3a513cfe73 caused a reversion in addurl.
The type of addSmall changed, but the void prevented the type checker
from helping notice this. Since it now returns a CommandPerform, the
cleanup action has to be run.
Sponsored-by: Dartmouth College's Datalad project
This is intended for users who want to see what it would output in order to
eg, check if a file would be added to git or the annex. It is not intended
as a way for scripts to get information.
Sponsored-by: Dartmouth College's Datalad project
On Windows, that does not support long paths
https://github.com/jacobstanley/unix-compat/issues/56
Instead, use System.Directory.renamePath, which does support long paths.
Sponsored-by: Dartmouth College's Datalad project
--backend is no longer a global option, and is only accepted by commands
that actually need it.
Three commands that used to support backend but don't any longer are
watch, webapp, and assistant. It would be possible to make them support it,
but I doubt anyone used the option with these. And in the case of webapp
and assistant, the option was handled inconsistently, only taking affect
when the command is run with an existing git-annex repo, not when it
creates a new one.
Also, renamed GlobalOption etc to AnnexOption. Because there are many
options of this type that are not actually global (any more) and get
added to commands that need them.
Sponsored-by: Kevin Mueller on Patreon
Some small wins, almost certianly swamped by the system calls, but still
worthwhile progress on the RawFilePath conversion.
Sponsored-by: Erik Bjäreholt on Patreon
When adding a small file, it does not get locked down, so can be modified
after git-annex checks that it's small. The use of queued git add made the
race window nice and wide too.
Fixed by checking if the file has changed, and by not using git add.
Instead, have to recapitulate git add's handling of things like symlinks
and executable files.
Sponsored-by: Jochen Bartl on Patreon
The remaining callers all did not rely on it checking gitignore, so were
easy to convert.
They were susceptable to the same overwrite race as add and fix,
although less likely to have it and a narrower window than add's race.
Command.Rekey in passing got an unncessary call to removeFile deleted.
addSymlink handles deleting any existing worktree file.
Similar to git-annex add, git-annex fix queued git add, so if a file
got modified before git add ran, the wrong content would be staged,
perhaps a large file content.
Sponsored-by: Brock Spratlen on Patreon
In the unlikely case where git-annex add is run on an annex symlink that
is not already added, and while it's processing it, the annex symlink is
overwritten with something else, avoid git-annex overwriting that with
the symlink again.
Sponsored-by: Jack Hill on Patreon
This is not a complete fix for all such races, only the one where a
large file gets changed while adding and gets added to git rather than
to the annex.
addLink needs to go away, any caller of it is probably subject to the
same kind of race. (Also, addLink itself fails to check gitignore when
symlinks are not supported.)
ingestAdd no longer checks gitignore. (It didn't check it consistently
before either, since there were cases where it did not run git add!)
When git-annex import calls it, it's already checked gitignore itself
earlier. When git-annex add calls it, it's usually on files found
by withFilesNotInGit, which handles checking ignores.
There was one other case, when git-annex add --batch calls it. In that
case, old git-annex behaved rather badly, it would seem to add the file,
but git add would later fail, leaving the file as an unstaged annex symlink.
That behavior has also been fixed.
Sponsored-by: Brett Eisenberg on Patreon
move: Improve resuming a move that succeeded in transferring the content,
but where dropping failed due to eg a network problem, in cases where
numcopies checks prevented the resumed move from dropping the object from
the source repository.
This was earlier done for moves that got interrupted during the drop stage.
Sponsored-by: Svenne Krap on Patreon
Use cases include using git-annex init --no-autoenable and then going back
and enabling the special remotes that have autoenable configured. As well
as just querying to remember which ones have it enabled.
It lists all special remotes that have autoenable=yes whether currently
enabled or not. And it can be used with --json.
I pondered making this "git-annex info autoenable", but that seemed wrong
because then if the use has a directory named "autoenable", it's unclear
what they are asking for. (Although "git-annex info remote" may be
similarly unclear.) Making it an option does mean that it can't be provided
via --batch though.
Sponsored-by: Dartmouth College's Datalad project
Someone may disagree with what repositories are set to autoenable and
it's good to have local overrides.
See https://github.com/datalad/datalad/issues/6634
Sponsored-by: Dartmouth College's Datalad project
The purpose of this is to fix situations where the annex object file is
stored in a directory structure other than where annex symlinks point to.
But it will also move object files from the hashdirmixed back to
hashdirlower if the repo configuration makes that the normal location.
It would have been more work to avoid that than to let it do it.
Sponsored-by: Dartmouth College's Datalad project
If the content directory does not exist, then it does not make sense to
lock the content file, as it also does not exist, and so it's ok for the
lock operation to fail.
This avoids potential races where the content file exists but is then
deleted/renamed, while another process sees that it exists and goes to
lock it, resulting in a dangling lock file in an otherwise empty object
directory.
Also renamed modifyContent to modifyContentDir since it is not only
necessarily used for modifying content files, but also other files in
the content directory.
Sponsored-by: Dartmouth College's Datalad project
None of the special remotes do it yet, but this lays the groundwork.
Added MustFinishIncompleteVerify so that, when an incremental verify is
started but not complete, it can be forced to finish it. Otherwise, it
would have skipped doing it when verification is disabled, but
verification must always be done when retrievin from export remotes
since files can be modified during retrieval.
Note that retrieveExportWithContentIdentifier doesn't support incremental
verification yet. And I'm not sure if it can -- it doesn't know the Key
before it downloads the content. It seems a new API call would need to
be split out of that, which is provided with the key.
Sponsored-by: Dartmouth College's Datalad project
Ignore annex.numcopies set to 0 in gitattributes or git config, or by
git-annex numcopies or by --numcopies, since that configuration would make
git-annex easily lose data. Same for mincopies.
This is a continuation of the work to make data only be able to be lost
when --force is used. It earlier led to the --trust option being disabled,
and similar reasoning applies here.
Most numcopies configs had docs that strongly discouraged setting it to 0
anyway. And I can't imagine a use case for setting to 0. Not that there
might not be one, but it's just so far from the intended use case of
git-annex, of managing and storing your data, that it does not seem like
it makes sense to cater to such a hypothetical use case, where any
git-annex drop can lose your data at any time.
Using a smart constructor makes sure every place avoids 0. Note that this
does mean that NumCopies is for the configured desired values, and not the
actual existing number of copies, which of course can be 0. The name
configuredNumCopies is used to make that clear.
Sponsored-by: Brock Spratlen on Patreon
add: Avoid unncessarily converting a newly unlocked file to be stored
in git when it is not modified, even when annex.largefiles does not
match it.
This fixes a reversion in version 10.20220222, where git-annex unlock
followed by git-annex add, followed by git commit file could result in
git thinking the file was modified after the commit.
I do have half a mind to remove the withUnmodifiedUnlockedPointers part
of git-annex add. It seems weird, despite that old bug report arguing
a case of consistency that it ought to behave that way. When git-annex
add surpises me, it seems likely it's wrong.. But for now, this is the
smallest possible fix.
Sponsored-by: Dartmouth College's Datalad project
The patch that removed it did not break anything, since the strings it's
used on are all ASCII not unicode. But I like making sure to use
packString everywhere just in case the code later changes in a way that
needs it.
In aeson 2.0, Text has been replaced by the Key type and HashMap by the
KeyMap interface. Accomodating this required adding some CPP in order to
still be able to compile with aeson < 2.0. The required changes were:
* Prevent Key from being re-exported by Utilities.Aeson, as it clashes
with git-annex's own Key type.
* Fix up convertion from String/Text to Key (or Text in aeson 1.*) in a
couple of places
* Import Data.Aeson.KeyMap instead of Data.HashMap.Strict, as they are
mostly API-compatible. insertWith needs to be replaced by unionWith,
however, as KeyMap lacks the former function.
It will then proceed to add the file the same as if it were any other
file containing possibly annexable content. Usually the file is one that
was annexed before, so the new, probably corrupt content will also be added
to the annex. If the file was not annexed before, the content will be added
to git.
It's not possible for the smudge filter to throw an error here, because
git then just adds the file to git anyway.
Sponsored-by: Dartmouth College's Datalad project
A few places were reading the max symlink size of a pointer file,
then passing tp parseLinkTargetOrPointer. Which is fine currently, but
to support pointer files with lines of data after the pointer, enough
has to be read that parseLinkTargetOrPointer can be assured of seeing
enough of that data to know if it's correctly formatted.
Sponsored-by: Dartmouth College's Datalad project
File matching options like --include will be rejected in situations where
there is no filename to match against. (Or where there is a filename but
it's not relative to the cwd, or otherwise seemed too bothersome to match
against.)
The addition of listKeys' was necessary to avoid using more memory in the
common case of "git-annex info". Adding a filterM would have caused the
list to buffer in memory and not stream. This is an ugly hack, but listKeys
had previously run Annex operations inside unafeInterleaveIO (for direct
mode). And matching against a matcher should hopefully not change any Annex
state.
