Commands that want to use it have to run their seek action inside
allowConcurrentOutput. Which seems reasonable; perhaps some future command
will want to support the -J flag but not use regions.
The region state moved from Annex to MessageState. This makes sense
organizationally, and note that some uses of onLocal use a different Annex
state, but pass the MessageState into it, which is what is needed.
There should be no behavior changes in this commit, it just adds a more
expressive data type and adjusts code that had been passing around a [UUID]
or sometimes a Maybe Remote to instead use [VerifiedCopy].
Although, since some functions were taking two different [UUID] lists,
there's some potential for me to have gotten it horribly wrong.
* When annex objects are received into git repositories, their checksums are
verified then too.
* To get the old, faster, behavior of not verifying checksums, set
annex.verify=false, or remote.<name>.annex-verify=false.
* setkey, rekey: These commands also now verify that the provided file
matches the key, unless annex.verify=false.
* reinject: Already verified content; this can now be disabled by
setting annex.verify=false.
recvkey and reinject already did verification, so removed now duplicate
code from them. fsck still does its own verification, which is ok since it
does not use getViaTmp, so verification doesn't happen twice when using fsck
--from.
Now it suffices to run git remote add, followed by git-annex sync. Now the
remote is automatically initialized for use by git-annex, where before the
git-annex branch had to manually be pushed before using git-annex sync.
Note that this involved changes to git-annex-shell, so if the remote is
using an old version, the manual push is still needed.
Implementation required git-annex-shell be changed, so configlist can
autoinit a repository even when no git-annex branch has been pushed yet.
Unfortunate because we'll have to wait for it to get deployed to servers
before being able to rely on this change in the documentation.
Did consider making git-annex sync push the git-annex branch to repos that
didn't have a uuid, but this seemed difficult to do without complicating it
in messy ways.
It would be cleaner to split a command out from configlist to handle
the initialization. But this is difficult without sacrificing backwards
compatability, for users of old git-annex versions which would not use the
new command.
This is a work in progress. It compiles and is able to do basic command
dispatch, including git autocorrection, while using optparse-applicative
for the core commandline parsing.
* Many commands are temporarily disabled before conversion.
* Options are not wired in yet.
* cmdnorepo actions don't work yet.
Also, removed the [Command] list, which was only used in one place.
The branch needs to be created when merging from the remote in sync,
since we diff between it and the remote's sync branch. But git annex merge
should not be creating sync branches.
This is needed because when preferred content matches on files,
the second pass would otherwise want to drop all keys. Using a bloom filter
avoids this, and in the case of a false positive, a key will be left
undropped that preferred content would allow dropping. Chances of that
happening are a mere 1 in 1 million.
This makes git annex unused use around 48 mb more memory than it did before,
but the massive increase in accuracy makes this worthwhile for all but the
smallest systems.
Also, I want to use the bloom filter for sync --all --content, to avoid
dropping files that the preferred content doesn't want, and 1/1000
false positives would be far too many in that use case, even if it were
acceptable for unused.
Actual memory use numbers:
1000: 21.06user 3.42system 0:26.40elapsed 92%CPU (0avgtext+0avgdata 501552maxresident)k
1000000: 21.41user 3.55system 0:26.84elapsed 93%CPU (0avgtext+0avgdata 549496maxresident)k
10000000: 21.84user 3.52system 0:27.89elapsed 90%CPU (0avgtext+0avgdata 549920maxresident)k
Based on these numbers, 10 million seemed a better pick than 1 million.
This works, and seems fairly robust. Clean get of 20 files at -J3. At -J10,
there are some messages about ssh multiplexing, probably due to a race
spinning up the ssh connection cacher. But, it manages to get all the files
ok regardless.
The progress bars are a scrambled mess though, due to bugs in
ascii-progress, which I've already filed. Particularly this one:
https://github.com/yamadapc/haskell-ascii-progress/issues/8
Seen for example, a newly checked out git submodule. In this case,
.git/HEAD is a raw sha, rather than the usual reference to a ref.
