init: probe if sqlite works

Help the user get annex.dbdir configured when their filesystem is not
one that sqlite works on.

The change in Database.Handle makes an error from sqlite not be ignored
besides being displayed, which it was before. I can't see any reason
git-annex would want to ignore these errors.

I chose to use the fsck database rather than the keys database because
opening the keys database populates it, and see commit
b3c4579c79.

The placement of the call to checkSqliteWorks inside checkInitializeAllowed
avoids annex.uuid getting set before it's called.

Sponsored-by: Dartmouth College's Datalad project

Annex/Init.hs

@@ -1,6 +1,6 @@
 {- git-annex repository initialization
  -
- - Copyright 2011-2021 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2022 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -27,6 +27,7 @@ import qualified Git.Objects
 import Git.Types (fromConfigValue)
 import Git.ConfigTypes (SharedRepository(..))
 import qualified Annex.Branch
+import qualified Database.Fsck
 import Logs.UUID
 import Logs.Trust.Basic
 import Logs.Config
@@ -69,7 +70,9 @@ import Control.Concurrent.Async
 
 checkInitializeAllowed :: Annex a -> Annex a
 checkInitializeAllowed a = guardSafeToUseRepo $ noAnnexFileContent' >>= \case
-	Nothing -> a
+	Nothing -> do
+		checkSqliteWorks
+		a
 	Just noannexmsg -> do
 		warning "Initialization prevented by .noannex file (remove the file to override)"
 		unless (null noannexmsg) $
@@ -391,6 +394,21 @@ checkFifoSupport = unlessM probeFifoSupport $ do
 	warning "Disabling ssh connection caching."
 	setConfig (annexConfig "sshcaching") (Git.Config.boolConfig False)
 
+{- Sqlite needs the filesystem to support range locking. Some like CIFS
+ - do not, which will cause sqlite to fail with ErrorBusy. -}
+checkSqliteWorks :: Annex ()
+checkSqliteWorks = do
+	u <- getUUID
+	tryNonAsync (Database.Fsck.openDb u >>= Database.Fsck.closeDb) >>= \case
+		Right () -> return ()
+		Left e -> do
+			showLongNote $ "Detected a filesystem where Sqlite does not work."
+			showLongNote $ "(" ++ show e ++ ")"
+			showLongNote $ "To work around this problem, you can set annex.dbdir " ++
+				"to a directory on another filesystem."
+			showLongNote $ "For example: git config annex.dbdir $HOME/cache/git-annex"
+			giveup "Not initialized."
+
 checkSharedClone :: Annex Bool
 checkSharedClone = inRepo Git.Objects.isSharedClone
 

Database/Handle.hs

@@ -123,7 +123,7 @@ workerThread db tablename jobs = newconn
 	newconn = do
 		v <- tryNonAsync (runSqliteRobustly tablename db loop)
 		case v of
-			Left e -> hPutStrLn stderr $
+			Left e -> giveup $
 				"sqlite worker thread crashed: " ++ show e
 			Right cont -> cont
 	

doc/bugs/crippled_filesystem__58___SQLite3_returned_ErrorBusy.mdwn

@@ -86,3 +86,5 @@ add file1 ok
 When initializing the repo with v5 git-annex (git annex init --version=5 test), then the legacy direct mode is used and file addition works well.
 
 [[!tag projects/datalad]]
+
+> [[done]] --[[Joey]]

doc/bugs/crippled_filesystem__58___SQLite3_returned_ErrorBusy/comment_13_baafac7f80ff4b7cc4cf078e4ab969c3._comment

@@ -0,0 +1,21 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 13"""
+ date="2022-08-17T17:05:25Z"
+ content="""
+I've implemented probing by `git-annex init`, and it will display
+this message to help the user get it configured:
+
+	init  
+	  Detected a filesystem where Sqlite does not work.
+	
+	  (sqlite worker thread crashed: user error (SQLite3 returned ErrorBusy while attempting to perform close(synthetic)(after successful open)))
+	
+	  To work around this problem, you can set annex.dbdir to a directory on another filesystem.
+	
+	  For example: git config annex.dbdir $HOME/cache/git-annex
+	
+	git-annex: Not initialized.
+
+Going to close the bug since I think this is the best that it can be handled.
+"""]]