This does allow for eg `git-annex info somefile --include=*.ext`
although why someone would want to do that I don't really know. But it
seems to make sense to allow it.
But, consider: `git-annex info ./somefile --include=somefile`
This does not match, so will not display info about somefile.
If the user really wants to, they can `--include=./somefile`.
Using matching options like --copies or --in=remote seems likely to be
slower than git-annex find with those options, because unlike such
commands, info does not have optimised streaming through the matcher.
Note that `git-annex info remote` is not the same as
`git-annex info --in remote`. The former shows info about all files in
the remote. The latter shows local keys that are also in that remote.
The output should make that clear, but this still seems like a point
where users could get confused.
Sponsored-by: Jochen Bartl on Patreon
This avoids a later git status or similar taking a long time to run
as it runs git-annex smudge once per file. While v9 repositories do
avoid that taking long when the files are small, large files can still
make git status take a very long time.
This does make unlock slower, because now git-annex smudge is being run
once per file unlocked. However, the next commit should speed that up in
many cases.
Sponsored-by: Boyd Stephen Smith Jr. on Patreon
* registerurl, unregisterurl: Improved output when reading from stdin
to be more like other batch commands.
* registerurl, unregisterurl: Added --json and --json-error-messages options.
Note that this did change the --batch output in a way that could possibly
break something that expected the old output to never change. I think it's
acceptable to break that because there has never been a guarantee of
unchanging output format except with --batch for most commands. The old
output was just really weird too!
One possible wart is that "git-annex registerurl" with no options now
seems to just hang, since it's waiting for stdin input. Before, it said
"registerurl (stdin)" which was clearer about what's happenening. But this
is a deprecated mode anyway, --batch makes clear what's happening. If
anything, this problem would be a reason to eventually remove the support
for reading from stdin w/o --batch.
Sponsored-by: Dartmouth College's Datalad project
Reject combinations of --batch (or --batch-keys) with options like --all or
--key or with filenames.
Most commands ignored the non-batch items when batch mode was enabled.
For some reason, addurl and dropkey both processed first the specified
non-batch items, followed by entering batch mode. Changed them to also
error out, for consistency.
Sponsored-by: Dartmouth College's Datalad project
Before it would pick one at random, though preferring ones that were not
dead over dead ones.
Now, if one is dead and the other not, it will use the non-dead one. But if
both are not dead, or both dead, it will error out, suggesting the user
clarify what they want to enable.
Sponsored-by: Luke Shumaker on Patreon
So that importing does not replace them with plain files.
This works similarly to how the previous handling of submodules and
matchers did, except that annexed symlinks still get exported as plain
files of course, it's only non-annexed symlinks that it does not make sense
to export.
When symlinks have previously been exported, updating the export will
unexport them after upgrading to this commit.
Sponsored-by: Kevin Mueller on Patreon
Started in 2017 in commit 3fe9d99f24.
Starting tomorrow, all versions of git-annex since then will provide
an appid, and so it will no longer be necessary to check the date.
Sponsored-by: Nicholas Golder-Manning on Patreon
Capstone to this feature. Any transitions that have been performed on an
unmerged remote ref but not on the local git-annex branch, or vice-versa
have to be applied on the fly when reading files.
Sponsored-by: Dartmouth College's Datalad project
It would display incomplete information, which would differ from the
information displayed with write access. So refuse to display anything.
Sponsored-by: Dartmouth College's Datalad project
It would be difficult to make Annex.Branch.files query the unmerged
git-annex branches. Might be possible, similar to what was discussed in
7f6b2ca49c but again I decided to make it
not do anything in that situation to start with before adding such a
complicated thing.
git-annex info uses it when getting info about a repostory. The choices
were to make that fail with an error, or display the info it can, and
change the output slightly for the bits of info it cannot access. While
that is a behavior change, and I want to avoid any behavior changes due
to unmerged git-annex branches in a read-only repo, displaying a message
that is not a number seems unlikely to break anything that was consuming
a number, any worse than throwing an exception would. Probably.
Also git-annex unused --from origin is made to throw an error, but
it would fail later anyway when trying to write to the unused log files.
Sponsored-by: Dartmouth College's Datalad project
This makes --all error out in that situation. Which is better than
ignoring information from the branches.
To really handle the branches right, overBranchFileContents would need
to both query all the branches and union merge file contents
(or perhaps not provide any file content), as well as diffing between
branches to find files that are only present in the unmerged branches.
And also, it would need to handle transitions..
Sponsored-by: Dartmouth College's Datalad project
sync: Better error message when unable to export to a remote because
remote.name.annex-tracking-branch is configured to a ref that does not
exist.
It does not suggest how to fix the problem because there are several
possible solutions: Change the git config to point to something that does
exist, git add some files, or put files on the special remote that will be
imported and so populate the ref.
I considered just silently not doing anything, which is what it does
when annex-tracking-branch = master and nothing has been committed to
master yet. But it seems better to be explicit about it, since this is a
fairly confusing situation to find yourself in.
Sponsored-By: Max Thoursie on Patreon
Commit b6e4ed9aa7 made non-annexed files
be re-uploaded every time, since they're not tracked in the location log,
and it made it check the location log. Don't do that for non-annexed files.
Sponsored-by: Brock Spratlen on Patreon
As mentioned in commit 2bd778a46e, there
was mojibake when LANG=C.
Looking at parseFeedFromFile, it is very particular to read the file as
unicode. parseFeedString looks like it will accept any old String,
but a String that was read using the filesystem encoding will not in
fact have the right encoding.
I think this is a bug in the feed library and will file one.
Sponsored-by: Svenne Krap on Patreon
See comment for analysis.
At first I thought I'd need to convert all T.unpack in git-annex, but
luckily not -- so long as the Text is read from a file, the filesystem
encoding is applied and T.unpack is fine. It's only when using Feed
that the filesystem encoding is not applied.
While this fixes the crash, it does result in some mojibake, eg:
itemid=http://www.manager-tools.com/2014/01/choosing-a-company-work-chapter-7-���-questions/
Have not tracked that down, but it must be unrelated, because
I've verified that it roundtrips when using encodeUf8:
joey@darkstar:~/src/git-annex>LANG=C ghci Utility/FileSystemEncoding.hs
ghci> useFileSystemEncoding
ghci> Just f <- Text.Feed.Import.parseFeedFromFile "/home/joey/tmp/career_tools_podcasts.xml"
ghci> Just (_, x) = Text.Feed.Query.getItemId (Text.Feed.Query.feedItems f !! 0)
ghci> decodeBS (Data.Text.Encoding.encodeUtf8 x)
"http://www.manager-tools.com/2014/01/choosing-a-company-work-chapter-7-\56546\56448\56467-questions/"
ghci> writeFile "foo" $ decodeBS (Data.Text.Encoding.encodeUtf8 x)
Writes a file containing the ENDASH character.
Sponsored-by: Jochen Bartl on Patreon
While intended for converting URL keys added by addurl --fast to be
as if added by addurl --relaxed, it can also be used to remove size
from other types of keys. Although that is not likely to be useful
for checksummed keys, I suppose it could be used for WORM or other
non-checksum keys.
Specifying the --remove-size option does not prevent other migrations
from taking effect if there's a key upgrade to perform, or if the
backend has changed. So --backend=URL needs to be used to prevent
migrating an URL key to the default backend.
Note that it's not possible to use git-annex migrate to convert from a
non-URL key to an URL key, as URL keys cannot be generated, except by
addurl. So while this can get the same effect as --relaxed would have
when addurl --fast was used, when --fast was not used, it won't work, or
if --backend=URL is not used will remove the size but not prevent
checksum verification, which is not useful. Due to this complexity, I
decided not to mention it in the git-annex addurl man page.
Sponsored-by: Jochen Bartl on Patreon
* uninit: Avoid error message when no commits have been made to the
repository yet.
* uninit: Avoid error message when there is no git-annex branch.
Sponsored-by: Svenne Krap on Patreon
filter-process: New command that can make git add/checkout faster when
there are a lot of unlocked annexed files or non-annexed files, but that
also makes git add of large annexed files slower.
Use it by running: git
config filter.annex.process 'git-annex filter-process'
Fully tested and working, but I have not benchmarked it at all.
And, incremental hashing is not done when git add uses it, so extra work is
done in that case.
Sponsored-by: Mark Reidenbach on Patreon
metadata --batch --json: Reject input whose "fields" does not consist of
arrays of strings. Such invalid input used to be silently ignored.
Used to be that parseJSON for a JSONActionItem ran parseJSON separately
for the itemAdded, and if that failed, did not propagate the error. That
allowed different items with differently named fields to be parsed.
But it was actually only used to parse "fields" for metadata, so that
flexability is not needed.
The fix is just to parse "fields" as-is. AddJSONActionItemFields is needed
only because of the wonky way Command.MetaData adds onto the started json
object.
Note that this line got a dummy type signature added,
just because the type checker needs it to be some type.
itemFields = Nothing :: Maybe Bool
Since it's Nothing, it doesn't really matter what type it is,
and the value gets turned into json and is then thrown away.
