Add back support for ftp urls, which was disabled as part of the fix for
security hole CVE-2018-10857 (except for configurations which enabled curl
and bypassed public IP address restrictions). Now it will work if allowed
by annex.security.allowed-ip-addresses.
Renamed annex.security.allowed-http-addresses to
annex.security.allowed-ip-addresses because it is not really specific to
the http protocol, also limiting eg, git-annex's use of ftp and via
youtube-dl, several other protocols.
The old name for the config will still work.
If both old and new name are set, the new name will win.
When a remote is configured to be readonly, don't allow changing what's
exported to it.
This was missed in the original export remote implementation, but it makes
sense for a readonly export remote to not be allowed to change.
~/.profile works for bash, but not all other login shells.
This setting PATH is a minor convenience for users, particuarly since
typing on android is so much harder. The usual linux standalone bundle
just expects the user to know how to add it to PATH. I don't want this
code to grow special cases for every possible login shell. So displaying a
message to the presumably minority who don't use bash seems like the best
choice.
Longer term, I'd hope termux gets some way to set an environment variable
for all login shells. Systems using PAM can, via ~/.pam_environment. Or
alternatively, add a git-annex package to termux, even if just an installer
package. I'd rather spend time on either of those than on making this minor
thing support more login shells.
This commit was sponsored by mo on Patreon.
* init: When the repository already has a description, don't change it.
* describe: When run with no description parameter it used to set
the description to "", now it will error out.
Importing from a special remote honors its preferred content too; unwanted
files are not imported. But, some preferred content expressions can't be
checked before files are imported, and trying to import with such an
expression will fail.
Tested this with scenarios including changing the preferred content
expression and making sure merging the import didn't delete files that were
no longer wanted.
There was one minor inefficiency mentioned in the todo that I punted on.
Make the import have the previous import as a parent, so eg `git log --stat`
displays a useful diff.
Also a minor optimisation, only calculate the depth of the imported history
once.
This includes a note about how include= and exclude= match when exporting
a subtree. I don't know if the note is prominent enough, but the
behavior seems unsurprising enough.
Added the ability to run one job per CPU (core), by setting annex.jobs=cpus,
or using option --jobs=cpus or -Jcpus.
Built with future expansion in mind, including not defaulting matching on
Concurrency so more constructors can later be added, and using "cpu"
instead of "0".
Fixes bug that caused git-annex to fail to add a file when another
git-annex process cleaned up the temp directory it was using.
Solution is just to push withOtherTmp out to a higher level, so that
the whole ingest process can be completed inside it.
But in the assistant, that was not practical to do, since withOtherTmp runs
in the Annex monad and the assistant does not. Worked around by introducing
a separate temp directory that only the assistant uses for lockdown.
Since only one assistant can run at a time, it's easy to clean up that
directory of old cruft at startup.
Fix reversion in last release that caused wrong tree to be written to
remote tracking branch after an export of a subtree.
The invariant "commitsha should have the treesha as its tree"
was not met due to a bug. Guarantee it's met by catting the commitsha
to find its actual tree. A little bit slower, but this is not run often.
* Added mimeencoding= term to annex.largefiles expressions.
This is probably mostly useful to match non-text files with eg
"mimeencoding=binary"
* git-annex matchexpression: Added --mimeencoding option.
Switch listContents to being a proper CommandStart, so if it throws an
exception, it will be treated like any other command action that fails.
downloadImport apparently does not ever throw an exception,
and itself uses commandAction, so it can't be a CommandStart.
Fix bug that caused importing from a special remote to repeatedly download
unchanged files when multiple files in the remote have the same content.
Unfortunately, there's really no good way to remove a uniqueness constraint
from a sqlite database. The best that can be done is to make a new table
and copy the data over. But that would require using persistent's
migrations or raw sql, and I don't want to do either.
Instead, a sledgehammer approach: Renamed .git/annex/cid to
.git/annex/cids. When the new database doesn't exist, it will be populated
from the git-annex branch.
Noting deletes the old database. Don't want to delete it out from under
some long-running git-annex process that might be using it. It could
eventually be deleted. But this is such a new feature, probably few repos
have the database in any case.
As well as adding the necessary methods, a few other changes to the adb
remote:
* Use ".annextmp" extension for temp files, to avoid conflict with other
temp files.
* Stop using "echo $?" to get exit status of command inside adb.
There were two problems; first the "echo" just before it meant it was
always 0! And secondly, it seems kind of random on my phone whether it's
1 or 0, not dependant on whether the command seems to have succeeded.
protocol=https implies port=443 and
port=443 implies protocol=https
-- this was necessary because the existing configs set port=443, but
with a protocol setting, users will naturally want to use it, and then
there's no need for them to supply the default https port. So we keep
back-compat, add a nicer way to enable https, and also add support for
non-standard https ports.
In particular, when two files had the same content, and one was unlocked
and modified, with annex.thin that can corrupt the content of the
annex object, and so fsck on the other file should detect that.
getKeyStatus was relying on Database.Keys.getAssociatedFiles to tell
when a file is unlocked, but that can false positive because the
database can list old associated files.
Instead, separate out the case of unlocked object which has multiple
hardlinks when annex.thin is in use.
To support filenames starting with dashes.
To update the config of existing repositories, you can re-run git-annex init.
Perhaps it should check every time for the old config and update it, but
that has several problems:
- read-only repos
- unexpected commands like `git annex find` changing git configs
might be surprising behavior
Since filenames starting with dashes are not super common and the user can
re-init easily enough if their repo needs fixed, I went for the simplest
fix.
Users may want sync to only export, or only import and this is broadly
analagous to push and pull, so it makes sense to use the same
configuration for it.
The branch is only updated once the export is 100% complete. This way,
if an export is started but interrupted and so the remote does not yet
contain some of the files, an import will make a commit on the old
branch, and so won't delete the missing files.
This log, unlike all other current top-level logs, is a new format log.
I have not checked what throwing it at the old log parser did, but it seems
likely it ignored unparsable lines, and so perhaps deleted all lines from
the log.
This fixes a reversion in the ByteString conversion. The old code used
isSpace to decide when the metadata value needs to be base64 encoded,
and that incorrectly changed to only checking if it contained ' '.
