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Thanks, Sean T Parsons
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This avoids all the complication about redundant work discussed in
the previous try at fixing this. At the expense of needing each command
that could have the problem to be patched to simply wrap the action in
onlyActionOn once the key is known. But there do not seem to be many
such commands.
onlyActionOn' should not be used with a CommandStart (or CommandPerform),
although the types do allow it. onlyActionOn handles running the whole
CommandStart chain. I couldn't immediately see a way to avoid mistken
use of onlyActionOn'.
This commit was supported by the NSF-funded DataLad project.
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After a false start, I found a fairly non-intrusive way to deal with it.
Although it only handles transfers -- there may be issues with eg
concurrent dropping of the same key, or other operations.
There is no added overhead when -J is not used, other than an added
inAnnex check. When -J is used, it has to maintain and check a small
Set, which should be negligible overhead.
It could output some message saying that the transfer is being done by
another thread. Or it could even display the same progress info for both
files that are being downloaded since they have the same content. But I
opted to keep it simple, since this is rather an edge case, so it just
doesn't say anything about the transfer of the file until the other
thread finishes.
Since the deferred transfer action still runs, actions that do more than
transfer content will still get a chance to do their other work. (An
example of something that needs to do such other work is P2P.Annex,
where the download always needs to receive the content from the peer.)
And, if the first thread fails to complete a transfer, the second thread
can resume it.
But, this unfortunately means that there's a risk of redundant work
being done to transfer a key that just got transferred.
That's not ideal, but should never cause breakage; the same
thing can occur when running two separate git-annex processes.
The get/move/copy/mirror --from commands had extra inAnnex checks added,
inside the download actions. Without those checks, the first thread
downloaded the content, and then the second thread woke up and
downloaded the same content redundantly.
move/copy/mirror --to is left doing redundant uploads for now. It
would need a second checkPresent of the remote inside the upload
to avoid them, which would be expensive. A better way to avoid
redundant work needs to be found..
This commit was supported by the NSF-funded DataLad project.
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Before, there was a window where interrupting an add could result in the
file being moved into the annex, with no symlink yet created.
This commit was supported by the NSF-funded DataLad project.
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Fix process and file descriptor leak that was exposed when git-annex was
built with ghc 8.2.1. Apparently ghc has changed its behavior of GC
of open file handles that are pipes to running processes. That
broke git-annex test on OSX due to running out of FDs.
Audited for all uses of Annex.new and made stopCoProcesses be called
once it's done with the state. Fixed several places that might have
leaked in other situations than running the test suite.
This commit was sponsored by Ewen McNeill.
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Using annexeval to run probeCrippledFileSystem' caused Git.CurrentRepo.get
to be run. Fixed easily since probeCrippledFileSystem' had no need to use
the Annex monad.
This commit was sponsored by Ethan Aubin.
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Also deletes any tagged pushes that the assistant might have done,
since those would also prevent resetting a branch back.
This commit was sponsored by andrea rota.
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to avoid the user being surprised in cases where that behavior is not desired or expected
This commit was supported by the NSF-funded DataLad project.
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Assistant still todo.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon
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Now when one repository has exported a tree, another repository can get
files from the export, after syncing.
There's a bug: While the database update works, somehow the database on
disk does not get updated, and so the database update is run the next
time, etc. Wasn't able to figure out why yet.
This commit was sponsored by Ole-Morten Duesund on Patreon.
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New table needed to look up what filenames are used in the currently
exported tree, for reasons explained in export.mdwn.
Also, added smart constructors for ExportLocation and ExportDirectory to
make sure they contain filepaths with the right direction slashes.
And some code refactoring.
This commit was sponsored by Francois Marier on Patreon.
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This commit was sponsored by Jack Hill on Patreon.
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It was not getting old lines removed, because the tree graft confused
the updater, so it union merged from the previous git-annex branch,
which still contained the old lines. Fixed by carefully using setIndexSha.
This commit was supported by the NSF-funded DataLad project.
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Don't allow "exporttree=yes" to be set when the special remote
does not support exports. That would be confusing since the user would
set up a special remote for exports, but `git annex export` to it would
later fail.
This commit was supported by the NSF-funded DataLad project.
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Straightforward enough, except for the needed belt-and-suspenders sanity
checks to avoid foot shooting due to exports not being key/value stores.
* Even when annex.verify=false, always verify from exports.
* Only get files from exports that use a backend that supports
checksum verification.
* Never trust exports, even if the user says to, because then
`git annex drop` would drop content if the export seemed to contain
a copy.
This commit was supported by the NSF-funded DataLad project.
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Went with a separate db per export remote, rather than a single export
database. Mostly because there will probably not be a lot of separate
export remotes, and it might be convenient to be able to delete a given
remote's export database.
This commit was supported by the NSF-funded DataLad project.
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* Only export to remotes that were initialized to support it.
* Prevent storing key/value on export remotes.
