migrate: Support adding size to URL keys that were added with --relaxed, by
running eg: git-annex migrate --backend=URL foo
Since url keys cannot be generated, that used to fail. Make it notice that
the backend is not changed, and just get the size of the content.
Sponsored-by: Brock Spratlen on Patreon
pull, sync: When operating on content, automatically hard link objects
that have been migrated.
Added annex.syncmigrations config that can be set to false to prevent
pull and sync from migrating object content.
I think that true is a good default for this config, because it avoids
users having to re-download migrated content or learning about migration.
But, some users will surely not like it, whether because it does take some
time (especially for the first git-annex branch scan when there is a long
history), or because they want to deal with it manually, or because their
filesystem doesn't support hard links and they don't want it to copy
objects.
Sponsored-by: k0ld on Patreon
And avoid migrate --update/--aply migrating when the new key was already
present in the repository, and got dropped. Luckily, the location log
allows distinguishing from the new key never having been present!
That is mostly useful for --apply because otherwise dropped files would
keep coming back until the old objects were reaped as unused. But it
seemed to make sense to also do it for --update. for consistency in edge
cases if nothing else. One case where --update can use it is when one
branch got migrated earlier, and we dropped the file, and now another
branch has migrated the same file.
Sponsored-by: Jack Hill on Patreon
This only avoids extra work and a warning messsage. It seems likely that
in such a situation, the user does not want migrations to insecure
hashes, and so best to ignore them as much as possible. If
the user merges a branch that switches annexed files to an insecure
hash, they will notice that the file contents are unavailable,
and git-annex get will tell them the problem then. So it does not seem
useful to have migrate --update also complain about it.
Could use some more testing.
When the old key is not present, Command.ReKey.linkKey' will return
False, so this handles that case ok.
But, I do wonder if distributed migration may need to deal with the old
key getting copied into the repository later. In that situation,
re-running migrate --update won't link it to the new key. It may be that
some users will need that. They can delete .git/annex/migrate.log and
run it again, but that is not a good user interface. Maybe either have
a way to re-run all distributed migrations, or record migrations
in a database and scan the db to find migrations to do in a future run?
Sponsored-by: Kevin Mueller on Patreon
This is most of the way there, but not quite working.
The layout of migrate.tree/ needs to be changed to follow this approach.
git log will list all the files in tree order, so the new layout needs
to alternate old and new keys. Can that be done? git may not document
tree order, or may not preserve it here.
Alternatively, change to using git log --format=raw and extract
the tree header from that, then use
git diff --raw $tree:migrate.tree/old $tree:migrate.tree/new
That will be a little more expensive, but only when there are lots of
migrations.
Sponsored-by: Joshua Antonishen on Patreon
This will allow distributed migration: Start a migration in one clone of
a repo, and then update other clones.
commitMigration is a bit of a bear.. There is some inversion of control
that needs some TMVars. Also streamLogFile's finalizer does not handle
recording the trees, so an interrupt at just the wrong time can cause
migration.log to be emptied but the git-annex branch not updated.
Sponsored-by: Graham Spencer on Patreon
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
The temporary URL key used for the download, before the real key is
generated, was blocked by annex.securehashesonly.
Fixed by passing the Backend that will be used for the final key into
runTransfer. When a Backend is provided, have preCheckSecureHashes
check that, rather than the key being transferred.
Sponsored-by: unqueued on Patreon
--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
While intended for converting URL keys added by addurl --fast to be
as if added by addurl --relaxed, it can also be used to remove size
from other types of keys. Although that is not likely to be useful
for checksummed keys, I suppose it could be used for WORM or other
non-checksum keys.
Specifying the --remove-size option does not prevent other migrations
from taking effect if there's a key upgrade to perform, or if the
backend has changed. So --backend=URL needs to be used to prevent
migrating an URL key to the default backend.
Note that it's not possible to use git-annex migrate to convert from a
non-URL key to an URL key, as URL keys cannot be generated, except by
addurl. So while this can get the same effect as --relaxed would have
when addurl --fast was used, when --fast was not used, it won't work, or
if --backend=URL is not used will remove the size but not prevent
checksum verification, which is not useful. Due to this complexity, I
decided not to mention it in the git-annex addurl man page.
Sponsored-by: Jochen Bartl on Patreon
Before only unlocked files were included.
