It takes a single key-value backend, rather than the unncessary and confusing list.
The old option still works if set.
Simplified some old old code too.
This commit was sponsored by Thomas Hochstein on Patreon.
fsck already special-cased dead keys to make --all not report errors with
them, and it makes sense to also expand that to whereis. I think it makes
sense for dead keys to be skipped by all uses of --all, so mistakes can be
completely forgotten about and not come back to haunt us.
The speed impact of testing if the key is dead is negligible for fsck and
whereis, since they use the location log anyway and it gets cached.
This does slow down a few commands that support --all, in particular
metadata --all runs around 2x as slow. I don't think metadata
--all is often used though. It might slow down copy/move/mirror
--all and get --all.
log --all is not affected (does not use the normal --all machinery).
Dead keys will still be processed by --incomplete, --branch,
--failed, and --key. Although it would be unlikely for a dead key to
ave in incomplete or failed transfer. It seems to make perfect sense for
--branch to process keys on the branch, even if dead.
(fsck's special-casing of dead keys was left in, so if one of these options
causes a dead key to be fscked, there will be a nice message.)
This commit was supported by the NSF-funded DataLad project.
Unlike git add -u, git annex add -u does not update the index for files
removed from the working tree. But then, "git add ." stages removals,
and "git annex add ." does not, so that's an existing divergence.
Seems that --update --batch would need to run git ls-files once per line of
batch input, which would surely be too slow, so just throw an error for
that.
This commit was supported by the NSF-funded DataLad project.
This was never supported before. And it doesn't re-encrypt the
gcrypt repo to the new gcrypt-participants, but it does at least now not
crash, and set gcrypt-participants.
This commit was sponsored by andrea rota.
They were silently ignored, a reversion introduced in 6.20160527.
I don't like this regular git remote special case in enableremote, but I
can't see a way to get rid of it. So, check if the existing remote is
a Remote.Git
This commit was sponsored by Trenton Cronholm on Patreon.
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.
The former can be useful to make remotes that don't get fully synced with
local changes, which comes up in a lot of situations.
The latter was mostly added for symmetry, but could be useful (though less
likely to be).
Implementing `remote.<name>.annex-pull` was a bit tricky, as there's no one
place where git-annex pulls/fetches from remotes. I audited all
instances of "fetch" and "pull". A few cases were left not checking this
config:
* Git.Repair can try to pull missing refs from a remote, and if the local
repo is corrupted, that seems a reasonable thing to do even though
the config would normally prevent it.
* Assistant.WebApp.Gpg and Remote.Gcrypt and Remote.Git do fetches
as part of the setup process of a remote. The config would probably not
be set then, and having the setup fail seems worse than honoring it if it
is already set.
I have not prevented all the code that does a "merge" from merging branches
from remotes with remote.<name>.annex-pull=false. That could perhaps
be done, but it would need a way to map from branch name to remote name,
and the way refspecs work makes that hard to get really correct. So if the
user fetches manually, the git-annex branch will get merged, for example.
Anther way of looking at/justifying this is that the setting is called
"annex-pull", not "annex-merge".
This commit was supported by the NSF-funded DataLad project.
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.
Fix bug when used with a recently cloned repository, where
"merging" messages were included in the output of configlist (and perhaps
other commands) and caused a "Failed to get annex.uuid configuration"
error.
This does not seem to have been a reversion.
I saw this with configlist, but it seems possible for other commands to be
effected, and it might not always happen only after a fresh clone. Eg, if a
foo/git-annex branch is pushed to the remote, the next git-annex-shell will
auto-merge it and display the message.
Decided to run all git-annex-shell commands with noMessages,
even ones that don't currently use stdout for structured communication.
Better to keep open the possibility for using stdout in the future.
This commit was supported by the NSF-funded DataLad project
The bug was that withFile closes the handle afterwards, but the content
of the file was not read due to laziness. Using readFile avoids it.
This commit was sponsored by Nick Daly on Patreon.
findShellCommand needs a full path to a file in order to check it for a
shebang on Windows. It was being run with only the base name of the external
special remote program, which would only work when it was in the current
directory.
This is why users in
https://github.com/DanielDent/git-annex-remote-rclone/pull/10 and elsewhere
were complaining that the previous improvements to git-annex didn't make
git-remote-rclone work on Windows.
