better dup key with -J fix

This avoids all the complication about redundant work discussed in
the previous try at fixing this. At the expense of needing each command
that could have the problem to be patched to simply wrap the action in
onlyActionOn once the key is known. But there do not seem to be many
such commands.

onlyActionOn' should not be used with a CommandStart (or CommandPerform),
although the types do allow it. onlyActionOn handles running the whole
CommandStart chain. I couldn't immediately see a way to avoid mistken
use of onlyActionOn'.

This commit was supported by the NSF-funded DataLad project.

Annex.hs

@@ -61,7 +61,6 @@ import Types.UUID
 import Types.FileMatcher
 import Types.NumCopies
 import Types.LockCache
-import Types.Transfer
 import Types.DesktopNotify
 import Types.CleanupActions
 import qualified Database.Keys.Handle as Keys
@@ -126,7 +125,6 @@ data AnnexState = AnnexState
 	, groupmap :: Maybe GroupMap
 	, ciphers :: M.Map StorableCipher Cipher
 	, lockcache :: LockCache
-	, currentprocesstransfers :: TVar (S.Set Transfer)
 	, sshstalecleaned :: TMVar Bool
 	, flags :: M.Map String Bool
 	, fields :: M.Map String String
@@ -140,6 +138,7 @@ data AnnexState = AnnexState
 	, existinghooks :: M.Map Git.Hook.Hook Bool
 	, desktopnotify :: DesktopNotify
 	, workers :: [Either AnnexState (Async AnnexState)]
+	, activekeys :: TVar (M.Map Key ThreadId)
 	, activeremotes :: MVar (M.Map (Types.Remote.RemoteA Annex) Integer)
 	, keysdbhandle :: Maybe Keys.DbHandle
 	, cachedcurrentbranch :: Maybe Git.Branch
@@ -149,9 +148,9 @@ data AnnexState = AnnexState
 newState :: GitConfig -> Git.Repo -> IO AnnexState
 newState c r = do
 	emptyactiveremotes <- newMVar M.empty
+	emptyactivekeys <- newTVarIO M.empty
 	o <- newMessageState
 	sc <- newTMVarIO False
-	cpt <- newTVarIO S.empty
 	return $ AnnexState
 		{ repo = r
 		, repoadjustment = return
@@ -182,7 +181,6 @@ newState c r = do
 		, groupmap = Nothing
 		, ciphers = M.empty
 		, lockcache = M.empty
-		, currentprocesstransfers = cpt
 		, sshstalecleaned = sc
 		, flags = M.empty
 		, fields = M.empty
@@ -196,6 +194,7 @@ newState c r = do
 		, existinghooks = M.empty
 		, desktopnotify = mempty
 		, workers = []
+		, activekeys = emptyactivekeys
 		, activeremotes = emptyactiveremotes
 		, keysdbhandle = Nothing
 		, cachedcurrentbranch = Nothing

Annex/Transfer.hs

@@ -32,9 +32,7 @@ import qualified Types.Remote as Remote
 import Types.Concurrency
 
 import Control.Concurrent
-import Control.Concurrent.STM
 import qualified Data.Map.Strict as M
-import qualified Data.Set as S
 import Data.Ord
 
 class Observable a where
@@ -91,8 +89,7 @@ alwaysRunTransfer :: Observable v => Transfer -> AssociatedFile -> RetryDecider
 alwaysRunTransfer = runTransfer' True
 
