When ssh connection caching is enabled (and when GIT_ANNEX_USE_GIT_SSH is
not set), only one ssh password prompt will be made per host, and only one
ssh password prompt will be made at a time.
This also fixes a race in prepSocket's stale ssh connection stopping
when run with -J. It was possible for one thread to start a cached ssh
connection, and another thread to immediately stop it, resulting in excess
connections being made.
This commit was supported by the NSF-funded DataLad project.
It takes a single key-value backend, rather than the unncessary and confusing list.
The old option still works if set.
Simplified some old old code too.
This commit was sponsored by Thomas Hochstein on Patreon.
It was distributing jobs to remotes that were not being used by any other
job. But, suppose that there are only 2 remotes, and -J10. In such a case,
the first 2 downloads would be distributed amoung the 2 remotes, but
the other 8 would all go to remote #1. Improved by keeping a counter
of how many jobs are assigned to a remote, and prefer remotes with fewer
jobs.
Note use of Data.Map.Strict to avoid blowing up space. I kept the
bang-patterns as-is, although probably not needed with Data.Map.Strict.
This commit was sponsored by Jack Hill on Patreon.
... to control the default behavior in all clones of a repository.
This includes a new Configurable data type, so the GitConfig type indicates
which values can be configured this way.
The implementation should be quite efficient; the config log is only read
once, and only when a Configurable value has not already been set by
git-config.
Indeed, it would be nice in the future to extend this, so that git-config
is itself only read on demand. Some commands may not need to look at the
git configuration at all.
This commit was sponsored by Trenton Cronholm on Patreon.
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.
Speeds up commands like "git-annex find --in remote" by over 50%.
Profiling showed that adjustGitEnv was 21% of the time and 37% of the
allocations of that command. It copied the environment each time with
getEnvironment.
The only repeated use of adjustGitEnv is in withIndexFile, which tends to
be run at least once per file. So, it was optimised by keeping a cache of
the environment, which can be reused.
There could be other better ways to optimise this. Maybe get the while
environment once at startup. But, then it would have to be serialized back
out each time running a child process, so I doubt that would be a net win.
It might be better to cache a version of the environment that is
pre-modified to use .git-annex/index. But, profiling doesn't show that
modifying the enviroment is taking any significant time.
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.
Only done in -J mode because only if there's concurrency can downloading
from two remotes be faster. Without concurrency, it's likely the case that
sequential downloads from the same remote are faster than switching back
and forth between two remotes.
There is some hairy MVar code here, but basically it just keeps
the activeremotes MVar full except when deciding which remote to assign
to a thread.
Also affects gets by sync --content -J
This commit was sponsored by Jochen Bartl.
* 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.
Writes are optimised by queueing up multiple writes when possible.
The queue is flushed after the Annex monad action finishes. That makes it
happen on program termination, and also whenever a nested Annex monad action
finishes.
Reads are optimised by checking once (per AnnexState) if the database
exists. If the database doesn't exist yet, all reads return mempty.
Reads also cause queued writes to be flushed, so reads will always be
consistent with writes (as long as they're made inside the same Annex monad).
A future optimisation path would be to determine when that's not necessary,
which is probably most of the time, and avoid flushing unncessarily.
Design notes for this commit:
- separate reads from writes
- reuse a handle which is left open until program
exit or until the MVar goes out of scope (and autoclosed then)
- writes are queued
- queue is flushed periodically
- immediate queue flush before any read
- auto-flush queue when database handle is garbage collected
- flush queue on exit from Annex monad
(Note that this may happen repeatedly for a single database connection;
or a connection may be reused for multiple Annex monad actions,
possibly even concurrent ones.)
- if database does not exist (or is empty) the handle
is not opened by reads; reads instead return empty results
- writes open the handle if it was not open previously
The problem is that shutdown is not always called, particularly in the test
suite. So, a database connection would be opened, possibly some changes
queued, and then not shut down.
One way this can happen is when using Annex.eval or Annex.run with a new
state. A better fix might be to make both of them call Keys.shutdown
(and be sure to do it even if the annex action threw an error).
Complication: Sometimes they're run reusing an existing state, so shutting
down a database connection could cause problems for other users of that
same state. I think this would need a MVar holding the database handle,
so it could be emptied once shut down, and another user of the database
connection could then start up a new one if it got shut down. But, what if
2 threads were concurrently using the same database handle and one shut it
down while the other was writing to it? Urgh.