Also, reworked checkearlytermination, which while it worked, seemed
to rely on a race condition. And, improved its error messages.
This commit was sponsored by Shane-o on Patreon.
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.
The slowdown is not going to be large in typical small-ish repos.
And it does not seem to matter if the assistant reacts a little bit slower
in situations involving the expensive scan, since:
a) Those situations typically involve getting back in sync after something
has changed on a remote, often after a disconnect of some duration.
So taking a few seconds more is not noticable.
b) If the scan finds things that it needs to do, it will start
blocking anyway after 10 transfers are queued (due to use of
queueTransferWhenSmall). So, only the speed of finding the first 10
transfers will be impacted by this change.
This commit was sponsored by Jochen Bartl on Patreon.
It was relying on segmentPaths to work correctly, so when it didn't,
sometimes the file that did not exist got matched up with a non-null
list of results. Fixed by always checking if each parameter exists.
There are two reason segmentPaths might not work correctly.
For one, it assumes that when the original list of paths
has more than 100 paths, it's not worth paying the CPU cost to
preserve input orders.
And then, it fails when a directory such as "." or ".." or
/path/to/repo is in the input list, and the list of found paths
does not start with that same thing. It should probably not be using
dirContains, but something else.
But, it's not clear how to handle this fully. Consider
when [".", "subdir"] has been expanded by git ls-files to
["subdir/1", "subdir/2"]
-- Both of the inputs contained those results, so there's
no one right answer for segmentPaths. All these would be equally valid:
[["subdir/1", "subdir/2"], []]
[[], ["subdir/1", "subdir/2"]]
[["subdir/1"], [""subdir/2"]]
So I've not tried to improve segmentPaths.
* 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.
Added --securehash option to match files using a secure hash function, and
corresponding securehash preferred content expression.
This commit was sponsored by Ethan Aubin.
Cryptographically secure hashes can be forced to be used in a repository,
by setting annex.securehashesonly. This does not prevent the git repository
from containing files with insecure hashes, but it does prevent the content
of such files from being pulled into .git/annex/objects from another
repository.
We want to make sure that at no point does git-annex accept content into
.git/annex/objects that is hashed with an insecure key. Here's how it
was done:
* .git/annex/objects/xx/yy/KEY/ is kept frozen, so nothing can be
written to it normally
* So every place that writes content must call, thawContent or modifyContent.
We can audit for these, and be sure we've considered all cases.
* The main functions are moveAnnex, and linkToAnnex; these were made to
check annex.securehashesonly, and are the main security boundary
for annex.securehashesonly.
* Most other calls to modifyContent deal with other files in the KEY
directory (inode cache etc). The other ones that mess with the content
are:
- Annex.Direct.toDirectGen, in which content already in the
annex directory is moved to the direct mode file, so not relevant.
- fix and lock, which don't add new content
- Command.ReKey.linkKey, which manually unlocks it to make a
copy.
* All other calls to thawContent appear safe.
Made moveAnnex return a Bool, so checked all callsites and made them
deal with a failure in appropriate ways.
linkToAnnex simply returns LinkAnnexFailed; all callsites already deal
with it failing in appropriate ways.
This commit was sponsored by Riku Voipio.
Yesterday's SHA1 collision attack could be used to generate eg:
SHA256-sfoo--whatever.good
SHA256-sfoo--whatever.bad
Such that they collide. A repository with the good one could have the
bad one swapped in and signed commits would still verify.
I've already mitigated this.
I am not happy that I had to put backend-specific code in file2key. But
it would be very difficult to avoid this layering violation.
Most of the time, when parsing a Key from a symlink target, git-annex
never looks up its Backend at all, so adding this check to a method of
the Backend object would not work.
The Key could be made to contain the appropriate
Backend, but since Backend is parameterized on an "a" that is fixed to
the Annex monad later, that would need Key to change to "Key a".
The only way to clean this up that I can see would be to have the Key
contain a LowlevelBackend, and put the validation in LowlevelBackend.
Perhaps later, but that would be an extensive change, so let's not do
it in this commit which may want to cherry-pick to backports.
This commit was sponsored by Ethan Aubin.
* Run curl with -S, so HTTP errors are displayed, even when
it's otherwise silent.
* When downloading in --json or --quiet mode, use curl in preference
to wget, since curl is able to display only errors to stderr, unlike
wget.
