lock: Fix edge cases where data loss could occur in v6 mode.

In the case where the pointer file is in place, and not the content
of the object, lock's  performNew was called with filemodified=True,
which caused it to try to repopulate the object from an unmodified
associated file, of which there were none. So, the content of the object
got thrown away incorrectly. This was the cause (although not the root
cause) of data loss in https://github.com/datalad/datalad/issues/1020

The same problem could also occur when the work tree file is modified,
but the object is not, and lock is called with --force. Added a test case
for this, since it's excercising the same code path and is easier to set up
than the problem above.

Note that this only occurred when the keys database did not have an inode
cache recorded for the annex object. Normally, the annex object would be in
there, but there are of course circumstances where the inode cache is out
of sync with reality, since it's only a cache.

Fixed by checking if the object is unmodified; if so we don't need to
try to repopulate it. This does add an additional checksum to the unlock
path, but it's already checksumming the worktree file in another case,
so it doesn't slow it down overall.

Further investigation found a similar problem occurred when smudge --clean
is called on a file and the inode cache is not populated. cleanOldKeys
deleted the unmodified old object file in this case. This was also
fixed by checking if the object is unmodified.

In general, use of getInodeCaches and sameInodeCache is potentially
dangerous if the inode cache has not gotten populated for some reason.
Better to use isUnmodified. I breifly auited other places that check the
inode cache, and did not see any immediate problems, but it would be easy
to miss this kind of problem.

Annex/Ingest.hs

@@ -244,10 +244,9 @@ cleanOldKeys file newkey = do
 	topf <- inRepo (toTopFilePath file)
 	oldkeys <- filter (/= newkey)
 		<$> Database.Keys.getAssociatedKey topf
-	forM_ oldkeys $ \key -> do
-		obj <- calcRepo (gitAnnexLocation key)
-		caches <- Database.Keys.getInodeCaches key
-		unlessM (sameInodeCache obj caches) $ do
+	forM_ oldkeys $ \key ->
+		unlessM (isUnmodified key =<< calcRepo (gitAnnexLocation key)) $ do
+			caches <- Database.Keys.getInodeCaches key
 			unlinkAnnex key
 			fs <- filter (/= ingestedf)
 				. map (`fromTopFilePath` g)

CHANGELOG

@@ -1,3 +1,10 @@
+git-annex (6.20161013) UNRELEASED; urgency=medium
+
+  * lock, smudge: Fix edge cases where data loss could occur in v6 mode
+    when the keys database was not populated.
+
+ -- Joey Hess <id@joeyh.name>  Mon, 17 Oct 2016 12:46:54 -0400
+
 git-annex (6.20161012) unstable; urgency=medium
 
   * Optimisations to time it takes git-annex to walk working tree and find

Command/Lock.hs

@@ -45,27 +45,27 @@ startNew file key = ifM (isJust <$> isAnnexLink file)
 	)
   where
 	go (Just key')
-		| key' == key = cont True
+		| key' == key = cont
 		| otherwise = errorModified
 	go Nothing = 
 		ifM (isUnmodified key file) 
-			( cont False
+			( cont
 			, ifM (Annex.getState Annex.force)
-				( cont True
+				( cont
 				, errorModified
 				)
 			)
-	cont = next . performNew file key
+	cont = next $ performNew file key
 
-performNew :: FilePath -> Key -> Bool -> CommandPerform
-performNew file key filemodified = do
+performNew :: FilePath -> Key -> CommandPerform
+performNew file key = do
 	lockdown =<< calcRepo (gitAnnexLocation key)
 	addLink file key
 		=<< withTSDelta (liftIO . genInodeCache file)
 	next $ cleanupNew file key
   where
 	lockdown obj = do
-		ifM (catchBoolIO $ sameInodeCache obj =<< Database.Keys.getInodeCaches key)
+		ifM (isUnmodified key obj)
 			( breakhardlink obj
 			, repopulate obj
 			)
@@ -83,20 +83,18 @@ performNew file key filemodified = do
 			Database.Keys.storeInodeCaches key [obj]
 
 	-- Try to repopulate obj from an unmodified associated file.
-	repopulate obj
-		| filemodified = modifyContent obj $ do
-			g <- Annex.gitRepo
-			fs <- map (`fromTopFilePath` g)
-				<$> Database.Keys.getAssociatedFiles key
-			mfile <- firstM (isUnmodified key) fs
-			liftIO $ nukeFile obj
-			case mfile of
-				Just unmodified ->
-					unlessM (checkedCopyFile key unmodified obj Nothing)
-						lostcontent
-				Nothing -> lostcontent
-		| otherwise = modifyContent obj $ 
-			liftIO $ renameFile file obj
+	repopulate obj = modifyContent obj $ do
+		g <- Annex.gitRepo
+		fs <- map (`fromTopFilePath` g)
+			<$> Database.Keys.getAssociatedFiles key
+		mfile <- firstM (isUnmodified key) fs
+		liftIO $ nukeFile obj
+		case mfile of
+			Just unmodified ->
+				unlessM (checkedCopyFile key unmodified obj Nothing)
+					lostcontent
+			Nothing -> lostcontent
+
 	lostcontent = logStatus key InfoMissing
 
 cleanupNew :: FilePath -> Key -> CommandCleanup

Test.hs

@@ -212,6 +212,7 @@ unitTests note = testGroup ("Unit Tests " ++ note)
 	, testCase "move" test_move
 	, testCase "copy" test_copy
 	, testCase "lock" test_lock
+	, testCase "lock (v6 --force)" test_lock_v6_force
 	, testCase "edit (no pre-commit)" test_edit
 	, testCase "edit (pre-commit)" test_edit_precommit
 	, testCase "partial commit" test_partial_commit
@@ -613,6 +614,23 @@ test_lock = intmpclonerepoInDirect $ do
 	r' <- git_annex "drop" [annexedfile]
 	not r' @? "drop wrongly succeeded with no known copy of modified file"
 
+-- Regression test: lock --force when work tree file
+-- was modified lost the (unmodified) annex object.
+-- (Only occurred when the keys database was out of sync.)
+test_lock_v6_force :: Assertion
+test_lock_v6_force = intmpclonerepoInDirect $ do
+	git_annex "upgrade" [] @? "upgrade failed"
+	whenM (annexeval Annex.Version.versionSupportsUnlockedPointers) $ do
+		git_annex "get" [annexedfile] @? "get of file failed"
+		git_annex "unlock" [annexedfile] @? "unlock failed in v6 mode"
+		annexeval $ do
+			dbdir <- Annex.fromRepo Annex.Locations.gitAnnexKeysDb
+			liftIO $ removeDirectoryRecursive dbdir
+		writeFile annexedfile "test_lock_v6_force content"
+		not <$> git_annex "lock" [annexedfile] @? "lock of modified file failed to fail in v6 mode"
+		git_annex "lock" ["--force", annexedfile] @? "lock --force of modified file failed in v6 mode"
+		annexed_present_locked annexedfile
+
 test_edit :: Assertion
 test_edit = test_edit' False