Removed currentSha in passing, since it was a more roundabout way of
doing what headSha does, and headSha is more robust.
See my comment in the bug report for analysis; basically this is safe
because it's a non-forced push, so won't lose history. Even if it was a
forced push or somehow races, things will eventually become consistent and
no git-annex branch info will be lost.
(This used to be done, but it forgot to do it since version 4.20130909.)
* sync: Use the ssh-options git config when doing git pull and push.
* remotedaemon: Use the ssh-options git config.
Note that the rename env var means that if a new git-annex calls an old one
for git-annex ssh, or a new calls an old, nothing much will go wrong;
just ssh caching won't happen.
Note that while the assistant detects changes made to remote names, I left
the commit message fixed rather than calculating it after every commit. It
doesn't seem worth the CPU to do the latter.
I think this is the last problimatic setCurrentDirectory. I also audited
for extrnal commands that git-annex might run with cwd = foo, and did not
find any that were passed any FilePath that might be absolute.
In the case where a remote of the bare repo has a fetch = configuration,
refs/remotes/origin/master will exist, and so the merge code path tried to
run in the bare repo.
This fixes all instances of " \t" in the code base. Most common case
seems to be after a "where" line; probably vim copied the two space layout
of that line.
Done as a background task while listening to episode 2 of the Type Theory
podcast.
Support users who have set commit.gpgsign, by disabling gpg signatures for
git-annex branch commits and commits made by the assistant.
The thinking here is that a user sets commit.gpgsign intending the commits
that they manually initiate to be gpg signed. But not commits made in the
background, whether by a deamon or implicitly to the git-annex branch.
gpg signing those would be at best a waste of CPU and at worst would fail,
or flood the user with gpg passphrase prompts, or put their signature on
changes they did not directly do.
See Debian bug #753720.
Also makes all commits done by git-annex go through a few central control
points, to make such changes easier in future.
Also disables commit.gpgsign in the test suite.
This commit was sponsored by Antoine Boegli.
When in direct mode, update the master branch after committing to the
annex/direct/master branch. Also, update the synced/master branch.
This fixes a topology A->B where both A and B are in direct mode and
running the assistant, and a change is made to B. Before this fix, A pulled
the changes from B, but since they were only on the annex/direct/master
branch, it did not merge them.
Note that I considered making the assistant merge the
remotes/B/annex/direct/master, but decided to keep it simple and only merge
the sync branches as before.
Only fsck and reinject and the test suite used the Backend, and they can
look it up as needed from the Key. This simplifies the code and also speeds
it up.
There is a small behavior change here. Before, all commands would warn when
acting on an annexed file with an unknown backend. Now, only fsck and
reinject show that warning.
For sync, saves 1 ssh connection per remote. For remotedaemon, the same
ssh connection that is already open to run git-annex-shell notifychanges
is reused to pull from the remote.
Only potential problem is that this also enables connection caching
when the assistant syncs with a ssh remote. Including the sync it does
when a network connection has just come up. In that case, cached ssh
connections are likely to be stale, and so using them would hang.
Until I'm sure such problems have been dealt with, this commit needs to
stay on the remotecontrol branch, and not be merged to master.
This commit was sponsored by Alexandre Dupas.
This is a new feature, it was not handled before, since it's a bit of an
edge case. However, it can be handled exactly the same as a file/dir
conflict, just leave the non-annexed item alone.
While implementing this, the core resolveMerge' function got a lot simpler
and clearer. Note especially that where before there was an asymetric call to
stagefromdirectmergedir, now graftin is called symmetrically in both cases.
And, in order to add that `graftin us`, the current branch needed to be
known (if there is no current branch, there cannot be a merge conflict).
This led to some cleanups of how autoMergeFrom behaved when there is no
current branch.