This does mean that downloadQuiet is only silent on stdout, not necessarily
on stderr, which affects a couple other calls of it. For example,
downloading the .git/config of a http remote may show an error message now,
perhaps with slightly suboptimal formatting due to other output.
This adds one extra line of output when a download is successful,
after the progress bar. I don't much like that, but wget does not provide a
way to show HTTP errors without it.
sync: When syncing with a local repository located on a crippled
filesystem, run the post-receive hook there, since it wouldn't get run
otherwise. This makes pushing to repos on FAT-formatted removable drives
update them when receive.denyCurrentBranch=updateInstead.
Made Remote.Git export onLocal, which was cleaned up to not have so many
caveats about its use.
This commit was sponsored by Jeff Goeke-Smith on Patreon.
* Added post-recieve hook, which makes updateInstead work with direct
mode and adjusted branches.
* init: Set up the post-receive hook.
This commit was sponsored by Fernando Jimenez on Patreon.
config group groupwanted numcopies schedule wanted required: Avoid
displaying extraneous messages about repository auto-init, git-annex branch
merging, etc, when being used to get information.
By displaying error messages from the remote then it fails to update
its checked out branch.
Error messages in the default receive.denyCurrentBranch are still
suppressed, which matches user expectations.
This commit was sponsored by Nick Daly on Patreon.
... to avoid it consuming stdin that it shouldn't.
This fixes git-annex-checkpresentkey --batch remote, which didn't output
results for all keys passed into it.
Other git-annex commands that communicate with a remote over ssh may also
have been consuming stdin that they shouldn't have, which could have
impacted using them in eg, shell scripts. For example, a shell script
reading files from stdin and passing them to git annex drop would be
impacted by this bug, whenever git annex drop ran git-annex-shell
checkpresent, it would consume part/all of the stdin that the shell script
was supposed to consume.
Fixed by adding a ConsumeStdin parameter to Annex.Ssh.sshOptions, which
is used throughout git-annex to run ssh (in order for ssh connection
caching to work). Every call site was checked to see if it used
CreatePipe for stdin, and if not was marked NoConsumeStdin.
At first I wanted to make it go ahead and merge into the newborn branch,
so made it use Git.Branch.currentUnsafe to get the current branch. But that
failed:
fatal: ambiguous argument 'refs/heads/master..refs/heads/synced/master':
unknown revision or path not in the working tree.
A whole nother code path to handle merging into newborn branches seemed
excessive, so went with displaying a warning and propigating failure
status.
This commit was sponsored by Brock Spratlen on Patreon.
Refactored some common code into initDb.
This only deals with the problem when creating new databases. If a repo
got bad permissions into it, it's up to the user to deal with it.
This commit was sponsored by Ole-Morten Duesund on Patreon.
The check was broken in two ways.. First, nowhere did it error out when
checkUUIDFile found a different UUID already in the file. Instead,
it overwrote the uuid file.
And, checkUUIDFile's implementation was for some reason always failing with
a ConnectionClosed exception. Apparently something to do with using two
different runResourceT's and a response getting GCed inbetween. I'm pretty
sure that used to work, but changed to a more obviously correct
implementation.
This commit was sponsored by Peter Hogg on Patreon.
Probing for hard link support in the pid locking code is redundant since
git-annex init already probes that. But, it didn't seem worth threading
that data through; the pid locking code runs at most once per git-annex
process, and only on unusual filesystems. Optimising a single hard link
and unlink isn't worth it.
This commit was sponsored by Francois Marier on Patreon.
Git does not provide a switch to find out where this directory is, and
while the git-init man page says it will always be in
/usr/share/git-core/templates, that's not the case on OSX with git
installed from homebrew. So, I used a hack taking the --man-path and
constructing a path from that. Works on both Debian and OSX at least.
This is the same as running git annex reinject --known, followed by
git-annex import. The advantage to having it in one command is that it
only has to hash each file once; the two commands have to
hash the imported files a second time.
This commit was sponsored by Shane-o on Patreon.
import: --deduplicate and --skip-duplicates were implemented inneficiently;
they unncessarily hashed each file twice. They have been improved to only
hash once.
The new approach is to lock down (minimally) and hash files, and then
reuse that information when importing them.
This was rather tricky, especially in detecting changes to files while
they are being imported.
