invalidate recorded content identifier tree when export changes
Fix bug that made changes to a special remote sometimes be missed when
importing a tree from it. The diff import would miss when a change was
exported, then manually undone on the special remote (eg deleting a newly
exported file). A full import is needed to catch such changes.
After upgrading, any such missed changes will be included in the next
tree imported from a special remote. This happens because the previously
recorded content identifier tree does not have export information included,
so it is treated as invalid, and a full import is done.
Unfortunately, this does mean that after each export, the next import will
be a full import. Which can take significantly longer than the diff import
does, when there are a lot of files in the tree.
It would be better if exporting also update the content identifier tree.
However, I don't know if that can be done inexpensively. It would be future
optimisation work, in any case.
(That could only be done for an export that is run in the same
repository as the import. When an export is run in a different repository,
the export.log gets updated, and that propagates to the repository where
import is later run. At that point, a full import is done.)
prevent deadlock when reconcileStaged runs restagePointerFiles
Fix hang that could occur when using git-annex adjust on a branch with a
number of files greater than annex.queuesize. Or potentially other
commands.
When reconcileStaged is running, the database is being opened. But
restagePointerFiles closes the database, and later writes to it. So it will
deadlock if called by reconcileStaged.
The deadlock occurred when the git queue happened to be full, causing
adding a call to restagePointerFiles to it to flush the queue and
restagePointerFiles to run at the wrong time.
Fixed by making reconcileStaged, when it populates or depopulates a pointer
file, arrange for restagePointerFiles to be run as a cleanup action, rather
than from the git queue.
But, what if restagePointerFiles is already in the git queue before
reconcileStaged is run? If it adds anything else to the git queue, causing
the queue to flush, it would still deadlock. To avoid this hypothetical
situation, added a Annex.inreconcilestaged, and made restagePointerFiles
check it and not do anything.
Note that, I did consider the simpler approach of only running
restagePointerFiles as a cleanup action, rather than from the git queue.
But see commit 6a3bd283b8af53f810982e002e435c0d7c040c59 for why it was made
to use the queue in the first place. I wanted to avoid tying this bug fix
to a behavior change.
enableremote: Disallow using type= to attempt to change the type of an existing remote
Changing the type out from under an existing special remote exposes the
existing config to something that may interpret it wildly differently. As
seen in the bug report, this can even result in behavior that makes
git-annex say it's buggy. So prevent the user from doing this. --sameas is
the better way.
tag repronim based on https://git-annex.branchable.com/forum/Is_there_a_way_to_have_assistant_add_files_locked__63__/#comment-096bedb2d22d5aae6a51a53179372d4f
improve error message when SETCREDS overwrites git-annex config
That is not allowed, so it's not a bug in git-annex when it happens and
instead tell the special remote developer how it's messed up.
Note that currently only Remote.External can overwrite the parsed remote
config with a PassedThrough value. PassedThrough values are otherwise
only generated for configs that are not parsed by the remote config
parser.
work around file-io not setting locale encoding when opening a Handle
Works around this bug https://github.com/haskell/file-io/issues/45
The fix is in Utility.FileIO.CloseOnExec because all use of file-io is
already wrapped through that module. Although perhaps that ought to be
refactored at this point.
I'd hope that file-io will eventually fix this bug, and also provide
CloseOnExec variants of its functions. That would allow depending on the
fixed version, and removing this ugly code.
Note that, functions like readFile that don't care about the encoding
due to reading/writing a ByteString were kept optimally fast by not
setting the encoding. This avoids an IORef read and write per open.
Improve performance when used with a local git remote that has a large working tree
git write-tree was being run once per file git-annex acts on when eg,
getting files, which is slow when the remote repository has a large
tree.
onLocal calls quiesce after each action, and quiesce closes the keys db
since [[!commit ba7ecbc6a9c]]. Which has a relevant comment about
performance. I have not addressed that, the keys db still gets closed and
reopened after each file.
Turns out that, since git write-tree was run by each call to
reconcileStaged, the .git/annex/keysdb.cache value was never the
same as the git index's inode. Because git write-tree updates the index's
mtime even when no changes have been made.
And so, when the database got closed and reopened, reconcileStaged would
see a changed index, and run git write-tree again. Over and over.
I considered writing the index's new inodecache after write-tree to the
keysdb.cache, but that would be vulnerable to a race, if the index was
changed just after write-tree.
The fix was to stop using keysb.cache at all. When the database is closed
and later reopened by the same process, avoid re-doing reconcileStaged.
Now that .git/annex/keysdb.cache is no longer used. It could be removed,
but the time overhead of removing it would be more than the space overhead
of keeping it. Defferred removal to the v11 upgrade.
convert withFile and withBinaryFile to close-on-exec safe versions
At this point, every call in git-annex to withFile, openBinaryFile,
withBinaryFile, appendFile, and openTempFile, readFile, and writeFile
have been converted.
Sponsored-by: the NIH-funded NICEMAN (ReproNim TR&D3) project
Exported by Common, so they will be available everywhere.
These are the same as readFile, writeFile, appendFile.
But have two benefits:
* They take OsPath, so using them avoids converting back and forth
unncessarily.
* They use the close-on-exec flag so can't leak FDs to child processes.
Unlike the standard Haskell versions which unfortunately have that
wart currently. (I do hope the standard versions get fixed
eventually.)
Sponsored-by: the NIH-funded NICEMAN (ReproNim TR&D3) project
Utility.FileIO: set close-on-exec flag for all functions
Utility.FileIO.CloseOnExec is largely copied from
System.File.OsPath.Internal with the simple modification of
setting the flag.
Unfortunately, openTempFile does not set the flag when
opening the file, but afterwards, leaving it vulnerable to a race.
A lot of code, including posix and windows specific code,
would need to be copied from file-io in order to fix that.
Still, I consider this implementation a placeholder, it doesn't truely
fix all instances of the problem.
I hope that this will be addressed in file-io itself, see
https://github.com/haskell/file-io/issues/44
Utility.FileIO.CloseOnExec could form the basis of a
file-io-closeonexec library, depending on how things go with that
issue.
Sponsored-by: the NIH-funded NICEMAN (ReproNim TR&D3) project
It was already default in stack builds, now it is default in cabal
builds as well.
Add build warnings when git-annex is built without the OsPath build flag.
git-annex version: Report on whether it was built with the OsPath build flag.
Having the flag on by default was always the plan, and this is a good time to
make the change. A bit of added urgency comes from the close-on-exec leak
issue. Fixing that is going to need reimplentation of things like openFile.
Needing to reimplenment it twice is not very appealing, especially since the
FilePath version of it has an implementation that cannot be easily copied and
tweaked. If OsPath is on by default, I can start with only implementing
openFile for it, and fix the bug in that build. And perhaps avoid doing the
extra work that will later get thrown away when this transition finishes.
Note that at this point, Debian still needs to package file-io. Hopefully, they
will package it, rather than turning off the OsPath build flag.
convert all bytestring readFile/writeFile to use Utility.FileIO
This is groundwork for setting the close-on-exec flag when opening
files, which will be done in Utility.FileIO or a similar module using the same
function names. The bytestring library does not set that flag, even though it
could, and IMHO should.
Note that there are many calls to the Prelude's readFile/writeFile/appendFile
still in git-annex, and this does not address those.
Sponsored-by: the NIH-funded NICEMAN (ReproNim TR&D3) project
projects / git-annex.git / log