This commit was sponsored by Philippe Gauthier.
I think that 751f496c11 didn't quite manage
to actually fix the bug, although I have not checked since its "fix" got
redone.
The test suite now actually checks the file staged in git is a symlink,
rather than relying on the bug casing a later sync failure. This seems a
more reliable way to detect it, and probably avoids a heisenbug in the test
suite.
Added test cases for both ways this can happen, with a conflict involving a
file, or a directory.
Cleaned up resolveMerge to not touch the work tree in direct mode, which
turned out to be the only way to handle things.. And makes it much nicer.
Still need to run test suite on windows.
Using the extract(1) program to do the heavy lifting.
Decided to make git-annex run pre-commit-annex when committing. Since
git-annex pre-commit also runs it, it'll be run when git commit is run too,
via the pre-commit hook. This basically gives back the pre-commit hook
that git-annex took away. The implementation avoids repeatedly looking
for the hook script when the assistant is running and committing
repeatedly; only checks if the hook is available once.
To make the script simpler, made git-annex metadata -s field?=value
only set a field when it's not already got a value.
This commit was sponsored by bak.
Removed instance, got it all to build using fromRef. (With a few things
that really need to show something using a ref for debugging stubbed out.)
Then added back Read instance, and made Logs.View use it for serialization.
This changes the view log format.
Fix bug in automatic merge conflict resolution code when used
on a filesystem not supporting symlinks, which resulted in it losing
track of the symlink bit of annexed files.
This was the underlying bug that was causing another test to fail,
which got worked around in 1c997fd08c.
I've chosen to keep 2 separate test cases since the old test case only
detected the problem accidentially.
Test suite passes on FAT & in windows, as well as on proper unix systems.
This commit was sponsored by Ellis Whitehead.
Need to include the uuid of the local repo in the list of belived locations
of a key after getting it, in order for the drop from remote to include it
in the numcopies calculation.
* sync --content: Honor annex-ignore configuration.
* sync: Don't try to sync with xmpp remotes, which are only currently
supported when using the assistant.
Several places assumed this would not happen, and when the AssociatedFile
was Nothing, did nothing.
As part of this, preferred content checks pass the Key around.
Note that checkMatcher is sometimes now called with Just Key and Just File.
It currently constructs a FileMatcher, ignoring the Key. However, if it
constructed a FileKeyMatcher, which contained both, then it might be
possible to speed up parts of Limit, which currently call the somewhat
expensive lookupFileKey to get the Key.
I have not made this optimisation yet, because I am not sure if the key is
always the same. Will need some significant checking to satisfy myself
that's the case..
I've been disliking how the command seek actions were written for some
time, with their inversion of control and ugly workarounds.
The last straw to fix it was sync --content, which didn't fit the
Annex [CommandStart] interface well at all. I have not yet made it take
advantage of the changed interface though.
The crucial change, and probably why I didn't do it this way from the
beginning, is to make each CommandStart action be run with exceptions
caught, and if it fails, increment a failure counter in annex state.
So I finally remove the very first code I wrote for git-annex, which
was before I had exception handling in the Annex monad, and so ran outside
that monad, passing state explicitly as it ran each CommandStart action.
This was a real slog from 1 to 5 am.
Test suite passes.
Memory usage is lower than before, sometimes by a couple of megabytes, and
remains constant, even when running in a large repo, and even when
repeatedly failing and incrementing the error counter. So no accidental
laziness space leaks.
Wall clock speed is identical, even in large repos.
This commit was sponsored by an anonymous bitcoiner.
Similar to the assistant, this honors any configured preferred content
expressions.
I am not entirely happpy with the implementation. It would be nicer if
the seek function returned a list of actions which included the individual
file gets and copies and drops, rather than the current list of calls to
syncContent. This would allow getting rid of the somewhat reundant display
of "sync file [ok|failed]" after the get/put display.
