* map: Run xdot if it's available in PATH. On OSX, the dot command
does not support graphical display, while xdot does.
* Debian: xdot is a better interactive viewer than dot, so Suggest
xdot, rather than graphviz.
The file matcher needs to be run on the destination file not the tmp
file, in order for filename matches to work properly. However, it also
needs to be able to probe the file for size and mime type.
This is a quick fix to a regression. The double rename is not pretty.
It would be good to either have a way to run the largeFileMatcher
such that it is matching on the final filename but looks at the temp
file, or to make addAnnexedFile not need the temp file in a different
location.
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.
This makes merging a remote into a freshly created direct mode repository
work the same as it works in indirect mode.
The git-annex branches would get merged in any case by a sync,
since that doesn't use git merge.
This might need to be revisited later to better mirror git's behavior.
This avoids needing to bind to the right port before something else
does.
The socket is in /var/run/user/$uid/ which ought to be writable by only
that uid. At least it is on linux systems using systemd.
For Windows, may need to revisit this and use ports or something.
The first version of tor to support sockets for hidden services
was 0.2.6.3. That is not in Debian stable, but is available in
backports.
This commit was sponsored by andrea rota.
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.
If a transfer fails for some reason, but some data managed to be sent, the
transfer will be retried. (The assistant already did this.)
Possible impacts:
* More ssh prompts if ssh needs to prompt for a password to connect to a
host, or is prompting about some other problem like a ssh key mismatch.
* More data transfer due to retrying, epecially when a remote does not
support resuming a transfer.
In the worst case, a lot of data will be transferred but it fails before
the end, and then all that data gets transferred again plus one byte more;
repeat until it manages to get the whole file.
Closes https://github.com/datalad/datalad/issues/1020
The use of runWriter in scanUnlockedFiles broke due to this change;
it failed with blocked indefinitely in mvar, because the database write
handle was taken while linkFromAnnex needed to also write to it (to update
the inode cache). So, switched to using a separate runWriter for each call
to addAssociatedFileFast. A little less efficient, but not greatly; the
writes should all still be cached.
In the case where the pointer file is in place, and not the content
of the object, lock's performNew was called with filemodified=True,
which caused it to try to repopulate the object from an unmodified
associated file, of which there were none. So, the content of the object
got thrown away incorrectly. This was the cause (although not the root
cause) of data loss in https://github.com/datalad/datalad/issues/1020
The same problem could also occur when the work tree file is modified,
but the object is not, and lock is called with --force. Added a test case
for this, since it's excercising the same code path and is easier to set up
than the problem above.
Note that this only occurred when the keys database did not have an inode
cache recorded for the annex object. Normally, the annex object would be in
there, but there are of course circumstances where the inode cache is out
of sync with reality, since it's only a cache.
Fixed by checking if the object is unmodified; if so we don't need to
try to repopulate it. This does add an additional checksum to the unlock
path, but it's already checksumming the worktree file in another case,
so it doesn't slow it down overall.
Further investigation found a similar problem occurred when smudge --clean
is called on a file and the inode cache is not populated. cleanOldKeys
deleted the unmodified old object file in this case. This was also
fixed by checking if the object is unmodified.
In general, use of getInodeCaches and sameInodeCache is potentially
dangerous if the inode cache has not gotten populated for some reason.
Better to use isUnmodified. I breifly auited other places that check the
inode cache, and did not see any immediate problems, but it would be easy
to miss this kind of problem.
Fixes a bug introduced with v6 mode that I didn't notice until now.
Probably not many v3 repos left out there, and upgrading them to v6 mode
is not disastrous, only a little premature.
This commit was sponsored by Riku Voipio
* sync: Previously, when run in a branch with a slash in its name,
such as "foo/bar", the sync branch was "synced/bar". That conflicted
with the sync branch used for branch "bar", so has been changed to
"synced/foo/bar".
* adjust: Previously, when adjusting a branch with a slash in its name,
such as "foo/bar", the adjusted branch was "adjusted/bar(unlocked)".
That conflicted with the adjusted branch used for branch "bar",
so has been changed to "adjusted/foo/bar(unlocked)"
* Also, running sync in an adjusted branch did not correctly sync
changes back to the parent branch when it had a slash in its name.
This bug has been fixed.
Eliminate use of Git.Ref.under and Git.Ref.basename; using
Git.Ref.underBase and Git.Ref.base make everything handle deep branches
correctly.
Probably noone was adjusting deep branches, and v6 is still experimental
anyway, so I'm not going to worry about the mess that was left by that bug.
In the case of git-annex sync, using a fixed git-annex with an old unfixed
one will mean they use different sync branches for a deep branch, and so
they may stop syncing until the old one is upgraded. However, that's only
a problem when syncing between repositories without going via a central
bare repository. Added a warning about this to the CHANGELOG, but it's
probably not going to affect many people at all.
This commit was sponsored by Riku Voipio.
Avoid threads emitting json at the same time and scrambling, which was
still possible even with the buffering, just less likely.
Converted json IO actions to JSONChunk data too.
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.
This was disabled in commit 61ccf95004,
because only the assistant used them, and they were clutter. But, now
--failed also uses them.
Remove the failure log files after successful transfers. Should avoid
most of the clutter problems.
Commit 61ccf95004 mentions a subtle behavior
change, which has now been reverted:
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.
