The new second pass sees the file as type changed because the first
pass's changes have typically not reached git yet. So, have to
explicitly check for unmodified files in the second pass.
Note that, if the file has been touched but not really modified,
the first pass will handle it, and so the second pass does nothing.
This commit was sponsored by Jochen Bartl on Patreon.
v6: When a file is unlocked but has not been modified, and the unlocking is
only staged, git-annex add did not lock it. Now it will, for consistency
with how modified files are handled and with v5.
Note the removal of the sameInodeCache check. Otherwise it would see
that the unmodified file is unmodified and stop there. That check seems to have
been copied from the direct mode branch. But, direct mode had a specific
reason to check for unmodified content, that does not apply to v6.
The second pass means there is potential for a race, eg the unlocked
file could be modified in between the first and second passes.
No problem with that, since both passes do the same thing.
This commit was sponsored by Jake Vosloo on Patreon.
When --batch is used with matching options like --in, --metadata, etc, only
operate on the provided files when they match those options. Otherwise, a
blank line is output in the batch protocol.
Affected commands: find, add, whereis, drop, copy, move, get
In the case of find, the documentation for --batch already said it honored
the matching options. The docs for the rest didn't, but it makes sense to
have them honor them. While this is a behavior change, why specify the
matching options with --batch if you didn't want them to apply?
Note that the batch output for all of the affected commands could
already output a blank line in other cases, so batch users should
already be prepared to deal with it.
git-annex metadata didn't seem worth making support the matching options,
since all it does is output metadata or set metadata, the use cases for
using it in combination with the martching options seem small. Made it
refuse to run when they're combined, leaving open the possibility for later
support if a use case develops.
This commit was sponsored by Brett Eisenberg on Patreon.
Useful for dropping old objects from cache repositories.
But also, quite a genrally useful thing to have..
Rather than imitiating find's -atime and other options, all of which are
pretty horrible to use, I made this match files accessed within a time
period, using the same duration format used by git-annex schedule and
--limit-time
In passing, changed the --limit-time option parser to parse the
duration, instead of having it later throw an error.
This commit was supported by the NSF-funded DataLad project.
Makes it allow writes, but not deletion of annexed content. Note that
securing pushes to the git repository is left up to the user.
This commit was sponsored by Jack Hill on Patreon.
In Annex.Branch.branch, the (++) was killing laziness.
Rewrote so it streams lazily.
filterM also kills laziness, so made loggedKeys use a Unchecked type,
and check if the key is dead in the seek loop.
Note that loggedKeysFor still buffers, so git-annex info <remote> and
git-annex unused --from remote still use more memory than necessary.
Also removed some unused functions from Annex.Journal.
Test case is 24 directories each containing files named 1..10000.
The concat and filterM destroyed what laziness there is in
dirContentsRecursive, making it buffer all the filenames. Memory
use was around 300 mb (possibly growing slightly as it progressed).
After this fix, memory use drops to a constant 59 mb.
Note that dirContentsRecursive still buffers the entire content of a
directory (not subdirectories) so this is still not optimal.
Unfortunately ReceiveMessage didn't handle unknown messages the way it
was documented to; client sending VERSION would cause the server to
return an ERROR and hang up. Fixed that, but old releases of git-annex
use the P2P protocol for tor and will still have that behavior.
So, version is not negotiated for Remote.P2P connections, only for
Remote.Git connections, which will support VERSION from their first
release. There will need to be a later flag day to change Remote.P2P;
left a commented out line that is the only thing that will need to be
changed then.
Version 1 of the P2P protocol is not implemented yet, but updated
the docs for the DATA change that will be allowed by that version.
This commit was sponsored by Jeff Goeke-Smith on Patreon.
Not yet used by git-annex, but this will allow faster transfers etc than
using individual ssh connections and rsync.
Not called git-annex-shell p2p, because git-annex p2p does something
else and I don't want two subcommands with the same name between the two
for sanity reasons.
This commit was sponsored by Øyvind Andersen Holm.
Added --json-error-messages option, which includes error messages in the
json output, rather than outputting them to stderr.
The actual rediretion of errors is not implemented yet, this is only
the docs and option plumbing.
This commit was supported by the NSF-funded DataLad project.
Fix behavior of --json-progress followed by --json, in which
the latter option disabled the former.
This commit was supported by the NSF-funded DataLad project.
