Improve behavior when -J transfers multiple files that point to the same key

After a false start, I found a fairly non-intrusive way to deal with it.
Although it only handles transfers -- there may be issues with eg
concurrent dropping of the same key, or other operations.

There is no added overhead when -J is not used, other than an added
inAnnex check. When -J is used, it has to maintain and check a small
Set, which should be negligible overhead.

It could output some message saying that the transfer is being done by
another thread. Or it could even display the same progress info for both
files that are being downloaded since they have the same content. But I
opted to keep it simple, since this is rather an edge case, so it just
doesn't say anything about the transfer of the file until the other
thread finishes.

Since the deferred transfer action still runs, actions that do more than
transfer content will still get a chance to do their other work. (An
example of something that needs to do such other work is P2P.Annex,
where the download always needs to receive the content from the peer.)
And, if the first thread fails to complete a transfer, the second thread
can resume it.

But, this unfortunately means that there's a risk of redundant work
being done to transfer a key that just got transferred.
That's not ideal, but should never cause breakage; the same
thing can occur when running two separate git-annex processes.

The get/move/copy/mirror --from commands had extra inAnnex checks added,
inside the download actions. Without those checks, the first thread
downloaded the content, and then the second thread woke up and
downloaded the same content redundantly.

move/copy/mirror --to is left doing redundant uploads for now. It
would need a second checkPresent of the remote inside the upload
to avoid them, which would be expensive. A better way to avoid
redundant work needs to be found..

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

12 files changed, 72 insertions, 31 deletions

diff --git a/Annex.hs b/Annex.hs
index add568a1b..8e79e63c1 100644
--- a/Annex.hs
+++ b/Annex.hs
@@ -61,6 +61,7 @@ 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
@@ -125,6 +126,7 @@ 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
@@ -149,6 +151,7 @@ newState c r = do
 	emptyactiveremotes <- newMVar M.empty
 	o <- newMessageState
 	sc <- newTMVarIO False
+	cpt <- newTVarIO S.empty
 	return $ AnnexState
 		{ repo = r
 		, repoadjustment = return
@@ -179,6 +182,7 @@ newState c r = do
 		, groupmap = Nothing
 		, ciphers = M.empty
 		, lockcache = M.empty
+		, currentprocesstransfers = cpt
 		, sshstalecleaned = sc
 		, flags = M.empty
 		, fields = M.empty
diff --git a/Annex/Transfer.hs b/Annex/Transfer.hs
index 3fcf1a1b9..35294ba2b 100644
--- a/Annex/Transfer.hs
+++ b/Annex/Transfer.hs
@@ -32,7 +32,9 @@ 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
@@ -89,22 +91,23 @@ 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 = checkSecureHashes t $ do
-	info <- liftIO $ startTransferInfo afile
-	(meter, tfile, metervar) <- mkProgressUpdater t info
-	mode <- annexFileMode
-	(lck, inprogress) <- prep tfile mode info
-	if inprogress && not ignorelock
-		then do
-			showNote "transfer already in progress, or unable to take transfer lock"
-			return observeFailure
-		else do
-			v <- retry info metervar $ transferaction meter
-			liftIO $ cleanup tfile lck
-			if observeBool v
-				then removeFailedTransfer t
-				else recordFailedTransfer t info
-			return v
+runTransfer' ignorelock t afile shouldretry transferaction = 
+	checkSecureHashes t $ currentProcessTransfer t $ do
+		info <- liftIO $ startTransferInfo afile
+		(meter, tfile, metervar) <- mkProgressUpdater t info
+		mode <- annexFileMode
+		(lck, inprogress) <- prep tfile mode info
+		if inprogress && not ignorelock
+			then do
+				showNote "transfer already in progress, or unable to take transfer lock"
+				return observeFailure
+			else do
+				v <- handleretry info metervar $ transferaction meter
+				liftIO $ cleanup tfile lck
+				if observeBool v
+					then removeFailedTransfer t
+					else recordFailedTransfer t info
+				return v
   where
 #ifndef mingw32_HOST_OS
 	prep tfile mode info = catchPermissionDenied (const prepfailed) $ do
@@ -153,7 +156,7 @@ runTransfer' ignorelock t afile shouldretry transferaction = checkSecureHashes t
 		dropLock lockhandle
 		void $ tryIO $ removeFile lck
 #endif
-	retry oldinfo metervar run = do
+	handleretry oldinfo metervar run = do
 		v <- tryNonAsync run
 		case v of
 			Right b -> return b
@@ -162,7 +165,7 @@ runTransfer' ignorelock t afile shouldretry transferaction = checkSecureHashes t
 				b <- getbytescomplete metervar
 				let newinfo = oldinfo { bytesComplete = Just b }
 				if shouldretry oldinfo newinfo
-					then retry newinfo metervar run
+					then handleretry newinfo metervar run
 					else return observeFailure
 	getbytescomplete metervar
 		| transferDirection t == Upload =
@@ -256,3 +259,20 @@ 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
diff --git a/Assistant/Types/DaemonStatus.hs b/Assistant/Types/DaemonStatus.hs
index 1166cd18a..f775e3064 100644
--- a/Assistant/Types/DaemonStatus.hs
+++ b/Assistant/Types/DaemonStatus.hs
@@ -38,7 +38,8 @@ data DaemonStatus = DaemonStatus
 	, lastSanityCheck :: Maybe POSIXTime
 	-- True when a scan for file transfers is running
 	, transferScanRunning :: Bool
-	-- Currently running file content transfers
+	-- Currently running file content transfers, for both this process
+	-- and other processes.
 	, currentTransfers :: TransferMap
 	-- Messages to display to the user.
 	, alertMap :: AlertMap
diff --git a/Assistant/Types/TransferQueue.hs b/Assistant/Types/TransferQueue.hs
index 7e2b4ce3b..f7ce33bda 100644
--- a/Assistant/Types/TransferQueue.hs
+++ b/Assistant/Types/TransferQueue.hs
@@ -8,7 +8,6 @@
 module Assistant.Types.TransferQueue where
 
 import Annex.Common
-import Types.Transfer
 
 import Control.Concurrent.STM
 import Utility.TList
diff --git a/CHANGELOG b/CHANGELOG
index 748fb2cc7..1c9d6132a 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -11,6 +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
+    same key.
   * stack.yaml: Update to lts-9.9.
 
