Annex.hs
index c9a4ef6a0..a8368f81e 100644
--- a/Annex.hs
+++ b/Annex.hs
@@ -60,6 +60,7 @@ import Types.NumCopies
 import Types.LockCache
 import Types.DesktopNotify
 import Types.CleanupActions
+import qualified Database.Keys.Handle as Keys
 #ifdef WITH_QUVI
 import Utility.Quvi (QuviVersion)
 #endif
@@ -134,6 +135,7 @@ data AnnexState = AnnexState
 	, desktopnotify :: DesktopNotify
 	, workers :: [Either AnnexState (Async AnnexState)]
 	, concurrentjobs :: Maybe Int
+	, keysdbhandle :: Maybe Keys.DbHandle
 	}
 
 newState :: GitConfig -> Git.Repo -> AnnexState
@@ -179,6 +181,7 @@ newState c r = AnnexState
 	, desktopnotify = mempty
 	, workers = []
 	, concurrentjobs = Nothing
+	, keysdbhandle = Nothing
 	}
 
 {- Makes an Annex state object for the specified git repo.
@@ -193,25 +196,26 @@ new r = do
 {- Performs an action in the Annex monad from a starting state,
  - returning a new state. -}
 run :: AnnexState -> Annex a -> IO (a, AnnexState)
-run s a = do
-	mvar <- newMVar s
+run s a = flip run' a =<< newMVar s
+
+run' :: MVar AnnexState -> Annex a -> IO (a, AnnexState)
+run' mvar a = do
 	r <- runReaderT (runAnnex a) mvar
 	s' <- takeMVar mvar
+	maybe noop Keys.flushDbQueue (keysdbhandle s')
 	return (r, s')
 
 {- Performs an action in the Annex monad from a starting state, 
  - and throws away the new state. -}
 eval :: AnnexState -> Annex a -> IO a
-eval s a = do
-	mvar <- newMVar s
-	runReaderT (runAnnex a) mvar
+eval s a = fst <$> run s a
 
 {- Makes a runner action, that allows diving into IO and from inside
  - the IO action, running an Annex action. -}
 makeRunner :: Annex (Annex a -> IO a)
 makeRunner = do
 	mvar <- ask
-	return $ \a -> runReaderT (runAnnex a) mvar
+	return $ \a -> fst <$> run' mvar a
 
 getState :: (AnnexState -> v) -> Annex v
 getState selector = do
diff --git a/Database/Fsck.hs b/Database/Fsck.hs
index d176690a6..da6e6263a 100644
--- a/Database/Fsck.hs
+++ b/Database/Fsck.hs
@@ -78,10 +78,6 @@ openDb u = do
 			rename tmpdbdir dbdir
 	lockFileCached =<< fromRepo (gitAnnexFsckDbLock u)
 	h <- liftIO $ H.openDbQueue db "fscked"
-
-	-- work around https://github.com/yesodweb/persistent/issues/474
-	liftIO setConsoleEncoding
-
 	return $ FsckHandle h u
 
 closeDb :: FsckHandle -> Annex ()
diff --git a/Database/Handle.hs b/Database/Handle.hs
index 8790b3218..748feaa97 100644
--- a/Database/Handle.hs
+++ b/Database/Handle.hs
@@ -19,6 +19,7 @@ module Database.Handle (
 ) where
 
 import Utility.Exception
+import Utility.FileSystemEncoding
 
 import Database.Persist.Sqlite
 import qualified Database.Sqlite as Sqlite
@@ -66,6 +67,10 @@ openDb :: FilePath -> TableName -> IO DbHandle
 openDb db tablename = do
 	jobs <- newEmptyMVar
 	worker <- async (workerThread (T.pack db) tablename jobs)
+	
+	-- work around https://github.com/yesodweb/persistent/issues/474
+	liftIO setConsoleEncoding
+
 	return $ DbHandle worker jobs
 
