faster associated file replacement with upsert

Rather than first deleting and then inserting, upsert lets the key
associated with a file be updated in place.

Benchmarked with 100,000 files, and an empty keys database, running
reconcileStaged. It improved from 47 seconds to 34 seconds.
So this got reconcileStaged to be as fast as scanAssociatedFiles,
or faster -- scanAssociatedFiles benchmarks at 37 seconds.

(Also checked for other users of deleteWhere that could be sped up by
upsert. There are a couple, but they are not in performance critical
code paths, eg recordExportTreeCurrent is only run once per tree
export.)

I would have liked to rename FileKeyIndex to FileKeyUnique since it is
being used as a uniqueness constraint now, not just to get an index.
But, that gets converted into part of the SQL schema, and the name
is used by the upsert, so it can't be changed.

Sponsored-by: Dartmouth College's Datalad project

Database/Keys/SQL.hs

@@ -1,6 +1,6 @@
 {- Sqlite database of information about Keys
  -
- - Copyright 2015-2019 Joey Hess <id@joeyh.name>
+ - Copyright 2015-2021 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -36,15 +36,12 @@ import Data.Maybe
 -- (Unfortunatly persistent does not support indexes that are not
 -- uniqueness constraints; https://github.com/yesodweb/persistent/issues/109)
 --
--- KeyFileIndex contains both the key and the file because the combined
--- pair is unique, whereas the same key can appear in the table multiple
--- times with different files.
+-- To speed up queries for a key, there's KeyFileIndex, 
+-- which makes there be a covering index for keys.
 --
--- The other benefit to including the file in the index is that it makes
--- queries that include the file faster, since it's a covering index.
---
--- The KeyFileIndex only speeds up selects for a key, since it comes first.
--- To also speed up selects for a file, there's a separate FileKeyIndex.
+-- FileKeyIndex speeds up queries that include the file, since
+-- it makes there be a covering index for files. Note that, despite the name, it is
+-- used as a uniqueness constraint now.
 share [mkPersist sqlSettings, mkMigrate "migrateKeysDb"] [persistLowerCase|
 Associated
   key Key
@@ -79,12 +76,15 @@ queueDb a (WriteHandle h) = H.queueDb h checkcommit a
 	-- commit queue after 1000 changes
 	checkcommit sz _lastcommittime = pure (sz > 1000)
 
+-- Insert the associated file.
+-- When the file was associated with a different key before,
+-- update it to the new key.
 addAssociatedFile :: Key -> TopFilePath -> WriteHandle -> IO ()
-addAssociatedFile k f = queueDb $ do
-	-- If the same file was associated with a different key before,
-	-- remove that.
-	deleteWhere [AssociatedFile ==. af, AssociatedKey !=. k]
-	void $ insertUnique $ Associated k af
+addAssociatedFile k f = queueDb $
+	void $ upsertBy
+		(FileKeyIndex af k)
+		(Associated k af)
+		[AssociatedFile =. af, AssociatedKey =. k]
   where
 	af = SFilePath (getTopFilePath f)
 
@@ -108,7 +108,7 @@ getAssociatedFiles k = readDb $ do
 	return $ map (asTopFilePath . (\(SFilePath f) -> f) . associatedFile . entityVal) l
 
 {- Gets any keys that are on record as having a particular associated file.
- - (Should be one or none but the database doesn't enforce that.) -}
+ - (Should be one or none.) -}
 getAssociatedKey :: TopFilePath -> ReadHandle -> IO [Key]
 getAssociatedKey f = readDb $ do
 	l <- selectList [AssociatedFile ==. af] []