Might have to go that route eventually to get the database access to run
fast enough. For now, a quick fix to get the test suite happier, at the
expense of speed.
Renamed the db to keys, since it is various info about a Keys.
Dropping a key will update its pointer files, as long as their content can
be verified to be unmodified. This falls back to checksum verification, but
I want it to use an InodeCache of the key, for speed. But, I have not made
anything populate that cache yet.
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.
The one exception is in Utility.Daemon. As long as a process only
daemonizes once, which seems reasonable, and as long as it avoids calling
checkDaemon once it's already running as a daemon, the fcntl locking
gotchas won't be a problem there.
Annex.LockFile has it's own separate lock pool layer, which has been
renamed to LockCache. This is a persistent cache of locks that persist
until closed.
This is not quite done; lockContent stil needs to be converted.
This works, and seems fairly robust. Clean get of 20 files at -J3. At -J10,
there are some messages about ssh multiplexing, probably due to a race
spinning up the ssh connection cacher. But, it manages to get all the files
ok regardless.
The progress bars are a scrambled mess though, due to bugs in
ascii-progress, which I've already filed. Particularly this one:
https://github.com/yamadapc/haskell-ascii-progress/issues/8
Seems to work, but still experimental until it's been tested more.
When repositories are on filesystems not supporting symlinks, the .git dir
symlink trick cannot be used. Since we're going to be in direct mode
anyway, the .git dir symlink is not strictly needed.
However, I have not fixed the code that creates new annex symlinks to
handle this case -- the committed symlinks will be wrong.
git annex sync happens to currently fail in a submodule using direct mode,
because there's no HEAD ref. That also needs to be dealt with to get
this fully working in crippled filesystems.
Leaving http://github.com/datalad/datalad/issues/44 open until these issues
are dealt with.
I think this is the last problimatic setCurrentDirectory. I also audited
for extrnal commands that git-annex might run with cwd = foo, and did not
find any that were passed any FilePath that might be absolute.
This allows the git repository to be moved while git-annex is running in
it, with fewer problems.
On Windows, this avoids some of the problems with the absurdly small
MAX_PATH of 260 bytes. In particular, git-annex repositories should
work in deeper/longer directory structures than before. See
http://git-annex.branchable.com/bugs/__34__git-annex:_direct:_1_failed__34___on_Windows/
There are several possible ways this change could break git-annex:
1. If it changes its working directory while it's running, that would
be Bad News. Good news everyone! git-annex never does so. It would also
break thread safety, so all such things were stomped out long ago.
2. parentDir "." -> "" which is not a valid path. I had to fix one
instace of this, and I should probably wipe all calls to parentDir out
of the git-annex code base; it was never a good idea.
3. Things like relPathDirToFile require absolute input paths,
and code assumes that the git repo path is absolute and passes it to it
as-is. In the case of relPathDirToFile, I converted it to not make
this assumption.
Currently, the test suite has 16 failures.
This does mean that eg, copying multiple files to a local remote will
become slightly slower, since it now restarts git-cat-file after each copy.
Should not be significant slowdown.
The reason git-cat-file is run on the remote at all is to update its
location log. In order to add an item to it, it needs to get the current
content of the log. Finding a way to avoid needing to do that would be a
good path to avoiding this slowdown if it does become a problem somehow.
This commit was sponsored by Evan Deaubl.
Removed old extensible-exceptions, only needed for very old ghc.
Made webdav use Utility.Exception, to work after some changes in DAV's
exception handling.
Removed Annex.Exception. Mostly this was trivial, but note that
tryAnnex is replaced with tryNonAsync and catchAnnex replaced with
catchNonAsync. In theory that could be a behavior change, since the former
caught all exceptions, and the latter don't catch async exceptions.
However, in practice, nothing in the Annex monad uses async exceptions.
Grepping for throwTo and killThread only find stuff in the assistant,
which does not seem related.
Command.Add.undo is changed to accept a SomeException, and things
that use it for rollback now catch non-async exceptions, rather than
only IOExceptions.
On Windows, changing the time zone causes the apparent mtime of files to
change. This confuses git-annex, which natually thinks this means the files
have actually been modified (since THAT'S WHAT A MTIME IS FOR, BILL <sheesh>).
Work around this stupidity, by using the inode sentinal file to detect if
the timezone has changed, and calculate a TSDelta, which will be applied
when generating InodeCaches.
