9cb250f7be got the ones in RawFilePath,
but there were others that used the one from unix-compat, which fails at
runtime on windows. To avoid this,
import System.PosixCompat.Files hiding removeLink
This commit was sponsored by Ethan Aubin.
Added annex.adjustedbranchrefresh git config to update adjusted branches
set up by git-annex adjust --unlock-present/--hide-missing.
Note, in a few cases, I was not able to make the adjusted branch
be updated in calls to moveAnnex, because information about what
file corresponds to a key is not available. They are:
* If two files point to one file, then eg, `git annex get foo` will
update the branch to unlock foo, but will not unlock bar, because it
does not know about it. Might be fixable by making `git annex get
bar` do something besides skipping bar?
* git-annex-shell recvkey likewise (so sends over ssh from old versions
of git-annex)
* git-annex setkey
* git-annex transferkey if the user does not use --file
* git-annex multicast sends keys with no associated file info
Doing a single full refresh at the end, after any incremental refresh,
will deal with those edge cases.
Warn when adding a annex symlink or pointer file that uses a key that is
not known to the repository, to prevent confusion if the user has copied it
from some other repository.
This commit was sponsored by Jake Vosloo on Patreon.
Lots of nice wins from this in avoiding unncessary work, and I think
nothing got slower.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
nukeFile replaced with removeWhenExistsWith removeLink, which allows
using RawFilePath. Utility.Directory cannot use RawFilePath since setup
does not depend on posix.
This commit was sponsored by Graham Spencer on Patreon.
The latter is for git-annex matchexpression and matching against it can
throw an exception. Splitting out the former reduces the potential for
mistakes and avoids needing to worry about matching against that
throwing an exception.
This is more groundwork for matching largefiles while importing,
without downloading content.
This commit was sponsored by Graham Spencer on Patreon.
Anything that needs to examine the file content will fail to match,
or fall back to other available information. But the intent is that the
matcher be checked for matchNeedsFileContent and only be used if it does
not, so the exact behavior doesn't much matter as it should never
happen.
The real point of this is to not need to provide a dummy content file
when matching.
This commit was sponsored by Martin D on Patreon.
add, addurl, importfeed, import: Added --no-check-gitignore option
for finer grained control than using --force.
(--force is used for too many different things, and at least one
of these also uses it for something else. I would like to reduce
--force's footprint until it only forces drops or a few other data
losses. For now, --force still disables checking ignores too.)
addunused: Don't check .gitignores when adding files. This is a behavior
change, but I justify it by analogy with git add of a gitignored file
adding it, asking to add all unused files back should add them all back,
not skip some. The old behavior was surprising.
In Command.Lock and Command.ReKey, CheckGitIgnore False does not change
behavior, it only makes explicit what is done. Since these commands are run
on annexed files, the file is already checked into git, so git add won't
check ignores.
Except for the assistant, which I think may use them between threads?
Most of the uses of SomeException were already catching only async exceptions.
But I did find a few places that were accidentially catching them.
retrieveExport is part of ongoing transition to make remote methods
throw exceptions, rather than silently hide them.
getKey very rarely fails, and when it does it's always for the same reason
(user configured annex.backend to url for some reason). So, this will
avoid dealing with Nothing everywhere it's used.
This commit was sponsored by Ilya Shlyakhter on Patreon.
Since it was used on both worktree and .git/annex files, split into
multiple functions.
In passing, this also improves permissions of created directories in
.git/annex, using createAnnexDirectory on those.
* annex.addunlocked can be set to an expression with the same format used by
annex.largefiles, in case you want to default to unlocking some files but
not others.
* annex.addunlocked can be configured by git-annex config.
Added a git-annex-matching-expression man page, broken out from
tips/largefiles.
A tricky consequence of this is that git-annex add --relaxed
honors annex.addunlocked, but an expression might want to know the size
or content of an url, which it's not going to download. I decided it was
better not to fail, and just dummy up some plausible data in that case.
Performance impact should be negligible. The global config is already
loaded for annex.largefiles. The expression only has to be parsed once,
and in the simple true/false case, it should not do any additional work
matching it.
git-annex find is now RawFilePath end to end, no string conversions.
So is git-annex get when it does not need to get anything.
So this is a major milestone on optimisation.
Benchmarks indicate around 30% speedup in both commands.
Probably many other performance improvements. All or nearly all places
where a file is statted use RawFilePath now.
