Make git-annex get/copy/move --from foo override configuration of
remote.foo.annex-ignore, as documented.
This already worked for remotes supporting hasKeyCheap. For others though,
git-annex copy --from foo would silently not do anything, while
git-annex copy --to foo would use the annex-ignored remote.
Also improved the annex-ignore docs, to reflect that `git-annex get`
without --from will skip using annex-ignored remotes, for example.
Sponsored-by: Dartmouth College's DANDI project
When a nonexistant file is passed to a command and --json-error-messages
is enabled, output a JSON object indicating the problem.
(But git ls-files --error-unmatch still displays errors about such files in
some situations.)
I don't like the duplication of the name of the command introduced by this,
but I can't see a great way around it. One way would be to pass the Command
instead.
When json is not enabled, the stderr is unchanged. This is necessary
because some commands like find have custom output. So dislaying
"find foo not found" would be wrong. So had to complicate things with
toplevelFileProblem having different output with and without json.
When not using --json-error-messages but still using --json, it displays
the error to stderr, but does display a json object without the error. It
does have an errorid though. Unsure how useful that behavior is.
Sponsored-by: Dartmouth College's Datalad project
This does, as a side effect, make long notes in json output not
be indented. The indentation is only needed to offset them
underneath the display of the file they apply to, so that's ok.
Sponsored-by: Brock Spratlen on Patreon
This serves two purposes. --remote=web bypasses other special remotes that
claim the url, same as addurl --raw. And, specifying some other remote
allows making sure that an url is claimed by the remote you expect,
which makes then using setpresentkey not be fragile.
Sponsored-By: the NIH-funded NICEMAN (ReproNim TR&D3) project
Use separate stages for download and upload. In the common case where
it downloads the file from one remote and then uploads to the other,
those are by far the most expensive operations, and there's a decent
chance the two remotes bottleneck on different resources.
Suppose it's being run with -J2 and a bunch of 10 mb files. Two threads
will be started both downloading from the src remote. They will probably
finish at the same time. Then two threads will be started uploading to
the dst remote. They will probably take the same time as well. Before
this change, it would alternate back and forth, bottlenecking on src and dst.
With this change, as soon as the two threads start uploading to dst, two
more threads are able to start, downloading from src. So bandwidth to
both remotes is saturated more often.
Other commands that use transferStages only send in one direction at a
time. So the worker threads for the other direction will sit idle, and
there will be no change in their behavior.
Sponsored-by: Dartmouth College's DANDI project
Prep for move --to --from, which needs to download from a src repo
without updating the location log for the local repo, before sending the
content on to the dest repo.
Note that caller of download' already update the log themselves.
See previous commit a422a056f2
that pushed it up to download from getViaTmpFrom.
(Also removed in passing a debug print + readline that I accidentially
committed last week on this branch.)
Sponsored-by: Dartmouth College's DANDI 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
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
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 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.
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.
No behavior changes (hopefully), just adding SeekInput and plumbing it
through to the JSON display code for later use.
Over the course of 2 grueling days.
withFilesNotInGit reimplemented in terms of seekHelper
should be the only possible behavior change. It seems to test as
behaving the same.
Note that seekHelper dummies up the SeekInput in the case where
segmentPaths' gives up on sorting the expanded paths because there are
too many input paths. When SeekInput later gets exposed as a json field,
that will result in it being a little bit wrong in the case where
100 or more paths are passed to a git-annex command. I think this is a
subtle enough problem to not matter. If it does turn out to be a
problem, fixing it would require splitting up the input
parameters into groups of < 100, which would make git ls-files run
perhaps more than is necessary. May want to revisit this, because that
fix seems fairly low-impact.
This removes all calls to inAnnex, except for some involving --batch.
It may be that the batch code could get a similar speedup, but I don't
know if people habitually pass a huge number of files through --batch
that git-annex does not need to do anything to process, so I skipped it
for now.
A few calls to ifAnnexed remain, and might be worth doing more to
convert. In particular, Command.Sync has one that would probably speed
it up by a good amount.
(also removed some dead code from Command.Lock)
This is only implemented for git-annex get so far. It makes git-annex
get nearly twice as fast in a repo with 10k files, all of them present!
But, see the TODO for some caveats.
Added annex.skipunknown git config, that can be set to false to change the
behavior of commands like `git annex get foo*`, to not skip over files/dirs
that are not checked into git and are explicitly listed in the command
line.
Significant complexity was needed to handle git-annex add, which uses some
git ls-files calls, but needs to not use --error-unmatch because of course
the files are not known to git.
annex.skipunknown is planned to change to default to false in a
git-annex release in early 2022. There's a todo for that.
move --to, copy --to, mirror --to: When concurrency is enabled, run cleanup
actions in separate job pool from uploads.
transferStages was confusingly named, it's only useful when doing downloads
as then the verify actions can be run concurrently with other downloads.