Sponsored-by: Kevin Mueller on Patreon
Turns out that CommandStart actions do not have their exceptions caught,
which is why the giveup was causing a crash. Mostly these actions
do not do very much work on their own, but it does seem possible there
are other commands whose CommandStart also throws an exception.
So, my first attempt at a fix was to catch those exceptions. But,
--json-error-messages then causes a difficulty, because in order to output
a json error message, an action needs to have been started; that sets up
the json object that the error message will be included in a field of.
While it would be possible to output an object with just an error field,
this would be json output of a format that the user has no reason to
expect, that happens only in an exceptional circumstance. That is something
I have always wanted to avoid with the json output; while git-annex man
pages don't document what the json looks like, the output has always
been made to be self-describing. Eg, it includes "error-messages":[]
even when there's no errors.
With that ruled out, it doesn't seem a good idea to catch CommandStart
exceptions and display the error to stderr when --json-error-messages
is set. And so I don't know if it makes sense to catch exceptions from that
at all. Maybe I'd have a different opinion if --json-error-messages did not
exist though.
So instead, output a blank line like other batch commands do.
This also leaves open the possibility of implementing support for matching
object with metadata --json, which would also want to output a blank line
when the input didn't match.
Sponsored-by: Dartmouth College's DANDI project
addurl: Support adding the same url to multiple files at the same time when
using -J with --batch --with-files.
Implementation was easier than expected, was able to reuse OnlyActionOn.
While it will download the url's content multiple times, that seems like
the best thing to do; see my comment for why.
Sponsored-by: Dartmouth College's DANDI project
* Removed support for accessing git remotes that use versions of
git-annex older than 6.20180312.
* git-annex-shell: Removed several commands that were only needed to
support git-annex versions older than 6.20180312.
(lockcontent, recvkey, sendkey, transferinfo, commit)
The P2P protocol was added in that version, and used ever since, so
this code was only needed for interop with older versions.
"git-annex-shell commit" is used by newer git-annex versions, though
unnecessarily so, because the p2pstdio command makes a single commit at
shutdown. Luckily, it was run with stderr and stdout sent to /dev/null,
and non-zero exit status or other exceptions are caught and ignored. So,
that was able to be removed from git-annex-shell too.
git-annex-shell inannex, recvkey, sendkey, and dropkey are still used by
gcrypt special remotes accessed over ssh, so those had to be kept.
It would probably be possible to convert that to using the P2P protocol,
but it would be another multi-year transition.
Some git-annex-shell fields were able to be removed. I hoped to remove
all of them, and the very concept of them, but unfortunately autoinit
is used by git-annex sync, and gcrypt uses remoteuuid.
The main win here is really in Remote.Git, removing piles of hairy fallback
code.
Sponsored-by: Luke Shumaker
This improves the borg special remote memory usage, by
letting it only load one archive's worth of filenames into memory at a
time, and building up a larger tree out of the chunks.
When a borg repository has many archives, git-annex could easily OOM
before. Now, it will use only memory proportional to the number of
annexed keys in an archive.
Minor implementation wart: Each new chunk re-opens the content
identifier database, and also a new vector clock is used for each chunk.
This is a minor innefficiency only; the use of continuations makes
it hard to avoid, although putting the database handle into a Reader
monad would be one way to fix it.
It may later be possible to extend the ImportableContentsChunkable
interface to remotes that are not third-party populated. However, that
would perhaps need an interface that does not use continuations.
The ImportableContentsChunkable interface currently does not allow
populating the top of the tree with anything other than subtrees. It
would be easy to extend it to allow putting files in that tree, but borg
doesn't need that so I left it out for now.
Sponsored-by: Noam Kremen on Patreon
This adds the overhead of a copy when serializing and deserializing keys.
I have not benchmarked much, but runtimes seem barely changed at all by that.
When a lot of keys are in memory, it improves memory use.
And, it prevents keys sometimes getting PINNED in memory and failing to GC,
which is a problem ByteString has sometimes. In particular, git-annex sync
from a borg special remote had that problem and this improved its memory
use by a large amount.
Sponsored-by: Shae Erisson on Patreon
Commit 4bf7940d6b introduced this
problem, but was otherwise doing a good thing. Problem being
that fileRef "/foo" used to return ":./foo", which was actually wrong,
but as long as there was no foo in the local repository, catKey
could operate on it without crashing. After that fix though, fileRef
would return eg "../../foo", resulting in fileRef returning
":./../../foo", which will make git cat-file crash since that's
not a valid path in the repo.
Fix is simply to make fileRef detect paths outside the repo and return
Nothing. Then catKey can be skipped. This needed several bugfixes to
dirContains as well, in previous commits.
In Command.Smudge, this led to needing to check for Nothing. That case
should actually never happen, because the fileoutsiderepo check will
detect it earlier.
Sponsored-by: Brock Spratlen on Patreon
sync --content: Avoid a redundant checksum of a file that was
incrementally verified, when used on NTFS and perhaps other filesystems.
When sync has just gotten the content, it does not need to check inAnnex a
second time. On NTFS, for some reason the write of the inode cache after
it gets the content is not immediately able to be read, and with an
empty/non-matching inode cache due to that stale data, inAnnex falls back
to hashing the whole object to determine if it's present.
Sponsored-by: Brock Spratlen on Patreon
Disabling git-annex branch update for this command is
ok, because it does not use any information from the branch,
but only logs the location when it adds a key.
Sponsored-by: Dartmouth College's Datalad project
Added annex.bwlimit and remote.name.annex-bwlimit config that works for git
remotes and many but not all special remotes.
This nearly works, at least for a git remote on the same disk. With it set
to 100kb/1s, the meter displays an actual bandwidth of 128 kb/s, with
occasional spikes to 160 kb/s. So it needs to delay just a bit longer...
I'm unsure why.
However, at the beginning a lot of data flows before it determines the
right bandwidth limit. A granularity of less than 1s would probably improve
that.
And, I don't know yet if it makes sense to have it be 100ks/1s rather than
100kb/s. Is there a situation where the user would want a larger
granularity? Does granulatity need to be configurable at all? I only used that
format for the config really in order to reuse an existing parser.
This can't support for external special remotes, or for ones that
themselves shell out to an external command. (Well, it could, but it
would involve pausing and resuming the child process tree, which seems
very hard to implement and very strange besides.) There could also be some
built-in special remotes that it still doesn't work for, due to them not
having a progress meter whose displays blocks the bandwidth using thread.
But I don't think there are actually any that run a separate thread for
downloads than the thread that displays the progress meter.
Sponsored-by: Graham Spencer on Patreon
This should complete the fix started in
6329997ac4, fixing the actual cause of the
test suite failure this time.
Sponsored-by: Dartmouth College's Datalad project
* When downloading urls fail, explain which urls failed for which
reasons.
* web: Avoid displaying a warning when downloading one url failed
but another url later succeeded.
Some other uses of downloadUrl use urls that are effectively internal use,
and should not all be displayed to the user on failure. Eg, Remote.Git
tries different urls where content could be located depending on how the
remote repo is set up. Exposing those urls to the user would lead to wild
goose chases. So had to parameterize it to control whether it displays urls
or not.
A side effect of this change is that when there are some youtube urls
and some regular urls, it will try regular urls first, even if the
youtube urls are listed first. This seems like an improvement if
anything, but in any case there's no defined order of urls that it's
supposed to use.
Sponsored-by: Dartmouth College's Datalad project
And fail with an informative message.
I don't think ACLs can prevent removing the write bit, but I'm not sure,
so kept it mentioning them as a possibility.
Should git-annex lock also check if the write bits are able to be removed?
Maybe, but the case I know about with xattrs involves cp -a copying NFS
xattrs, and it's the copy of the file that is the problem. So when locking
a file, I guess it will not be the copy.
Sponsored-by: Dartmouth College's Datalad project
New --batch-keys option added to these commands: get, drop, move, copy, whereis
git-annex-matching-options had to be reworded since some of its options
can be used to match on keys, not only files.
Sponsored-by: Luke Shumaker on Patreon
This was unlikely to cause any problem, but it is unsightly to mention
normally hidden refs, and it might have done a bit of unnecessary work to
check that ref.
Sponsored-by: Noam Kremen on Patreon
Except when configuration makes curl be used. It did not seem worth
trying to tail the file when curl is downloading.
But when an interrupted download is resumed, it does not read the whole
existing file to hash it. Same reason discussed in
commit 7eb3742e4b76d1d7a487c2c53bf25cda4ee5df43; that could take a long
time with no progress being displayed. And also there's an open http
request, which needs to be consumed; taking a long time to hash the file
might cause it to time out.
Also in passing implemented it for git and external special remotes when
downloading from the web. Several others like S3 are within striking
distance now as well.
Sponsored-by: Dartmouth College's DANDI project
This fixes the recent reversion that annex.verify is not honored,
because retrieveChunks was passed RemoteVerify baser, but baser
did not have export/import set up.