 {- This is optional; when the DbHandle gets garbage collected it will
diff --git a/Database/Keys.hs b/Database/Keys.hs
index 425f1d54b..c51a163c4 100644
--- a/Database/Keys.hs
+++ b/Database/Keys.hs
@@ -12,8 +12,6 @@
 
 module Database.Keys (
 	DbHandle,
-	openDb,
-	closeDb,
 	addAssociatedFile,
 	getAssociatedFiles,
 	getAssociatedKey,
@@ -27,7 +25,7 @@ module Database.Keys (
 ) where
 
 import Database.Types
-import Database.Keys.Types
+import Database.Keys.Handle
 import qualified Database.Queue as H
 import Locations
 import Common hiding (delete)
@@ -35,12 +33,12 @@ import Annex
 import Types.Key
 import Annex.Perms
 import Annex.LockFile
-import Messages
 import Utility.InodeCache
 import Annex.InodeSentinal
 
 import Database.Persist.TH
 import Database.Esqueleto hiding (Key)
+import Data.Time.Clock
 
 share [mkPersist sqlSettings, mkMigrate "migrateKeysDb"] [persistLowerCase|
 Associated
@@ -53,7 +51,86 @@ Content
   KeyCacheIndex key cache
 |]
 
-{- Opens the database, creating it if it doesn't exist yet.
+newtype ReadHandle = ReadHandle H.DbQueue
+
+type Reader v = ReadHandle -> Annex v
+
+{- Runs an action that reads from the database.
+ -
+ - If the database doesn't already exist, it's not created; mempty is
+ - returned instead. This way, when the keys database is not in use,
+ - there's minimal overhead in checking it.
+ -
+ - If the database is already open, any writes are flushed to it, to ensure
+ - consistency.
+ -
+ - Any queued writes will be flushed before the read.
+ -}
+runReader :: Monoid v => Reader v -> Annex v
+runReader a = do
+	h <- getDbHandle
+	withDbState h go
+  where
+	go DbEmpty = return (mempty, DbEmpty)
+	go st@(DbOpen qh) = do
+		liftIO $ H.flushDbQueue qh
+		v <- a (ReadHandle qh)
+		return (v, st)
+	go DbClosed = do
+		st' <- openDb False DbClosed
+		v <- case st' of
+			(DbOpen qh) -> a (ReadHandle qh)
+			_ -> return mempty
+		return (v, st')
+
+readDb :: SqlPersistM a -> ReadHandle -> Annex a
+readDb a (ReadHandle h) = liftIO $ H.queryDbQueue h a
+
+newtype WriteHandle = WriteHandle H.DbQueue
+
+type Writer = WriteHandle -> Annex ()
+
+{- Runs an action that writes to the database. Typically this is used to
+ - queue changes, which will be flushed at a later point.
+ -
+ - The database is created if it doesn't exist yet. -}
+runWriter :: Writer -> Annex ()
+runWriter a = do
+	h <- getDbHandle
+	withDbState h go
+  where
+	go st@(DbOpen qh) = do
+		v <- a (WriteHandle qh)
+		return (v, st)
+	go st = do
+		st' <- openDb True st
+		v <- case st' of
+			DbOpen qh -> a (WriteHandle qh)
+			_ -> error "internal"
+		return (v, st)
+
+queueDb :: SqlPersistM () -> WriteHandle -> Annex ()
+queueDb a (WriteHandle h) = liftIO $ H.queueDb h checkcommit a
+  where
+	-- commit queue after 1000 changes or 5 minutes, whichever comes first
+	checkcommit sz lastcommittime
+		| sz > 1000 = return True
+		| otherwise = do
+			now <- getCurrentTime
+			return $ diffUTCTime lastcommittime now > 300
+
+{- Gets the handle cached in Annex state; creates a new one if it's not yet
+ - available, but doesn't open the database. -}
+getDbHandle :: Annex DbHandle
+getDbHandle = go =<< getState keysdbhandle
+  where
+	go (Just h) = pure h
+	go Nothing = do
+		h <- liftIO newDbHandle
+		changeState $ \s -> s { keysdbhandle = Just h }
+		return h
+
+{- Opens the database, perhaps creating it if it doesn't exist yet.
  -
  - Multiple readers and writers can have the database open at the same
  - time. Database.Handle deals with the concurrency issues.
@@ -61,32 +138,32 @@ Content
  - the database doesn't exist yet, one caller wins the lock and
  - can create it undisturbed.
  -}
-openDb :: Annex DbHandle
-openDb = withExclusiveLock gitAnnexKeysDbLock $ do
+openDb :: Bool -> DbState -> Annex DbState
+openDb _ st@(DbOpen _) = return st
+openDb False DbEmpty = return DbEmpty
+openDb createdb _ = withExclusiveLock gitAnnexKeysDbLock $ do
 	dbdir <- fromRepo gitAnnexKeysDb
 	let db = dbdir </> "db"
-	unlessM (liftIO $ doesFileExist db) $ do
-		liftIO $ do
-			createDirectoryIfMissing True dbdir
-			H.initDb db $ void $
-				runMigrationSilent migrateKeysDb
-		setAnnexDirPerm dbdir
-		setAnnexFilePerm db
-	h <- liftIO $ H.openDbQueue db "content"
-
-	-- work around https://github.com/yesodweb/persistent/issues/474
-	liftIO setConsoleEncoding
-
-	return $ DbHandle h
-
-closeDb :: DbHandle -> IO ()
-closeDb (DbHandle h) = H.closeDbQueue h
-
-withDbHandle :: (H.DbQueue -> IO a) -> Annex a
-withDbHandle a = bracket openDb (liftIO . closeDb) (\(DbHandle h) -> liftIO (a h))
+	dbexists <- liftIO $ doesFileExist db
+	case (dbexists, createdb) of
+		(True, _) -> open db
+		(False, True) -> do
+			liftIO $ do
+				createDirectoryIfMissing True dbdir
+				H.initDb db $ void $
+					runMigrationSilent migrateKeysDb
+			setAnnexDirPerm dbdir
+			setAnnexFilePerm db
+			open db
+		(False, False) -> return DbEmpty
+  where
+	open db = liftIO $ DbOpen <$> H.openDbQueue db "content"
 
