* Perform a clean shutdown when --time-limit is reached.
This includes running queued git commands, and cleanup actions normally
run when a command is finished.
* fsck: Commit incremental fsck database when --time-limit is reached.
Previously, some of the last files fscked did not make it into the
database when using --time-limit.
Note that this changes Annex.addCleanup hooks, to run after --time-limit
expires. Fsck was using such a hook to clean up after a
--incremental-schedule, and that shouldn't run when --time-limit exipires
it. So, instead, moved that cleanup code to be run by cleanupIncremental.
Resulted in some data type juggling.
I've seen rss feeds that have no permalinks, only guids (which are
sometimes in the form of permalinks, argh/sigh).
I had previously avoided trusting guids to be globally unique, because my
survey of rss feeds that I subscribe to shows a lot of pretty bad
"guids" like "2 at http://serialpodcast.org" or even worse "oth20150401-hq".
Worry was that two podcasts that are generating guids so badly, that
there's no guarantee they're actually globally unique.
But, I'm seeing too many url changes that result in redundant files, so
let's try this. If feeds are so broken that guids overlap, they could just
as well incorrectly call them permalinks too.
"checkPresent baser" was wrong; the baser has a dummy checkPresent action
not the real one. So, to fix this, we need to call preparecheckpresent to
get a checkpresent action that can be used to check if chunks are present.
Note that, for remotes like S3, this means that the preparer is run,
which opens a S3 handle, that will be used for each checkpresent of a
chunk. That's a good thing; if we're resuming an upload that's already many
chunks in, it'll reuse that same http connection for each chunk it checks.
Still, it's not a perfectly ideal thing, since this is a different http
connection that the one that will be used to upload chunks. It would be
nice to improve the API so that both use the same http connection.
The branch needs to be created when merging from the remote in sync,
since we diff between it and the remote's sync branch. But git annex merge
should not be creating sync branches.
This was a reversion caused by the relative path changes in 5.20150113.
Other uses of addAuthorizedKeys seem to be ok. If the user enters a
directory like ~/annex, it writes GIT_ANNEX_SHELL_DIRECTORY=annex, and
git-annex-shell assumes that's relative to HOME.
This makes git annex unused use around 48 mb more memory than it did before,
but the massive increase in accuracy makes this worthwhile for all but the
smallest systems.
Also, I want to use the bloom filter for sync --all --content, to avoid
dropping files that the preferred content doesn't want, and 1/1000
false positives would be far too many in that use case, even if it were
acceptable for unused.
Actual memory use numbers:
1000: 21.06user 3.42system 0:26.40elapsed 92%CPU (0avgtext+0avgdata 501552maxresident)k
1000000: 21.41user 3.55system 0:26.84elapsed 93%CPU (0avgtext+0avgdata 549496maxresident)k
10000000: 21.84user 3.52system 0:27.89elapsed 90%CPU (0avgtext+0avgdata 549920maxresident)k
Based on these numbers, 10 million seemed a better pick than 1 million.
backup: Use new "anything" terminal. This means that content that
is not unused, but has no associated file will be wanted by backup repos.
unwanted: "not anything" will result in any and all content moving
off of these repos.
incremental backup: Remove the "(include=* or unused)",
so it matches content that has no associated files
but is not unused.
client: Add a include=* to the expression. This limits it to matching
only files in the work tree. Without this change, sync --all --content
would match a key against the expression, and since it matches
exclude=archive/*, the client repo would have wanted the file content.
The "and not unused" would have kept unused objects out, but not
objects that were not known to be unused, or objects that another branch
referred to. In practice, everything would have flooded into client repos
without this change.
In my tests, this has to be set when uploading a file to the bucket
and then the file can be accessed using the bucketname.s3.amazonaws.com
url.
Setting it when creating the bucket didn't seem to make the whole bucket
public, or allow accessing files stored in it. But I have gone ahead and
also sent it when creating the bucket just in case that is needed in some
case.
This reverts commit cf650eaa99.
It's too early to do this; the linux and android autobuilder will need to
be updated to use the new version of shakespeare, and that will require a
complete refresh of them. In the meantime, this has knocked the webapp out
of the autobuilders.
This is especially useful because the caller doesn't need to generate valid
url keys, which involves some escaping of characters, and may involve
taking a md5sum of the url if it's too long.
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.
Only the assistant uses these, and only the assistant cleans them up, so
make only git annex transferkeys write them,
There is one behavior change from this. If glacier is being used, and a
manual git annex get --from glacier fails because the file isn't available
yet, the assistant will no longer later see that failed transfer file and
retry the get. Hope no-one depended on that old behavior.