Sponsored-by: Dartmouth College's DANDI project
This eliminates the distinction between decodeBS and decodeBS', encodeBS
and encodeBS', etc. The old implementation truncated at NUL, and the
primed versions had to do extra work to avoid that problem. The new
implementation does not truncate at NUL, and is also a lot faster.
(Benchmarked at 2x faster for decodeBS and 3x for encodeBS; more for the
primed versions.)
Note that filepath-bytestring 1.4.2.1.8 contains the same optimisation,
and upgrading to it will speed up to/fromRawFilePath.
AFAIK, nothing relied on the old behavior of truncating at NUL. Some
code used the faster versions in places where I was sure there would not
be a NUL. So this change is unlikely to break anything.
Also, moved s2w8 and w82s out of the module, as they do not involve
filesystem encoding really.
Sponsored-by: Shae Erisson on Patreon
* Deal with clock skew, both forwards and backwards, when logging
information to the git-annex branch.
* GIT_ANNEX_VECTOR_CLOCK can now be set to a fixed value (eg 1)
rather than needing to be advanced each time a new change is made.
* Misuse of GIT_ANNEX_VECTOR_CLOCK will no longer confuse git-annex.
When changing a file in the git-annex branch, the vector clock to use is now
determined by first looking at the current time (or GIT_ANNEX_VECTOR_CLOCK
when set), and comparing it to the newest vector clock already in use in
that file. If a newer time stamp was already in use, advance it forward by
a second instead.
When the clock is set to a time in the past, this avoids logging with
an old timestamp, which would risk that log line later being ignored in favor
of "newer" line that is really not newer.
When a log entry has been made with a clock that was set far ahead in the
future, this avoids newer information being logged with an older timestamp
and so being ignored in favor of that future-timestamped information.
Once all clocks get fixed, this will result in the vector clocks being
incremented, until finally enough time has passed that time gets back ahead
of the vector clock value, and then it will return to usual operation.
(This latter situation is not ideal, but it seems the best that can be done.
The issue with it is, since all writers will be incrementing the last
vector clock they saw, there's no way to tell when one writer made a write
significantly later in time than another, so the earlier write might
arbitrarily be picked when merging. This problem is why git-annex uses
timestamps in the first place, rather than pure vector clocks.)
Advancing forward by 1 second is somewhat arbitrary. setDead
advances a timestamp by just 1 picosecond, and the vector clock could
too. But then it would interfere with setDead, which wants to be
overrulled by any change. So it could use 2 picoseconds or something,
but that seems weird. It could just as well advance it forward by a
minute or whatever, but then it would be harder for real time to catch
up with the vector clock when forward clock slew had happened.
A complication is that many log files contain several different peices of
information, and it may be best to only use vector clocks for the same peice
of information. For example, a key's location log file contains
InfoPresent/InfoMissing for each UUID, and it only looks at the vector
clocks for the UUID that is being changed, and not other UUIDs.
Although exactly where the dividing line is can be hard to determine.
Consider metadata logs, where a field "tag" can have multiple values set
at different times. Should it advance forward past the last tag?
Probably. What about when a different field is set, should it look at
the clocks of other fields? Perhaps not, but currently it does, and
this does not seems like it will cause any problems.
Another one I'm not entirely sure about is the export log, which is
keyed by (fromuuid, touuid). So if multiple repos are exporting to the
same remote, different vector clocks can be used for that remote.
It looks like that's probably ok, because it does not try to determine
what order things occurred when there was an export conflict.
Sponsored-by: Jochen Bartl on Patreon
git-annex get when run as the first git-annex command in a new repo did not
populate unlocked files. (Reversion in version 8.20210621)
I am not entirely happy with this, because I don't understand how
428c91606b caused the problem in the first
place, and I don't fully understand how skipping calling scanAnnexedFiles
during autoinit avoids the problem.
Kept the explicit call to scanAnnexedFiles during git-annex init,
so that when reconcileStaged is expensive, it can be made to run then,
rather than at some later point when the information is needed.
Sponsored-by: Brock Spratlen on Patreon
The pass was needed to populate files when annex.thin was set,
but in commit 73e0cbbb19,
reconcileStaged started to do that. So, this second pass is not needed
any longer.
An easy way to see this in action is to have an unlocked file, and touch the
object file.
While all code that compares inode caches for object files needs to be
prepared for this kind of problem and fall back to verification, having
fsck notice it and correct it is cheap (as long as fsck is being run
anyway) and ensures that if it happens for some unusual reason, there's a
way for the user to notice that it's happening.
Not that, when annex.thin is in use, the earlier call to isUnmodified
(and also potentially earlier calls to inAnnex in eg, verifyLocationLog)
will fix up the same problem silently. That might prevent the warning
being displayed, although probably it still will be, because the
Database.Keys write of the InodeCache will be queued but will not have
happened yet. I can't see a way to improve this, but it's not great.
Sponsored-by: Dartmouth College's Datalad project
This avoids it calling enteringStage VerifyStage when it's used in
places that only fall back to verification rarely, and which might be
called while in TransferStage and be going to perform a transfer after
the verification.
Some uses of linkFromAnnex are inside replaceWorkTreeFile, which was
already safe, but others use it directly on the work tree file, which
was race-prone. Eg, if the work tree file was first removed, then
linkFromAnnex called to populate it, the user could have re-written it in
the interim.
This came to light during an audit of all calls of addInodeCaches,
looking for such races. All the other uses of it seem ok.
Sponsored-by: Brett Eisenberg on Patreon
In Annex.Content, the object file was statted after pointer files were
populated. But if annex.thin is set, once the pointer files are
populated, the object file can potentially be modified via the hard
link. So, it was possible, though seemingly very unlikely, for the inode
of the modified object file to be cached.
Command.Fix and Command.Fsck had similar problems, statting the work
tree files after they were in place. Changed them to stat the temp file
that gets moved into place. This does rely on .git/annex being on the
same filesystem. If it's not, the cached inode will not be the same as
the one that the temp file gets moved to. Result will be that git-annex
will later need to do an expensive verification of the content of the
worktree files. Note that the cross-filesystem move of the temp file
already is a larger amount of extra work, so this seems acceptable.
Sponsored-by: Luke Shumaker on Patreon
When git-annex lock repopulates the object file by copying an associated
file that still has its content, it negected to update the inode cache.
I was not able to actually get this code to successfully repopulate the
object file; the associated file gets replaced with a dangling pointer
before unlock is able to do that. (By what I'm not sure..
reconcileStaged?) Which might be itself a bug, but
anyway this makes me doubtful that this was really leading to a stale
inode cache. Still, in case there is some situation in which it does
work, fixed it to update the inode cache.
Which is the same as the git merge option.
After last commit, this turns out to be needed in the test suite, and when
doing git-annex import from special remote, followed by a git-annex merge.
Sponsored-by: Svenne Krap on Patreon
sync, merge, post-receive: Avoid merging unrelated histories, which used to
be allowed only to support direct mode repositories.
(However, sync does still merge unrelated histories when importing trees
from special remotes, and the assistant still merges unrelated histories
always.)
See 556b2ded2b for why this was added
back in 2016, for direct mode.
This is a behavior change, which might break something that was relying
on sync merging unrelated histories, but git had a good reason to
prevent it, since it's easy to foot shoot with it, and git-annex should
follow suit.
Sponsored-by: Noam Kremen on Patreon
* sync: When --quiet is used, run git commit, push, and pull without
their ususual output.
* merge: When --quiet is used, run git merge without its usual output.
This might also make --quiet work better for some other commands
that make commits, like git-annex adjust.
Sponsored-by: Kevin Mueller on Patreon
Handles keys that are substrings of other keys, as well as pointer files
that contain a newline after the key.
Note that -S does not match regexp, while -G does by default. Docs are
not clear, determined experimentally. The only other difference in
changing to -G is that if a file used to contain the key and changed
in some way, while still containing the key, -G will match and -S would
not. So eg, annex links that git annex fix rewrites will match, and
files that change lock status will match. Which is an improvement anyway.
Sponsored-by: Jochen Bartl on Patreon
Does not check the reflog, but otherwise works.
It's possible for it to display something that is not an annexed file,
if a non-annexed file somehow ends up containing something that looks
like the key's name. This seems very unlikely to happen, and it would
add a lot of complexity to detect it and somehow skip over that file,
since the git log would need to either be run again, or not limited to 1
result and canceled once enough results have been read.
Also, it kind of seems ok, if a file refers to a key, to consider that
as a place the key was used, for some definition of used. So, I punted
on dealing with that. May revisit later.
Sponsored-by: Brock Spratlen on Patreon
Forces eg, download with youtube-dl without falling back to raw download.
Since youtube-dl failing due to an url not being supported is difficult to
distinguish from it failing due to being blocked in some way, this can be
useful to avoid the fallback of git-annex downloading the raw web page and
adding that.
Since --raw also prevents using special remotes, --no-raw also
allows special remote downloads. Although it's always possible that some
special remote may claim an url and fall back to raw download of the
content, which --no-raw cannot prevent.