Note that only '\n' and '\r' were added and not other sorts of
whitespace that isSpace matches, like '\t' and '\v'. Only the former
would cause problems.
Installing git-annex with stack rsync won't be available.
Also, using the git-annex installer with 64 bit git installs a non-working
rsync binary because it's linked with libraries provided by 32 bit git.
Like with the network-uri split, cabal will automatically turn off the flag
when building with an old network.
I have not tested building with the new network-3.0.0.0 yet; several
other dependencies including aws are still pinned on network-2.*
xporting files with '#' or '?' in their name won't work because urls get
truncated on those. Fail in a better way in this case, and avoid failing
when removing such files from the export, so after the user has renamed the
problem files the export will succeed.
Avoid performing repository fixups for submodules and git-worktrees
when there's a .noannex file that will prevent git-annex from being
used in the repository.
This change is ok as long as the .noannex file is really going to prevent
git-annex from being used. But, init --force could override the file.
Which would result in the repo being initialized without the fixups
having run.
To avoid that situation decided to change init, to not let --force be used
to override a .noannex file. Instead the user can just delete the file.
* fromkey: Added --json.
* fromkey --batch output changed to support using it with --json.
The old output was not parseable for any useful information, so
this is not expected to break anything.
If the worktree file already exists, and is annexed and uses the same
key, avoid failing, nothing needs to be done.
Had to add lookupFileNotHidden to handle the case where an adjust --hide-missing
is in use, and the worktree file was hidden due to the object content
being missing. lookupFile would return the key of the hidden file,
but it makes sense that after fromkey succeeds, the worktree must
contain the file it was supposed to set up.
Need to create the directory after the lock is held, not before.
The other racing process would need to shut down at just the wrong time,
running cleanupOtherTmp.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
This gets back any speed lost in commit
9cebfd7002, and speeds up all uses of S3
remotes that operate on them more than once.
This commit was sponsored by Brett Eisenberg on Patreon.
When key-based retrieval from a S3 remote with exporttree=yes
appendonly=yes fails, fall back to trying to retrieve from the exported
tree. This allows downloads of files that were exported to such a remote
before versioning was enabled on it.
This is useful at least for a transition for users who got into that
situation, so they can download content from their S3 remote. May want to
remove this in the future though, since normally trying to download the
second time is only extra work.
This commit was sponsored by Brock Spratlen on Patreon.
Like the earlier fixed one in Command.Export, it occurred when the same
tree was exported by multiple clones. Previous fix was incomplete since
several other places looked at the list of exported trees to detect when
there was an export conflict. Added a single unified function to avoid
missing any places it needed to be fixed.
This commit was sponsored by mo on Patreon.
Because when git-annex lacks S3 version IDs for files stored in the bucket,
deleting them would cause data loss.
Also because git-annex is not able to download unversioned objects from a bucket
when versioning=yes.
This also prevents setting versioning=no. While that would perhaps be
possible to do safely, it would add complexity, and would mean that if
the user accidentially did enableremote versioning=no, they would not be
able to undo it.
This commit was sponsored by Trenton Cronholm on Patreon.
Needs not yet released version 0.22 of aws library; with older versions
asks the user to configure the bucket versioning themselves.
Note that S3 endpoints that don't support versioning will cause putBucketVersioning
to throw an exception, so initremote will fail.
This commit was sponsored by Jake Vosloo on Patreon.
* webapp: Remove configurator for box.com repository, since their
webdav support is going away at the end of this January.
* webapp: Remove configurator for gitlab, which stopped supporting git-annex
some time ago.
This commit was sponsored by Brock Spratlen on Patreon.
However, rsync still won't work with 64 bit git and
this is still not the documented way to install it.
So, if both 64 and 32 are installed, go with 32.
And if neither git can be found, default to 32.
* Switch to using .git/annex/othertmp for tmp files other than partial
downloads, and make stale files left in that directory when git-annex
is interrupted be cleaned up promptly by subsequent git-annex processes.
* The .git/annex/misctmp directory is no longer used and git-annex will
delete anything lingering in there after it's 1 week old.
Also, in Annex.Ingest, made the filename it uses in the tmp dir be
prefixed with "ingest-" to avoid potentially using a filename used by
some other code.
This will speed up the common case where a Key is deserialized from
disk, but is then serialized to build eg, the path to the annex object.
It means that every place a Key has any of its fields changed, the cache
has to be dropped. I've grepped and found them all. But, it would be
better to avoid that gotcha somehow..
A keyName could contain "/", though this is unlikely and certianly only
ever could happen with WORM keys.
The change to addunused to escape that is no problem at all.
The change to VariantFile to escape it means that different versions of
git-annex could resolve a merge conflict differently in this case, which
is unfortunate. There would be different .variant files used, so the two
resolutions would themselves merge together without additional
conflicts, but the user would have to clean up the extra .variant
files.
Not likely to be any speed gain here, but this completes porting every
log file over.
And, it let me get rid of code copied from ghc and modified, so
simplifying the licensing.
This preserves the workaround for the old bug that caused NoUUID items
to be stored in the log, prefixing log lines with " ". It's now handled
implicitly, by using takeWhile1 (/= ' ') to get the uuid.
There is a behavior change from the old parser, which split the value
into words and then recombined it. That meant that "foo bar" and "foo\tbar"
came out as "foo bar". That behavior was not documented, and seems
surprising; it meant that after a git-annex describe here "foo bar",
you wouldn't get that same string back out when git-annex displayed repo
descriptions.
Otoh, some other parsers relied on the old behavior, and the attoparsec
rewrites had to deal with the issue themselves...
For group.log, there are some edge cases around the user providing a
group name with a leading or trailing space. The old parser would ignore
such excess whitespace. The new parser does too, because the alternative
is to refuse to parse something like " group1 group2 " due to excess
whitespace, which would be even more confusing behavior.
The only git-annex branch log file that is not converted to attoparsec
and bytestring-builder now is transitions.log.
Mostly didn't push the ByteStrings down very deep, but all of these log
files are not written to frequently at all, so slight remaining
innefficiency doesn't matter.