The output of import changed slightly. While before it silently skipped
over files with eg --skip-duplicates, now it shows each file as it starts
to act on it. Since every file is hashed first thing, it would otherwise
not be clear what file import is chewing on. (Actually, it wasn't clear
before when any of the duplicates switches were used.)
This commit was sponsored by Alexander Thompson on Patreon.
Before, only content known to be present somewhere was considered a
duplicate. Now, any content that has been annexed before will be considered
a duplicate, even if all annexed copies of the data have been lost.
Note that --clean-duplicates and --deduplicate still check numcopies,
so won't delete duplicate files unless there's an annexed copy.
This makes import use the same method as reinject --known.
The man page already said that duplicate meant "its content is either
present in the local repository already, or git-annex knows of another
repository that contains it, or it was present in the annex before but has
been removed now". So, this is really only bringing the implementation into
line with the man page.
This commit was sponsored by Jochen Bartl on Patreon.
Wormhole pairing will start to provide an appid to wormhole on 2021-12-31.
An appid can't be provided now because Debian stable is going to ship a
older version of git-annex that does not provide an appid. Assumption is
that by 2021-12-31, this version of git-annex will be shipped in a Debian
stable release. If that turns out to not be the case, this change will need
to be cherry-picked into the git-annex in Debian stable, or its wormhole
pairing will break.
This commit was sponsored by Thomas Hochstein on Patreon.
.. which can be set to true to make git annex sync default to --content.
This may become the default at some point in the future.
As well as being configuable by git config, it can be configured by
git-annex config to control the default behavior in all clones of a
repository.
Had to add a separate --no-content switch to we can tell if it's been
explicitly set, and should override annex.synccontent. If --content was the
default, this complication would not be necessary.
This commit was sponsored by Jake Vosloo on Patreon.
... to control the default behavior in all clones of a repository.
This includes a new Configurable data type, so the GitConfig type indicates
which values can be configured this way.
The implementation should be quite efficient; the config log is only read
once, and only when a Configurable value has not already been set by
git-config.
Indeed, it would be nice in the future to extend this, so that git-config
is itself only read on demand. Some commands may not need to look at the
git configuration at all.
This commit was sponsored by Trenton Cronholm on Patreon.
Argh, didn't need an accumulator here!
I think I use accumulators a lot more than I need to when recusively
processing lists..
This commit was sponsored by Jeff Goeke-Smith on Patreon.
This makes it a little bit slower since it has to check file size,
but worth it to fix a potential memory use problem.
This commit was sponsored by Fernando Jimenez on Patreon.
Turns out that Data.List.Utils.split is slow and makes a lot of
allocations. Here's a much simpler single character splitter that behaves
the same (even in wacky corner cases) while running in half the time and
75% the allocations.
As well as being an optimisation, this helps move toward eliminating use of
missingh.
(Data.List.Split.splitOn is nearly as slow as Data.List.Utils.split and
allocates even more.)
I have not benchmarked the effect on git-annex, but would not be surprised
to see some parsing of eg, large streams from git commands run twice as
fast, and possibly in less memory.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
esqueleto finally got fixed, thanks to @bitemyapp
Since XMPP was removed, the previous build failures related to it should
no longer be a problem either.
Meanwhile, lts-5.18 fails to build anymore on Debian due to linker
hardening breaking the version of ghc stack uses with that version.
This commit was sponsored by Francois Marier on Patreon.
Any config names can be set using this; git-annex commands will only look
at specific ones that make sense and are worth the overhead of querying the
branch.
This might also be useful for storing whatever other config-type stuff the
user might want to shove into the git-annex branch.
This commit was sponsored by Jochen Bartl on Patreon.
Docs say vicfg can configure everything from git-annex branch,
so it ought to configure numcopies.
Note that commenting out existing numcopies does not unset it.
This commit was sponsored by Thom May on Patreon.
This way we know that after enable-tor, the tor hidden service is fully
published and working, and so there should be no problems with it at
pairing time.
It has to start up its own temporary listener on the hidden service. It
would be nice to have it start the remotedaemon running, so that extra
step is not needed afterwards. But, there may already be a remotedaemon
running, in communication with the assistant and we don't want to start
another one. I thought about trying to HUP any running remotedaemon, but
Windows does not make it easy to do that. In any case, having the user
start the remotedaemon themselves lets them know it needs to be running
to serve the hidden service.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
weasel explained that apparmor limits on what files tor can read do not
apply to sockets (because they're not files). And apparently the
problems I was seeing with hidden services not being accessible had to
do with onion address propigation and not the location of the socket
file.
remotedaemon looks up the HiddenServicePort in torrc, so if it was
previously configured with the socket in /etc, that will still work.