Adds a dependency on filepath-bytestring, an as yet unreleased fork of
filepath that operates on RawFilePath.
Git.Repo also changed to use RawFilePath for the path to the repo.
This does eliminate some RawFilePath -> FilePath -> RawFilePath
conversions. And filepath-bytestring's </> is probably faster.
But I don't expect a major performance improvement from this.
This is mostly groundwork for making Annex.Location use RawFilePath,
which will allow for a conversion-free pipleline.
No behavior changes, but this shows everywhere that a progress meter
could be displayed when hashing a file to add to the annex.
Many of the places don't make sense to display a progress meter though,
eg when importing the copy of the file probably swamps the hashing of
the file.
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.
This does not change the overall license of the git-annex program, which
was already AGPL due to a number of sources files being AGPL already.
Legally speaking, I'm adding a new license under which these files are
now available; I already released their current contents under the GPL
license. Now they're dual licensed GPL and AGPL. However, I intend
for all my future changes to these files to only be released under the
AGPL license, and I won't be tracking the dual licensing status, so I'm
simply changing the license statement to say it's AGPL.
(In some cases, others wrote parts of the code of a file and released it
under the GPL; but in all cases I have contributed a significant portion
of the code in each file and it's that code that is getting the AGPL
license; the GPL license of other contributors allows combining with
AGPL code.)
* 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.
Both Command.Sync and Annex.Ingest had their own versions of this.
The one in Annex.Ingest used Git.Branch.currentUnsafe, but does not seem
to need it. That is only checking to see if it's in an adjusted unlocked
branch, and when in an adjusted branch, the branch does in fact exist,
so the added check that Git.Branch.current does is fine.
This commit was sponsored by Denis Dzyubenko on Patreon.
Combinations like --hide-misssing --unlocked seem very useful. On the
other hand, combining --fix with --unlock doesn't make sense because a
file can be either unlocked or a symlink that can be fixed, but not
both.
Changed the serialization of HideMissingAdjustment in passing, but it
has not actually been used yet so nothing will be broken.
This commit was sponsored by Trenton Cronholm on Patreon.
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.
Needs ghc 7.6.1, so minimum base version increased slightly. All builds
are well above this version of ghc, and debian oldstable is as well.
Code that could use lambdacase can be found by running:
git grep -B 1 'case ' | less
and searching in less for "<-"
This commit was sponsored by andrea rota.
Before, there was a window where interrupting an add could result in the
file being moved into the annex, with no symlink yet created.
This commit was supported by the NSF-funded DataLad project.
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.
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.
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.
When annex.thin is set, adding an object will add the execute bits to the
work tree file, and this does mean that the annex object file ends up
executable.
This doesn't add any complexity that wasn't already present, because git
annex add of an executable file has always ingested it so that the annex
object ends up executable.
But, since an annex object file can be executable or not, when populating
an unlocked file from one, the executable bit is always added or removed
to match the mode of the pointer file.
* add, addurl, import, importfeed: When in a v6 repository on a crippled
filesystem, add files unlocked.
* annex.addunlocked: New configuration setting, makes files always be
added unlocked. (v6 only)
Linking the file to the tmp dir was not necessary in the clean
filter, and it caused the ctime to change, which caused git to think
the file was changed. This caused git status to get slow as it kept
re-cleaning unchanged files.
Fixes several bugs with updates of pointer files. When eg, running
git annex drop --from localremote
it was updating the pointer file in the local repository, not the remote.
Also, fixes drop ../foo when run in a subdir, and probably lots of other
problems. Test suite drops from ~30 to 11 failures now.
TopFilePath is used to force thinking about what the filepath is relative
to.
The data stored in the sqlite db is still just a plain string, and
TopFilePath is a newtype, so there's no overhead involved in using it in
DataBase.Keys.
Decided it's too scary to make v6 unlocked files have 1 copy by default,
but that should be available to those who need it. This is consistent with
git-annex not dropping unused content without --force, etc.
* Added annex.thin setting, which makes unlocked files in v6 repositories
be hard linked to their content, instead of a copy. This saves disk
space but means any modification of an unlocked file will lose the local
(and possibly only) copy of the old version.
* Enable annex.thin by default on upgrade from direct mode to v6, since
direct mode made the same tradeoff.
* fix: Adjusts unlocked files as configured by annex.thin.