In Logs.UUID, removed the fixBadUUID code that cleaned up after a bug in
git-annex versions 3.20111105-3.20111110. In the unlikely event that a repo was
last touched by that ancient git-annex version, the descriptions of remotes
would appear missing when used with this version of git-annex. That is such minor
breakage, and so unlikely to still be a problem for any repos, that it was not
worth forward-porting that code to ByteString.
Tested on an older ghc by enabling MonadFailDesugaring globally.
In TransferQueue, the lack of a MonadFail for STM exposed what would
normally be a bug in the pattern matching, although in this case an
earlier check that the queue was not empty avoided a pattern match
failure.
This is not as efficient as using ByteStrings throughout, but converting
the String to ByteString is actually significantly faster than the old
parser.
benchmarking parse/old
time 9.657 μs (9.600 μs .. 9.732 μs)
1.000 R² (0.999 R² .. 1.000 R²)
mean 9.703 μs (9.645 μs .. 9.785 μs)
std dev 231.6 ns (161.5 ns .. 323.7 ns)
variance introduced by outliers: 25% (moderately inflated)
benchmarking parse/new
time 834.6 ns (797.1 ns .. 886.9 ns)
0.987 R² (0.976 R² .. 0.999 R²)
mean 816.4 ns (802.7 ns .. 845.1 ns)
std dev 62.39 ns (37.66 ns .. 108.4 ns)
variance introduced by outliers: 82% (severely inflated)
There is a small behavior change from the old parsePOSIXTime,
which accepted any amount of trailing whitespace after the timestamp.
That behavior was not documented, and it doesn't seem anything relied on it.
It used to display the "bad feed content" message indicating there were no
enclosures found, which was misleading when the http request for the feed
failed.
This commit was sponsored by Ewen McNeill on Patreon.
downloadUrl uses meteredFile, which sets up one progress meter,
and Remote.Web also uses metered, so two progress meters are displayed for
the same download.
Reversion introduced with the http-conduit switch in
c34152777b -- I don't know why the extra
call to metered was added there.
When -J is not used, the extra progress meter didn't display,
but an extra blank line did get output, which is also fixed.
This commit was sponsored by John Pellman on Patreon.
init: When --version=5 is passed on a crippled filesystem, use a v5 direct
mode repo as requested, rather than upgrading to v7 adjusted unlocked.
Fixed test suite on crippled filesystems, making it request --version=5
to test direct mode.
Deleting directories is one of the great unsolved problems of CS, thanks to
abominations like NFS lock files and Windows and races with other processes
cleaning up after themselves in the background. The gpg test harness
sometimes failed to delete its temp directory on NFS. Avoid the problem
class by not deleting it at all, and putting it inside the tmp repo being
tested. The test suite's more robust (and/or nonsensical) workarounds for
deleting its test dir will thus be used, hopefully avoiding the problem
until an OS finds a new way to violate POSIX and the laws of nature.
Note that this means that the .gnupg directory will be on whatever
filesystem the test suite is being run on, which may be a lesser quality
filesystem than gpg is really expecting. Gpg does not seem to need to
write sockets etc to there so this seems ok. The only known problem is
that if the filesystem forces a directory mode like 777, gpg will warn
about unsafe home directory perms, but it still works.
This fixes a bug with the numcopies counting when using sync --content.
It did not always pass the local repo uuid to handleDropsFrom, and so the
numcopies counting was off by one, and unwanted local content would only be
dropped when there were numcopies+1 remote copies.
Also, support dropping local content that has reached an
exporttree remote that is not untrusted (currently only S3 remotes
with versioning).
* Fix bug upgrading from direct mode to v7: when files in the repository
were already committed as v7 unlocked files elsewhere, and the
content was present in the direct mode repository, the annexed files
got their full content checked into git.
* Fix bug that caused v7 unlocked files in a direct mode repository
to get locked when committing.
This commit was sponsored by Nick Piper on Patreon.
When a file was already unlocked, but the annex object was present, the
upgrade process populated the unlocked file, but neglected to update the
index.
This commit was sponsored by Jochen Bartl on Patreon.
webdav: When initializing, avoid trying to make a directory at the top of
the webdav server, which could never accomplish anything and failed on
nextcloud servers. (Reversion introduced in version 6.20170925.)
This commit was sponsored by mo on patreon.
No deprecation warning at run time, just one on the man page.
One thing findref remains able to do that find cannot is to run in a bare
repo. Find was made to refuse to run in a bare repo because it seemed
confusing for it to not list any files ever in that situation. It would be
better for find --branch to work in a bare repo but not without --branch
but I don't currently have a way to do that.
Probably a better solution would be to make git-annex in a bare repo
default to --branch master or something like that instead of --all.
This commit was sponsored by Denis Dzyubenko on Patreon.
* findref: Support file matching options: --include, --exclude,
--want-get, --want-drop, --largerthan, --smallerthan, --accessedwithin
* Commands supporting --branch now apply file matching options --include,
--exclude, --want-get, --want-drop to filenames from the branch.
Previously, combining --branch with those would fail to match anything.
* add, import, findref: Support --time-limit.
This commit was sponsored by Jake Vosloo on Patreon.
When public access is used for the remote, it complained that the user
needed to set creds to use it, which was just wrong.
When creds were being used, it fell back from trying to use the version ID
to just accessing the key in the bucket, which was ok for non-export
remotes, but wrong for buckets.
In both cases, display a hopefully useful warning.
This should only come up when an existing S3 remote has been exported
to, and then later versioning was enabled.
Note that it would perhaps be possible to fall back from trying to use
retrieveKeyFile when it fails and instead use retrieveKeyFileFromExport,
which may work when S3 version ID is missing. But there are problems
with that approach; how to tell when retrieveKeyFile has failed due to this
rather than a network problem etc? Anyway, that approach would only work
until the file in the export got overwritten, and then it would no
longer be accessible. And with versioning enabled, the user wants old
versions of objects to remain accessible, so it seems better to warn
about the problem as soon as possible, so they can go back and add S3
version IDs.
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
Note that it does not prevent storing p2p access tokens or multicast
encryption keys, since those are not cached; the previous commit
established the distinction.