And for tab completion, by not unnessessarily statting paths to remotes,
which used to cause eg, spin-up of removable drives.
Got rid of the remotes member of Git.Repo. This was a bit painful.
Remote.Git modifies the list of remotes as it reads their configs,
so still need a persistent list of remotes. So, put it in as
Annex.gitremotes. It's only populated by getGitRemotes, so commands
like examinekey that don't care about remotes won't do so.
This commit was sponsored by Jake Vosloo on Patreon.
Chose to make this only handle files actively being downloaded, not temp
files for downloads that were interrupted or files that have been fully
downloaded.
This commit was sponsored by Ole-Morten Duesund on Patreon.
Test suite is always included.
Building with this flag disabled has actually been broken for some time,
since Command.TestRemote uses tasty. Fewer build flags are better, so good
time to drop it.
This commit was sponsored by Thomas Hochstein on Patreon.
This avoids all the complication about redundant work discussed in
the previous try at fixing this. At the expense of needing each command
that could have the problem to be patched to simply wrap the action in
onlyActionOn once the key is known. But there do not seem to be many
such commands.
onlyActionOn' should not be used with a CommandStart (or CommandPerform),
although the types do allow it. onlyActionOn handles running the whole
CommandStart chain. I couldn't immediately see a way to avoid mistken
use of onlyActionOn'.
This commit was supported by the NSF-funded DataLad project.
git annex add, git annex lock etc make multiple seek passes,
and each seek pass checked that files existed. That was unncessary
redundant work.
Fixed by adding a new WorkTreeItem type, make seek actions use it,
and check that the files exist when constructing it.
This commit was supported by the NSF-funded DataLad project.
optparse-applicative-0.14.0.0 adds support for these, so have the
Makefile install their scripts when built with it.
CmdLine/GitAnnex/Options.hs now uses action "file" in cmdParams,
which affects the bash and zsh completions, letting them complete
filenames for subcommands that use that. This is not needed for
bash, since bash-completion.bash enables -o bashdefault, which
lets it complete filenames too. But it does not seem to break the bash
completions. It is needed for zsh; the zsh completion otherwise
does not complete filenames. The fish completion will always complete
filenames no matter what. Messy.
This commit was sponsored by Denis Dzyubenko on Patreon.
When setting metadata of a file that did not exist, no error message was
displayed, unlike getting metadata and most other git-annex commands. Fixed
this oversight.
Note that, if the file exists but is not annexed, there's no error.
This is the same behavior as other git-annex commands.
This commit was supported by the NSF-funded DataLad project.
Reworked remote name parsing to allow things like that. Command.Move
uses it for --to=here, although there's not yet an implementation of
that option.
This commit was sponsored by Ignacio on Patreon.
See my comment. This only avoids the problem for -J; two git-annex
processes started at the same time could still both try to write to
.git/config and one fail. That would be very unlikely though, and it
doesn't really seem worth adding an additional layer of locking around
.git/config.
This commit was supported by the NSF-funded DataLad project.
Fix bug when used with a recently cloned repository, where
"merging" messages were included in the output of configlist (and perhaps
other commands) and caused a "Failed to get annex.uuid configuration"
error.
This does not seem to have been a reversion.
I saw this with configlist, but it seems possible for other commands to be
effected, and it might not always happen only after a fresh clone. Eg, if a
foo/git-annex branch is pushed to the remote, the next git-annex-shell will
auto-merge it and display the message.
Decided to run all git-annex-shell commands with noMessages,
even ones that don't currently use stdout for structured communication.
Better to keep open the possibility for using stdout in the future.
This commit was supported by the NSF-funded DataLad project
It was relying on segmentPaths to work correctly, so when it didn't,
sometimes the file that did not exist got matched up with a non-null
list of results. Fixed by always checking if each parameter exists.
There are two reason segmentPaths might not work correctly.
For one, it assumes that when the original list of paths
has more than 100 paths, it's not worth paying the CPU cost to
preserve input orders.
And then, it fails when a directory such as "." or ".." or
/path/to/repo is in the input list, and the list of found paths
does not start with that same thing. It should probably not be using
dirContains, but something else.