For commands that upload, there will be more concurrency from running
cleanup actions in a separate job pool.
As for sync, I left it using downloadStages although that's not optimal
for the part of a sync that uploads. Perhaps it should use the union of
both?
This means that Command.Move and Command.Get don't need to
manually set the stage, and is a lot cleaner conceptually.
Also, this makes Command.Sync.syncFile use the worker pool better.
In the scenario where it first downloads content and then uploads it to
some other remotes, it will start in TransferStage, then enter VerifyStage
and then go back to TransferStage for each transfer to the remotes.
Before, it entered CleanupStage after the download, and stayed in it for
the upload, so too many transfer jobs could run at the same time.
Note that, in Remote.Git, it uses runTransfer and also verifyKeyContent
inside onLocal. That has a Annex state for the remote, with no worker pool.
So the resulting calls to enteringStage won't block in there.
While Remote.Git.copyToRemote does do checksum verification, I
realized that should not use a verification slot in the WorkerPool
to do it. Because, it's reading back from eg, a removable disk to checksum.
That will contend with other writes to that disk. It's best to treat
that checksum verification as just part of the transer. So, removed the todo
item about that, as there's nothing needing to be done.
Rather than limiting it to PerformStage and CleanupStage, this opens it
up so any number of stages can be added as needed by commands.
Each concurrent command has a set of stages that it uses, and only
transitions between those can block waiting for a free slot in the
worker pool. Calling enteringStage for some other stage does not block,
and has very little overhead.
Note that while before the Annex state was duplicated on the first call
to commandAction, this now happens earlier, in startConcurrency.
That means that seek stage actions should that use startConcurrency
and then modify Annex state won't modify the state of worker threads
they then start. I audited all of them, and only Command.Seek
did so; prepMerge changes the working directory and so has to come
before startConcurrency.
Also, the remote list is built before duplicating the state, which means
that it gets built earlier now than it used to. This would only have an
effect of making commands that end up not needing to perform any actions
unncessary build the remote list (only when they're run with concurrency
enable), but that's a minor overhead compared to commands seeking
through the work tree and determining they don't need to do anything.
get, move, copy, sync: When -J or annex.jobs has enabled concurrency,
checksum verification uses a separate job pool than is used for
downloads, to keep bandwidth saturated.
Not yet done for upload checksum verification, but that only affects
remotes on local disks.
The hoped for optimisation of CommandStart with -J did not materialize.
In fact, not runnign CommandStart in parallel is slower than -J3.
So, CommandStart are still run in parallel.
(The actual bad performance I've been seeing with -J in my big repo
has to do with building the remoteList.)
But, this is still progress toward making -J faster, because it gets rid
of the onlyActionOn roadblock in the way of making CommandCleanup jobs
run separate from CommandPerform jobs.
Added OnlyActionOn constructor for ActionItem which fixes the
onlyActionOn breakage in the last commit.
Made CustomOutput include an ActionItem, so even things using it can
specify OnlyActionOn.
In Command.Move and Command.Sync, there were CommandStarts that used
includeCommandAction, so output messages, which is no longer allowed.
Fixed by using startingCustomOutput, but that's still not quite right,
since it prevents message display for the includeCommandAction run
inside it too.
The goal is to be able to run CommandStart in the main thread when -J is
used, rather than unncessarily passing it off to a worker thread, which
incurs overhead that is signficant when the CommandStart is going to
quickly decide to stop.
To do that, the message it displays needs to be displayed in the worker
thread, after the CommandStart has run.
Also, the change will mean that CommandStart will no longer necessarily
run with the same Annex state as CommandPerform. While its docs already
said it should avoid modifying Annex state, I audited all the
CommandStart code as part of the conversion. (Note that CommandSeek
already sometimes runs with a different Annex state, and that has not been
a source of any problems, so I am not too worried that this change will
lead to breakage going forward.)
The only modification of Annex state I found was it calling
allowMessages in some Commands that default to noMessages. Dealt with
that by adding a startCustomOutput and a startingUsualMessages.
This lets a command start with noMessages and then select the output it
wants for each CommandStart.
One bit of breakage: onlyActionOn has been removed from commands that used it.
The plan is that, since a StartMessage contains an ActionItem,
when a Key can be extracted from that, the parallel job runner can
run onlyActionOn' automatically. Then commands won't need to worry about
this detail. Future work.
Otherwise, this was a fairly straightforward process of making each
CommandStart compile again. Hopefully other behavior changes were mostly
avoided.
In a few cases, a command had a CommandStart that called a CommandPerform
that then called showStart multiple times. I have collapsed those
down to a single start action. The main command to perhaps suffer from it
is Command.Direct, which used to show a start for each file, and no
longer does.
Another minor behavior change is that some commands used showStart
before, but had an associated file and a Key available, so were changed
to ShowStart with an ActionItemAssociatedFile. That will not change the
normal output or behavior, but --json output will now include the key.