How well this works depends on how often getRemoteCredPair is called and
how expensive it is. In some cases setting this will result in an annoying
number of gpg password prompts and/or slowdowns due to reading creds
from the git-annex branch and decrypting, which could be improved by calling
getRemoteCredPair less often.
This commit was sponsored by Ilya Shlyakhter on Patreon.
dropunused: When an unused object file has gotten modified, eg due to
annex.thin being set, don't silently skip it, but display a warning and let
--force drop it.
This commit was sponsored by Ethan Aubin.
info: When used with an exporttree remote, includes an "exportedtree" info,
which is the tree last exported to the remote. During an export conflict,
multiple values will be listed.
This commit was sponsored by John Pellman on Patreon.
* init: When a crippled filesystem causes an adjusted unlocked branch to
be used, set repo version to 7, which it neglected to do before.
* init: When on a crippled filesystem, and the git version is too old
to use an adjusted unlocked branch, fall back to using direct mode.
This commit was sponsored by Ilya Shlyakhter on Patreon.
Seems that youtube-dl --get-filename on a playlist lists all the filenames
for the playlist, which can take quite some time. The code already only
took the first name, so --no-playlist can speed it up a lot.
This commit was sponsored by Brett Eisenberg on Patreon.
And added stack-lts-9.9.yaml to support old versions of stack.
The i386 ancient autobuilder needs stack-lts-9.9.yaml; the OSX autobuilder
may also use it for a while, and it's needed to build on eg debian stable.
That didn't actually happen, newer lts like that one are not supported
by the version of stack in Debian stable, used for the i386-ancient
autobuild, and generally I want git-annex to be buildable on stable
releases of linux distros etc. So stack.yaml is going to be stuck on old
versions for some time until some years after stack stops breaking backwards
compatability.
When a command is operating on multiple files and there's an error with
one, try harder to continue to the rest. (As was already done for many
types of errors including IO errors.)
This handles cases like lockContentForRemoval throwing an exception when
the content is already locked. Just because a drop of one file fails, does
not mean it shouldn't go on to try to drop other files.
I looked over uses of `giveup` in Command/*; there are too many to check
them all extensively, but none stood out as being problems that should let
one commandAction stop running other commandActions. Worst case, something
bad will happen and rather than stopping right away with an error,
git-annex will display multiple errors as it fails over and over on each
file. I don't think I ever really intended `error`/`giveup` to stop other
commandActions; this was a relic of old confusion over haskell exception
handling.
Test suite passes.
This commit was sponsored by Ethan Aubin.
* drop -J: Avoid processing the same key twice at the same time when
multiple annexes files use it.
This prevents a drop of a key conflicting with another drop of the same
key.
This commit was sponsored by Brock Spratlen on Patreon.
export, sync --content: Avoid unnecessarily trying to upload files to an
exporttree remote that already contains the files.
When the export was origianly made in one repo and now git-annex is
running in a different repo, the export database is not yet populated with
information about the exportLocation of files. So, it was trying to upload
the files to the export, even when it already contained them.
sync --content would first download the content from the export, and then
re-upload the content back.
And this also led to "not available" failures for each file that was not
locally present yet.
Fix: Just use checkPresentExport before uploading; if it succeeds update
the database.
This is a surprising oversight, it's possible it fixes a reversion because
I would have thought I'd have noticed this problem when originally
developing exporttree remotes.
This commit was sponsored by Jochen Bartl on Patreon.
When an export conflict prevents accessing a special remote, be clearer
about what the problem is and how to resolve it.
This commit was sponsored by Trenton Cronholm on Patreon.
Don't much like that there's no way to distinguish between having the whole
content and having an old version of the file that's bigger, but of course
resuming a http transfer can always yield the wrong result if the file on
the http server is changing, and git-annex will detect that when it
verifies the downloaded content.
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
Fix bash completion of "git annex" to propertly handle files with spaces
and other problem characters. (Completion of "git-annex" already did.)
This commit was sponsored by Jake Vosloo on Patreon.
Finishes the start made in 983c9d5a53, by
handling the case where `transfer` fails for some other reason, and so the
ReadContent callback does not get run. I don't know of a case where
`transfer` does fail other than the locking dealt with in that commit, but
it's good to have a guarantee.
StoreContent and StoreContentTo had a similar problem.
Things like `getViaTmp` may decide not to run the transfer action.
And `transfer` could certianly fail, if another transfer of the same
object was in progress. (Or a different object when annex.pidlock is set.)
If the transfer action was not run, the content of the object would
not all get consumed, and so would get interpreted as protocol commands,
which would not go well.
My approach to fixing all of these things is to set a TVar only
once all the data in the transfer is known to have been read/written.
This way the internals of `transfer`, `getViaTmp` etc don't matter.
So in ReadContent, it checks if the transfer completed.
If not, as long as it didn't throw an exception, send empty and Invalid
data to the callback. On an exception the state of the protocol is unknown
so it has to raise ProtoFailureException and close the connection,
same as before.
In StoreContent, if the transfer did not complete
some portion of the DATA has been read, so the protocol is in an unknown
state and it has to close the conection as well.
(The ProtoFailureMessage used here matches the one in Annex.Transfer, which
is the most likely reason. Not ideal to duplicate it..)
StoreContent did not ever close the protocol connection before. So this is
a protocol change, but only in an exceptional circumstance, and it's not
going to break anything, because clients already need to deal with the
connection breaking at any point.
The way this new behavior looks (here origin has annex.pidlock = true so will
only accept one upload to it at a time):
git annex copy --to origin -J2
copy x (to origin...) ok
copy y (to origin...)
Lost connection (fd:25: hGetChar: end of file)
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
Fix hang when transferring the same objects to two different clients at the
same time. (Or when annex.pidlock is used, two different objects to the
same or different clients.)
Could also potentially occur if a client was downloading an object and
somehow lost connection but that git-annex-shell was still running and
holding the transfer lock.
This does not guarantee that, if `transfer` fails for some other reason,
a DATA response will be made.
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
Not the first time this kind of test suite breakage has happened..
It would be good to avoid somehow it looking up from .t and finding a git
repo. But just running the test suite from time to time outside of
git-annex would also let me notice these before the distribution packagers
do.
This commit was sponsored by mo on Patreon.