This should add no overhead at all on unix. Indeed, I sped up a few
things slightly in the refactoring.
Seems to basically work! But it has a big known problem:
If the timezone changes while the assistant (or a long-running command)
runs, it won't notice, since it only checks the inode cache once, and
so will use the old delta for all new inode caches it generates for new
files it's added. Which will result in them seeming changed the next time
it runs.
This commit was sponsored by Vincent Demeester.
Motivation: Hook scripts for nautilus or other file managers
need to provide the user with feedback that a file is being downloaded.
This commit was sponsored by THM Schoemaker.
Benchmarking this with 1000 small files being copied, the time reduced from
15.98s to 14.64s -- an 8% improvement in the non-data-transfer overhead of
git-annex copy.
Using the extract(1) program to do the heavy lifting.
Decided to make git-annex run pre-commit-annex when committing. Since
git-annex pre-commit also runs it, it'll be run when git commit is run too,
via the pre-commit hook. This basically gives back the pre-commit hook
that git-annex took away. The implementation avoids repeatedly looking
for the hook script when the assistant is running and committing
repeatedly; only checks if the hook is available once.
To make the script simpler, made git-annex metadata -s field?=value
only set a field when it's not already got a value.
This commit was sponsored by bak.
* numcopies: New command, sets global numcopies value that is seen by all
clones of a repository.
* The annex.numcopies git config setting is deprecated. Once the numcopies
command is used to set the global number of copies, any annex.numcopies
git configs will be ignored.
* assistant: Make the prefs page set the global numcopies.
This global numcopies setting is needed to let preferred content
expressions operate on numcopies.
It's also convenient, because typically if you want git-annex to preserve N
copies of files in a repo, you want it to do that no matter which repo it's
running in. Making it global avoids needing to warn the user about gotchas
involving inconsistent annex.numcopies settings.
(See changes to doc/numcopies.mdwn.)
Added a new variety of git-annex branch log file, that holds only 1 value.
Will probably be useful for other stuff later.
This commit was sponsored by Nicolas Pouillard.
I've been disliking how the command seek actions were written for some
time, with their inversion of control and ugly workarounds.
The last straw to fix it was sync --content, which didn't fit the
Annex [CommandStart] interface well at all. I have not yet made it take
advantage of the changed interface though.
The crucial change, and probably why I didn't do it this way from the
beginning, is to make each CommandStart action be run with exceptions
caught, and if it fails, increment a failure counter in annex state.
So I finally remove the very first code I wrote for git-annex, which
was before I had exception handling in the Annex monad, and so ran outside
that monad, passing state explicitly as it ran each CommandStart action.
This was a real slog from 1 to 5 am.
Test suite passes.
Memory usage is lower than before, sometimes by a couple of megabytes, and
remains constant, even when running in a large repo, and even when
repeatedly failing and incrementing the error counter. So no accidental
laziness space leaks.
Wall clock speed is identical, even in large repos.
This commit was sponsored by an anonymous bitcoiner.
0980f3dae6 broke support for local remotes
from direct mode repos, because the relative path was taken to be from the
gitdir, rather than from the work tree.
Direct mode repositories can now have core.bare=true set, to prevent
accidentally running git commands that try to operate on the work tree,
and so do the wrong thing.
This is not yet the default, and it causes known problems for git-annex sync
due to receive.denyCurrentBranch not working in bare repositories.
This commit was sponsored by Richard Hartmann.
Overridable with --user-agent option.
Not yet done for S3 or WebDAV due to limitations of libraries used --
nether allows a user-agent header to be specified.
This commit sponsored by Michael Zehrer.
Requires git 1.8.4 or newer. When it's installed, a background
git check-ignore process is run, and used to efficiently check ignores
whenever a new file is added.
Thanks to Adam Spiers, for getting the necessary support into git for this.
A complication is what to do about files that are gitignored but have
been checked into git anyway. git commands assume the ignore has been
overridden in this case, and not need any more overriding to commit a
changed version.
However, for the assistant to do the same, it would have to run git ls-files
to check if the ignored file is in git. This is somewhat expensive. Or it
could use the running git-cat-file process to query the file that way,
but that requires transferring the whole file content over a pipe, so it
can be quite expensive too, for files that are not git-annex
symlinks.
Now imagine if the user knows that a file or directory tree will be getting
frequent changes, and doesn't want the assistant to sync it, so gitignores
it. The assistant could overload the system with repeated ls-files checks!