But, it's not clear how to handle this fully. Consider
when [".", "subdir"] has been expanded by git ls-files to
["subdir/1", "subdir/2"]
-- Both of the inputs contained those results, so there's
no one right answer for segmentPaths. All these would be equally valid:
[["subdir/1", "subdir/2"], []]
[[], ["subdir/1", "subdir/2"]]
[["subdir/1"], [""subdir/2"]]
So I've not tried to improve segmentPaths.
Added --securehash option to match files using a secure hash function, and
corresponding securehash preferred content expression.
This commit was sponsored by Ethan Aubin.
Where before the "name" of a key and a backend was a string, this makes
it a concrete data type.
This is groundwork for allowing some varieties of keys to be disabled
in file2key, so git-annex won't use them at all.
Benchmarks ran in my big repo:
old git-annex info:
real 0m3.338s
user 0m3.124s
sys 0m0.244s
new git-annex info:
real 0m3.216s
user 0m3.024s
sys 0m0.220s
new git-annex find:
real 0m7.138s
user 0m6.924s
sys 0m0.252s
old git-annex find:
real 0m7.433s
user 0m7.240s
sys 0m0.232s
Surprising result; I'd have expected it to be slower since it now parses
all the key varieties. But, the parser is very simple and perhaps
sharing KeyVarieties uses less memory or something like that.
This commit was supported by the NSF-funded DataLad project.
* Added post-recieve hook, which makes updateInstead work with direct
mode and adjusted branches.
* init: Set up the post-receive hook.
This commit was sponsored by Fernando Jimenez on Patreon.
Any config names can be set using this; git-annex commands will only look
at specific ones that make sense and are worth the overhead of querying the
branch.
This might also be useful for storing whatever other config-type stuff the
user might want to shove into the git-annex branch.
This commit was sponsored by Jochen Bartl on Patreon.
Still a couple bugs:
* Closing the connection to the server leaves git upload-pack /
receive-pack running, which could be used to DOS.
* Sometimes the data is transferred, but it fails at the end, sometimes
with:
git-remote-tor-annex: <socket: 10>: commitBuffer: resource vanished (Broken pipe)
Must be a race condition around shutdown.
Almost working, but there's a bug in the relaying.
Also, made tor hidden service setup pick a random port, to make it harder
to port scan.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
ghc 8 added backtraces on uncaught errors. This is great, but git-annex was
using error in many places for a error message targeted at the user, in
some known problem case. A backtrace only confuses such a message, so omit it.
Notably, commands like git annex drop that failed due to eg, numcopies,
used to use error, so had a backtrace.
This commit was sponsored by Ethan Aubin.
I've long considered the XMPP support in git-annex a wart.
It's nice to remove it.
(This also removes the NetMessager, which was only used for XMPP, and the
daemonstatus's desynced list (likewise).)
Existing XMPP remotes should be ignored by git-annex.
This commit was sponsored by Brock Spratlen on Patreon.
Tor unfortunately does not come out of the box configured to let hidden
services register themselves on the fly via the ControlPort.
And, changing the config to enable the ControlPort and a particular type
of auth for it may break something already using the ControlPort, or
lessen the security of the system.
So, this leaves only one option to us: Add a hidden service to the
torrc. git-annex enable-tor does so, and picks an unused high port for
tor to listen on for connections to the hidden service.
It's up to the caller to somehow pick a local port to listen on
that won't be used by something else. That may be difficult to do..
This commit was sponsored by Jochen Bartl on Patreon.
This makes -Jn work with --json and --quiet, where before
setting -Jn disabled those options.
Concurrent json output is currently a mess though since threads output
chunks over top of one-another.
Note that get --from foo --failed will get things that a previous get --from bar
tried and failed to get, etc. I considered making --failed only retry
transfers from the same remote, but it was easier, and seems more useful,
to not have the same remote requirement.
Noisy due to some refactoring into Types/
Show branch:file that is being operated on.
I had to make ActionItem a type and not a type class because
withKeyOptions' passed two different types of values when using the type
class, and I could not get the type checker to accept that.
Added --branch option to copy, drop, fsck, get, metadata, mirror, move, and
whereis commands. This option makes git-annex operate on files that are
included in a specified branch (or other treeish).
The names of the files from the branch that are being operated on are not
displayed yet; only the keys. Displaying the filenames will need changes
to every affected command.
Also, note that --branch can be specified repeatedly. This is not really
documented, but seemed worth supporting, especially since we may later want
the ability to operate on all branches matching a refspec. However, when
operating on two branches that contain the same key, that key will be
operated on twice.
