incremental hashing for fileRetriever

It uses tailVerify to hash the file while it's being written.

This is able to sometimes avoid a separate checksum step. Although
if the file gets written quickly enough, tailVerify may not see it
get created before the write finishes, and the checksum still happens.

Testing with the directory special remote, incremental checksumming did
not happen. But then I disabled the copy CoW probing, and it did work.
What's going on with that is the CoW probe creates an empty file on
failure, then deletes it, and then the file is created again. tailVerify
will open the first, empty file, and so fails to read the content that
gets written to the file that replaces it.

The directory special remote really ought to be able to avoid needing to
use tailVerify, and while other special remotes could do things that
cause similar problems, they probably don't. And if they do, it just
means the checksum doesn't get done incrementally.

Sponsored-by: Dartmouth College's DANDI project

Backend/Hash.hs

@@ -124,7 +124,7 @@ checkKeyChecksum hash key file = catchIOErrorType HardwareFault hwfault $ do
 	exists <- liftIO $ R.doesPathExist file
 	case (exists, fast) of
 		(True, False) -> do
-			showAction "checksum"
+			showAction descChecksum
 			sameCheckSum key 
 				<$> hashFile hash file nullMeterUpdate
 		_ -> return True
@@ -293,8 +293,12 @@ mkIncrementalVerifier ctx key = do
 					return $ sameCheckSum key (show digest)
 				Nothing -> return False
 		, failIncremental = writeIORef v Nothing
+		, descVerify = descChecksum
 		}
 
+descChecksum :: String
+descChecksum = "checksum"
+
 {- A varient of the SHA256E backend, for testing that needs special keys
  - that cannot collide with legitimate keys in the repository.
  -

CHANGELOG

@@ -8,9 +8,10 @@ git-annex (8.20210804) UNRELEASED; urgency=medium
   * add: When adding a dotfile, avoid treating its name as an extension.
   * rsync special remote: Stop displaying rsync progress, and use
     git-annex's own progress display.
-  * Several special remotes verify content while it is being retrieved,
-    avoiding a separate checksum pass. They are: S3, bup, ddar,
-    and gcrypt (with a local repository).
+  * Special remotes now checksum content while it is being retrieved,
+    instead of in a separate pass at the end. This is supported for all
+    special remotes on Linux (except for web and bittorrent), and for a
+    few on other OSs (S3, bup, ddar, gcrypt).
 
  -- Joey Hess <id@joeyh.name>  Tue, 03 Aug 2021 12:22:45 -0400
 

Remote/Directory/LegacyChunked.hs

@@ -98,7 +98,7 @@ store repotop chunksize finalizer k b p = storeHelper repotop finalizer k $ \des
  - :/ This is legacy code..
  -}
 retrieve :: (RawFilePath -> Key -> [RawFilePath]) -> RawFilePath -> Retriever
-retrieve locations d basek p c = withOtherTmp $ \tmpdir -> do
+retrieve locations d basek p miv c = withOtherTmp $ \tmpdir -> do
 	showLongNote "This remote uses the deprecated chunksize setting. So this will be quite slow."
 	let tmp = tmpdir P.</> keyFile basek <> ".directorylegacy.tmp"
 	let tmp' = fromRawFilePath tmp
@@ -110,7 +110,7 @@ retrieve locations d basek p c = withOtherTmp $ \tmpdir -> do
 		b <- liftIO $ L.readFile tmp'
 		liftIO $ removeWhenExistsWith R.removeLink tmp
 		sink b
-	byteRetriever go basek p c
+	byteRetriever go basek p miv c
 
 checkKey :: RawFilePath -> (RawFilePath -> Key -> [RawFilePath]) -> Key -> Annex Bool
 checkKey d locations k = liftIO $

Remote/GCrypt.hs

@@ -407,9 +407,9 @@ store' repo r rsyncopts accessmethod
 	storersync = fileStorer $ Remote.Rsync.store rsyncopts
 
 retrieve :: Remote -> Remote.Rsync.RsyncOpts -> AccessMethod -> Retriever
-retrieve r rsyncopts accessmethod k p sink = do
+retrieve r rsyncopts accessmethod k p miv sink = do
 	repo <- getRepo r
-	retrieve' repo r rsyncopts accessmethod k p sink
+	retrieve' repo r rsyncopts accessmethod k p miv sink
 
 retrieve' :: Git.Repo -> Remote -> Remote.Rsync.RsyncOpts -> AccessMethod -> Retriever
 retrieve' repo r rsyncopts accessmethod