So, I've decided that the assistant will not automatically commit changes
to files that are gitignored. This is a tradeoff. Hopefully it won't be a
problem to adjust .gitignore settings to not ignore files you want the
assistant to autocommit, or to manually git annex add files that are listed
in .gitignore.
(This could be revisited if git-annex gets access to an interface to check
the content of the index w/o forking a git command. This could be libgit2,
or perhaps a separate git cat-file --batch-check process, so it wouldn't
need to ship over the whole file content.)
This commit was sponsored by Francois Marier. Thanks!
As seen in this bug report, the lifted exception handling using the StateT
monad throws away state changes when an action throws an exception.
http://git-annex.branchable.com/bugs/git_annex_fork_bombs_on_gpg_file/
.. Which can result in cached values being redundantly calculated, or other
possibly worse bugs when the annex state gets out of sync with reality.
This switches from a StateT AnnexState to a ReaderT (MVar AnnexState).
All changes to the state go via the MVar. So when an Annex action is
running inside an exception handler, and it makes some changes, they
immediately go into affect in the MVar. If it then throws an exception
(or even crashes its thread!), the state changes are still in effect.
The MonadCatchIO-transformers change is actually only incidental.
I could have kept on using lifted-base for the exception handling.
However, I'd have needed to write a new instance of MonadBaseControl
for the new monad.. and I didn't write the old instance.. I begged Bas
and he kindly sent it to me. Happily, MonadCatchIO-transformers is
able to derive a MonadCatchIO instance for my monad.
This is a deep level change. It passes the test suite! What could it break?
Well.. The most likely breakage would be to code that runs an Annex action
in an exception handler, and *wants* state changes to be thrown away.
Perhaps the state changes leaves the state inconsistent, or wrong. Since
there are relatively few places in git-annex that catch exceptions in the
Annex monad, and the AnnexState is generally just used to cache calculated
data, this is unlikely to be a problem.
Oh yeah, this change also makes Assistant.Types.ThreadedMonad a bit
redundant. It's now entirely possible to run concurrent Annex actions in
different threads, all sharing access to the same state! The ThreadedMonad
just adds some extra work on top of that, with its own MVar, and avoids
such actions possibly stepping on one-another's toes. I have not gotten
rid of it, but might try that later. Being able to run concurrent Annex
actions would simplify parts of the Assistant code.
* since this is a crippled filesystem anyway, git-annex doesn't use
symlinks on it
* so there's no reason to use the mixed case hash directories that we're
stuck using to avoid breaking everyone's symlinks to the content
* so we can do what is already done for all bare repos, and make non-bare
repos on crippled filesystems use the all-lower case hash directories
* which are, happily, all 3 letters long, so they cannot conflict with
mixed case hash directories
* so I was able to 100% fix this and even resuming `git annex add` in the
test case will recover and it will all just work.
Now there's a Config type, that's extracted from the git config at startup.
Note that laziness means that individual config values are only looked up
and parsed on demand, and so we get implicit memoization for all of them.
So this is not only prettier and more type safe, it optimises several
places that didn't have explicit memoization before. As well as getting rid
of the ugly explicit memoization code.
Not yet done for annex.<remote>.* configuration settings.
It occurs to me that all config settings should be parsed once at startup,
into a proper ADT, rather than all this ad-hoc parsing and memoization. One
day..
I had been using -ignore-package monads-tf to deal with this, but
the XMPP library uses monads-tf, so that also ignores it. Instead,
use PackageImports to force use of mtl in my own code.
Monitors git-annex branch for changes, which are noticed by the Merger
thread whenever the branch ref is changed (either due to an incoming push,
or a local change), and refreshes cached config values for modified config
files.
Rate limited to run no more often than once per minute. This is important
because frequent git-annex branch changes happen when files are being
added, or transferred, etc.
A primary use case is that, when preferred content changes are made,
and get pushed to remotes, the remotes start honoring those settings.
Other use cases include propigating repository description and trust
changes to remotes, and learning when a remote has added a new special
remote, so the webapp can present the GUI to enable that special remote
locally.
Also added a uuid.log cache. All other config files already had caches.
When in a subdir, both the normal filepath, and the filepath relative to
the top of the git repo are needed for matching. The former for key lookup,
and the latter for include/exclude to match against. Previously, key lookup
didn't work in this situation.