* Prevent enabling exporttree=yes and encryption in the same remote.
SetupStage Enable was changed to take the old RemoteConfig.
This allowed only setting exporttree when initially setting up a
remote, and not configuring it later after stuff might already be stored
in the remote.
Went with =yes rather than =true for consistency with other parts of
git-annex. Changed docs accordingly.
This commit was supported by the NSF-funded DataLad project.
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So it will be available later and elsewhere, even after GC.
I first though to use git update-index to do this, but feeding it a line
with a tree object seems to always cause it to generate a git subtree
merge. So, fell back to using the Git.Tree interface to maniupulate the
trees, and not involving the git-annex branch index file at all.
This commit was sponsored by Andreas Karlsson.
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writing to files whose write bit is not set.
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Security fix: Disallow hostname starting with a dash, which would get
passed to ssh and be treated an option. This could be used by an attacker
who provides a crafted ssh url (for eg a git remote) to execute arbitrary
code via ssh -oProxyCommand.
No CVE has yet been assigned for this hole.
The same class of security hole recently affected git itself,
CVE-2017-1000117.
Method: Identified all places where ssh is run, by git grep '"ssh"'
Converted them all to use a SshHost, if they did not already, for
specifying the hostname.
SshHost was made a data type with a smart constructor, which rejects
hostnames starting with '-'.
Note that git-annex already contains extensive use of Utility.SafeCommand,
which fixes a similar class of problem where a filename starting with a
dash gets passed to a program which treats it as an option.
This commit was sponsored by Jochen Bartl on Patreon.
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anymore
To work around the problem that the external special remote protocol does
not support keys containing spaces.
This commit was sponsored by Denis Dzyubenko on Patreon.
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handing spaces in keys would complicate things like the external special remote protocol.
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Added remote configuration settings annex-ignore-command and
annex-sync-command, which are dynamic equivilants of the annex-ignore
and annex-sync configurations.
For this I needed a new DynamicConfig infrastructure. Its implementation
should be as fast as before when there is no dynamic config, and it caches
so shell commands are only run once.
Note that annex-ignore-command exits nonzero when the remote should be ignored.
While that may seem backwards, it allows using the same command for it as
for annex-sync-command when you want to disable both.
This commit was sponsored by Trenton Cronholm on Patreon.
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Removed its Show instance.
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Can be used to override the default timestamps used in log files in the
git-annex branch. This is a dangerous environment variable; use with
caution.
Note that this only affects writing to the logs on the git-annex branch.
It is not used for metadata in git commits (other env vars can be set for
that).
There are many other places where timestamps are still used, that don't
get committed to git, but do touch disk. Including regular timestamps
of files, and timestamps embedded in some files in .git/annex/, including
the last fsck timestamp and timestamps in transfer log files.
A good way to find such things in git-annex is to get for getPOSIXTime and
getCurrentTime, although some of the results are of course false positives
that never hit disk (unless git-annex gets swapped out..)
So this commit does NOT necessarily make git-annex comply with some HIPPA
privacy regulations; it's up to the user to determine if they can use it in
a way compliant with such regulations.
Benchmarking: It takes 0.00114 milliseconds to call getEnv
"GIT_ANNEX_VECTOR_CLOCK" when that env var is not set. So, 100 thousand log
files can be written with an added overhead of only 0.114 seconds. That
should be by far swamped by the actual overhead of writing the log files
and making the commit containing them.
This commit was supported by the NSF-funded DataLad project.
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a git remote where git-annex-shell is not installed.
This commit was sponsored by andrea rota.
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* Added annex.resolvemerge configuration, which can be set to false to
disable the usual automatic merge conflict resolution done by git-annex
sync and the assistant.
* sync: Added --no-resolvemerge option.
Note that disabling merge conflict resolution is probably not a good idea
in a direct mode repo or adjusted branch. Since updates to both are done
outside the usual work tree, if it fails the tree is not left in a
conflicted state, and it would be hard to manually resolve the conflict.
Still, made annex.resolvemerge be supported in those cases for consistency.
This commit was sponsored by Riku Voipio.
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orElse is great, but was not the right thing to use here because
waitTakeLock could retry for other reasons than the lock being held,
which made tryTakeLock fail when it shouldn't.
Instead, move the code to tryTakeLock and implement waitTakeLock using
tryTakeLock and retry.
(Also, in runTransfer, when checkSaneLock fails, dropLock to avoid leaking a
lock handle.)
This commit was supported by the NSF-funded DataLad project.
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When built with concurrent-output 1.9, ssh password prompts will no longer
interfere with the -J display.
To avoid flicker, only done when ssh actually does need to prompt;
ssh is first run in batch mode and if that succeeds the connection is up
and no need to clear regions.
This commit was supported by the NSF-funded DataLad project.
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(and remove debug print)
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changes into adjusted branches.
Might want to remove this when it gets fixed, in case adjusted branches are
used in a repo with a great many refs, which would become unnecessarily
slow.