Sponsored-by: Boyd Stephen Smith Jr. on Patreon
Dropping an object with drop --unused or dropunused will mark it as
dead, preventing fsck --all from complaining about it after it's been
dropped from all repositories.
If another repository still has a copy, it won't be treated as dead
until it's also dropped from there.
The drop has to use --unused, can't be --key or something else, because
this indicates that the user has recently ran git-annex unused. If it
checked the unused log on every drop, bad things would happen when the
unused log was out of date, eg a file used to be unused but then got
re-added. Marking such a file as dead could be confusing. When the user
uses --unused/dropunused, they must consider the unused information to be
up-to-date.
The particular workflow this enables is:
git annex add foo
git annex unannex foo
git annex unused
git annex drop --unused / dropunused
git annex fsck --all # no warnings
The docs for git-annex unannex say to use git-annex unused and dropunused,
so the user should be pointed in this direction when they want to undo an
accidental add.
Sponsored-by: Brock Spratlen on Patreon
sync: Partly work around github behavior that first branch to be pushed to
a new repository is assumed to be the head branch, by not pushing
synced/git-annex first.
github expects master (or whatever the name is) to be pushed first, but
git-annex sync can't, because it's got to also support pushes to non-bare
repos where pushing master fails, as explained in the big comment. So
pushing synced/master is not entirely a fix, but at least it makes github
default to a branch with the stuff the user expects in it, not a bunch of
annex log files.
Aside from fixing github to not make this assumption, or improving
the git push protocol to include what the current HEAD is, the only other
approach I can think of is to identify git push's progress messages and
display those when pushing master, while filtering out error messages
about non-fast-forward etc. But git doesn't provide a way to separate out
or identify its progress messages.
Sponsored-by: Luke Shumaker on Patreon
Eg, before with a .gitattributes like:
*.2 annex.numcopies=2
*.1 annex.numcopies=1
And foo.1 and foo.2 having the same content and key, git-annex drop foo.1 foo.2
would succeed, leaving just 1 copy, despite foo.2 needing 2 copies.
It dropped foo.1 first and then skipped foo.2 since its content was gone.
Now that the keys database includes locked files, this longstanding wart
can be fixed.
Sponsored-by: Noam Kremen on Patreon
When the log has an activity that is not known, eg added by a future
version of git-annex, it used to be treated as no activity at all,
which would make git-annex expire think it should expire the repository,
despite it having some kind of recent activity.
Hopefully there will be no reason to add a new activity until enough
time has passed that this commit is in use everywhere.
Sponsored-by: Jake Vosloo on Patreon
This makes git checkout and git merge hooks do the work to catch up with
changes that they made to the tree. Rather than doing it at some later
point when the user is not thinking about that past operation.
Sponsored-by: Dartmouth College's Datalad project
When two files have the same content, and a required content expression
matches one but not the other, dropping the latter file will fail as it
would also remove the content of the required file.
This will slow down drop (w/o --auto), dropunused, mirror, and move, by one
keys db lookup per file. But I did include an optimisation to avoid a
double db lookup in the drop --auto / sync --content case. I suspect that
dropunused could also use PreferredContentChecked True, but haven't
entirely thought it through and it's rarely used with enough files for the
optimisation to matter.
Sponsored-by: Dartmouth College's Datalad project
* drop: When two files have the same content, and a preferred content
expression matches one but not the other, do not drop the file.
* sync --content, assistant: Fix an edge case where a file that is not
preferred content did not get dropped.
The sync --content edge case is that handleDropsFrom loaded associated files
and used them without verifying that the information from the database was
not stale.
It seemed best to avoid changing --want-drop's behavior, this way when
debugging a preferred content expression with it, the files matched will
still reflect the expression. So added a note to the --want-drop documentation,
to make clear it may not behave identically to git-annex drop --auto.
While it would be possible to introspect the preferred content
expression to see if it matches on filenames, and only look up the
associated files when it does, it's generally fairly rare for 2 files to
have the same content, and the database lookup is already avoided when
there's only 1 file, so I did not implement that further optimisation.
Note that there are still some situations where the associated files
database does not get locked files recorded in it, which will prevent
this fix from working.
Sponsored-by: Dartmouth College's Datalad project
Before only unlocked files were included.
The initial scan now scans for locked as well as unlocked files. This
does mean it gets a little bit slower, although I optimised it as well
as I think it can be.
reconcileStaged changed to diff from the current index to the tree of
the previous index. This lets it handle deletions as well, removing
associated files for both locked and unlocked files, which did not
always happen before.
On upgrade, there will be no recorded previous tree, so it will diff
from the empty tree to current index, and so will fully populate the
associated files, as well as removing any stale associated files
that were present due to them not being removed before.
reconcileStaged now does a bit more work. Most of the time, this will
just be due to running more often, after some change is made to the
index, and since there will be few changes since the last time, it will
not be a noticable overhead. What may turn out to be a noticable
slowdown is after changing to a branch, it has to go through the diff
from the previous index to the new one, and if there are lots of
changes, that could take a long time. Also, after adding a lot of files,
or deleting a lot of files, or moving a large subdirectory, etc.
Command.Lock used removeAssociatedFile, but now that's wrong because a
newly locked file still needs to have its associated file tracked.
Command.Rekey used removeAssociatedFile when the file was unlocked.
It could remove it also when it's locked, but it is not really
necessary, because it changes the index, and so the next time git-annex
run and accesses the keys db, reconcileStaged will run and update it.
There are probably several other places that use addAssociatedFile and
don't need to any more for similar reasons. But there's no harm in
keeping them, and it probably is a good idea to, if only to support
mixing this with older versions of git-annex.
However, mixing this and older versions does risk reconcileStaged not
running, if the older version already ran it on a given index state. So
it's not a good idea to mix versions. This problem could be dealt with
by changing the name of the gitAnnexKeysDbIndexCache, but that would
leave the old file dangling, or it would need to keep trying to remove
it.
They're only needed to cover a gc edge case, and it's better someone
gets caught by that edge case than that someone who does not know about
them ends up with a filtered git-annex branch that contains such a tree
when some of the files listed in it are ones they wanted to *remove*
from the repository.
It's not currently possible to exclude a sameas repo using its
annex-config-uuid. (Remote.nameToUUID rejects them).
Since there's no real documented way to learn those, this seems ok, at
least for now. Also it avoids the problem of someone excluding the
parent but including the sameas, which would probably make the sameas
repo not usable when using the filtered branch.
Added a note to man page about what happens to information that is
recorded in the private journal. Since it uses Branch.get, that
information will be copied when options allow. It seemed better to allow
it and document it than not allow it, since the options allow excluding
repositories and so can be used to exclude private repos if desired.
Not tested yet but should work.
Noted a possible optimisation, which should probably be added, to
speed it up in cases where there is no uuid filtering being done.
It would need Annex.Branch to add a function like getRef that uses
catFileDetails, so the sha is also returned. The difficulty would be
making it support the precached file content; if it didn't it would
probably not be any faster and could even be slower. So probably the
precaching would need to be changed to also cache the sha.
This is less erorr-prone, and easier for the user to reason about; it
preserves the man page's promise that only explicitly included
information will be copied.
ghc 8.8.4 seems to have changed something that broke code that has been
successfully using forkProcess since 2012. Likely a change to GC internals.
Since forkProcess has never had clear documentation about how to
use it safely, avoid using it at all. Instead, when git-annex needs to
daemonize itself, re-run the git-annex command, in a new process group
and session.
This commit was sponsored by Luke Shumaker on Patreon.
Similar to what commit 675556fd9a did for
adding a non-annexed file, this prevents the smudge clean filter
recognising the inode if git add is later run on the unannexed file.
smudge: Fix a case where an unlocked annexed file that annex.largefiles
does not match could get its unchanged content checked into git, due to git
running the smudge filter unecessarily.
When the file has the same inodecache as an already annexed file,
we can assume that the user is not intending to change how it's stored in
git.
Note that checkunchangedgitfile already handled the inverse case, where the
file was added to git previously. That goes further and actually sha1
hashes the new file and checks if it's the same hash in the index.
It would be possible to generate a key for the file and see if it's the
same as the old key, however that could be considerably more expensive than
sha1 of a small file is, and it is not necessary for the case I have, at
least, where the file is not modified or touched, and so its inode will
match the cache.
git-annex add was changed, when adding a small file, to remove the inode
cache for it. This is necessary to keep the recipe in
doc/tips/largefiles.mdwn for converting from annex to git working.
It also avoids bugs/case_where_using_pathspec_with_git-commit_leaves_s.mdwn
which the earlier try at this change introduced.
Fix behavior of several commands, including reinject, addurl, and rmurl
when given an absolute path to an unlocked file, or a relative path that
leaves and re-enters the repository.
To avoid slowing down all the cases where the paths are already ok
with an unncessary call to getCurrentDirectory, put in an optimisation
in relPathCwdToFile. That will probably also speed up other parts of
git-annex by some small amount, but I have not benchmarked.