That can leave other imported files not checked into git, because the git
command queue is not flushed when git-annex errors out. And since it only
happens once git-annex has concluded a feed is broken, it's an intermittent
bug, worst kind. Been seeing it for a while, only tracked down today.
Instead, by returning False, git-annex importfeed will cleanly shutdown and
still exit nonzero.
This commit was sponsored by Denis Dzyubenko on Patreon.
When readContent got Nothing from prepSendAnnex, it did not run its
callback, and the callback is what sends the DATA reply.
sendContent checks with contentSize that the object file is present, but
that doesn't really guarantee that prepSendAnnex won't return Nothing.
So, it was possible for a P2P protocol GET to not receive a response,
and appear to hang. When what it's really doing is waiting for the next
protocol command.
This seems most likely to happen when the annex is in direct mode, and the
file being requested has been modified. It could also happen in an indirect
mode repository if genInodeCache somehow failed. Perhaps due to a race
with a drop of the content file.
Fixed by making readContent behave the way its spec said it should,
and run the callback with L.empty in this case.
Note that, it's finee for readContent to send any amount of data
to the callback, including L.empty. sendBytes deals with that
by making sure it sends exactly the specified number of bytes,
aborting the protocol if it's too short. So, when L.empty is sent,
the protocol will end up aborting.
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
Cache high-resolution mtimes for improved detection of modified files in v7
(and direct mode).
Including on Windows.
With back-compat support so old low-res mtimes won't break anything, and
so the new information also won't break old versions of git-annex.
Removed undocumented special case in handling of a CHECKURL-MULTI response
with only a single file listed. Rather than ignoring the url that was in
the response, use it. This allows external special remotes that want to
provide some better url to do so, although I don't entirely agree with
using CHECKURL-MULTI to accomplish that. I'm more of the feeling that an
undocumented special case that throws data away is just not a good idea.
This could in theory break some external special remote program that relied
on the current behavior, but its seems unlikely that it would because such
a program must already handle the multiple url case, unless it only ever
provides a single url response to CHECKURL-MULTI.
Make addurl --file work with a single item CHECKURL-MULTI response.
It already did for external special remotes due to the special case,
but now it also will for builtin ones like the BitTorrent special remote.
This commit was sponsored by Ilya Shlyakhter on Patron.
This is safe, because while the annex object ends up executable,
there were already at least two other cases where it ended up executable:
1. git add an an executable file
2. chmod +x of a a non-executable worktree file that was hard linked to the
annex object
After copy/hard link, it always fixes up the permissions to match the mode
of the worktree file, so when an executable annex object gets hard linked
to a non-executable worktree file, its execute bit gets removed.
Commit b7c8bf5274 already *said* it would do
this; I suspect the line of code I've removed was included in that commit
accidentially.
Also improves annex.thin documentation.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
This makes --version=6 still work, despite v6 not being in
supportedVersions. Which is useful for scripts that use it.
I didn't document it on the man page, because it's indistinguishable
from an automatic upgrade after initting as v6.
init: When in a crippled filesystem, initialize a v7 repository using an
adjusted unlocked branch, instead of a direct mode repository.
Direct mode is deprecated, so this makes sense to do already I hope.
This commit was sponsored by Ole-Morten Duesund on Patreon.
Install new git hooks in this version.
This does beg the question of what to do if git later gets eg a
post-smudge hook, that could run git-annex smudge --update. I think the
thing to do in that case would be to make git-annex smudge --update
install the new hooks. That way, as the user uses git-annex, the hook
would be created pretty quickly and without needing any extra syscalls
except for when git-annex smudge --update is called.
I considered doing something like that for installation of the
post-checkout and post-merge hooks, which would have avoided the need
for v7. But the only place it was cheap to do it would be in git-annex smudge
which could cheaply notice that smudge.log didn't exist yet and so know
the hooks needed to be installed. But since smudge used to populate pointer
files, it would be quite surprising if a single git checkout/merge failed
to update the work tree, and so that idea didn't work out.
The other reason for v7 is psychological -- users don't need to worry
about whether they might be running an old version of git-annex that
doesn't support their v7 repository very well. And bug reports about
"v6" have gotten a bit of a bad association in my head since they often
hit one of the known limitations and didn't realize it was experimental.
newtyped RepoVersion Int to avoid needing 2 comparisons in
versionSupportsUnlockedPointers etc. Also it's just nicer.
This commit was sponsored by John Pellman on Patreon.
* init, upgrade: Install git post-checkout and post-merge hooks that run
git annex smudge --update.
* precommit: Run git annex smudge --update, because the post-merge
hook is not run when there is a merge conflict. So the work tree will
be updated when a commit is made to resolve the merge conflict.
* precommit: Run git annex smudge --update, because the post-merge
hook is not run when there is a merge conflict. So the work tree will
be updated when a commit is made to resolve the merge conflict.
* Note that git has no hooks run after git stash or git cherry-pick,
so the user will have to manually run git annex smudge --update
after such commands.
Nothing currently installs the hooks into v6 repos that already exist.
Something will need to be done about that, either move this behavior to v7,
or document that the user will need to manually fix up their v6 repos.
This commit was sponsored by Eric Drechsel on Patreon.
The smuge filter no longer provides git with annexed file content, to
avoid a git memory leak, and because that did not honor annex.thin.
git annex smudge --update has to be run after a checkout to update
unlocked files in the working tree with annexed file contents.
No hooks yet to run it.
This commit was sponsored by Nick Piper on Patreon.
Block other threads while the export database is being constructed (or
updated) by the first thread to try to access it.
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
This completes initial support for --hide-missing, although the
assistant still needs to be updated and it perhaps needs to be sped up,
and maybe there needs to be a way for git-annex get to operate on
missing files. Opened some more todos for those things.
This commit was sponsored by Henrik Riomar.
This relies on git ls-files --with-tree, which I'm using in a way that
its man page does not document. Hm. I emailed the git list to try to get
the docs improved, but at least the git test suite does test the same
kind of use case I'm using here.
Performance impact when not in an adjusted branch is limited to some
additional MVar accesses, and a single git call to determine the name of
the current branch. So very minimal.