 addAssociatedFile :: Key -> FilePath -> Annex ()
-addAssociatedFile k f = withDbHandle $ \h -> H.queueDb h (\_ _ -> pure True) $ do
+addAssociatedFile k f = runWriter $ addAssociatedFile' k f
+
+addAssociatedFile' :: Key -> FilePath -> Writer
+addAssociatedFile' k f = queueDb $ do
 	-- If the same file was associated with a different key before,
 	-- remove that.
 	delete $ from $ \r -> do
@@ -98,11 +175,10 @@ addAssociatedFile k f = withDbHandle $ \h -> H.queueDb h (\_ _ -> pure True) $ d
 {- Note that the files returned were once associated with the key, but
  - some of them may not be any longer. -}
 getAssociatedFiles :: Key -> Annex [FilePath]
-getAssociatedFiles k = withDbHandle $ \h -> H.queryDbQueue h $
-	getAssociatedFiles' $ toSKey k
+getAssociatedFiles = runReader . getAssociatedFiles' . toSKey
 
-getAssociatedFiles' :: SKey -> SqlPersistM [FilePath]
-getAssociatedFiles' sk = do
+getAssociatedFiles' :: SKey -> Reader [FilePath]
+getAssociatedFiles' sk = readDb $ do
 	l <- select $ from $ \r -> do
 		where_ (r ^. AssociatedKey ==. val sk)
 		return (r ^. AssociatedFile)
@@ -111,22 +187,22 @@ getAssociatedFiles' sk = do
 {- Gets any keys that are on record as having a particular associated file.
  - (Should be one or none but the database doesn't enforce that.) -}
 getAssociatedKey :: FilePath -> Annex [Key]
-getAssociatedKey f = withDbHandle $ \h -> H.queryDbQueue h $
-	getAssociatedKey' f
+getAssociatedKey = runReader . getAssociatedKey'
 
-getAssociatedKey' :: FilePath -> SqlPersistM [Key]
-getAssociatedKey' f = do
+getAssociatedKey' :: FilePath -> Reader [Key]
+getAssociatedKey' f = readDb $ do
 	l <- select $ from $ \r -> do
 		where_ (r ^. AssociatedFile ==. val f)
 		return (r ^. AssociatedKey)
 	return $ map (fromSKey . unValue) l
 
 removeAssociatedFile :: Key -> FilePath -> Annex ()
-removeAssociatedFile k f = withDbHandle $ \h -> H.queueDb h (\_ _ -> pure True) $
+removeAssociatedFile k = runWriter . removeAssociatedFile' (toSKey k)
+
+removeAssociatedFile' :: SKey -> FilePath -> Writer
+removeAssociatedFile' sk f = queueDb $ 
 	delete $ from $ \r -> do
 		where_ (r ^. AssociatedKey ==. val sk &&. r ^. AssociatedFile ==. val f)
-  where
-	sk = toSKey k
 