This commit was sponsored by Denis Dzyubenko on Patreon.
This reverts commit 3037feb1bf.
On second thought, this was an overcomplication of what should be the
lowest-level primitive. Let's build bi-directional links at the pairing
level with eg magic wormhole.
Both the local and remote git repositories get remotes added
pointing at one-another.
Makes pairing twice as easy!
Security: The new LINK command in the protocol can be sent repeatedly,
but only by a peer who has authenticated with us. So, it's entirely safe to
add a link back to that peer, or to some other peer it knows about.
Anything we receive over such a link, the peer could send us over the
current connection.
There is some risk of being flooded with LINKs, and adding too many
remotes. To guard against that, there's a hard cap on the number of remotes
that can be set up this way. This will only be a problem if setting up
large p2p networks that have exceptional interconnectedness.
A new, dedicated authtoken is created when sending LINK.
This also allows, in theory, using a p2p network like tor, to learn about
links on other networks, like telehash.
This commit was sponsored by Bruno BEAUFILS on Patreon.
Revert ServerAliveInterval change in 6.20161111, which caused problems
with too many old versions of ssh and unusual ssh configurations.
It should have not been needed anyway since ssh is supposted to
have TCPKeepAlive enabled by default.
1 microsecond delay is ugly.. but, maintaining an queue of a list of timestamps
and taking a new one from the queue each time around, or maintaining a timestamp
counter, would probably be slower.
The attacker could just send a very lot of data, with no \n and it would
all be buffered in memory until the kernel killed git-annex or perhaps OOM
killed some other more valuable process.
This is a low impact security hole, only affecting communication between
local git-annex and git-annex-shell on the remote system. (With either
able to be the attacker). Only those with the right ssh key can do it. And,
there are probably lots of ways to construct git repositories that make git
use a lot of memory in various ways, which would have similar impact as
this attack.
The fix in P2P/IO.hs would have been higher impact, if it had made it to a
released version, since it would have allowed DOSing the tor hidden
service without needing to authenticate.
(The LockContent and NotifyChanges instances may not be really
exploitable; since the line is read and ignored, it probably gets read
lazily and does not end up staying buffered in memory.)
Would have liked to make the Parser parse the file and key pairs, but it
seems that optparse-applicative is unable to handle eg:
many ((,) <$> argument <*> argument)
This commit was sponsored by Thomas Hochstein on Patreon.
* rmurl: Multiple pairs of files and urls can be provided on the
command line.
* rmurl: Added --batch mode.
This commit was sponsored by Trenton Cronholm on Patreon.
* map: Run xdot if it's available in PATH. On OSX, the dot command
does not support graphical display, while xdot does.
* Debian: xdot is a better interactive viewer than dot, so Suggest
xdot, rather than graphviz.
Building w/o the webapp is not supposed to pull in any AGPLed files.
I appear to have written all the code in these files;
the only commit by anyone else is 64e844e1fe
and is a spelling fix that is not copyrightable.
Almost working, but there's a bug in the relaying.
Also, made tor hidden service setup pick a random port, to make it harder
to port scan.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
ghc 8 added backtraces on uncaught errors. This is great, but git-annex was
using error in many places for a error message targeted at the user, in
some known problem case. A backtrace only confuses such a message, so omit it.
Notably, commands like git annex drop that failed due to eg, numcopies,
used to use error, so had a backtrace.
This commit was sponsored by Ethan Aubin.
This makes merging a remote into a freshly created direct mode repository
work the same as it works in indirect mode.
The git-annex branches would get merged in any case by a sync,
since that doesn't use git merge.
This might need to be revisited later to better mirror git's behavior.
git-annex.cabal: Loosen bounds on persistent to allow 2.5, which on Debian
has been patched to work with esqueleto. This may break cabal's resolver on
non-Debian systems; if so, either use stack to build, or run cabal with
--constraint='persistent ==2.2.4.1' Hopefully this mess with esqueleto will
be resolved soon.
https://github.com/prowdsponsor/esqueleto/issues/137
Yesod didn't used to do auth checks for that, but this may have changed.