Remote/Helper/Chunked.hs

@@ -267,8 +267,7 @@ retrieveChunks retriever u vc chunkconfig encryptor basek dest basep enc encc
 		-- Optimisation: Try the unchunked key first, to avoid
 		-- looking in the git-annex branch for chunk counts
 		-- that are likely not there.
-		iv <- startVerifyKeyContentIncrementally vc basek
-		tryNonAsync (getunchunked iv) >>= \case
+		tryNonAsync getunchunked >>= \case
 			Right r -> finalize r
 			Left e -> go (Just e) 
 				=<< chunkKeysOnly u chunkconfig basek
@@ -287,9 +286,7 @@ retrieveChunks retriever u vc chunkconfig encryptor basek dest basep enc encc
 	firstavail (Just e) _ [] = throwM e
 	firstavail pe currsize ([]:ls) = firstavail pe currsize ls
 	firstavail _ currsize ((k:ks):ls)
-		| k == basek = do
-			iv <- startVerifyKeyContentIncrementally vc basek
-			getunchunked iv
+		| k == basek = getunchunked
 			`catchNonAsync` (\e -> firstavail (Just e) currsize ls)
 		| otherwise = do
 			let offset = resumeOffset currsize k
@@ -297,12 +294,12 @@ retrieveChunks retriever u vc chunkconfig encryptor basek dest basep enc encc
 				(offsetMeterUpdate basep . toBytesProcessed)
 				offset
 			v <- tryNonAsync $
-				retriever (encryptor k) p $ \content ->
+				retriever (encryptor k) p Nothing $ \content ->
 					bracket (maybe opennew openresume offset) (liftIO . hClose . fst) $ \(h, iv) -> do
-						iv' <- retrieved iv (Just h) p content
+						retrieved iv (Just h) p content
 						let sz = toBytesProcessed $
 							fromMaybe 0 $ fromKey keyChunkSize k
-						getrest p h iv' sz sz ks
+						getrest p h iv sz sz ks
 			case v of
 				Left e
 					| null ls -> throwM e
@@ -313,12 +310,21 @@ retrieveChunks retriever u vc chunkconfig encryptor basek dest basep enc encc
 	getrest p h iv sz bytesprocessed (k:ks) = do
 		let p' = offsetMeterUpdate p bytesprocessed
 		liftIO $ p' zeroBytesProcessed
-		iv' <- retriever (encryptor k) p' $ 
+		retriever (encryptor k) p' Nothing $ 
 			retrieved iv (Just h) p'
-		getrest p h iv' sz (addBytesProcessed bytesprocessed sz) ks
+		getrest p h iv sz (addBytesProcessed bytesprocessed sz) ks
 
-	getunchunked iv = retriever (encryptor basek) basep $
+	getunchunked = do
+		iv <- startVerifyKeyContentIncrementally vc basek
+		case enc of
+			Just _ -> retriever (encryptor basek) basep Nothing $
 				retrieved iv Nothing basep
+			-- Not chunked and not encrypted, so ask the
+			-- retriever to incrementally verify when it
+			-- retrieves to a file.
+			Nothing -> retriever (encryptor basek) basep iv $
+				retrieved iv Nothing basep
+		return iv
 
 	opennew = do
 		iv <- startVerifyKeyContentIncrementally vc basek
@@ -365,13 +371,11 @@ retrieveChunks retriever u vc chunkconfig encryptor basek dest basep enc encc
  - will be provided, and instead the content will be written to the
  - dest file.
  -
+ - The IncrementalVerifier is updated as the file content is read.
+ -
  - Note that when neither chunking nor encryption is used, and the remote
  - provides FileContent, that file only needs to be renamed
  - into place. (And it may even already be in the right place..)
- -
- - The IncrementalVerifier is updated as the file content is read.
- - If it was not able to be updated, due to the file not needing to be read,
- - Nothing will be returned.
  -}
 writeRetrievedContent
 	:: LensGpgEncParams encc
@@ -382,32 +386,25 @@ writeRetrievedContent
 	-> Maybe MeterUpdate
 	-> ContentSource
 	-> Maybe IncrementalVerifier
-	-> Annex (Maybe IncrementalVerifier)
+	-> Annex ()
 writeRetrievedContent dest enc encc mh mp content miv = case (enc, mh, content) of
 	(Nothing, Nothing, FileContent f)
-		| f == dest -> return Nothing
-		| otherwise -> do
-			liftIO $ moveFile f dest
-			return Nothing
+		| f == dest -> noop
+		| otherwise -> liftIO $ moveFile f dest
 	(Just (cipher, _), _, ByteContent b) -> do
 		cmd <- gpgCmd <$> Annex.getGitConfig
 		decrypt cmd encc cipher (feedBytes b) $
 			readBytes write
-		return miv
 	(Just (cipher, _), _, FileContent f) -> do
 		cmd <- gpgCmd <$> Annex.getGitConfig
 		withBytes content $ \b ->
 			decrypt cmd encc cipher (feedBytes b) $
 				readBytes write
 		liftIO $ removeWhenExistsWith R.removeLink (toRawFilePath f)
-		return miv
 	(Nothing, _, FileContent f) -> do
 		withBytes content write
 		liftIO $ removeWhenExistsWith R.removeLink (toRawFilePath f)
-		return miv
-	(Nothing, _, ByteContent b) -> do
-		write b
-		return miv
+	(Nothing, _, ByteContent b) -> write b
   where
 	write b = case mh of
 		Just h -> liftIO $ write' b h

