uninit: Fix crash due to trying to write to deleted keys db.

Reversion introduced by v6 mode support, affects v5 too.

Also fix a similar crash when the webapp is used to delete a repository.

Assistant/WebApp/Configurators/Delete.hs

@@ -17,17 +17,15 @@ import Assistant.Sync
 import qualified Remote
 import qualified Git
 import Config.Files
-import Utility.FileMode
 import Logs.Trust
 import Logs.Remote
 import Logs.PreferredContent
 import Types.StandardGroups
 import Annex.UUID
+import Command.Uninit (prepareRemoveAnnexDir)
 
-import System.IO.HVFS (SystemFS(..))
 import qualified Data.Text as T
 import qualified Data.Map as M
-import System.Path
 
 notCurrentRepo :: UUID -> Handler Html -> Handler Html
 notCurrentRepo uuid a = do
@@ -99,12 +97,8 @@ deleteCurrentRepository = dangerPage $ do
 				rs <- syncRemotes <$> getDaemonStatus
 				mapM_ (\r -> changeSyncable (Just r) False) rs
 
-			{- Make all directories writable and files writable
-			 - so all annexed content can be deleted. -}
-			liftIO $ do
-				recurseDir SystemFS dir
-					>>= mapM_ (void . tryIO . allowWrite)
-				removeDirectoryRecursive =<< absPath dir
+			liftAnnex $ prepareRemoveAnnexDir dir
+			liftIO $ removeDirectoryRecursive =<< absPath dir
 			
 			redirect ShutdownConfirmedR
 		_ -> $(widgetFile "configurators/delete/currentrepository")

CHANGELOG

@@ -15,6 +15,9 @@ git-annex (6.20160614) UNRELEASED; urgency=medium
   * fsck: Fix a reversion in direct mode fsck of a file that is
     present when the location log thinks it is not. Reversion introduced
     in version 5.20151208.
+  * uninit: Fix crash due to trying to write to deleted keys db.
+    Reversion introduced by v6 mode support, affects v5 too.
+  * Fix a similar crash when the webapp is used to delete a repository.
 
  -- Joey Hess <id@joeyh.name>  Mon, 13 Jun 2016 21:52:24 -0400
 

Command/Uninit.hs

@@ -13,6 +13,7 @@ import qualified Git
 import qualified Git.Command
 import qualified Command.Unannex
 import qualified Annex.Branch
+import qualified Database.Keys
 import Annex.Content
 import Annex.Init
 import Utility.FileMode
@@ -61,7 +62,7 @@ finish = do
 	annexdir <- fromRepo gitAnnexDir
 	annexobjectdir <- fromRepo gitAnnexObjectDir
 	leftovers <- removeUnannexed =<< getKeysPresent InAnnex
-	liftIO $ prepareRemoveAnnexDir annexdir
+	prepareRemoveAnnexDir annexdir
 	if null leftovers
 		then liftIO $ removeDirectoryRecursive annexdir
 		else error $ unlines
@@ -89,9 +90,17 @@ finish = do
 	liftIO exitSuccess
 
 {- Turn on write bits in all remaining files in the annex directory, in
- - preparation for removal. -}
-prepareRemoveAnnexDir :: FilePath -> IO ()
-prepareRemoveAnnexDir annexdir =
+ - preparation for removal. 
+ -
+ - Also closes sqlite databases that might be in the directory,
+ - to avoid later failure to write any cached changes to them. -}
+prepareRemoveAnnexDir :: FilePath -> Annex ()
+prepareRemoveAnnexDir annexdir = do
+	Database.Keys.closeDb
+	liftIO $ prepareRemoveAnnexDir' annexdir
+
+prepareRemoveAnnexDir' :: FilePath -> IO ()
+prepareRemoveAnnexDir' annexdir =
 	recurseDir SystemFS annexdir >>= mapM_ (void . tryIO . allowWrite)
 
 {- Keys that were moved out of the annex have a hard link still in the

Test.hs

@@ -1837,7 +1837,7 @@ cleanup = cleanup' False
 
 cleanup' :: Bool -> FilePath -> IO ()
 cleanup' final dir = whenM (doesDirectoryExist dir) $ do
-	Command.Uninit.prepareRemoveAnnexDir dir
+	Command.Uninit.prepareRemoveAnnexDir' dir
 	-- This sometimes fails on Windows, due to some files
 	-- being still opened by a subprocess.
 	catchIO (removeDirectoryRecursive dir) $ \e ->

doc/bugs/git_uninit_on_OS_X_causes_SqlLite3_error.mdwn

@@ -1,3 +1,5 @@
+[[!meta title="git annex uninit causes SqlLite3 error"]]
+
 ### Please describe the problem.
 I am basically having issues with `git annex uninit`
 
@@ -74,3 +76,5 @@ Now if I add a local file I get a different error
 ### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
 
 I am super excited about what I can do with git-annex. I hope to setup and maintain encrypted repo(s) of some of my files, and access them by cloning a local copy of the encrypted repo and getting the files I want, using them, and then deleting the local copy.
+
+> [[fixed|done]] --[[Joey]]

doc/bugs/git_uninit_on_OS_X_causes_SqlLite3_error/comment_1_be3aaa58fd3adfa5eeb893c205aa871c._comment

@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 1"""
+ date="2016-07-12T17:48:50Z"
+ content="""
+Not OSX specific; reproduced on Linux.
+
+Instrumentation shows that removeInodeCaches is being called, when it
+unannexes the annexed file. This is why a file has to have been added to
+the repo to get the crash.
+
+It's actually not necessary for removeInodeCaches to be called in a v5
+repo, only in v6. If the code checked for v6 mode before writing to the
+database, such problems would be avoided except for in v6 mode.
+
+But, the actual fix is to make uninit close this and all other sqlite
+db's before deleting the .git/annex directory.
+"""]]