But, do that, withFilesInGit would need to somehow be able to construct
such a mixed action list. And it would be less efficient than the current
implementation, which is able to reuse several values between eg get and
drop.
Note that currently this does not try to satisfy numcopies when
getting/putting files (numcopies are of course checked when dropping
files!) This makes it like the assistant, and unlike get --auto
and copy --auto, which do duplicate files when numcopies is not yet
satisfied. I don't know if this is the right decision; it only seemed to
make sense to have this parallel the assistant as far as possible to start
with, since I know the assistant works.
This commit was sponsored by Øyvind Andersen Holm.
The assistant's commit code also always avoids git commit, for simplicity.
Indirect mode sync still does a git commit -a to catch unstaged changes.
Note that this means that direct mode sync no longer runs the pre-commit
hook or any other hooks git commit might call. The git annex pre-commit
hook action for direct mode is however explicitly run. (The assistant
already ran git commit with hooks disabled, so no change there.)
Now that direct mode sets core.bare=true, git's normal prohibition about
pushing into the currently checked out branch doesn't work.
A simple fix for this would be an update hook which blocks the pushes..
but git hooks must be executable, and git-annex needs to be usable on eg,
FAT, which lacks x bits.
Instead, enabling direct mode switches the branch (eg master) to a special
purpose branch (eg annex/direct/master). This branch is not pushed when
syncing; instead any changes that git annex sync commits get written to
master, and it's pushed (along with synced/master) to the remote.
Note that initialization has been changed to always call setDirect,
even if it's just setDirect False for indirect mode. This is needed because
if the user has just cloned a direct mode repo, that nothing has synced
with before, it may have no master branch, and only a annex/direct/master.
Resulting in that branch being checked out locally too. Calling setDirect False
for indirect mode moves back out of this branch, to a new master branch,
and ensures that a manual "git push" doesn't push changes directly to
the annex/direct/master of the remote. (It's possible that the user
makes a commit w/o using git-annex and pushes it, but nothing I can do
about that really.)
This commit was sponsored by Jonathan Harrington.
Note that this case is only fully automatically resolved in direct mode.
In indirect mode, git merge moves the file to file~HEAD, and replaces it
with the directory, and leaves the file in unmerged state, and sync doesn't
yet change that.
Done using a mode witness, which ensures it's fixed everywhere.
Fixing catFileKey was a bear, because git cat-file does not provide a
nice way to query for the mode of a file and there is no other efficient
way to do it. Oh, for libgit2..
Note that I am looking at tree objects from HEAD, rather than the index.
Because I cat-file cannot show a tree object for the index.
So this fix is technically incomplete. The only cases where it matters
are:
1. A new large file has been directly staged in git, but not committed.
2. A file that was committed to HEAD as a symlink has been staged
directly in the index.
This could be fixed a lot better using libgit2.
Ie, when there'a a conflicted merge we may get foo.variant-xxxx
created in a merge. If a second merge conflict occurs on that new file,
it was not falling back to putting in the whole key (which should stop
the merge conflicts happening for good, but is ugly).
There may be already staged changes from a prior `git annex add`,
so always commit.
Also, suppressed the commit output, since it contains noise due to
typechanged files in direct mode.
This is so git remotes on servers without git-annex installed can be used
to keep clients' git repos in sync.
This is a behavior change, but since annex-sync can be set to disable
syncing with a remote, I think it's acceptable.
* since this is a crippled filesystem anyway, git-annex doesn't use
symlinks on it
* so there's no reason to use the mixed case hash directories that we're
stuck using to avoid breaking everyone's symlinks to the content
* so we can do what is already done for all bare repos, and make non-bare
repos on crippled filesystems use the all-lower case hash directories
* which are, happily, all 3 letters long, so they cannot conflict with
mixed case hash directories
* so I was able to 100% fix this and even resuming `git annex add` in the
test case will recover and it will all just work.