Remote/Helper/Special.hs

@@ -1,6 +1,6 @@
 {- helpers for special remotes
  -
- - Copyright 2011-2020 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2021 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -39,6 +39,7 @@ import Annex.Common
 import Annex.SpecialRemote.Config
 import Types.StoreRetrieve
 import Types.Remote
+import Annex.Verify
 import Annex.UUID
 import Config
 import Config.Cost
@@ -54,6 +55,8 @@ import Git.Types
 import qualified Data.ByteString as S
 import qualified Data.ByteString.Lazy as L
 import qualified Data.Map as M
+import Control.Concurrent.STM
+import Control.Concurrent.Async
 
 {- Special remotes don't have a configured url, so Git.Repo does not
  - automatically generate remotes for them. This looks for a different
@@ -101,19 +104,33 @@ fileStorer a k (ByteContent b) m = withTmp k $ \f -> do
 byteStorer :: (Key -> L.ByteString -> MeterUpdate -> Annex ()) -> Storer
 byteStorer a k c m = withBytes c $ \b -> a k b m
 
--- A Retriever that writes the content of a Key to a provided file.
--- It is responsible for updating the progress meter as it retrieves data.
-fileRetriever :: (FilePath -> Key -> MeterUpdate -> Annex ()) -> Retriever
-fileRetriever a k m callback = do
-	f <- prepTmp k
-	a (fromRawFilePath f) k m
-	pruneTmpWorkDirBefore f (callback . FileContent . fromRawFilePath)
-
 -- A Retriever that generates a lazy ByteString containing the Key's
 -- content, and passes it to a callback action which will fully consume it
 -- before returning.
-byteRetriever :: (Key -> (L.ByteString -> Annex a) -> Annex a) -> Key -> MeterUpdate -> (ContentSource -> Annex a) -> Annex a
-byteRetriever a k _m callback = a k (callback . ByteContent)
+byteRetriever :: (Key -> (L.ByteString -> Annex a) -> Annex a) -> Key -> MeterUpdate -> Maybe IncrementalVerifier -> (ContentSource -> Annex a) -> Annex a
+byteRetriever a k _m _miv callback = a k (callback . ByteContent)
+
+-- A Retriever that writes the content of a Key to a provided file.
+-- The action is responsible for updating the progress meter as it 
+-- retrieves data. The incremental verifier is updated in the background as
+-- the action writes to the file.
+fileRetriever :: (FilePath -> Key -> MeterUpdate -> Annex ()) -> Retriever
+fileRetriever a k m miv callback = do
+	f <- prepTmp k
+	let retrieve = a (fromRawFilePath f) k m
+	case miv of
+		Nothing -> retrieve
+		Just iv -> do
+			finished <- liftIO newEmptyTMVarIO
+			t <- liftIO $ async $ tailVerify iv f finished
+			retrieve
+			liftIO $ atomically $ putTMVar finished ()
+			liftIO (wait t) >>= \case
+				Nothing -> noop
+				Just deferredverify -> do
+					showAction (descVerify iv)
+					liftIO deferredverify
+	pruneTmpWorkDirBefore f (callback . FileContent . fromRawFilePath)
 
 {- The base Remote that is provided to specialRemote needs to have
  - storeKey, retrieveKeyFile, removeKey, and checkPresent methods,

Types/Backend.hs

@@ -52,4 +52,6 @@ data IncrementalVerifier = IncrementalVerifier
 	-- if the hash verified.
 	, failIncremental :: IO ()
 	-- ^ Call if the incremental verification needs to fail.
+	, descVerify :: String
+	-- ^ A description of what is done to verify the content.
 	}

Types/StoreRetrieve.hs

@@ -1,6 +1,6 @@
 {- Types for Storer and Retriever actions for remotes.
  -
- - Copyright 2014 Joey Hess <id@joeyh.name>
+ - Copyright 2014-2021 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -11,6 +11,7 @@ module Types.StoreRetrieve where
 
 import Annex.Common
 import Utility.Metered
+import Types.Backend (IncrementalVerifier)
 
 import qualified Data.ByteString.Lazy as L
 
@@ -29,8 +30,17 @@ type Storer = Key -> ContentSource -> MeterUpdate -> Annex ()
 
 -- Action that retrieves a Key's content from a remote, passing it to a
 -- callback, which will fully consume the content before returning.
+--
 -- Throws exception if key is not present, or remote is not accessible.
-type Retriever = forall a. Key -> MeterUpdate -> (ContentSource -> Annex a) -> Annex a
+--
+-- When it retrieves FileContent, it is responsible for updating the
+-- MeterUpdate. And when the IncrementalVerifier is passed to it,
+-- and it retrieves FileContent, it should feed the content to the
+-- verifier before running the callback. 
+-- This should not be done when it retrieves ByteContent.
+type Retriever = forall a.
+	Key -> MeterUpdate -> Maybe IncrementalVerifier
+		-> (ContentSource -> Annex a) -> Annex a
 
 -- Action that removes a Key's content from a remote.
 -- Succeeds if key is already not present.