When in an adjusted branch, the performance impact is
in Annex.WorkTree.lookupFile, which starts doing an equal amount of work
for files that didn't exist as it already did for files that were
unlocked.
This commit was sponsored by Jochen Bartl on Patreon.
* At long last there's a way to hide annexed files whose content
is missing from the working tree: git-annex adjust --hide-missing
* When already in an adjusted branch, running git-annex adjust
again will update the branch as needed. This is mostly
useful with --hide-missing to hide/unhide files after their content
has been dropped or received.
Still needs integration with sync and the assistant, and not as fast as it
could be, but already usable.
This commit was sponsored by Ethan Aubin.
That could cause git-annex to get confused about whether a locked file's
content was present, when the object file got touched.
Unfortunately this means more work sometimes when annex.thin is set,
since it has to checksum the file to tell if it's still got the right
content.
Had to suppress output when inAnnex calls isUnmodified, otherwise
"(checksum...)" would be printed in places it ought not to be,
eg "git annex get" could turn out not need to get anything, and
so only display that.
This commit was sponsored by Ole-Morten Duesund on Patreon.
This is to work around https://github.com/datalad/datalad/issues/2769
which I don't know how to reproduce outside that environment, nor do I
understand the root cause of. For some time, Neurodebian has been working
around it by building its standalone debs with a patch that disables use
of the locales bundled with the standalone build, letting the system
locales be used.
Using the system locales is asking for trouble if there's
significant version skew between the system and bundled glibc, and
possibly also if the architeciture is different, or whatever. That's why
git-annex bundles and uses its own locales, because numerous users
reported real problems with using the system locales.
... However, in the specific case of the Neurodebian standalone debs,
the deb is built on a system very like the one it's targeted to be
installed on. Or well, so they assure me, although doc/install/Ubuntu.mdwn
also promotes those for use across all versions of Ubuntu, and the deb
is built avoiding xz so it will work with old versions of dpkg, so I wonder
how true it is. It does seem that, at least currently, there is no bad
version skew in the locales of the systems the deb is used on, since
it's already been using the system locales for some time.
Anyway, since the Neurodebian build already is setting
GIT_ANNEX_PACKAGE_INSTALL=1 in runshell, I made runshell use system
locales when that's set. This is a small scope creep for
GIT_ANNEX_PACKAGE_INSTALL, but it's not documented and AFAIK only used
for the Neurodebian build, so that seems ok. This will let them stop
carrying their patch for this forward.
This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
The bundled uname -o says Linux in termux; have runshell on Android
delete it so the termux one is used instead.
This fixes the webapp so it will enter Android mode.
This commit was sponsored by mo on Patreon.
Running git-annex linux builds in termux seems to work well enough that the
only reason to keep the Android app would be to support Android 4-5, which
the old Android app supported, and which I don't know if the termux method
works on (although I see no reason why it would not).
According to [1], Android 4-5 remains on around 29% of devices, down from
51% one year ago.
[1] https://www.statista.com/statistics/271774/share-of-android-platforms-on-mobile-devices-with-android-os/
This is a rather large commit, but mostly very straightfoward removal of
android ifdefs and patches and associated cruft.
Also, removed support for building with very old ghc < 8.0.1, and with
yesod < 1.4.3, and without concurrent-output, which were only being used
by the cross build.
Some documentation specific to the Android app (screenshots etc) needs
to be updated still.
This commit was sponsored by Brett Eisenberg on Patreon.
* Added arm64 Linux standalone build. (No autobuilder yet.)
* Improved termux installation process.
Added git-annex-install.sh script to avoid user needing to type as much in
termux. The scope of this script is limited; runshell handles the rest.
Runshell runs termux-fix-shebang on the shell scripts. The problem is
the bundled bin/sh script, deleting that script also works, but then the
others probably use the system Android /bin/sh, which could be old or
broken or not posix or whatever. Using termux sh to run the scripts is
better.
This commit was sponsored by Eric Drechsel on Patreon.
On android arm64, I saw the cp fail with "Bad system call", because proot
has not run yet. runshell only recently started using cp, and it's bundled
with git-annex, so this fixes a reversion.
This commit was sponsored by Nick Piper on Patreon.
Made it impossible to recover from setting a bad value since enableremote
to change it would crash.
This commit was sponsored by Henrik Riomar on Patreon.
I don't know the circumstances, but have a report of this:
git-annex: failed to commit changes to sqlite database: Just SQLite3 returned
ErrorConstraint while attempting to perform step.
All 3 tables in the export db have uniqueness constraints on them,
insertUnique is used for all the rest, but this use of insertMany
means it doesn't check the constraint. I guess that's what caused the
crash, but I have not been able to test it yet.
Use putMany when available, as it should be faster than mapM of insertMany.
This commit was sponsored by Brock Spratlen on Patreon.
* rmurl: Fix a case where removing the last url left git-annex thinking
content was still present in the web special remote.
* SETURLPRESENT, SETURIPRESENT, SETURLMISSING, and SETURIMISSING
used to update the presence information of the external special remote
that called them; this was not documented behavior and is no longer done.
Done by making setUrlPresent and setUrlMissing only update presence info
for the web, and only when the url is a web url. See the comment for
reasoning about why that's the right thing to do.
In AddUrl, had to make it update location tracking, to handle the
non-web-url case.
This commit was sponsored by Ewen McNeill on Patreon.
Inverted logic added as part of the url security fix made it always use
curl when annex.security.allowed-http-addresses=all unless annex.web-options
was set.
That nobody noticed kind of makes me wonder if anyone uses
annex.web-options..
This commit was sponsored by Denis Dzyubenko on Patreon.
Added annex.jobs setting, which is like using the -J option.
Of course, -J overrides annex.jobs.
This commit was sponsored by Trenton Cronholm on Patreon.
The error message displayed used to only come from curl/wget and perhaps
was clearer than the one displayed now that http-client is used. In any
case, it does make sense to hide it because git-annex prints its own
warning message.
This commit was sponsored by Jake Vosloo on Patreon.
Only display the warning when the current branch has a tree that is not
the same as the tree in the export.
Note that it doesn't check to see if the current tree is
in incompleteExportedTreeish; it might be worth checking that and reminding
the user about an incomplete export, but when export tracking is not
configured, they are probably not in the right clone of the repository to
resolve the incomplete export.