  -- Joey Hess <id@joeyh.name>  Sat, 07 Oct 2017 14:11:00 -0400
diff --git a/Command/Get.hs b/Command/Get.hs
index 5cb0245d9..e91798eba 100644
--- a/Command/Get.hs
+++ b/Command/Get.hs
@@ -109,9 +109,10 @@ getKey' key afile = dispatch
 		| Remote.hasKeyCheap r =
 			either (const False) id <$> Remote.hasKey r key
 		| otherwise = return True
-	docopy r witness = getViaTmp (RemoteVerify r) key $ \dest ->
-		download (Remote.uuid r) key afile forwardRetry
-			(\p -> do
+	docopy r = download (Remote.uuid r) key afile forwardRetry $ \p ->
+		ifM (inAnnex key)
+			( return True
+			, getViaTmp (RemoteVerify r) key $ \dest -> do
 				showAction $ "from " ++ Remote.name r
 				Remote.retrieveKeyFile r key afile dest p
-			) witness
+			)
diff --git a/Command/Move.hs b/Command/Move.hs
index b9e0b6548..9e6c03e3b 100644
--- a/Command/Move.hs
+++ b/Command/Move.hs
@@ -200,8 +200,11 @@ fromPerform src move key afile = do
   where
 	go = notifyTransfer Download afile $ 
 		download (Remote.uuid src) key afile forwardRetry $ \p ->
-			getViaTmp (RemoteVerify src) key $ \t ->
-				Remote.retrieveKeyFile src key afile t p
+			ifM (inAnnex key)
+				( 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
diff --git a/Logs/Transfer.hs b/Logs/Transfer.hs
index 3e90ae1ee..91683b1d0 100644
--- a/Logs/Transfer.hs
+++ b/Logs/Transfer.hs
@@ -9,6 +9,7 @@
 
 module Logs.Transfer where
 
+import Types
 import Types.Transfer
 import Types.ActionItem
 import Annex.Common
diff --git a/Types.hs b/Types.hs
index 884c91a6b..ec7709a0e 100644
--- a/Types.hs
+++ b/Types.hs
@@ -15,6 +15,8 @@ module Types (
 	RemoteGitConfig(..),
 	Remote,
 	RemoteType,
+	Transfer,
+	TransferInfo,
 ) where
 
 import Annex
@@ -23,7 +25,9 @@ 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
diff --git a/Types/ActionItem.hs b/Types/ActionItem.hs
index 73d845101..0b53bec01 100644
--- a/Types/ActionItem.hs
+++ b/Types/ActionItem.hs
@@ -10,6 +10,7 @@
 module Types.ActionItem where
 
 import Key
+import Types
 import Types.Transfer
 import Git.FilePath
 
diff --git a/Types/Transfer.hs b/Types/Transfer.hs
index ade8fc763..093307ea9 100644
--- a/Types/Transfer.hs
+++ b/Types/Transfer.hs
@@ -7,10 +7,13 @@
 
 module Types.Transfer where
 
-import Types
+import Types.Remote
+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
@@ -30,18 +33,18 @@ 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 TransferInfo = TransferInfo
+data TransferInfoA a = TransferInfo
 	{ startedTime :: Maybe POSIXTime
 	, transferPid :: Maybe PID
 	, transferTid :: Maybe ThreadId
-	, transferRemote :: Maybe Remote
+	, transferRemote :: Maybe (RemoteA a)
 	, bytesComplete :: Maybe Integer
 	, associatedFile :: AssociatedFile
 	, transferPaused :: Bool
 	}
 	deriving (Show, Eq, Ord)
 
-stubTransferInfo :: TransferInfo
+stubTransferInfo :: TransferInfoA a
 stubTransferInfo = TransferInfo Nothing Nothing Nothing Nothing Nothing (AssociatedFile Nothing) False
 
 data Direction = Upload | Download
@@ -56,7 +59,7 @@ parseDirection "upload" = Just Upload
 parseDirection "download" = Just Download
 parseDirection _ = Nothing
 
-instance Arbitrary TransferInfo where
+instance Arbitrary (TransferInfoA a) where
 	arbitrary = TransferInfo
 		<$> arbitrary
 		<*> arbitrary
diff --git a/doc/bugs/get_-J___34__fails__34___to_get_files_with_the_same_key.mdwn b/doc/bugs/get_-J___34__fails__34___to_get_files_with_the_same_key.mdwn
index fade3b331..80c16d6e1 100644
--- a/doc/bugs/get_-J___34__fails__34___to_get_files_with_the_same_key.mdwn
+++ b/doc/bugs/get_-J___34__fails__34___to_get_files_with_the_same_key.mdwn
@@ -46,3 +46,5 @@ so at the end we get a run of git-annex which exits with error 1... and in json
 I wondered if annex should first analyze passed paths to get actual keys to be fetched?
 
 [[!meta author=yoh]]
+
+> [[fixed|done]] --[[Joey]]