I've tested all the dataenc to sandi conversions except Assistant.XMPP,
and all have unchanged behavior, including behavior on large unicode code
points.
For example, it failed to get files from a bucket named S3.
Also fixes `git annex initremote UPPERCASE type=S3`, which failed with the
new aws library, with a signing error message.
The setDifferences that got added to initialize turns out to make a git
commit, and before ensureCommit has been used. Thus, repo init can fail
when the system has a broken hostname etc.
Move the ensureCommit to the very first thing to avoid this kind of breakage.
The directory special remote was not affected in its normal configuration,
since annex-directory is an absolute path normally. But it could fail
when a relative path was used.
The git remote was affected even when an absolute path to it was used in
.git/config, since git-annex now converts all such paths to relative.
Since we started using this for git repos, when a remote was on another
drive, it resulted in a bogus relative path to it being used by git-annex,
which didn't work.
This is a nearly free feature; it piggybacks on the location log lookups
done for the numcopies stats. So, the only extra overhead is updating
the map of repository sizes.
However, I had to switch to Data.Map.Strict, which needs containers 0.5.
If backporting to wheezy, will probably need to revert this commit.
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
webapp: When adding another local repository, and combining it with the
current repository, the new repository's remote path was set to "." rather
than the path to the current repository. This was a reversion caused by the
relative path changes in 5.20150113.
git-checkignore refuses to work if any pathspec options are set. Urgh.
I audited the rest of git, and no other commands used by git-annex have
such limitations. Indeed, AFAICS, *all* other commands support
--literal-pathspecs. So, worked around this where git-checkignore is
called.
I don't quite understand the cause of the deadlock. It only occurred
when git-annex-shell transferinfo was being spawned over ssh to feed
download transfer progress back. And if I removed this line from
feedprogressback, the deadlock didn't occur:
bytes <- readSV v
The problem was not a leaked FD, as far as I could see. So what was it?
I don't know.
Anyway, this is a nice clean implementation, that avoids the deadlock.
Just fork off the async threads to handle filtering the stdout and stderr,
and let them clean up their handles whenever they decide to exit.
I've verified that the handles do get promptly closed, although a little
later than I would expect. Presumably that "little later" is what
was making waiting on the threads deadlock.
Despite the late exit, the last line of stdout and stderr appears where
I'd want it to, so I guess this is ok..
Stderr reader blocks waiting for all stderr, and so blocks the process ever
exiting.
I tried several ways to get around this, but no success yet. For now,
disable the stderr reader entirely.
New approach is to do it the expensive way for the first 100 paths
on the command line, but then assume the user doesn't care about order too
much and fall back to the cheap way that does not preserve order.
This will only ever result in a few more git-ls-files being run than were run
before. (Only 1 more is really needed, but around 10 more are currently run
for a max length command line.)
So, no need to worry about the extra zombie, or lost laziness due to concat.
Note that previously, `git annex find *.jpg` would find eg, foo/bar.jpg.
That was never intended or documented behavior, so I'm going to change it.
But this is potentially a behavior change if someone discovered that
behavior and relied on it despite it being accidental. Oh well.. can't make
an omlette w/o breaking some eggs.
This was introduced by commit 450ee53ab6
However, the same problem could affect other calls to programPath,
specifically some on the assistant. So, I fixed it at a deeper level.
In this situation, curl -o exits successfully without creating the output
file.
There was already a workaround for curl file:/// but I did not realize this
also affected regular url downloads.
To fix it, pre-create the destination file before starting curl.
Since we cannot always know the size of an url before trying to download
it, let's always do this.
Note that since curl is told -C -, we have to consider if this
makes curl try to do a ranged download, which might fail on some servers
where a regular download would have succeeded. My testing indicates
this isn't a problem; since the file is empty, curl seems to not try to
do a ranged download.
Original report: https://github.com/datalad/datalad/issues/79
Curl bug report: https://github.com/bagder/curl/issues/183
Useful for things like ipfs that don't use regular urls.
An external special remote can add a regular url to a key, and then
git-annex get will download it from the web. But for ipfs, we want to
instead tell git-annex that the uri uses OtherDownloader. Before this
change, the external special remote protocol lacked a way to do that.
Seen for example, a newly checked out git submodule. In this case,
.git/HEAD is a raw sha, rather than the usual reference to a ref.
Removed currentSha in passing, since it was a more roundabout way of
doing what headSha does, and headSha is more robust.
The fix is to stop using w82s, which does not properly reconstitute unicode
strings. Instrad, use utf8 bytestring to get the [Word8] to base64. This
passes unicode through perfectly, including any invalid filesystem encoded
characters.