Note that I did not convert branchFileRef, because it seems likely that
it will be used with a file that is not provided by the user, so is already
in a sane format. This is certainly true for the way git-annex uses it,
though maybe arguable to the extent Git.Ref is a reusable library.
GHC was complaining about it possibly being a homoglyph:
Command/Multicast.hs:111:36: error:
warning: treating Unicode character <U+2212> as identifier character rather than as '-' symbol [-Wunicode-homoglyph]
-- using a nice prime, namely 2521−1 but the sheer size of this
^
|
111 | -- using a nice prime, namely 2521−1 but the sheer size of this
| ^
1 warning generated.
smudge: Fix a case where an unlocked annexed file that annex.largefiles
does not match could get its unchanged content checked into git, due to git
running the smudge filter unecessarily.
When the file has the same inodecache as an already annexed file,
we can assume that the user is not intending to change how it's stored in
git.
Note that checkunchangedgitfile already handled the inverse case, where the
file was added to git previously. That goes further and actually sha1
hashes the new file and checks if it's the same hash in the index.
It would be possible to generate a key for the file and see if it's the
same as the old key, however that could be considerably more expensive than
sha1 of a small file is, and it is not necessary for the case I have, at
least, where the file is not modified or touched, and so its inode will
match the cache.
fromkey: Create an unlocked file when used in an adjusted branch where the
file should be unlocked, or when configured by annex.addunlocked.
There is some overlap with code in Annex.Ingest, however it's not quite the
same because ingesting has a temp file with the content, where here the
content, if any, is in the annex object file. So it eg, makes sense for
Annex.Ingest to copy the execute mode of the content file, but it does not make
sense for fromkey to do that.
Also changed in passing to stage the file in git directly, rather than
using git add. One consequence of that is that if the file is gitignored,
it will still get added, rather than the old behavior:
The following paths are ignored by one of your .gitignore files:
ignored
hint: Use -f if you really want to add them.
hint: Turn this message off by running
hint: "git config advice.addIgnoredFile false"
git-annex: user error (xargs ["-0","git","--git-dir=.git","--work-tree=.","--literal-pathspecs","add","--"] exited 123)
That old behavior was a surprise to me, and so I consider it a bug, and doubt
anyone would have relied on it.
Note that, when on an --hide-missing branch, it is possible to fromkey a key
that is not present (needs --force). The annex link or pointer file still gets
written in this case. It doesn't seem to make any sense not to write it,
because then fromkey would not do anything useful in this case, and this way
the file can be committed and synced to master, and the branch re-adjusted to
hide the new missing file.
This commit was sponsored by Noam Kremen on Patreon.
* Fix bug that could make git-annex importfeed not see recently recorded
state when configured with annex.alwayscommit=false.
* importfeed: Made "checking known urls" phase run 12 times faster.
The massive speedup is because it no longer queries for metadata
accompanying each url. Instead it processes the whole git-annex branch and
checks all metadata files for feed item ids, and uses any it finds.
This could result in a behavior change, in an unlikely situation: If a feed
id is recorded in a key's metadata, but the url gets removed, the old code
would not see that item id and would re-download it if it finds an url for
it in a feed, while the new code will see the item id. I don't think
the old behavior was intentional, and it may be that the new behavior is
better. Not gonna worry about this.
This adds a separate journal, which does not currently get committed to
an index, but is planned to be committed to .git/annex/index-private.
Changes that are regarding a UUID that is private will get written to
this journal, and so will not be published into the git-annex branch.
All log writing should have been made to indicate the UUID it's
regarding, though I've not verified this yet.
Currently, no UUIDs are treated as private yet, a way to configure that
is needed.
The implementation is careful to not add any additional IO work when
privateUUIDsKnown is False. It will skip looking at the private journal
at all. So this should be free, or nearly so, unless the feature is
used. When it is used, all branch reads will be about twice as expensive.
It is very lucky -- or very prudent design -- that Annex.Branch.change
and maybeChange are the only ways to change a file on the branch,
and Annex.Branch.set is only internal use. That let Annex.Branch.get
always yield any private information that has been recorded, without
the risk that Annex.Branch.set might be called, with a non-private UUID,
and end up leaking the private information into the git-annex branch.
And, this relies on the way git-annex union merges the git-annex branch.
When reading a file, there can be a public and a private version, and
they are just concacenated together. That will be handled the same as if
there were two diverged git-annex branches that got union merged.
When downloading content from a remote, if the content is able to be
verified during the transfer, skip checksumming it a second time.
Note that in this case, the fsck output does not include "(checksum)"
which it does when the checksumming is done separately from the download.
This commit was sponsored by Brock Spratlen on Patreon.
This uses a DebugSelector, rather than debug levels, which will allow
for a later option like --debug-from=Process to only
see debuging about running processes.
The module name that contains the thing being debugged is used as the
DebugSelector (in most cases; does not need to be a hard and fast rule).
Debug calls were changed to add that. hslogger did not display
that first parameter to debugM, but the DebugSelector does get
displayed.
Also fastDebug will allow doing debugging in places that are used in
tight loops, with the DebugSelector coming from the Annex Reader
essentially for free. Not done yet.
Values in AnnexRead can be read more efficiently, without MVar overhead.
Only a few things have been moved into there, and the performance
increase so far is not likely to be noticable.
This is groundwork for putting more stuff in there, particularly a value
that indicates if debugging is enabled.
The obvious next step is to change option parsing to not run in the
Annex monad to set values in AnnexState, and instead return a pure value
that gets stored in AnnexRead.
Not yet used, but allows getting the size of items in the tree fairly
cheaply.
I noticed that CmdLine.Seek uses ls-tree and the feeds the files into
another long-running process to check their size. That would be an
example of a place that might be sped up by using this. Although in that
particular case, it only needs to know the size of unlocked files, not
locked. And since enabling --long probably doubles the ls-tree runtime
or more, the overhead of using it there may outwweigh the benefit.
I don't think this was really intentional behavior. It may be that it was
useful to include it so it could be passed to rmurl, since without it rmurl
would not actually remove the url. Since that was changed earlier today,
now seems like a good time to clean up the display of these urls.
This commit was sponsored by Jochen Bartl on Patreon.
fsck: When --from is used in combination with --all or similar options, do
not verify required content, which can't be checked properly when operating
on keys.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
unregisterurl: Fix a bug that caused an url to not be unregistered when it
is claimed by a special remote other than the web.
See commit f175d4cc90 for rationalle.
* rmurl: When youtube-dl was used for an url, it no longer needs to be
prefixed with "yt:" in order to be removed.
* rmurl: If an url is both used by the web and also claimed by another
special remote, fix a bug that caused the url to to not be removed.
The youtube-dl change is a consequence of how the bug fix is implemented.
But I also think it's the right thing to do. Consider that, before,
git-annex addurl $url followed by git-annex rmurl $url would not remove the
url in the case where youtube-dl was used. That was surprising behavior.
In the unlikely case where a special remote claims an url, and it's been
added using OtherDownloader, but it was also added already as a web url,
it seems better for rmurl to remove both than to arbitrarily remove only one.
And in the case the bug report was filed for, when an url was added as a
web url, but a special remote now claims it, that should not prevent rmurl
removing the web url.
Calling setUrlMissing lets other callers of it behave differently.
Probably the calls to it in eg, Remote.External and Remote.BitTorrent are
fine, since they don't mangle the url and just remove what was provided,
and the OtherDownloader form of a bittorrent url, respectively.
I suspect unregisterurl needs to have a similar change made to rmurl, for
similar reasons.
Like import was using ActionItemWorkTreeFile, it's ok to use it for export,
even though it might not correspond with a file in the work tree.
And renamed it to ActionItemTreeFile to make that clearer.
Note that when an export has to rename files, it still uses
ActionItemOther, so file will still be null in that case, but as no file is
being transferred, that seems ok.
import: When the previously exported tree contained a submodule,
preserve it in the imported tree so it does not get deleted.
The export exclude log, which was used for non-preferred content,
now also includes the submodules. Since the log format is git ls-tree
output, this does not break backwards compatibility.
It's not necessary to log location of GIT keys, because these files are
not annexed files and so git-annex will never need to get them.
This corresponds to code in Annex.Import that already checked before
updating the location log when handling deleted files.
Older versions of git-annex that used SHA1 keys for non-annexed files
also unncessarily updated the location log for them.
GIT keys still appear in the git-annex branch for content identifier
logs, so kept the documentation of them in backends.mdwn
This commit was sponsored by Jake Vosloo on Patreon.
This solves the problem that import of such files gets confused and
converts them back to annexed files.
The import code already used GIT keys internally when it determined a
file should not be annexed. So now when it sees a GIT key that export
used, it already does the right thing.
This also means that even older version of git-annex can import and will
do the right thing, once a fixed version has exported. Still, there may
be other complications around upgrades; still need to think it all
through.
Moved gitShaKey and keyGitSha from Key to Annex.Export since they're
only used for export/import.