 {- Stats the files, and stores their InodeCaches. -}
 storeInodeCaches :: Key -> [FilePath] -> Annex ()
@@ -134,23 +210,28 @@ storeInodeCaches k fs = withTSDelta $ \d ->
 	addInodeCaches k . catMaybes =<< liftIO (mapM (`genInodeCache` d) fs)
 
 addInodeCaches :: Key -> [InodeCache] -> Annex ()
-addInodeCaches k is = withDbHandle $ \h -> H.queueDb h (\_ _ -> pure True) $
-	forM_ is $ \i -> insertUnique $ Content (toSKey k) (toSInodeCache i)
+addInodeCaches k is = runWriter $ addInodeCaches' (toSKey k) is
+
+addInodeCaches' :: SKey -> [InodeCache] -> Writer
+addInodeCaches' sk is = queueDb $
+	forM_ is $ \i -> insertUnique $ Content sk (toSInodeCache i)
 
 {- A key may have multiple InodeCaches; one for the annex object, and one
  - for each pointer file that is a copy of it. -}
 getInodeCaches :: Key -> Annex [InodeCache]
-getInodeCaches k = withDbHandle $ \h -> H.queryDbQueue h $ do
+getInodeCaches = runReader . getInodeCaches' . toSKey
+
+getInodeCaches' :: SKey -> Reader [InodeCache]
+getInodeCaches' sk = readDb $ do
 	l <- select $ from $ \r -> do
 		where_ (r ^. ContentKey ==. val sk)
 		return (r ^. ContentCache)
 	return $ map (fromSInodeCache . unValue) l
-  where
-	sk = toSKey k
 
 removeInodeCaches :: Key -> Annex ()
-removeInodeCaches k = withDbHandle $ \h -> H.queueDb h (\_ _ -> pure True) $
+removeInodeCaches = runWriter . removeInodeCaches' . toSKey
+
+removeInodeCaches' :: SKey -> Writer
+removeInodeCaches' sk = queueDb $ 
 	delete $ from $ \r -> do
 		where_ (r ^. ContentKey ==. val sk)
-  where
-	sk = toSKey k
diff --git a/Database/Keys/Handle.hs b/Database/Keys/Handle.hs
new file mode 100644
index 000000000..5a5912b0b
--- /dev/null
+++ b/Database/Keys/Handle.hs
@@ -0,0 +1,55 @@
+{- Handle for the Keys database.
+ -
+ - Copyright 2015 Joey Hess <id@joeyh.name>
+ -:
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Database.Keys.Handle (
+	DbHandle,
+	newDbHandle,
+	DbState(..),
+	withDbState,
+	flushDbQueue,
+) where
+
+import qualified Database.Queue as H
+import Utility.Exception
+
+import Control.Concurrent
+import Control.Monad.IO.Class (liftIO, MonadIO)
+
+-- The MVar is always left full except when actions are run
+-- that access the database.
+newtype DbHandle = DbHandle (MVar DbState)
+
+-- The database can be closed or open, but it also may have been
+-- tried to open (for read) and didn't exist yet.
+data DbState = DbClosed | DbOpen H.DbQueue | DbEmpty
+
+newDbHandle :: IO DbHandle
+newDbHandle = DbHandle <$> newMVar DbClosed
+
+-- Runs an action on the state of the handle, which can change its state.
+-- The MVar is empty while the action runs, which blocks other users
+-- of the handle from running.
+withDbState
+	:: (MonadIO m, MonadCatch m)
+	=> DbHandle
+	-> (DbState
+	-> m (v, DbState))
+	-> m v
+withDbState (DbHandle mvar) a = do
+	st <- liftIO $ takeMVar mvar
+	go st `onException` (liftIO $ putMVar mvar st)
+  where
+	go st = do
+		(v, st') <- a st
+		liftIO $ putMVar mvar st'
+		return v
+
+flushDbQueue :: DbHandle -> IO ()
+flushDbQueue (DbHandle mvar) = go =<< readMVar mvar
+  where
+	go (DbOpen qh) = H.flushDbQueue qh
+	go _ = return ()
diff --git a/Database/Keys/Types.hs b/Database/Keys/Types.hs
deleted file mode 100644
index 3fabafcf2..000000000
--- a/Database/Keys/Types.hs
+++ /dev/null
@@ -1,14 +0,0 @@
-{- Sqlite database of information about Keys, data types.
- -
- - Copyright 2015 Joey Hess <id@joeyh.name>
- -:
- - Licensed under the GNU GPL version 3 or higher.
- -}
-
-module Database.Keys.Types (
-	DbHandle(..)
-) where
-
-import qualified Database.Queue as H
-
-newtype DbHandle = DbHandle H.DbQueue
diff --git a/Database/Queue.hs b/Database/Queue.hs
index 11cc23b2d..99fbacb9b 100644
--- a/Database/Queue.hs
+++ b/Database/Queue.hs
@@ -22,7 +22,6 @@ import Utility.Monad
 import Database.Handle
 