 runTransfer' :: Observable v => Bool -> Transfer -> AssociatedFile -> RetryDecider -> (MeterUpdate -> Annex v) -> Annex v
-runTransfer' ignorelock t afile shouldretry transferaction = 
+runTransfer' ignorelock t afile shouldretry transferaction = checkSecureHashes t $ do
-	checkSecureHashes t $ currentProcessTransfer t $ do
 	info <- liftIO $ startTransferInfo afile
 	(meter, tfile, metervar) <- mkProgressUpdater t info
 	mode <- annexFileMode
@@ -102,7 +99,7 @@ runTransfer' ignorelock t afile shouldretry transferaction =
 			showNote "transfer already in progress, or unable to take transfer lock"
 			return observeFailure
 		else do
-				v <- handleretry info metervar $ transferaction meter
+			v <- retry info metervar $ transferaction meter
 			liftIO $ cleanup tfile lck
 			if observeBool v
 				then removeFailedTransfer t
@@ -156,7 +153,7 @@ runTransfer' ignorelock t afile shouldretry transferaction =
 		dropLock lockhandle
 		void $ tryIO $ removeFile lck
 #endif
-	handleretry oldinfo metervar run = do
+	retry oldinfo metervar run = do
 		v <- tryNonAsync run
 		case v of
 			Right b -> return b
@@ -165,7 +162,7 @@ runTransfer' ignorelock t afile shouldretry transferaction =
 				b <- getbytescomplete metervar
 				let newinfo = oldinfo { bytesComplete = Just b }
 				if shouldretry oldinfo newinfo
-					then handleretry newinfo metervar run
+					then retry newinfo metervar run
 					else return observeFailure
 	getbytescomplete metervar
 		| transferDirection t == Upload =
@@ -259,20 +256,3 @@ lessActiveFirst :: M.Map Remote Integer -> Remote -> Remote -> Ordering
 lessActiveFirst active a b
 	| Remote.cost a == Remote.cost b = comparing (`M.lookup` active) a b
 	| otherwise = compare a b
-
-{- Runs a transfer action. Only one thread can run for a given Transfer
- - at a time; other threads will block. -}
-currentProcessTransfer :: Transfer -> Annex a -> Annex a
-currentProcessTransfer t a = go =<< Annex.getState Annex.concurrency
-  where
-	go NonConcurrent = a
-	go (Concurrent _) = do
-		tv <- Annex.getState Annex.currentprocesstransfers
-		bracket_ (setup tv) (cleanup tv) a
-	setup tv = liftIO $ atomically $ do
-		s <- readTVar tv
-		if S.member t s
-			then retry
-			else writeTVar tv $! S.insert t s
-	cleanup tv = liftIO $ atomically $
-		modifyTVar' tv $ S.delete t

Assistant/Types/DaemonStatus.hs

@@ -38,8 +38,7 @@ data DaemonStatus = DaemonStatus
 	, lastSanityCheck :: Maybe POSIXTime
 	-- True when a scan for file transfers is running
 	, transferScanRunning :: Bool
-	-- Currently running file content transfers, for both this process
+	-- Currently running file content transfers
-	-- and other processes.
 	, currentTransfers :: TransferMap
 	-- Messages to display to the user.
 	, alertMap :: AlertMap

Assistant/Types/TransferQueue.hs

@@ -8,6 +8,7 @@
 module Assistant.Types.TransferQueue where
 
 import Annex.Common
+import Types.Transfer
 
 import Control.Concurrent.STM
 import Utility.TList

Assistant/WebApp/Types.hs

@@ -22,6 +22,7 @@ import Utility.NotificationBroadcaster
 import Utility.AuthToken
 import Utility.WebApp
 import Utility.Yesod
+import Types.Transfer
 import Utility.Gpg (KeyId)
 import Build.SysConfig (packageversion)
 import Types.ScheduledActivity

CHANGELOG

@@ -11,8 +11,8 @@ git-annex (6.20171004) UNRELEASED; urgency=medium
     where interrupting an add could result in the file being
     moved into the annex, with no symlink yet created.
   * Avoid repeated checking that files passed on the command line exist.
-  * Improve behavior when -J transfers multiple files that point to the
+  * get -J/move -J/copy -J/mirror -J/sync -J: Avoid "transfer already in
-    same key.
+    progress" errors when two files use the same key.
   * stack.yaml: Update to lts-9.9.
 