Documented GIT keys in backends, since they do appear in the git-annex
branch now.
This commit was sponsored by Graham Spencer on Patreon.
Added LinkType to ProvidedInfo, and unified MatchingKey with
ProvidedInfo. They're both used in the same way, so there was no real
reason to keep separate.
Note that addLocked and addUnlocked still set matchNeedsFileName,
because to handle MatchingFile, they do need it. However, they
don't use it when MatchingInfo is provided. This should be ok,
the --branch case will be able skip checking matchNeedsFileName,
since it will provide a filename in any case.
Implemented by generalizing registerurl. Without the implicit batch mode
of registerurl since that is only a backwards compatability thing
(see commit 1d1054faa6).
unannex, uninit: When an annexed file is modified, don't overwrite the
modified version with an older version from the annex
This commit was sponsored by Mark Reidenbach on Patreon.
When a git remote is configured with an absolute path, use that path,
rather than making it relative. If it's configured with a relative path,
use that.
Git.Construct.fromPath changed to preserve the path as-is,
rather than making it absolute. And Annex.new changed to not
convert the path to relative. Instead, Git.CurrentRepo.get
generates a relative path.
A few things that used fromAbsPath unncessarily were changed in passing to
use fromPath instead. I'm seeing fromAbsPath as a security check,
while before it was being used in some cases when the path was
known absolute already. It may be that fromAbsPath is not really needed,
but only git-annex-shell uses it now, and I'm not 100% sure that there's
not some input that would cause a relative path to be used, opening a
security hole, without the security check. So left it as-is.
Test suite passes and strace shows the configured remote url is used
unchanged in the path into it. I can't be 100% sure there's not some code
somewhere that takes an absolute path to the repo and converts it to
relative and uses it, but it seems pretty unlikely that the code paths used
for a git remote would call such code. One place I know of is gitAnnexLink,
but I'm pretty sure that git remotes never deal with annex symlinks. If
that did get called, it generates a path relative to cwd, which would have
been wrong before this change as well, when operating on a remote.
When annex.stalldetection is not enabled, and a likely stall is detected,
display a suggestion to enable it.
Note that the progress meter display is not taken down when displaying
the message, so it will display like this:
0% 8 B 0 B/s
Transfer seems to have stalled. To handle stalling transfers, configure annex.stalldetection
0% 10 B 0 B/s
Although of course if it's really stalled, it will never update
again after the message. Taking down the progress meter and starting
a new one doesn't seem too necessary given how unusual this is,
also this does help show the state it was at when it stalled.
Use of uninterruptibleCancel here is ok, the thread it's canceling
only does STM transactions and sleeps. The annex thread that gets
forked off is separate to avoid it being canceled, so that it
can be joined back at the end.
A module cycle required moving from dupState the precaching of the
remote list. Doing it at startConcurrency should cover all the cases
where the remote list is used in concurrent actions.
This commit was sponsored by Kevin Mueller on Patreon.
Missed this when implementing it because of the default case catching
the new constructor. So, removed that default case to make sure
future types of adjusted branches don't make the same mistake.
Complicated by git-annex addurl --fast which adds the file whose content
is not present, so it needs to stay unlocked when on such a branch.
This commit was sponsored by Brock Spratlen on Patreon.
34a535ebea broke the test suite.
Getting a file started failing in one case, because the annex object did
not have its inode cached, so was not trusted to be unmodified.
This adds something very similar to what was added to linkAnnex
in commit 2e9341a47d -- if there are not
yet any inodes cached for a key, add the inode of the annex object when
adding the inode of the unlocked file.
Feels like this should be handled in a more principled way. How
do we know the addInodeCaches call in getMoveRaceRecovery just above
this change is currently correct? It doesn't add the annex object inode
cache. Ah well, maybe sometime when I've not had my entire evening eaten
by a reversion that the test suite caught as I was cooking dinner.
Avoids the smudge --clean filter failing because URL keys do not support
genKey. Instead the modified content will be added using the default
backend.
This commit was sponsored by Jochen Bartl on Patreon.
This avoids the smudge --clean filter failing on the URL keys.
git checkout runs the post-checkout hook, which runs smudge --update.
That populates all the pointer files, but it neglected to store their inode
caches in the keys db. With that done, and the keys db flushed before
smudge --clean gets run (by restagePointerFile), the isUnmodifiedCheap
check can tell the file is not modified, so will not try to re-ingest it,
which does not work with URL keys because they do not support genKey.
It also seems possible that the isUnmodifiedCheap was also failing for
non-URL keys, which would cause them to be re-ingested, leading to a lot of
extra work. I have not verified that, but don't see why it wouldn't have
happened. So this probably also speeds up checking out adjusted branches.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
Configuring chunking and encryption for a git remote has no effect, so
skip testing those variants in the TestRemote call.
It would be better if TestRemote itself could do this, but it
doesn't seem possible there. There is no way to look at a Remote and
tell if it supports chunking or encryption.
Note that, while the test suite displays output as it it's testing
exporting, it actually skips doing anything for the tests when run on
the git remote. So at least does not waste time even though the output
is not ideal.
This commit was sponsored by Noam Kremen on Patreon.
Since unconsidered use of trusted repositories can lead to data loss.
Trusted has always been this way, but it used to be acceptable for
git-annex to be set up so that data could be lost without using --force,
and most or all other ways that can happen have already been eliminated.
This commit was sponsored by Mark Reidenbach on Patreon.
This is conceptually very simple, just making a 1 that was hard coded be
exposed as a config option. The hard part was plumbing all that, and
dealing with complexities like reading it from git attributes at the
same time that numcopies is read.
Behavior change: When numcopies is set to 0, git-annex used to drop
content without requiring any copies. Now to get that (highly unsafe)
behavior, mincopies also needs to be set to 0. It seemed better to
remove that edge case, than complicate mincopies by ignoring it when
numcopies is 0.
This commit was sponsored by Denis Dzyubenko on Patreon.
* add: Significantly speed up adding lots of non-large files to git,
by disabling the annex smudge filter when running git add.
* add --force-small: Run git add rather than updating the index itself,
so any other smudge filters than the annex one that may be enabled will
be used.
Especially from borg, where the content identifier logs
all end up being the same identical file!
But also, for other imports, the location tracking logs can,
in some cases, be identical files.
Bonus optimisation: Avoid looking up (and parsing when set)
GIT_ANNEX_VECTOR_CLOCK env var every time a log is written to.
Although the lookup does happen at startup even when no
log will be written now.
May actually work now.
Note that, importKey now has to add the size to the key if it's supposed
to have size. Remote.Directory relied on the importer adding the size,
which is no longer done, so it was changed; it was the only one.
This way, importKey does not need to behave differently between regular
and thirdpartypopulated imports.
These don't have importTree in their config, because they don't support
tree import, but they do still support import, and do not support export
or key/value modification.
This is to support, eg a borg repo as a special remote, which is
populated not by running git-annex commands, but by using borg. Then
git-annex sync lists the content of the remote, learns which files are
annex objects, and treats those as present in the remote.
So, most of the import machinery is reused, to a new purpose. While
normally importtree maintains a remote tracking branch, this does not,
because the files stored in the remote are annex object files, not
user-visible filenames. But, internally, a git tree is still generated,
of the files on the remote that are annex objects. This tree is used
by retrieveExportWithContentIdentifier, etc. As with other import/export
remotes, that the tree is recorded in the export log, and gets grafted
into the git-annex branch.
importKey changed to be able to return Nothing, to indicate when an
ImportLocation is not an annex object and so should be skipped from
being included in the tree.
It did not seem to make sense to have git-annex import do this, since
from the user's perspective, it's not like other imports. So only
git-annex sync does it.
Note that, git-annex sync does not yet download objects from such
remotes that are preferred content. importKeys is run with
content downloading disabled, to avoid getting the content of all
objects. Perhaps what's needed is for seekSyncContent to be run with these
remotes, but I don't know if it will just work (in particular, it needs
to avoid trying to transfer objects to them), so I skipped that for now.
(Untested and unused as of yet.)
This commit was sponsored by Jochen Bartl on Patreon.
Don't want to try to use these remotes as key/value remotes, which will
surely fail. It only recently became possible for importtree to be set
w/o exporttree, so before this code was ok.
(cherry picked from commit 97599cb0f7f4115aa5a3e81a91ee3d1d6c52dc84)
In cd1676d604, it stopped using that to avoid surprising behavior
when the location log and remote content were out of sync.
But, it seems that may have changed some behavior users relied on as
well, and also Remote.hasKeyCheap should be faster than checking then
location log.
So, try Remote.hasKeyCheap first, and only if it does not have the key,
fall back to checking the location log. If the location log still thinks
it's present, go ahead and try to get it, so the user will see a failure
rather than silently skipping a file what whereis says is on the remote.
This does make slightly slower the case where the remote does not have
the key, and location log and Remote.hasKeyCheap agree, since it now
checks both. But only 1 stat slower.