This should not break it for anyone using a real json parser.
This does not change the overall license of the git-annex program, which
was already AGPL due to a number of sources files being AGPL already.
Legally speaking, I'm adding a new license under which these files are
now available; I already released their current contents under the GPL
license. Now they're dual licensed GPL and AGPL. However, I intend
for all my future changes to these files to only be released under the
AGPL license, and I won't be tracking the dual licensing status, so I'm
simply changing the license statement to say it's AGPL.
(In some cases, others wrote parts of the code of a file and released it
under the GPL; but in all cases I have contributed a significant portion
of the code in each file and it's that code that is getting the AGPL
license; the GPL license of other contributors allows combining with
AGPL code.)
This is groundwork for nested seek loops, eg seeking over all files and
then performing commandActions on a list of remotes, which can be done
concurrently.
This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
Added -z option to git-annex commands that use --batch, useful for
supporting filenames containing newlines.
It only controls input to --batch, the output will still be line delimited
unless --json or etc is used to get some other output. While git often
makes -z affect both input and output, I don't like trying them together,
and making it affect output would have been a significant complication,
and also git-annex output is generally not intended to be machine parsed,
unless using --json or a format option.
Commands that take pairs like "file key" still separate them with a space
in --batch mode. All such commands take care to support filenames with
spaces when parsing that, so there was no need to change it, and it would
have needed significant changes to the batch machinery to separate tose
with a null.
To make fromkey and registerurl support -z, I had to give them a --batch
option. The implicit batch mode they enter when not provided with input
parameters does not support -z as that would have complicated option
parsing. Seemed better to move these toward using the same --batch as
everything else, though the implicit batch mode can still be used.
This commit was sponsored by Ole-Morten Duesund 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.
Leveraged the existing verification code by making it also check the
retrievalSecurityPolicy.
Also, prevented getViaTmp from running the download action at all when the
retrievalSecurityPolicy is going to prevent verifying and so storing it.
Added annex.security.allow-unverified-downloads. A per-remote version
would be nice to have too, but would need more plumbing, so KISS.
(Bill the Cat reference not too over the top I hope. The point is to
make this something the user reads the documentation for before using.)
A few calls to verifyKeyContent and getViaTmp, that don't
involve downloads from remotes, have RetrievalAllKeysSecure hard-coded.
It was also hard-coded for P2P.Annex and Command.RecvKey,
to match the values of the corresponding remotes.
A few things use retrieveKeyFile/retrieveKeyFileCheap without going
through getViaTmp.
* Command.Fsck when downloading content from a remote to verify it.
That content does not get into the annex, so this is ok.
* Command.AddUrl when using a remote to download an url; this is new
content being added, so this is ok.
This commit was sponsored by Fernando Jimenez on Patreon.
move: Added --safe option, which makes move honor numcopies settings.
Also --unsafe enables the default behavior, anticipating that the
default may one day change.
This commit was sponsored by Ethan Aubin.
Added annex.retry, annex.retry-delay, and per-remote versions to configure
transfer retries.
This commit was supported by the NSF-funded DataLad project.
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.
Clean up some uses of showStart with "" for the file,
or in some cases, a non-filename description string. That would
generate bad json, although none of the commands doing that
supported --json.
Using "" for the file resulted in output like "foo rest";
now the extra space is eliminated.
This commit was sponsored by Fernando Jimenez 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.
After a false start, I found a fairly non-intrusive way to deal with it.
Although it only handles transfers -- there may be issues with eg
concurrent dropping of the same key, or other operations.
There is no added overhead when -J is not used, other than an added
inAnnex check. When -J is used, it has to maintain and check a small
Set, which should be negligible overhead.
It could output some message saying that the transfer is being done by
another thread. Or it could even display the same progress info for both
files that are being downloaded since they have the same content. But I
opted to keep it simple, since this is rather an edge case, so it just
doesn't say anything about the transfer of the file until the other
thread finishes.
Since the deferred transfer action still runs, actions that do more than
transfer content will still get a chance to do their other work. (An
example of something that needs to do such other work is P2P.Annex,
where the download always needs to receive the content from the peer.)
And, if the first thread fails to complete a transfer, the second thread
can resume it.
But, this unfortunately means that there's a risk of redundant work
being done to transfer a key that just got transferred.
That's not ideal, but should never cause breakage; the same
thing can occur when running two separate git-annex processes.
The get/move/copy/mirror --from commands had extra inAnnex checks added,
inside the download actions. Without those checks, the first thread
downloaded the content, and then the second thread woke up and
downloaded the same content redundantly.
move/copy/mirror --to is left doing redundant uploads for now. It
would need a second checkPresent of the remote inside the upload
to avoid them, which would be expensive. A better way to avoid
redundant work needs to be found..
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.
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.
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.