  -- Joey Hess <id@joeyh.name>  Sat, 07 Oct 2017 14:11:00 -0400

CmdLine/Action.hs

@@ -1,6 +1,6 @@
 {- git-annex command-line actions
  -
- - Copyright 2010-2015 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2017 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU GPL version 3 or higher.
  -}
@@ -18,9 +18,12 @@ import Messages.Concurrent
 import Types.Messages
 import Remote.List
 
+import Control.Concurrent
 import Control.Concurrent.Async
+import Control.Concurrent.STM
 import Control.Exception (throwIO)
 import Data.Either
+import qualified Data.Map.Strict as M
 
 #ifdef WITH_CONCURRENTOUTPUT
 import qualified System.Console.Regions as Regions
@@ -177,3 +180,36 @@ allowConcurrentOutput a = go =<< Annex.getState Annex.concurrency
 #else
 allowConcurrentOutput = id
 #endif
+
+{- Ensures that only one thread processes a key at a time.
+ - Other threads will block until it's done. -}
+onlyActionOn :: Key -> CommandStart -> CommandStart
+onlyActionOn k a = onlyActionOn' k run
+  where
+	run = do
+		-- Run whole action, not just start stage, so other threads
+		-- block until it's done.
+		r <- callCommandAction' a
+		case r of
+			Nothing -> return Nothing
+			Just r' -> return $ Just $ return $ Just $ return r'
+
+onlyActionOn' :: Key -> Annex a -> Annex a
+onlyActionOn' k a = go =<< Annex.getState Annex.concurrency
+  where
+	go NonConcurrent = a
+	go (Concurrent _) = do
+		tv <- Annex.getState Annex.activekeys
+		bracket (setup tv) id (const a)
+	setup tv = liftIO $ do
+		mytid <- myThreadId
+		atomically $ do
+			m <- readTVar tv
+			case M.lookup k m of
+				Just tid
+					| tid /= mytid -> retry
+					| otherwise -> return (return ())
+				Nothing -> do
+					writeTVar tv $! M.insert k mytid m
+					return $ liftIO $ atomically $
+						modifyTVar tv $ M.delete k

Command/Get.hs

@@ -62,8 +62,8 @@ startKeys from key ai = checkFailedTransferDirection ai Download $
 	start' (return True) from key (AssociatedFile Nothing) ai
 
 start' :: Annex Bool -> Maybe Remote -> Key -> AssociatedFile -> ActionItem -> CommandStart
-start' expensivecheck from key afile ai = stopUnless (not <$> inAnnex key) $
+start' expensivecheck from key afile ai = onlyActionOn key $
-	stopUnless expensivecheck $
+	stopUnless (not <$> inAnnex key) $ stopUnless expensivecheck $
 		case from of
 			Nothing -> go $ perform key afile
 			Just src ->
@@ -109,10 +109,9 @@ getKey' key afile = dispatch
 		| Remote.hasKeyCheap r =
 			either (const False) id <$> Remote.hasKey r key
 		| otherwise = return True
-	docopy r = download (Remote.uuid r) key afile forwardRetry $ \p ->
+	docopy r witness = getViaTmp (RemoteVerify r) key $ \dest ->
-		ifM (inAnnex key)
+		download (Remote.uuid r) key afile forwardRetry
-			( return True
+			(\p -> do
-			, getViaTmp (RemoteVerify r) key $ \dest -> do
 				showAction $ "from " ++ Remote.name r
 				Remote.retrieveKeyFile r key afile dest p
-			)
+			) witness

Command/Mirror.hs

@@ -53,7 +53,7 @@ start o file k = startKey o afile k (mkActionItem afile)
 	afile = AssociatedFile (Just file)
 
 startKey :: MirrorOptions -> AssociatedFile -> Key -> ActionItem -> CommandStart
-startKey o afile key ai = case fromToOptions o of
+startKey o afile key ai = onlyActionOn key $ case fromToOptions o of
 	ToRemote r -> checkFailedTransferDirection ai Upload $ ifM (inAnnex key)
 		( Command.Move.toStart False afile key ai =<< getParsed r
 		, do

Command/Move.hs

@@ -74,7 +74,7 @@ startKey :: MoveOptions -> Bool -> Key -> ActionItem -> CommandStart
 startKey o move = start' o move (AssociatedFile Nothing)
 
 start' :: MoveOptions -> Bool -> AssociatedFile -> Key -> ActionItem -> CommandStart
-start' o move afile key ai = 
+start' o move afile key ai = onlyActionOn key $
 	case fromToOptions o of
 		Right (FromRemote src) ->
 			checkFailedTransferDirection ai Download $
@@ -200,11 +200,8 @@ fromPerform src move key afile = do
   where
 	go = notifyTransfer Download afile $ 
 		download (Remote.uuid src) key afile forwardRetry $ \p ->
-			ifM (inAnnex key)
+			getViaTmp (RemoteVerify src) key $ \t ->
-				( return True
-				, getViaTmp (RemoteVerify src) key $ \t ->
 				Remote.retrieveKeyFile src key afile t p
-				)
 	dispatch _ False = stop -- failed
 	dispatch False True = next $ return True -- copy complete
 	-- Finish by dropping from remote, taking care to verify that