This is common in some feeds, which might mix some items with enclosures,
with others that link to posts or whatever. Before this, it would try to
use youtube-dl and fail, or if youtube-dl was not allowed, it would
incorrectly complain that an url was supported by youtube-dl.
MatchingKey is not the thing to use when matching on actual worktreee
files.
Fix reversion in 8.20201116 that made include= and exclude= in
preferred/required content expressions match a path relative to the current
directory, rather than the path from the top of the repository.
Done on unix, could not implement it on windows quite.
The signal library gets part of the way needed for windows.
But I had to open https://github.com/pmlodawski/signal/issues/1 because
it lacks raiseSignal.
Also, I don't know what the equivilant of getProcessGroupIDOf is on
windows. And System.Process does not provide a way to send any signal to
a process group except for SIGINT.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
All callers adjusted to update it themselves.
In Command.ReKey, and Command.SetKey, the cleanup action already did,
so it was updating the log twice before.
This fixes a bug when annex.stalldetection is set, as now
Command.Transferrer can skip updating the location log, and let it be
updated by the calling process.
Rather than using Read/Show, which would force me to preserve data types
into the future.
I considered just deriving json and sending that, but I don't much like
deriving json with data types that have named constructors (like Key
does) because again it locks in data type details.
So instead, used SimpleProtocol, with a fairly complex and unreadable
protocol. But it is as efficient as the p2p protocol at least, and as
future proof.
(Writing my own custom json instances would have worked but I thought
of it too late and don't want to do all the work twice. The only real
benefit might be that aeson could be faster.)
Note that, when a new protocol request type is added later, git-annex
trying to use it will cause the git-annex transferrer to display a
protocol error message. That seems ok; it would only happen if a new
git-annex found an old version of itself in PATH or the program
file. So it's unlikely, and all it can do anyway is display an error.
(The error message could perhaps be improved..)
This commit was sponsored by Jack Hill on Patreon.
This is to avoid breakage when upgrading or downgrading git-annex with a
process running that uses the interface. It's better to keep the
compatability code for a few years than worry about such breakage.
This commit was sponsored by Brett Eisenberg on Patreon.
Seems to work! Even progress bars. Have not tested prompting or various
error message displays yet.
transferkeys had to be made to operate in different modes for the
Assistant and Annex monads. A bit ugly, but it did relegate that
really ugly Database.Keys.closeDb in transferkeys to only the assistant
code path.
This commit was sponsored by Noam Kremen.
This is groundwork for using git-annex transferkeys to run transfers,
in order to allow stalled transfers to be interrupted and retried.
The new upload and download are closer to what git-annex transferkeys
does, so the plan is to make them use it.
Then things that were left using upload' and download' won't recover
from stalls. Notably, that includes import and export. But
at least get/move/copy will be able to. (Also the assistant hopefully,
but not yet.)
This commit was sponsored by Jake Vosloo on Patreon.
That seems to be the last thing needed for message serialization.
Although it's only used in the assistant currently, so hard to tell if I
forgot something.
At this point, it should be possible to start using transferkeys
when performing transfers, which will allow killing a transferkeys
process if a transfer times out or stalls. But that's for another day.
This commit was sponsored by Ethan Aubin.
Necessarily threw out the old protocol, so if an old git-annex assistant
is running, and starts a transferkeys from the new git-annex, it would
fail. But, that seems unlikely; the assistant starts up transferkeys
processes and then keeps them running. Still, may need to test that
scenario.
The new protocol is simple read/show and looks like this:
TransferRequest Download (Right "origin") (Key {keyName = "f8f8766a836fb6120abf4d5328ce8761404e437529e997aaa0363bdd4fecd7bb", keyVariety = SHA2Key (HashSize 256) (HasExt True), keySize = Just 30, keyMtime = Nothing, keyChunkSize = Nothing, keyChunkNum = Nothing}) (AssociatedFile (Just "foo"))
TransferOutput (ProgressMeter (Just 30) (MeterState {meterBytesProcessed = BytesProcessed 0, meterTimeStamp = 1.6070268727892535e9}) (MeterState {meterBytesProcessed = BytesProcessed 30, meterTimeStamp = 1.6070268728043e9}))
TransferOutput (OutputMessage "(checksum...) ")
TransferResult True
Granted, this is not optimally fast, but it seems good enough, and is
probably nearly as fast as the old protocol anyhow.
emitSerializedOutput for ProgressMeter is not yet implemented. It needs
to somehow start or update a progress meter. There may need to be a new
message that allocates a progress meter, and then have ProgressMeter
update it.
This commit was sponsored by Ethan Aubin
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.
An --unlock-present branch reverses back to a branch where
all files that get modified or renamed become locked, even if they were
originally unlocked. This is the same that reversing a --unlock branch
works, and the new name makes that commonality more clear.
Like --hide-missing the branch does not get updated when content
availability changes.
Seems to basically work, but sync does not update it yet.
Also, when a file is present and so unlocked, git mv followed by
git-annex sync results in the basis branch being updated to contain the
file with the new name, unlocked. This seems different than what
happens in an adjusted unlocked branch, where the commit propigates back
locked. Probably the reverse adjustment code needs to be improved to
handle this case.
Note that, the way the SeekInput parser is written to support batch mode,
it's actually possible to do git-annex examinekey
"SHA1--foo foo.tar.gz" --migrate-to-backend=SHA1E
While that might be kind of useful to support multiple migrations not using
batch mode, I have not documented it. It would be better to take pairs of
key and file in that case.
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.
In cases where numcopies checks prevented the resumed move from dropping
the object from the source repository, it now relies on a log of recent
moves to replicate the behavior of the interrupted command.
Performance: Probably noticable impact, since it has to add to the log,
check the log, and remove from the log. Seems worth it to avoid this
annoying edge case. The log functions are pretty well optimised to avoid
unncessary work.
An performance improvement to make later would be to avoid cleanup doing
anything if it's not written to the log file, and has confirmed that the
log file does not contain the log line.
This commit was sponsored by Jake Vosloo on Patreon.
When I put in Haskell98 this spring, I was under the mistaken
apprehension that ghc defaulted to that. But it actually its default
is a third mode, which is closer to Haskell2010 but with some differences.
The manual says "By default, GHC mainly aims to behave (mostly) like a
Haskell 2010 compiler"
Fixed two cases where the Haskell98 do indentation flexability let
wrongly indented code build. That is one of the places where
ghc does not behave like Haskell2010 by default.
The other place that I think I was concerned about, is GHC manual
section 19.1.1.3. Expressions and patterns. But that only seems to
affect code using bottoms, so would only affect pure functions throwing
an error, which I don't think git-annex does in many places as it's
pretty horrid style. And it would only affect rare cases like shown in
that section. If it did happen, it would mean that the error was not
thrown before specifying Haskell98, and then was. Haskell2010 behaves
the same as Haskell98.
This commit was sponsored by Denis Dzyubenko on Patreon.
It seemed best to do this, for consistency with every other way files can
get into a git-annex repo. Although it's just a bit strange that a local
.gitignore file affects the pseudo-commits made for the remote that's
imported from.
This commit was sponsored by Brett Eisenberg on Patreon.
Which lets progress be displayed when doing concurrent downloads.
Amoung other things, like --json-progress etc.
The youtube-dl output is no longer displayed, except for any errors.
This commit was sponsored by Denis Dzyubenko on Patreon.
Ensure that checkCanAdd is used everywhere a file is added to git,
so git add is run with -f, presumably avoiding the work it would usually
do to check ignores.
sync: When run without --content, import without copying from
importtree=yes directory special remotes. (Other special remotes may
support this later as well.)
This commit was sponsored by Svenne Krap on Patreon.
This avoids import with --no-content and with --content potentially
generating two different trees, leading to a merge conflict when run in
two different clones of a repo. And it's necessary groundwork to make
git-annex sync --no-content import from special remotes that support
importKey.
Only the directory special remote currently supports importKey, and it
generates the same key as git-annex usually does, so there is no
behavior change for it.
Future special remotes will need to take care when adding importKey,
if it generates different keys. Added some warnings about that to
comments.
This commit was sponsored by Noam Kremen 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.
This was the last one marked as a zombie. There might be others I don't
know about, but except for in the hypothetical case of a thread dying
due to an async exception before it can wait on a process it started, I
don't know of any.
It would probably be safe to remove the reapZombies now, but let's wait
and so that in its own commit in case it turns out to cause problems.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
Eliminate a zombie that was only cleaned up by the later zombie cleanup
code.
This is still not ideal, it would be cleaner if it used conduit or
something, and if the thread gets killed before waiting, it won't stop
the process.
Only remaining zombies are in CmdLine.Seek
Sped up seeking to around twice as fast, by avoiding a pass over the
worktree files when preferred content expressions of the local repo and
remotes don't use include=/exclude=.
Thanks to Lukey for identifying the optimisation.
This commit was sponsored by Brock Spratlen on Patreon.
Otherwise the bloom filter may not be fully populated when the second
pass starts, which could have led to incorrect behavior with --all -J,
probably in very rare circumstances.