This commit was sponsored by Ethan Aubin.
Added remote.name.annex-security-allow-unverified-downloads, a per-remote
setting for annex.security.allow-unverified-downloads.
This commit was sponsored by Brock Spratlen on Patreon.
* init: Improve generated post-receive hook, so it won't fail when
run on a system whose git-annex is too old to support git-annex post-receive
* init: Update the post-receive hook when re-run in an existing repository.
This commit was sponsored by Jack Hill on Patreon.
This reverts commit b18fb1e343.
That broke support for old git-annex-shell before p2pstdio was added.
The immediate problem is that postAuth had a fallthrough case
that sent an error back to the peer, but sending an error back when the
connection is closed is surely not going to work.
But thinking about it some more, making every function that uses receiveMessage
need to handle ProtocolEOF adds a lot of complication, so I don't want
to do that.
The commit only cleaned up the test suite output a tiny bit, so I'm just
gonna revert it for now.
Added annex.maxextensionlength for use cases where extensions longer than 4
characters are needed.
This commit was sponsored by Henrik Riomar on Patreon.
Untested, on FreeBSD but enough to fix the listed build errors.
Seems that System.Posix.Files must have used to export this stuff and it
was split.
This commit was sponsored by Peter on Patreon.
Added -z option to git-annex commands that use --batch, useful for
supporting filenames containing newlines.
It only controls input to --batch, the output will still be line delimited
unless --json or etc is used to get some other output. While git often
makes -z affect both input and output, I don't like trying them together,
and making it affect output would have been a significant complication,
and also git-annex output is generally not intended to be machine parsed,
unless using --json or a format option.
Commands that take pairs like "file key" still separate them with a space
in --batch mode. All such commands take care to support filenames with
spaces when parsing that, so there was no need to change it, and it would
have needed significant changes to the batch machinery to separate tose
with a null.
To make fromkey and registerurl support -z, I had to give them a --batch
option. The implicit batch mode they enter when not provided with input
parameters does not support -z as that would have complicated option
parsing. Seemed better to move these toward using the same --batch as
everything else, though the implicit batch mode can still be used.
This commit was sponsored by Ole-Morten Duesund on Patreon.
Work around git cat-file --batch's protocol not supporting newlines by
running git cat-file not batched and passing the filename as a
parameter.
Of course this is quite a lot less efficient, especially because it
currently runs it multiple times to query for different pieces of
information.
Also, it has subtly different behavior when the batch process was
started and then some changes were made, in which case the batch process
sees the old index but this workaround sees the current index. Since
that batch behavior is mostly a problem that affects the assistant and has
to be worked around in it, I think I can get away with this difference.
I don't know of any other problems with newlines in filenames, everything
else in git I can think of supports -z. And git-annex's json output
supports newlines in filenames so downstream parsers from git-annex will be ok.
git-annex commands that use --batch themselves don't support newlines
in input filenames; using --json --batch is currently a way around that
problem.
This commit was sponsored by Ewen McNeill on Patreon.
When git-annex used wget and curl, --debug would show urls. So there can't
be any new security problem with doing so.
This commit was sponsored by John Pellman on Patreon.
When the publicurl has been set to an url that does not end with a slash,
we need to add one in between it and the rest of the url.
As far as I can see, git-annex does not default to such publicurls; it's
careful to end them with slashes. But this was observed in the wild, and
there may be documentation that doesn't include the slash. And it's an easy
mistake to make in any case.
This commit was sponsored by Eric Drechsel on Patreon.
S3: Multipart uploads are now only supported when git-annex is built
with aws-0.16.0 or later, as earlier versions of the library don't
support versioning with multipart uploads.
This will affect the android build, and debian stable also has a too old
aws to support both features at the same time.
This commit was sponsored by Nick Piper on Patreon.
v6: When a file is unlocked but has not been modified, and the unlocking is
only staged, git-annex add did not lock it. Now it will, for consistency
with how modified files are handled and with v5.
Note the removal of the sameInodeCache check. Otherwise it would see
that the unmodified file is unmodified and stop there. That check seems to have
been copied from the direct mode branch. But, direct mode had a specific
reason to check for unmodified content, that does not apply to v6.
The second pass means there is potential for a race, eg the unlocked
file could be modified in between the first and second passes.
No problem with that, since both passes do the same thing.
This commit was sponsored by Jake Vosloo on Patreon.
* Don't use GIT_PREFIX when GIT_WORK_TREE=. because it seems git
does not intend GIT_WORK_TREE to be relative to GIT_PREFIX in that
case, despite GIT_WORK_TREE=.. being relative to GIT_PREFIX.
* Don't use GIT_PREFIX to fix up a relative GIT_DIR, because
git 2.11 sets GIT_PREFIX set to a path it's not relative to.
and apparently GIT_DIR is never relative to GIT_PREFIX.
Commit e50ed4ba48 led us down this path
by working around a git bug by relying on the barely documented GIT_PREFIX.
This commit was sponsored by Trenton Cronholm on Patreon.
v6: Fix annex object file permissions when git-annex add is run on a
modified unlocked file, and in some related cases.
If a hard link is made, don't freeze it; annex.thin
uses writable object files.
Also: For some reason, linkToAnnex used to thawContent src. I can see no
reason why it needed to do that, so I eliminated that.
This commit was sponsored by Brock Spratlen on Patreon.
In 2013, I wrote "Cryptohash benchmarks 90 to 101% faster than external
hashers". Re-benchmarking today, I found cryptonite's sha256 consistently
outperformed coreutils by 10% for large files. Tested 10 mb, 100 mb, 1 gb
files with both sha256 and sha512. And for smaller files, the external
process startup time swamps the hash time.
Perhaps cryptonite has improved. Or it could just do better on my
current CPU Intel(R) Pentium(R) CPU 4410Y @ 1.50GHz). Anyway, even if cryptonite
is slower in some situations, seems likely it would only be marginally slower;
it's got the same class of highly optimised C code under the hood as coreutils.
The main difference between the two sha256 implementations seems to be
how much of the inner loop they unroll..
This commit was sponsored by Henrik Riomar on Patreon.