I don't have a way to reproduce the reported problem yet, but this change
certianly won't hurt anything.
This commit was sponsored by Thom May on Patreon.
ghc 8.0.2 may make this unncessary, but it's not in a stackage version yet,
so put in a workaround.
Note that the linux builds already delete the RPATHs for similar reasons.
This commit was sponsored by Josh Taylor on Patreon.
* S3: Support the special case endpoint needed for the cn-north-1 region.
* Webapp: Don't list the Frankfurt region, as this (and some other new
regions) need V4 authorization which the aws library does not yet use.
This commit was sponsored by Nick Daly on Patreon.
When used with an older version of ssh, any ServerAliveInterval in
~/.ssh/config will be overridden by .git/annex/ssh.config.
This commit was sponsored by Josh Taylor on Patreon.
Restarting a crashing git process could result in filename encoding issues
when not in a unicode locale, as the restarted processes's handles were not
read in raw mode.
Since rawMode is always used when starting a coprocess, didn't bother
to parameterise it and just always enable it for simplicity.
This commit was sponsored by Jake Vosloo on Patreon.
The Makefile was putting them in git-annex.linux/i18n/i18n, and so I18NPATH
did not point to the files. I think that on close enough to Debian systems,
localedef then fell back to using the system-wide locale files, while on
other systems it would fail to generate locales.
So that stalled transfers will be noticed within about 3 minutes,
even if TCPKeepAlive is disabled or doesn't work.
Rather than setting with -o, use -F with another config file,
so that any settings in ~/.ssh/config or /etc/ssh/ssh_config overrides this.
If a transfer fails for some reason, but some data managed to be sent, the
transfer will be retried. (The assistant already did this.)
Possible impacts:
* More ssh prompts if ssh needs to prompt for a password to connect to a
host, or is prompting about some other problem like a ssh key mismatch.
* More data transfer due to retrying, epecially when a remote does not
support resuming a transfer.
In the worst case, a lot of data will be transferred but it fails before
the end, and then all that data gets transferred again plus one byte more;
repeat until it manages to get the whole file.
gpg-agent started deleting its socket file on shutdown, and this tickled an
ugly behavior in removeDirectoryRecursive,
https://github.com/haskell/directory/issues/60
Running removeDirectoryRecursive again on exception avoids the problem.
Closes https://github.com/datalad/datalad/issues/1020
The use of runWriter in scanUnlockedFiles broke due to this change;
it failed with blocked indefinitely in mvar, because the database write
handle was taken while linkFromAnnex needed to also write to it (to update
the inode cache). So, switched to using a separate runWriter for each call
to addAssociatedFileFast. A little less efficient, but not greatly; the
writes should all still be cached.
In the case where the pointer file is in place, and not the content
of the object, lock's performNew was called with filemodified=True,
which caused it to try to repopulate the object from an unmodified
associated file, of which there were none. So, the content of the object
got thrown away incorrectly. This was the cause (although not the root
cause) of data loss in https://github.com/datalad/datalad/issues/1020
The same problem could also occur when the work tree file is modified,
but the object is not, and lock is called with --force. Added a test case
for this, since it's excercising the same code path and is easier to set up
than the problem above.
Note that this only occurred when the keys database did not have an inode
cache recorded for the annex object. Normally, the annex object would be in
there, but there are of course circumstances where the inode cache is out
of sync with reality, since it's only a cache.
Fixed by checking if the object is unmodified; if so we don't need to
try to repopulate it. This does add an additional checksum to the unlock
path, but it's already checksumming the worktree file in another case,
so it doesn't slow it down overall.
Further investigation found a similar problem occurred when smudge --clean
is called on a file and the inode cache is not populated. cleanOldKeys
deleted the unmodified old object file in this case. This was also
fixed by checking if the object is unmodified.
In general, use of getInodeCaches and sameInodeCache is potentially
dangerous if the inode cache has not gotten populated for some reason.
Better to use isUnmodified. I breifly auited other places that check the
inode cache, and did not see any immediate problems, but it would be easy
to miss this kind of problem.
The modification flag was not being set when making modifications deep
in a tree, so parent trees were not updated to contain the modified tree.
Seems to have exposed another bug where the wrong filename gets grafted in.
This commit was sponsored by Brock Spratlen on Patreon.
