Commit graph

500 commits

Author SHA1 Message Date
Joey Hess
b646a85c4a
oops, fixed wrong change 2019-05-23 12:44:27 -04:00
Joey Hess
e1aa8b9001
avoid build failure with older base 2019-05-23 12:16:57 -04:00
Joey Hess
16a2bed710
avoid build warning on Windows about unused import 2019-05-23 12:15:33 -04:00
Joey Hess
e06feb7316
honor preferred content when importing
Importing from a special remote honors its preferred content too; unwanted
files are not imported. But, some preferred content expressions can't be
checked before files are imported, and trying to import with such an
expression will fail.

Tested this with scenarios including changing the preferred content
expression and making sure merging the import didn't delete files that were
no longer wanted.

There was one minor inefficiency mentioned in the todo that I punted on.
2019-05-21 14:38:06 -04:00
Joey Hess
97fd9da6e7
add back non-preferred files to imported tree
Prevents merging the import from deleting the non-preferred files from
the branch it's merged into.

adjustTree previously appended the new list of items to the old, which
could result in it generating a tree with multiple files with the same
name. That is not good and confuses some parts of git. Gave it a
function to resolve such conflicts.

That allowed dealing with the problem of what happens when the import
contains some files (or subtrees) with the same name as files that were
filtered out of the export. The files from the import win.
2019-05-20 16:43:52 -04:00
Joey Hess
354c0eb57f
support standard and groupwanted in keyless mode
Only when the preferred content expression includes them will a parse
failure due to them needing keys result in the preferred content
expression not parsing in keyless mode.
2019-05-14 14:59:03 -04:00
Joey Hess
9411a7c93c
matching preferred content before key is known
This will let import try to match preferred content expressions before
downloading the content and generating its key.

If an expression needs a key, it preferredContentParser with
preferredContentKeylessTokens will fail to parse it.

standard and groupwanted are not in preferredContentKeylessTokens
because they may refer to an expression that refers to a key.
That needs further work to support them.
2019-05-14 14:28:23 -04:00
Joey Hess
aa7710982b
avoid list lookup by parseToken
Minor optimisation to parsing of a preferred content expression.
2019-05-14 13:11:29 -04:00
Joey Hess
40ecf58d4b
update licenses from GPL to AGPL
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.)
2019-03-13 15:48:14 -04:00
Joey Hess
ee251b2e2e
implement updating the ContentIdentifier db with info from the git-annex branch
untested

This won't be super slow, but it does need to diff two likely large
trees, and since the git-annex branch rarely sits still, it will most
likely be run at the beginning of every import.

A possible speed improvement would be to only run this when the database
did not contain a ContentIdentifier. But that would only speed up
imports when there is no new version of a file on the special remote,
at most renames of existing files being imported.

A better speed improvement would be to record something in the git-annex
branch that indicates when an import has been run, and only do the diff
if the git-annex branch has record of a newer import than we've seen
before. Then, it would only run when there is in fact new
ContentIdentifier information available from a remote. Certianly doable,
but didn't want to complicate things yet.
2019-03-06 18:04:30 -04:00
Joey Hess
1b3d04979e
speed up slow quickcheck test
Only test parsing of ContentIdentifier lists, not the whole log.
2019-03-06 16:43:41 -04:00
Joey Hess
6ef38df881
fix another parser bug 2019-03-06 14:51:31 -04:00
Joey Hess
c0bd202147
fix failing test case
An empty list of [ContentIdenfier] serialized to the same thing
as a single ContentIdentifier "". Avoid this ambiguity by requiring the
list be non-empty.
2019-03-06 14:27:15 -04:00
Joey Hess
b0fe4916b7
forgot to change list delimiter in parser 2019-03-06 11:59:42 -04:00
Joey Hess
7af55de83c
optimisation: use graftTree to remember the export branch
Sped up git-annex export in repositories with lots of keys.

Old method read whole git-annex branch tree into memory.
2019-02-22 11:16:22 -04:00
Joey Hess
56137ce0d2
use colon not space to delimit content identifier list
InodeCache serializes to a value with spaces, and seems likely other
things will too, and want to avoid unncessary base64 of content
identifiers when possible.
2019-02-21 13:45:16 -04:00
Joey Hess
1f6339ade7
fix parsing of empty content identifier
Seems very unlikely an empty content identifier would be used, but
quickcheck found this bug.
2019-02-21 13:44:09 -04:00
Joey Hess
9887a378fe
renamings to make clean when old-format logs are being used 2019-02-21 13:43:44 -04:00
Joey Hess
936aee6a60
quickcheck property for parsing of content identifier logs 2019-02-21 13:17:43 -04:00
Joey Hess
5a294f0dd7
add Logs.ContentIdentifier 2019-02-20 17:22:56 -04:00
Joey Hess
a818bc5e73
add Database.ContentIdentifier
Does not yet have a way to update with new information from the
git-annex branch, which will be needed when multiple repos are importing
from the same remote.
2019-02-20 16:59:10 -04:00
Joey Hess
e8bfc3640b
storing ContentIdentifier in the git-annex branch 2019-02-20 15:40:07 -04:00
Joey Hess
ad1d422dd7
fix false positive in export conflict detection
Like the earlier fixed one in Command.Export, it occurred when the same
tree was exported by multiple clones. Previous fix was incomplete since
several other places looked at the list of exported trees to detect when
there was an export conflict. Added a single unified function to avoid
missing any places it needed to be fixed.