Solves the issue with preferred content expressions and dropping that
I mentioned yesterday. My solution was to add a parameter to specify a set
of repositories where content should be assumed not to be present. When
deciding whether to drop, it can put the current repository in, and then
if the expression fails to match, the content can be dropped.
Using yesterday's example "(not copies=trusted:2) and (not in=usbdrive)",
when the local repo is one of the 2 trusted copies, the drop check will
see only 1 trusted copy, so the expression matches, and so the content will
not be dropped.
This includes a full parser for the boolean expressions in the log,
that compiles them into Matchers. Those matchers are not used yet.
A complication is that matching against an expression should never
crash git-annex with an error. Instead, vicfg checks that the expressions
parse. If a bad expression (or an expression understood by some future
git-annex version) gets into the log, it'll be ignored.
Most of the code in Limit couldn't fail anyway, but I did have to make
limitCopies check its parameter first, and return an error if it's bad,
rather than erroring at runtime.
Uses a MVar again, as there seems no other way to thread the state through
inotify events.
This is a rather unsatisfactory result. I had wanted to run them in
the same monad so that the git queue could be used to coleasce git commands
and speed things up. But, that led to fragility: If several files are
added, and one is removed before queue flush, git add will fail to add
any of them. So, the queue is still explicitly flushed after each add for
now.
TODO: Investigate using git add --ignore-errors. This would need to be done
in Command.Add. And, git add still exits nonzero with it, so would need
to avoid crashing on queue flush.
The environment needs to override git-config. Changed when git config is
read, and avoid rereading it once it's been read.
chdir for both worktree settings.
This option avoids gpg key distribution, at the expense of flexability, and
with the requirement that all clones of the git repository be equally
trusted.
A bit tricky to avoid printing it twice in a row when there are queued git
commands to run and journal to stage.
Added a generic way to run an action that may output multiple side
messages, with only the first displayed.
Added Annex.cleanup, which is a general purpose interface for adding
actions to run at the end.
Remotes with the old git-annex-shell will commit every time, and have no
commit command, so hide stderr when running the commit command.
useful when adding hundreds of thousands of files on a system with plenty
of memory.
git add gets quite slow in such a large repository, so if the system has
more than the ~32 mb of memory the queue can use by default, it's a useful
optimisation to increase the queue size, in order to decrease the number
of times git add is run.
Now gitattributes are looked up, efficiently, in only the places that
really need them, using the same approach used for cat-file.
The old CheckAttr code seemed very fragile, in the way it streamed files
through git check-attr.
I actually found that cad8824852
was still deadlocking with ghc 7.4, at the end of adding a lot of files.
This should fix that problem, and avoid future ones.
The best part is that this removes withAttrFilesInGit and withNumCopies,
which were complicated Seek methods, as well as simplfying the types
for several other Seek methods that had a Backend tupled in.
I had not realized what a memory leak the lazy state monad could be,
although I have not seen much evidence of actual leaking in git-annex.
However, if running git-annex on a great many files, this could matter.
The additional Utility.State.changeState adds even more strictness,
avoiding a problem I saw in github-backup where repeatedly modifying
state built up a huge pile of thunks.
Ssh connection caching is now enabled automatically by git-annex. Only one
ssh connection is made to each host per git-annex run, which can speed some
things up a lot, as well as avoiding repeated password prompts. Concurrent
git-annex processes also share ssh connections. Cached ssh connections are
shut down when git-annex exits.
Note: The rsync special remote does not yet participate in the ssh
connection caching.
This overrides the trust.log, and is overridden by the command-line trust
parameters.
It would have been nicer to have Logs.Trust.trustMap just look up the
configuration for all remotes, but a dependency loop prevented that
(Remotes depends on Logs.Trust in several ways). So instead, look up
the configuration when building remotes, storing it in the same forcetrust
field used for the command-line trust parameters.
Made --from and --to command-specific options.
Added generic storage for values of command-specific options,
which allows removing some of the special case fields in AnnexState.
(Also added generic storage for command-specific flags, although there are
not yet any.)
Note that this storage uses a Map, so repeatedly looking up the same value
is slightly more expensive than looking up an AnnexState field. But, the
value can be looked up once in the seek stage, transformed as necessary,
and passed in a closure to the start stage, and this avoids that overhead.
Still, I'm hesitant to use this for things like force or fast flags.
It's probably best to reserve it for flags that are only used by a few
commands, or options like --from and --to that it's important only be
allowed to be used with commands that implement them, to avoid user
confusion.