Probably not noticed until now because the queue is large enough that two
threads each filling theirs at the same time and flushing is unlikely to
happen.
Also made explicit that each worker thread gets its own queue.
I think that was the case before, but if something was put in the queue
before worker threads were forked off, they could have each inherited the
same queue.
Could have gone with a single shared queue, but per-worker queues is more
efficient, because a worker can add lots of stuff to its own queue without
any locking.
This commit was sponsored by Ole-Morten Duesund on Patreon.
v6: When annex.largefiles is not configured for a file, running git add or
git commit, or otherwise using git to stage a file will add it to the annex
if the file was in the annex before, and to git otherwise. This is to avoid
accidental conversion.
Note that git-annex add's behavior has not changed, for reasons explained
in the added comment.
Performance: No added overhead when annex.largefiles is configured.
When not configured, there is an added call to catObjectMetaData,
which involves a round trip through git cat-file --batch.
However, the earlier catKeyFile primes the cache for it.
This commit was supported by the NSF-funded DataLad project.
Update pointer file next time reconcileStaged is run to recover from the
race.
Note that restagePointerFile causes git to run the clean filter,
and that will run reconcileStaged. So, normally by the time the git
annex get/drop command finishes, the race has already been dealt with.
It may be that, in some case, that won't happen and the race will be
dealt with at a later point. git-annex could run reconcileStaged at
shutdown if that becomes a problem.
This does not handle the situation where the git mv is committed before
git-annex gets a chance to run again. git commit does run the clean
filter, and that happens to re-inject the content if it was supposed to
be dropped but is still populated. But, the case where the file was
supposed to be gotten but is not populated is not handled yet.
This commit was supported by the NSF-funded DataLad project.
It can be set to an empty string to use the system locales too. Of course
whether that will work depends on the amount of divergence.
This commit was supported by the NSF-funded DataLad project.
After updating the worktree for an add/drop, update git's index, so git
status will not show the files as modified.
What actually happens is that the index update removes the inode
information from the index. The next git status (or similar) run
then has to do some work. It runs the clean filter.
So, this depends on the clean filter being reasonably fast and on git
not leaking memory when running it. Both problems were fixed in
a96972015d, but only for git 2.5. Anyone
using an older git will see very expensive git status after an add/drop.
This uses the same git update-index queue as other parts of git-annex, so
the actual index update is fairly efficient. Of course, updating the index
does still have some overhead. The annex.queuesize config will control how
often the index gets updated when working on a lot of files.
This is an imperfect workaround... Added several todos about new
problems this workaround causes. Still, this seems a lot better than the
old behavior.
This commit was supported by the NSF-funded DataLad project.
v6 add: Take advantage of improved SIGPIPE handler in git 2.5 to speed up
the clean filter by not reading the file content from the pipe. This also
avoids git buffering the whole file content in memory.
When built with an older git, still consumes stdin. If built with a newer
git and used with an older one, it breaks, but that's acceptable --
checking the git version every time would make repeated smudge runs slow.
This commit was supported by the NSF-funded DataLad project.
When --batch is used with matching options like --in, --metadata, etc, only
operate on the provided files when they match those options. Otherwise, a
blank line is output in the batch protocol.
Affected commands: find, add, whereis, drop, copy, move, get
In the case of find, the documentation for --batch already said it honored
the matching options. The docs for the rest didn't, but it makes sense to
have them honor them. While this is a behavior change, why specify the
matching options with --batch if you didn't want them to apply?
Note that the batch output for all of the affected commands could
already output a blank line in other cases, so batch users should
already be prepared to deal with it.
git-annex metadata didn't seem worth making support the matching options,
since all it does is output metadata or set metadata, the use cases for
using it in combination with the martching options seem small. Made it
refuse to run when they're combined, leaving open the possibility for later
support if a use case develops.
This commit was sponsored by Brett Eisenberg on Patreon.
Added getStaged, to get the versions of git-annex branch files staged in its
index, and use during transitions so the result of merging sibling branches
is used.
The catFileStop in performTransitionsLocked is absolutely necessary,
without that the bug still occurred, because git cat-file was already
running and was looking at the old index file.
Note that getLocal still has cat-file look at the git-annex branch, not the
index. It might be faster if it looked at the index, but probably only
marginally so, and I've not benchmarked it to see if it's faster at all. I
didn't want to change unrelated behavior as part of this bug fix. And as
the need for catFileStop shows, using the index file has added
complications.
Anyway, it still seems fine for getLocal to look at the git-annex branch,
because normally the index file is updated just before the git-annex branch
is committed, and so they'll contain the same information. It's only during
a transition that the two diverge.
This commit was sponsored by Paul Walmsley in honor of Mark Phillips.
It was sorting by uuid, rather than cost!
Avoid future bugs of this kind by changing the Ord to primarily compare
by cost, with uuid only used when the cost is the same.
This commit was supported by the NSF-funded DataLad project.
Added annex.commitmessage config that can specify a commit message for the
git-annex branch instead of the usual "update".
This commit was supported by the NSF-funded DataLad project.
Useful for dropping old objects from cache repositories.
But also, quite a genrally useful thing to have..
Rather than imitiating find's -atime and other options, all of which are
pretty horrible to use, I made this match files accessed within a time
period, using the same duration format used by git-annex schedule and
--limit-time
In passing, changed the --limit-time option parser to parse the
duration, instead of having it later throw an error.
This commit was supported by the NSF-funded DataLad project.
Added remote.name.annex-speculate-present config that can be used to
make cache remotes.
Implemented it in Remote.keyPossibilities, which is used by the
get/move/copy/mirror commands, and nothing else. This way, things like
whereis will not show content that's speculatively present.
The assistant and sync --content were not using Remote.keyPossibilities,
and were changed to use it.
The efficiency hit should be small; Remote.keyPossibilities is only
used before transferring a file, which is the expensive operation.
And, it's only doing one lookup of the remoteList and a very cheap
filter over it.
Note that, git-annex still updates the location log when copying content
to a remote with annex-speculate-present set. In this case, the location
tracking will indicate that content is present in the remote. This may
not be wanted for caches, or may not be a real problem for them. TBD.
This commit was supported by the NSF-funded DataLad project.