"git annex adjust" may be a temporary interface, but works for a proof of
concept.
It is pretty fast at creating the adjusted branch. The main overhead is
injecting pointer files. It might be worth optimising that by reusing the
symlink target as the pointer file content. When I tried to do that,
the problem was that the clean filter doesn't use that same format, and so
git thought files had changed. Could be dealt with, perhaps make the clean
filter use symlink format for pointer files when on an adjusted branch?
But the real overhead is in checking out the branch, when git runs the
smudge filter once per file. That is perhaps too slow to be usable,
although it may only affect initial checkout of the branch, and not
updates. TBD.
Instead -J will behave as if it was built without concurrent-output support
in this situation. Ie, it will be mostly quiet, except when there's an
error.
Note that it's not a problem for a filename to contain invalid utf-8 when
in a utf-8 locale. That is handled ok by concurrent-output. It's only
displaying unicode characters in a non-unicode locale that doesn't work.
* Removed the webapp-secure build flag, rolling it into the webapp build
flag.
* Removed the quvi and tahoe build flags, which only adds aeson to
the core dependencies.
* Removed the feed build flag, which only adds feed to the core
dependencies.
Build flags have cost in both code complexity and also make Setup configure
have to work harder to find a usable set of build flags when some
dependencies are missing.
When Config.setConfig runs, it throws away the old Repo and loads a new
one. So, add an action to adjust the Repo so that -c settings will persist
across that.
This allows things like Command.Find to use noMessages and generate their
own complete json objects. Previouly, Command.Find managed that only via a
hack, which wasn't compatable with batch mode.
Only Command.Find, Command.Smudge, and Commange.Status use noMessages
currently, and none except for Command.Find are impacted by this change.
Fixes find --json --batch output
Previously, it only flushed when the queue got larger than 1.
Also, make the queue auto-flush when items are added, rather than needing
to be flushed as a separate step. This simplifies the code and make it more
efficient too, as it avoids needing to read the queue out of the state to
check if it should be flushed.
The benchmark shows that the database access is quite fast indeed!
And, it scales linearly to the number of keys, with one exception,
getAssociatedKey.
Based on this benchmark, I don't think I need worry about optimising
for cases where all files are locked and the database is mostly empty.
In those cases, database access will be misses, and according to this
benchmark, should add only 50 milliseconds to runtime.
(NB: There may be some overhead to getting the database opened and locking
the handle that this benchmark doesn't see.)
joey@darkstar:~/src/git-annex>./git-annex benchmark
setting up database with 1000
setting up database with 10000
benchmarking keys database/getAssociatedFiles from 1000 (hit)
time 62.77 μs (62.70 μs .. 62.85 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 62.81 μs (62.76 μs .. 62.88 μs)
std dev 201.6 ns (157.5 ns .. 259.5 ns)
benchmarking keys database/getAssociatedFiles from 1000 (miss)
time 50.02 μs (49.97 μs .. 50.07 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 50.09 μs (50.04 μs .. 50.17 μs)
std dev 206.7 ns (133.8 ns .. 295.3 ns)
benchmarking keys database/getAssociatedKey from 1000 (hit)
time 211.2 μs (210.5 μs .. 212.3 μs)
1.000 R² (0.999 R² .. 1.000 R²)
mean 211.0 μs (210.7 μs .. 212.0 μs)
std dev 1.685 μs (334.4 ns .. 3.517 μs)
benchmarking keys database/getAssociatedKey from 1000 (miss)
time 173.5 μs (172.7 μs .. 174.2 μs)
1.000 R² (0.999 R² .. 1.000 R²)
mean 173.7 μs (173.0 μs .. 175.5 μs)
std dev 3.833 μs (1.858 μs .. 6.617 μs)
variance introduced by outliers: 16% (moderately inflated)
benchmarking keys database/getAssociatedFiles from 10000 (hit)
time 64.01 μs (63.84 μs .. 64.18 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 64.85 μs (64.34 μs .. 66.02 μs)
std dev 2.433 μs (547.6 ns .. 4.652 μs)
variance introduced by outliers: 40% (moderately inflated)
benchmarking keys database/getAssociatedFiles from 10000 (miss)
time 50.33 μs (50.28 μs .. 50.39 μs)
1.000 R² (1.000 R² .. 1.000 R²)
mean 50.32 μs (50.26 μs .. 50.38 μs)
std dev 202.7 ns (167.6 ns .. 252.0 ns)
benchmarking keys database/getAssociatedKey from 10000 (hit)
time 1.142 ms (1.139 ms .. 1.146 ms)
1.000 R² (1.000 R² .. 1.000 R²)
mean 1.142 ms (1.140 ms .. 1.144 ms)
std dev 7.142 μs (4.994 μs .. 10.98 μs)
benchmarking keys database/getAssociatedKey from 10000 (miss)
time 1.094 ms (1.092 ms .. 1.096 ms)
1.000 R² (1.000 R² .. 1.000 R²)
mean 1.095 ms (1.095 ms .. 1.097 ms)
std dev 4.277 μs (2.591 μs .. 7.228 μs)
The direct flag is also set when sending unlocked content, to support old
versions of git-annex-shell. At some point, the direct flag will be
removed, and only the unlocked flag will be used.