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/
metadata --json output format has changed, adding a inner json object
named "fields" which contains only the fields and their values.
This should be easier to parse than the old format, which mixed up
metadata fields with other keys in the json object.
Any consumers of the old format will need to be updated.
This adds a dependency on unordered-containers for parsing MetaData
from JSON, but it's a free dependency; aeson pulls in that library.
Keeping Text.JSON use for now, because it seems a better fit for most of
the commands, which don't use very structured JSON objects, but just output
whatever fields suites them. But this lets Aeson be used when a more
structured data type is available to serialize to JSON.
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.
I noticed move --to failing when there was no disk space. The file was sent
to the remote, but it crashed before it could be dropped locally. This
could fix that.
Added guard in Annex.Transfer to prevent this problem at a deeper level.
I'm unhappy ith NoUUID, but having Maybe UUID instead wouldn't help either
if nothing checked that there was a UUID. Since there legitimately need to
be Remotes that do not have a UUID, I can't see a way to fix it at the type
level, short making there be two separate types of Remotes.
Removed the instance LensGpgEncParams RemoteConfig because it encouraged
code that does not take the RemoteGitConfig into account.
RemoteType's setup was changed to take a RemoteGitConfig,
although the only place that is able to provide a non-empty one is
enableremote, when it's changing an existing remote. This led to several
folow-on changes, and got RemoteGitConfig plumbed through.
There's a potential race where the smudge filter is run at the same time an
object is being downloaded. If the download finished after the inAnnex
check, and before the keys db was updated, the associated file would not
get updated with the downloaded content.
I'm not sure this closes the race; it may only narrow the window. Problem
is, the keys database needs to communicate between two different processes.
In the case of the assistant, the transferkeys command is the other
process, and it closes the db handle after getting the file. So, it should
re-open the database and so see the update that the smudge filter has
written to it. But, what if the smudge filter takes a while to update the
database?
The keys database handle needs to be closed after merging, because the
smudge filter, in another process, updates the database. Old cached info
can be read for a while from the open database handle; closing it ensures
that the info written by the smudge filter is available.
This is pretty horribly ad-hoc, and it's especially nasty that the
transferrer closes the database every time.
Could not think of a foolproof way to detect if the old adjusted branch was
just behind the current branch. It's possible that the user amended the
adjusting commit at the head of the adjusted branch, for example.
I decided to bail in this situation, instead of just entering the old
branch, so that if git annex adjust succeeds the user is always in a
*current* adjusted branch, not some old and out of date one.
What could perhaps be done is enter the old branch and then update it. But
that seems too magical; the user may have rebased master or something or
may not want to propigate the changes from the old branch. Best to error
out.
git 2.8.1 (or perhaps 2.9.0) is going to prevent git merge from merging in
unrelated branches. Since the webapp's pairing etc features often combine
together repositories with unrelated histories, work around this behavior
change by setting GIT_MERGE_ALLOW_UNRELATED_HISTORIES when the assistant
merges.
Note though that this is not done for git annex sync's merges, so
it will follow git's default or configured behavior.
When git-annex is used with a git version older than 2.2.0, disable support for
adjusted branches, since GIT_COMMON_DIR is needed to update them and was first
added in that version of git.
Made all Annex.Perms file mode changing functions ignore errors when
core.sharedRepository is set, because the file might be owned by someone
else. I don't fancy getting bug reports about crashes due to set modes in
this configuration, which is a very foot-shooty configuration in the first
place.
The fsck warning is necessary because old repos kept files mode 444, which
doesn't allow locking them, and so if the mode remains 444 due to the file
being owned by someone else, the user should be told about it.
When annex.thin is set, adding an object will add the execute bits to the
work tree file, and this does mean that the annex object file ends up
executable.
This doesn't add any complexity that wasn't already present, because git
annex add of an executable file has always ingested it so that the annex
object ends up executable.
But, since an annex object file can be executable or not, when populating
an unlocked file from one, the executable bit is always added or removed
to match the mode of the pointer file.
This is how direct mode does it too, and somehow, for reasons that
currently escape me, this makes git merge not care if it's run with an
empty work tree.
Rationalle: User might have hook scripts whose output they want to see.
Also, git commit output may tell the user they forgot to add a file.
The output is not too ugly when there's nothing to commit.
An unlocked present file does not have a pointer file in the worktree, so
info skipped counting it.
It may be that unused was also affected by the problem, but it seemed not
to be in my tests. I think because of the use of the associatedFilesFilter.
This fix slows down both info and unused a little bit, since they have to
query the contents of files from git, but only when handling unlocked files.
So, it will pull and push the original branch, not the adjusted one.
And, for merging, it will use updateAdjustedBranch (not implemented yet).
Note that remaining uses of Git.Branch.current need to be checked too;
for things that should act on the original branch, and not the adjusted
branch.
"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.
* add, addurl, import, importfeed: When in a v6 repository on a crippled
filesystem, add files unlocked.
* annex.addunlocked: New configuration setting, makes files always be
added unlocked. (v6 only)
The type checker should have noticed this, but the changes to mapM
that make it accept any Traversable hid the fact that it was not being
passed a list at all. Thus, what should have returned an empty list most
of the time instead returned [""] which was treated as the name of the
associated file, with disasterout consequences.
When I have time, I should add a test case checking what sync --content
drops. I should also consider replacing mapM with one re-specialized to
lists.
* 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.
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