This commit was supported by the NSF-funded DataLad project.
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Removed dependency on MissingH, instead depending on the split
library.
After laying groundwork for this since 2015, it
was mostly straightforward. Added Utility.Tuple and
Utility.Split. Eyeballed System.Path.WildMatch while implementing
the same thing.
Since MissingH's progress meter display was being used, I re-implemented
my own. Bonus: Now progress is displayed for transfers of files of
unknown size.
This commit was sponsored by Shane-o on Patreon.
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Cryptonite is faster and allocates less, and I want to get rid of
MissingH use.
Note that the new dependency on memory is free; it's a dependency of
cryptonite.
This commit was supported by the NSF-funded DataLad project.
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Moving toward dropping MissingH dep.
I think I've addressed the problem identified earlier in
7141943075211f9dd4959ca4c8b0a274f48dc9ff. On Windows,
absPathFrom "/tmp/repo/xxx" "y/bar" would be "/tmp/repo/xxx\\y/bar",
which then confuses relPathDirToFile. Fixed by converting to unix (git)
style paths.
Also, relPathDirToFile was splitting only on \\ on windows and not /
which broke the example in 7141943075211f9dd4959ca4c8b0a274f48dc9ff of
relPathDirToFile (absPathFrom "/tmp/repo/xxx" "y/bar") "/tmp/repo/.git/annex/objects/xxx"
Now, on windows, that will yield "..\\..\\..\\.git/annex/objects/xxx"
which once converted to unix style paths is what we want.
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When ssh connection caching is enabled (and when GIT_ANNEX_USE_GIT_SSH is
not set), only one ssh password prompt will be made per host, and only one
ssh password prompt will be made at a time.
This also fixes a race in prepSocket's stale ssh connection stopping
when run with -J. It was possible for one thread to start a cached ssh
connection, and another thread to immediately stop it, resulting in excess
connections being made.
This commit was supported by the NSF-funded DataLad project.
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GIT_ANNEX_USE_GIT_SSH=1 is also set in the environment.
This is necessary because as feared, the extra -n parameter that git-annex
passes breaks uses of these environment variables that expect exactly the
parameters that git passes.
For example, see https://github.com/datalad/datalad/issues/1456
It would of course be possible to pre-close stdin before running ssh so not
needing the -n, and I think that would not even break ssh's password
caching. But it would probably involve a lot of work, possibly would need
to deal with some layering violations, and would be error-prone. The really
clean fix would be to make all the ssh stuff return a CreateProcess, which
could have the handle closed when appropriate, but that would be a large
reworing of the code base.
This commit was supported by the NSF-funded DataLad project.
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classroom setting.
This commit was supported by the NSF-funded DataLad project.
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fbf69ca7b3eee84c2284d260aa70f106ff9d6d57 was incomplete
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They are handled close the same as they are by git. However, unlike git,
git-annex sometimes needs to pass the -n parameter when using these.
So, this has the potential for breaking some setup, and perhaps there ought
to be a ANNEX_USE_GIT_SSH=1 needed to use these. But I'd rather avoid that
if possible, so let's see if anyone complains.
Almost all places where "ssh" was run have been changed to support the env
vars. Anything still calling sshOptions does not support them. In
particular, rsync special remotes don't. Seems that annex-rsync-transport
already gives sufficient control there.
(Fixed in passing: Remote.Helper.Ssh.toRepo used to extract
remoteAnnexSshOptions and pass them to sshOptions, which was redundant
since sshOptions also extracts those.)
This commit was sponsored by Jeff Goeke-Smith on Patreon.
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To prevent any further mistakes like 1a497cefb47557f0b4788c606f9071be422b2511
This commit was sponsored by Francois Marier on Patreon.
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than remotes.
It was distributing jobs to remotes that were not being used by any other
job. But, suppose that there are only 2 remotes, and -J10. In such a case,
the first 2 downloads would be distributed amoung the 2 remotes, but
the other 8 would all go to remote #1. Improved by keeping a counter
of how many jobs are assigned to a remote, and prefer remotes with fewer
jobs.
Note use of Data.Map.Strict to avoid blowing up space. I kept the
bang-patterns as-is, although probably not needed with Data.Map.Strict.
This commit was sponsored by Jack Hill on Patreon.
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Just totally wrong logic, oops. Caught by test suite.
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* init: When annex.securehashesonly has been set with git-annex config,
copy that value to the annex.securehashesonly git config.
* config --set: As well as setting value in git-annex branch,
set local gitconfig. This is needed especially for
annex.securehashesonly, which is read only from local gitconfig and not
the git-annex branch.
doc/todo/sha1_collision_embedding_in_git-annex_keys.mdwn has the
rationalle for doing it this way. There's no perfect solution; this
seems to be the least-bad one.
This commit was supported by the NSF-funded DataLad project.
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Joey Hess