This only adds 1 stat to each file fscked for locked files, so
added overhead is minimal.
For unlocked files it has to access the database to see if a file
is modified.
Backend.lookupFile is changed to always fall back to catKey when
operating on a file that's not a symlink.
catKey is changed to understand pointer files, as well as annex symlinks.
Before, catKey needed a file mode witness, to be sure it was looking at a
symlink. That was complicated stuff. Now, it doesn't actually care if a
file in git is a symlink or not; in either case asking git for the content
of the file will get the pointer to the key.
This does mean that git-annex will treat a link
foo -> WORM--bar as a git-annex file, and also treats
a regular file containing annex/objects/WORM--bar as a git-annex file.
Calling catKey could make git-annex commands need to do more work than
before. This would especially be the case if a repo contained many regular
files, and only a few annexed files, as now git-annex will need to ask
git about the contents of the regular files.
The git filter config can be used to map the single git-annex command to
the 2 actions, and this avoids "git annex clean" being used for this thing,
it might have a better use for that name later.
Commands that want to use it have to run their seek action inside
allowConcurrentOutput. Which seems reasonable; perhaps some future command
will want to support the -J flag but not use regions.
The region state moved from Annex to MessageState. This makes sense
organizationally, and note that some uses of onLocal use a different Annex
state, but pass the MessageState into it, which is what is needed.
This was potentially a hole in the readonly mode armor even before my last
commit. If the user could push a git-annex branch to a repo, they could get
git-annex-shell to initialize the repo. After my last commit, the user
didn't even need to be allowed to push a branch to init the repo, so
this hole certianly needs to be closed now.
Now it suffices to run git remote add, followed by git-annex sync. Now the
remote is automatically initialized for use by git-annex, where before the
git-annex branch had to manually be pushed before using git-annex sync.
Note that this involved changes to git-annex-shell, so if the remote is
using an old version, the manual push is still needed.
Implementation required git-annex-shell be changed, so configlist can
autoinit a repository even when no git-annex branch has been pushed yet.
Unfortunate because we'll have to wait for it to get deployed to servers
before being able to rely on this change in the documentation.
Did consider making git-annex sync push the git-annex branch to repos that
didn't have a uuid, but this seemed difficult to do without complicating it
in messy ways.
It would be cleaner to split a command out from configlist to handle
the initialization. But this is difficult without sacrificing backwards
compatability, for users of old git-annex versions which would not use the
new command.
Work around https://github.com/pcapriotti/optparse-applicative/issues/146
by not using action "file" and instead passing -o bashdefault -o default
to complete. This way, when optparse fails to complete a filename, bash
will fall back to regular filename completion.
Unfortunately, optparse-applicative does not provide a way to control the
options passed to complete, so I had to modify its generated completion script.
Note that for "git annex" command completion, git's completion script already
used -o bashdefault -o default, so that works too.
Note that I ran into a problem where parsing the global options looped
forever, eating memory. It was somehow caused by stacking
combineGlobalSetters inside a combineGlobalSetters. Maybe due to both
using "many"? Anyway, changed things to avoid that.
This is a work in progress. It compiles and is able to do basic command
dispatch, including git autocorrection, while using optparse-applicative
for the core commandline parsing.
* Many commands are temporarily disabled before conversion.
* Options are not wired in yet.
* cmdnorepo actions don't work yet.
Also, removed the [Command] list, which was only used in one place.
