Split lines in the git-annex branch on \r as well as \n, to deal with \r\n terminated lines written by some versions of git-annex on Windows.

This fixes strange displays in some cases, including whereis showing
many duplicate locations, and showing more total copies than actually
exist.

It's unknown if that lead to data loss when eg, dropping. At the moment,
it seems unlikely it could, since the UUID with \r's appended is not the
same as a UUID without, and so no remote matches it.

It's also unknown if \r's can leak in on windows, perhaps when merging the
git-annex branch.

CHANGELOG

@@ -1,5 +1,8 @@
 git-annex (6.20160512) UNRELEASED; urgency=medium
 
+  * Split lines in the git-annex branch on \r as well as \n, to deal
+    with \r\n terminated lines written by some versions of git-annex on
+    Windows. This fixes strange displays in some cases.
   * Change git annex info remote encryption description to use wording
     closer to what's used in initremote.
   * webapp: Avoid confusing display of dead remotes.

COPYRIGHT

@@ -95,6 +95,38 @@ License: MIT-twitter
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
 
+Files: Logs/Line.hs
+Copyright: 2001, The University Court of the University of Glasgow.
+License: other
+  All rights reserved.
+  .
+  Redistribution and use in source and binary forms, with or without
+  modification, are permitted provided that the following conditions are met:
+  .
+  - Redistributions of source code must retain the above copyright notice,
+  this list of conditions and the following disclaimer.
+  .
+  - Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+  .
+  - Neither name of the University nor the names of its contributors may be
+  used to endorse or promote products derived from this software without
+  specific prior written permission.
+  .
+  THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY COURT OF THE UNIVERSITY OF
+  GLASGOW AND THE CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+  FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+  UNIVERSITY COURT OF THE UNIVERSITY OF GLASGOW OR THE CONTRIBUTORS BE LIABLE
+  FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+  DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+  CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+  LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+  OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+  DAMAGE.
+
 License: GPL-3+
  The full text of version 3 of the GPL is distributed as doc/license/GPL in
  this package's source, or in /usr/share/common-licenses/GPL-3 on

Logs/Line.hs

@@ -0,0 +1,51 @@
+{- 
+
+The Glasgow Haskell Compiler License
+
+Copyright 2001, The University Court of the University of Glasgow.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+- Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+- Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+- Neither name of the University nor the names of its contributors may be
+used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY COURT OF THE UNIVERSITY OF
+GLASGOW AND THE CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
+FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+UNIVERSITY COURT OF THE UNIVERSITY OF GLASGOW OR THE CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+-}
+
+module Logs.Line where
+
+-- This is the same as Data.List.lines, with \r added.
+-- This works around some versions of git-annex which wrote \r
+-- into git-annex branch files on Windows. Those \r's sometimes
+-- accumulated over time, so a single line could end with multiple \r's
+-- before the \n.
+splitLines :: String -> [String]
+splitLines "" =  []
+splitLines s =  cons (case break (\c -> c == '\n' || c == '\r') s of
+	(l, s') -> (l, case s' of
+		[]      -> []
+		_:s''   -> splitLines s''))
+  where
+	cons ~(h, t) = h : t

Logs/MapLog.hs

@@ -18,6 +18,7 @@ import Data.Time.Clock.POSIX
 
 import Common
 import Logs.TimeStamp
+import Logs.Line
 
 data TimeStamp = Unknown | Date POSIXTime
 	deriving (Eq, Ord, Show)
@@ -38,7 +39,7 @@ showMapLog fieldshower valueshower = unlines . map showpair . M.toList
 		unwords ["0", fieldshower f, valueshower v]
 
 parseMapLog :: Ord f => (String -> Maybe f) -> (String -> Maybe v) -> String -> MapLog f v
-parseMapLog fieldparser valueparser = M.fromListWith best . mapMaybe parse . lines
+parseMapLog fieldparser valueparser = M.fromListWith best . mapMaybe parse . splitLines
   where
 	parse line = do
 		let (ts, rest) = splitword line

Logs/Presence/Pure.hs

@@ -12,6 +12,7 @@ import qualified Data.Map as M
 
 import Annex.Common
 import Logs.TimeStamp
+import Logs.Line
 import Utility.QuickCheck
 
 data LogLine = LogLine {
@@ -25,7 +26,7 @@ data LogStatus = InfoPresent | InfoMissing | InfoDead
 
 {- Parses a log file. Unparseable lines are ignored. -}
 parseLog :: String -> [LogLine]
-parseLog = mapMaybe parseline . lines
+parseLog = mapMaybe parseline . splitLines
   where
 	parseline l = LogLine
 		<$> parsePOSIXTime d

Logs/SingleValue.hs

@@ -16,6 +16,7 @@ module Logs.SingleValue where
 import Annex.Common
 import qualified Annex.Branch
 import Logs.TimeStamp
+import Logs.Line
 
 import qualified Data.Set as S
 import Data.Time.Clock.POSIX
@@ -37,7 +38,7 @@ showLog = unlines . map showline . S.toList
 	showline (LogEntry t v) = unwords [show t, serialize v]
 
 parseLog :: (Ord v, SingleValueSerializable v) => String -> Log v
-parseLog = S.fromList . mapMaybe parse . lines
+parseLog = S.fromList . mapMaybe parse . splitLines
   where
 	parse line = do
 		let (ts, s) = splitword line

Logs/Transitions.hs

@@ -19,6 +19,7 @@ import qualified Data.Set as S
 
 import Annex.Common
 import Logs.TimeStamp
+import Logs.Line
 
 transitionsLog :: FilePath
 transitionsLog = "transitions.log"
@@ -50,7 +51,7 @@ showTransitions = unlines . map showTransitionLine . S.elems
 
 {- If the log contains new transitions we don't support, returns Nothing. -}
 parseTransitions :: String -> Maybe Transitions
-parseTransitions = check . map parseTransitionLine . lines
+parseTransitions = check . map parseTransitionLine . splitLines
   where
 	check l
 		| all isJust l = Just $ S.fromList $ catMaybes l

Logs/UUIDBased.hs

@@ -35,6 +35,7 @@ import Common
 import Types.UUID
 import Logs.MapLog
 import Logs.TimeStamp
+import Logs.Line
 
 type Log v = MapLog UUID v
 
@@ -50,7 +51,7 @@ parseLog :: (String -> Maybe a) -> String -> Log a
 parseLog = parseLogWithUUID . const
 
 parseLogWithUUID :: (UUID -> String -> Maybe a) -> String -> Log a
-parseLogWithUUID parser = M.fromListWith best . mapMaybe parse . lines
+parseLogWithUUID parser = M.fromListWith best . mapMaybe parse . splitLines
   where
 	parse line
 		-- This is a workaround for a bug that caused

doc/bugs/Whereis_reports_same_UUID_multiple_times/comment_5_2355fd90d4ff8dd440bf11348a8daa73._comment

@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 5"""
+ date="2016-05-27T15:40:16Z"
+ content="""
+I've developed a patch which yields a good whereis display in this repo.
+
+Still remains to be seen if there's some code path that currently causes
+'\r' to get added in the current version of git-annex on Windows.
+"""]]