Note that toB64 / fromB64 are also used for creds and cipher
embedding. It would be unfortunate if this change broke those uses.
For cipher embedding, note that ciphers can contain arbitrary bytes (should
really be using ByteString.Char8 there). Testing indicated it's not safe to
use the new fromB64 there; I think that characters were incorrectly
combined.
For credpair embedding, the username or password could contain unicode.
Before, that unicode would fail to round-trip through the b64.
So, I guess this is not going to break any embedded creds that worked
before.
This bug may have affected some creds before, and if so,
this change will not fix old ones, but should fix new ones at least.
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.
Most of the time, there will be no discreprancy between programPath and
readProgramFile.
But, the programFile might have been written by an old version of git-annex
that is still installed, while a newer one is currently running. In this
case, we want to run the same one that's currently running.
This is especially important for things like the GIT_SSH=git-annex used for
ssh connection caching.
The only code that still uses readProgramFile directly is the upgrade code,
which needs to know where the standalone git-annex was installed, in order to
upgrade it.
See my comment in the bug report for analysis; basically this is safe
because it's a non-forced push, so won't lose history. Even if it was a
forced push or somehow races, things will eventually become consistent and
no git-annex branch info will be lost.
(This used to be done, but it forgot to do it since version 4.20130909.)
* sync: Use the ssh-options git config when doing git pull and push.
* remotedaemon: Use the ssh-options git config.
Note that the rename env var means that if a new git-annex calls an old one
for git-annex ssh, or a new calls an old, nothing much will go wrong;
just ssh caching won't happen.
Note that while the assistant detects changes made to remote names, I left
the commit message fixed rather than calculating it after every commit. It
doesn't seem worth the CPU to do the latter.
hGetSomeString reads one byte at a time, so unicode bytes are not composed.
The problem comes when outputting that to the console with hPut; that
tried to apply the handle's encoding, and so we get mojibake.
Instead, use ByteStrings, and only convert it to a string for parsing, not
for display.
Note that there are a couple of other things that use hGetSomeString,
which I've left as-is for now.
--deduplicate, --skip-duplicates, and --clean-duplicates still checksum the
file twice, the first time to determine if it's a duplicate. This cannot be
easily merged with the checksumming done to add the file, since the file
needs to be locked down before that second checksum is taken.
I hope this doesn't impact speed much -- it does have to pull out a value
from Annex state every time it accesses the branch now.
The test case I dropped has never caught any problems that I can remember,
and would have been rather difficult to convert.
* init: Repository tuning parameters can now be passed when initializing a
repository for the first time. For details, see
http://git-annex.branchable.com/tuning/
* merge: Refuse to merge changes from a git-annex branch of a repo
that has been tuned in incompatable ways.
Avoid using fileSize which maxes out at just 2 gb on Windows.
Instead, use hFileSize, which doesn't have a bounded size.
Fixes support for files > 2 gb on Windows.
Note that the InodeCache code only needs to compare a file size,
so it doesn't matter it the file size wraps. So it has been
left as-is. This was necessary both to avoid invalidating existing inode
caches, and because the code passed FileStatus around and would have become
more expensive if it called getFileSize.
This commit was sponsored by Christian Dietrich.
* info: Can now display info about a given uuid.
* Added to remote/uuid info: Count of the number of keys present
on the remote, and their size. This is rather expensive to calculate,
so comes last and --fast will disable it.
* Git remote info now includes the date of the last sync with the remote.
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.
It's ok to probe every time for git-branch remove because that's
run quite rarely. For git-checkattr, it's run only once, when
starting the --batch mode, and so again the overhead is pretty minimal.
This leaves 2 places where the build version is still used.
git merge might be interactive or fail if one skews, and --no-gpg-sign
might not be pased, or might be passed to a git that doesn't understand it
if the other skews. It seems a little expensive to check the git version
each time these are used.
This doesn't seem likely to cause many problems, at least compared with
check-attr hanging on skew.
In the case where a remote of the bare repo has a fetch = configuration,
refs/remotes/origin/master will exist, and so the merge code path tried to
run in the bare repo.
Getting rid of build warning
warning: 'statfs64' is deprecated: first deprecated in OS X 10.6
[-Wdeprecated-declarations]
10.6 is much older than the oldest git-annex OSX port, so won't break
anything.
More aggressive rsync params fixup for windows. Param may contain a url, or
a file path, so check if it looks like a local file path and if so, fix it
up.
On windows only, rsyncUrlIsPath will treat c:foo as a path, rather than as
a rsyncurl starting with a host "c".