 import Database.Persist.Sqlite
-import Control.Monad
 import Control.Concurrent
 import Data.Time.Clock
 
diff --git a/Messages.hs b/Messages.hs
index a49f20711..b62e6d2a7 100644
--- a/Messages.hs
+++ b/Messages.hs
@@ -31,7 +31,6 @@ module Messages (
 	showHeader,
 	showRaw,
 	setupConsole,
-	setConsoleEncoding,
 	enableDebugOutput,
 	disableDebugOutput,
 	debugEnabled,
@@ -183,13 +182,6 @@ setupConsole = do
 	updateGlobalLogger rootLoggerName (setLevel NOTICE . setHandlers [s])
 	setConsoleEncoding
 
-{- This avoids ghc's output layer crashing on invalid encoded characters in
- - filenames when printing them out. -}
-setConsoleEncoding :: IO ()
-setConsoleEncoding = do
-	fileEncoding stdout
-	fileEncoding stderr
-
 {- Log formatter with precision into fractions of a second. -}
 preciseLogFormatter :: LogFormatter a
 preciseLogFormatter = tfLogFormatter "%F %X%Q" "[$time] $msg"
diff --git a/Utility/FileSystemEncoding.hs b/Utility/FileSystemEncoding.hs
index 67341d371..eab98337a 100644
--- a/Utility/FileSystemEncoding.hs
+++ b/Utility/FileSystemEncoding.hs
@@ -19,6 +19,7 @@ module Utility.FileSystemEncoding (
 	encodeW8NUL,
 	decodeW8NUL,
 	truncateFilePath,
+	setConsoleEncoding,
 ) where
 
 import qualified GHC.Foreign as GHC
@@ -164,3 +165,10 @@ truncateFilePath n = reverse . go [] n . L8.fromString
 					else go (c:coll) (cnt - x') (L8.drop 1 bs)
 			_ -> coll
 #endif
+
+{- This avoids ghc's output layer crashing on invalid encoded characters in
+ - filenames when printing them out. -}
+setConsoleEncoding :: IO ()
+setConsoleEncoding = do
+	fileEncoding stdout
+	fileEncoding stderr
diff --git a/doc/todo/smudge.mdwn b/doc/todo/smudge.mdwn
index 2e8479e99..a62e19f68 100644
--- a/doc/todo/smudge.mdwn
+++ b/doc/todo/smudge.mdwn
@@ -331,18 +331,6 @@ files to be unlocked, while the indirect upgrades don't touch the files.
 	# fails to drop content from associated file othername,
 	# because it doesn't know it has that name
 	# git commit clears up this mess
-* A new connection to the Keys database is opened each time.
-  It would be more efficient to reuse a connection. 
-  However, that needs a way to close the connection, which was a problem.
-  See 38a23928e9d45b56d6836a4eac703862d63cf93c for details.
-* See if the cases where the Keys database is not used can be
-  optimised. Eg, if the Keys database doesn't exist at all,
-  we know smudge/clean are not used, so queries don't
-  need to open the database or do reconciliation, but can simply return none.
-  Also, no need for Backend.lookupFile to catKeyFile in this case
-  (when not in direct mode).
-  However, beware over-optimisation breaking the assistant or perhaps other
-  long-lived processes.
 * Interaction with shared clones. Should avoid hard linking from/to a
   object in a shared clone if either repository has the object unlocked.
   (And should avoid unlocking an object if it's hard linked to a shared clone,
@@ -368,6 +356,14 @@ files to be unlocked, while the indirect upgrades don't touch the files.
   smudged files.)
 * Audit code for all uses of isDirect. These places almost always need
   adjusting to support v6, if they haven't already.
+* Optimisation: See if the database schema can be improved to speed things
+  up. Are there enough indexes? getAssociatedKey in particular does a
+  reverse lookup and might benefit from an index.
+* Optimisation: Reads from the Keys database avoid doing anything if the
+  database doesn't exist. This makes v5 repos, or v6 with all locked files
+  faster. However, if a v6 repo unlocks and then re-locks a file, its
+  database will exist, and so this optimisation will no longer apply.
+  Could try to detect when the database is empty, and remove it or avoid reads.
 
 * Eventually (but not yet), make v6 the default for new repositories.
   Note that the assistant forces repos into direct mode; that will need to