Pass subcommand as a regular param, which allows passing git parameters
like -c before it. This was already done in the pipeing set of functions,
but not the command running set.
Refactored annex link code into nice clean new library.
Audited and dealt with calls to createSymbolicLink.
Remaining calls are all safe, because:
Annex/Link.hs: ( liftIO $ createSymbolicLink linktarget file
only when core.symlinks=true
Assistant/WebApp/Configurators/Local.hs: createSymbolicLink link link
test if symlinks can be made
Command/Fix.hs: liftIO $ createSymbolicLink link file
command only works in indirect mode
Command/FromKey.hs: liftIO $ createSymbolicLink link file
command only works in indirect mode
Command/Indirect.hs: liftIO $ createSymbolicLink l f
refuses to run if core.symlinks=false
Init.hs: createSymbolicLink f f2
test if symlinks can be made
Remote/Directory.hs: go [file] = catchBoolIO $ createSymbolicLink file f >> return True
fast key linking; catches failure to make symlink and falls back to copy
Remote/Git.hs: liftIO $ catchBoolIO $ createSymbolicLink loc file >> return True
ditto
Upgrade/V1.hs: liftIO $ createSymbolicLink link f
v1 repos could not be on a filesystem w/o symlinks
Audited and dealt with calls to readSymbolicLink.
Remaining calls are all safe, because:
Annex/Link.hs: ( liftIO $ catchMaybeIO $ readSymbolicLink file
only when core.symlinks=true
Assistant/Threads/Watcher.hs: ifM ((==) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file))
code that fixes real symlinks when inotify sees them
It's ok to not fix psdueo-symlinks.
Assistant/Threads/Watcher.hs: mlink <- liftIO (catchMaybeIO $ readSymbolicLink file)
ditto
Command/Fix.hs: stopUnless ((/=) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file)) $ do
command only works in indirect mode
Upgrade/V1.hs: getsymlink = takeFileName <$> readSymbolicLink file
v1 repos could not be on a filesystem w/o symlinks
Audited and dealt with calls to isSymbolicLink.
(Typically used with getSymbolicLinkStatus, but that is just used because
getFileStatus is not as robust; it also works on pseudolinks.)
Remaining calls are all safe, because:
Assistant/Threads/SanityChecker.hs: | isSymbolicLink s -> addsymlink file ms
only handles staging of symlinks that were somehow not staged
(might need to be updated to support pseudolinks, but this is
only a belt-and-suspenders check anyway, and I've never seen the code run)
Command/Add.hs: if isSymbolicLink s || not (isRegularFile s)
avoids adding symlinks to the annex, so not relevant
Command/Indirect.hs: | isSymbolicLink s -> void $ flip whenAnnexed f $
only allowed on systems that support symlinks
Command/Indirect.hs: whenM (liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f) $ do
ditto
Seek.hs:notSymlink f = liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f
used to find unlocked files, only relevant in indirect mode
Utility/FSEvents.hs: | Files.isSymbolicLink s = runhook addSymlinkHook $ Just s
Utility/FSEvents.hs: | Files.isSymbolicLink s ->
Utility/INotify.hs: | Files.isSymbolicLink s ->
Utility/INotify.hs: checkfiletype Files.isSymbolicLink addSymlinkHook f
Utility/Kqueue.hs: | Files.isSymbolicLink s = callhook addSymlinkHook (Just s) change
all above are lower-level, not relevant
Audited and dealt with calls to isSymLink.
Remaining calls are all safe, because:
Annex/Direct.hs: | isSymLink (getmode item) =
This is looking at git diff-tree objects, not files on disk
Command/Unused.hs: | isSymLink (LsTree.mode l) = do
This is looking at git ls-tree, not file on disk
Utility/FileMode.hs:isSymLink :: FileMode -> Bool
Utility/FileMode.hs:isSymLink = checkMode symbolicLinkMode
low-level
Done!!