The initial scan now scans for locked as well as unlocked files. This
does mean it gets a little bit slower, although I optimised it as well
as I think it can be.
reconcileStaged changed to diff from the current index to the tree of
the previous index. This lets it handle deletions as well, removing
associated files for both locked and unlocked files, which did not
always happen before.
On upgrade, there will be no recorded previous tree, so it will diff
from the empty tree to current index, and so will fully populate the
associated files, as well as removing any stale associated files
that were present due to them not being removed before.
reconcileStaged now does a bit more work. Most of the time, this will
just be due to running more often, after some change is made to the
index, and since there will be few changes since the last time, it will
not be a noticable overhead. What may turn out to be a noticable
slowdown is after changing to a branch, it has to go through the diff
from the previous index to the new one, and if there are lots of
changes, that could take a long time. Also, after adding a lot of files,
or deleting a lot of files, or moving a large subdirectory, etc.
Command.Lock used removeAssociatedFile, but now that's wrong because a
newly locked file still needs to have its associated file tracked.
Command.Rekey used removeAssociatedFile when the file was unlocked.
It could remove it also when it's locked, but it is not really
necessary, because it changes the index, and so the next time git-annex
run and accesses the keys db, reconcileStaged will run and update it.
There are probably several other places that use addAssociatedFile and
don't need to any more for similar reasons. But there's no harm in
keeping them, and it probably is a good idea to, if only to support
mixing this with older versions of git-annex.
However, mixing this and older versions does risk reconcileStaged not
running, if the older version already ran it on a given index state. So
it's not a good idea to mix versions. This problem could be dealt with
by changing the name of the gitAnnexKeysDbIndexCache, but that would
leave the old file dangling, or it would need to keep trying to remove
it.
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)
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.
retrieveExport is part of ongoing transition to make remote methods
throw exceptions, rather than silently hide them.
getKey very rarely fails, and when it does it's always for the same reason
(user configured annex.backend to url for some reason). So, this will
avoid dealing with Nothing everywhere it's used.
This commit was sponsored by Ilya Shlyakhter on Patreon.
git-annex find is now RawFilePath end to end, no string conversions.
So is git-annex get when it does not need to get anything.
So this is a major milestone on optimisation.
Benchmarks indicate around 30% speedup in both commands.
Probably many other performance improvements. All or nearly all places
where a file is statted use RawFilePath now.
This will speed up the common case where a Key is deserialized from
disk, but is then serialized to build eg, the path to the annex object.
Previously attempted in 4536c93bb2
and reverted in 96aba8eff7.
The problems mentioned in the latter commit are addressed now:
Read/Show of KeyData is backwards-compatible with Read/Show of Key from before
this change, so Types.Distribution will keep working.
The Eq instance is fixed.
Also, Key has smart constructors, avoiding needing to remember to update
the cached serialization.
Used git-annex benchmark:
find is 7% faster
whereis is 3% faster
get when all files are already present is 5% faster
Generally, the benchmarks are running 0.1 seconds faster per 2000 files,
on a ram disk in my laptop.
No behavior changes, but this shows everywhere that a progress meter
could be displayed when hashing a file to add to the annex.
Many of the places don't make sense to display a progress meter though,
eg when importing the copy of the file probably swamps the hashing of
the file.
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.
In particular, when two files had the same content, and one was unlocked
and modified, with annex.thin that can corrupt the content of the
annex object, and so fsck on the other file should detect that.
getKeyStatus was relying on Database.Keys.getAssociatedFiles to tell
when a file is unlocked, but that can false positive because the
database can list old associated files.
Instead, separate out the case of unlocked object which has multiple
hardlinks when annex.thin is in use.
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.)
* rmurl: Fix a case where removing the last url left git-annex thinking
content was still present in the web special remote.
* SETURLPRESENT, SETURIPRESENT, SETURLMISSING, and SETURIMISSING
used to update the presence information of the external special remote
that called them; this was not documented behavior and is no longer done.
Done by making setUrlPresent and setUrlMissing only update presence info
for the web, and only when the url is a web url. See the comment for
reasoning about why that's the right thing to do.
In AddUrl, had to make it update location tracking, to handle the
non-web-url case.
This commit was sponsored by Ewen McNeill on Patreon.
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 annex.maxextensionlength for use cases where extensions longer than 4
characters are needed.
This commit was sponsored by Henrik Riomar on Patreon.
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.
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.
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.
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.