Command/Sync.hs

@@ -609,7 +609,7 @@ seekSyncContent o rs = do
  - Returns True if any file transfers were made.
  -}
 syncFile :: Either (Maybe (Bloom Key)) (Key -> Annex ()) -> [Remote] -> AssociatedFile -> Key -> Annex Bool
-syncFile ebloom rs af k = do
+syncFile ebloom rs af k = onlyActionOn' k $ do
 	locs <- Remote.keyLocations k
 	let (have, lack) = partition (\r -> Remote.uuid r `elem` locs) rs
 

Logs/Transfer.hs

@@ -9,7 +9,6 @@
 
 module Logs.Transfer where
 
-import Types
 import Types.Transfer
 import Types.ActionItem
 import Annex.Common

Types.hs

@@ -15,8 +15,6 @@ module Types (
 	RemoteGitConfig(..),
 	Remote,
 	RemoteType,
-	Transfer,
-	TransferInfo,
 ) where
 
 import Annex
@@ -25,9 +23,7 @@ import Types.GitConfig
 import Types.Key
 import Types.UUID
 import Types.Remote
-import Types.Transfer
 
 type Backend = BackendA Annex
 type Remote = RemoteA Annex
 type RemoteType = RemoteTypeA Annex
-type TransferInfo = TransferInfoA Annex

Types/ActionItem.hs

@@ -10,7 +10,6 @@
 module Types.ActionItem where
 
 import Key
-import Types
 import Types.Transfer
 import Git.FilePath
 

Types/Transfer.hs

@@ -7,13 +7,10 @@
 
 module Types.Transfer where
 
-import Types.Remote
+import Types
-import Types.Key
-import Types.UUID
 import Utility.PID
 import Utility.QuickCheck
 
-import Control.Concurrent.STM
 import Data.Time.Clock.POSIX
 import Control.Concurrent
 import Control.Applicative
@@ -33,18 +30,18 @@ data Transfer = Transfer
  - git repository. It's some file, possibly relative to some directory,
  - of some repository, that was acted on to initiate the transfer.
  -}
-data TransferInfoA a = TransferInfo
+data TransferInfo = TransferInfo
 	{ startedTime :: Maybe POSIXTime
 	, transferPid :: Maybe PID
 	, transferTid :: Maybe ThreadId
-	, transferRemote :: Maybe (RemoteA a)
+	, transferRemote :: Maybe Remote
 	, bytesComplete :: Maybe Integer
 	, associatedFile :: AssociatedFile
 	, transferPaused :: Bool
 	}
 	deriving (Show, Eq, Ord)
 
-stubTransferInfo :: TransferInfoA a
+stubTransferInfo :: TransferInfo
 stubTransferInfo = TransferInfo Nothing Nothing Nothing Nothing Nothing (AssociatedFile Nothing) False
 
 data Direction = Upload | Download
@@ -59,7 +56,7 @@ parseDirection "upload" = Just Upload
 parseDirection "download" = Just Download
 parseDirection _ = Nothing
 
-instance Arbitrary (TransferInfoA a) where
+instance Arbitrary TransferInfo where
 	arbitrary = TransferInfo
 		<$> arbitrary
 		<*> arbitrary

doc/bugs/get_-J___34__fails__34___to_get_files_with_the_same_key.mdwn

@@ -47,4 +47,6 @@ I wondered if annex should first analyze passed paths to get actual keys to be f
 
 [[!meta author=yoh]]
 
-> [[fixed|done]] --[[Joey]]
+> [[fixed|done]]; also fixed for several other commands, but the final 
+> fix needed each command that could have the problem to be modified, so 
+> there could possibly be some I missed.. --[[Joey]]