This commit was sponsored by mo on Patreon.
2019-01-30 12:36:30 -04:00
Joey Hess
d913961b7b
avoid shadowing warning 2019-01-21 20:40:30 -04:00
Joey Hess
b79ef475ac
still fixing this sigh 2019-01-21 18:39:25 -04:00
Joey Hess
f603fc252d
fixed a different way this test case could fail in LANG=C 2019-01-21 16:46:40 -04:00
Joey Hess
0aea1a7b93
fix inverted logic 2019-01-21 15:41:35 -04:00
Joey Hess
e15d18058b
add back exclusion of whitespace and = 2019-01-21 12:38:00 -04:00
Joey Hess
928e08904d
avoid two test failures with LANG=C
Log.Remote.prop_parse_show_Config failed on an input of fromList [("\28162","")]
in LANG=C, encodeBS "\28162" == "\STX=", while in UTF-8 locale,
encodeBS "\28162" == "\230\184\130". So in the C locale, the String
that's the parsed Map key ends up being encoded differently than it was
in the input Map.

Logs.Presence.Pure.prop_parse_build_log was failing in LANG=C because
the Arbitrary LogLine for some reason sometimes generated LogInfo values
containing \n or \r, despite using suchThat to prevent that. I don't
understand why at all, but switching the suchThat to filter the
ByteString instead of the String before conversion with encodeBS
somehow avoids the problem.

Both of these suggest something wonky with encodeBS in LANG=C, but
I *think* it's not a problem except for with test data generated by
Arbitrary.
2019-01-18 13:33:48 -04:00
Joey Hess
d3ab5e626b
rename key2file and file2key
What these generate is not really suitable to be used as a filename,
which is why keyFile and fileKey further escape it. These are just
serializing Keys.

Also removed a quickcheck test that was very unlikely to test anything
useful, since it relied on random chance creating something that looks
like a serialized key. The other test is sufficient for testing what
that was intended to test anyway.
2019-01-14 13:03:35 -04:00
Joey Hess
2eadb6cd68
convert transitions.log to attoparsec and bytestring-builder
Not likely to be any speed gain here, but this completes porting every
log file over.

And, it let me get rid of code copied from ghc and modified, so
simplifying the licensing.
2019-01-10 17:13:30 -04:00
Joey Hess
591e4b145f
convert old uuid-based log parsers to attoparsec
This preserves the workaround for the old bug that caused NoUUID items
to be stored in the log, prefixing log lines with " ". It's now handled
implicitly, by using takeWhile1 (/= ' ') to get the uuid.

There is a behavior change from the old parser, which split the value
into words and then recombined it. That meant that "foo  bar" and "foo\tbar"
came out as "foo bar". That behavior was not documented, and seems
surprising; it meant that after a git-annex describe here "foo  bar",
you wouldn't get that same string back out when git-annex displayed repo
descriptions.

Otoh, some other parsers relied on the old behavior, and the attoparsec
rewrites had to deal with the issue themselves...

For group.log, there are some edge cases around the user providing a
group name with a leading or trailing space. The old parser would ignore
such excess whitespace. The new parser does too, because the alternative
is to refuse to parse something like " group1  group2 " due to excess
whitespace, which would be even more confusing behavior.

The only git-annex branch log file that is not converted to attoparsec
and bytestring-builder now is transitions.log.
2019-01-10 16:34:20 -04:00
Joey Hess
66603d6f75
attoparsec parsers for all new-format uuid-based logs
There should be some speed gains here, especially for chunk and remote
state logs, which are queried once per key.

Now only old-format uuid-based logs still need to be converted to attoparsec.
2019-01-10 13:30:36 -04:00
Joey Hess
7e54c215b4
Remove redundant endOfInput
parseLogLines consumes till endOfInput
2019-01-10 12:42:59 -04:00
Joey Hess
6f66b53a30
newtype Group to ByteString
This may speed up queries for things in groups, due to Eq and Ord being faster.
2019-01-09 15:05:49 -04:00
Joey Hess
2fef43dd71
convert all per-uuid log files to use Builder
Mostly didn't push the ByteStrings down very deep, but all of these log
files are not written to frequently at all, so slight remaining
innefficiency doesn't matter.

In Logs.UUID, removed the fixBadUUID code that cleaned up after a bug in
git-annex versions 3.20111105-3.20111110. In the unlikely event that a repo was
last touched by that ancient git-annex version, the descriptions of remotes
would appear missing when used with this version of git-annex. That is such minor
breakage, and so unlikely to still be a problem for any repos, that it was not
worth forward-porting that code to ByteString.
2019-01-09 14:00:35 -04:00
Joey Hess
de4980ef85
simplify Show instance by deriving 2019-01-09 13:13:31 -04:00
Joey Hess
11f4d993b5
fix format of show instance
It's only used to show test suite failures..
2019-01-09 13:12:25 -04:00
Joey Hess
2d46038754
converting more log files to use Builder
Probably not any particular speedup in this, since most of these logs
are not written to often. Possibly chunk log writing is sped up, but
writes to chunk logs are interleaved with expensive data transfers to
remotes, so unlikely to be a noticiable speedup.
2019-01-09 13:06:37 -04:00
Joey Hess
cb375977a6
follow-on changes from MetaData type changes
Including writing and parsing the metadata log files with
bytestring-builder and attoparsec.
2019-01-07 15:51:05 -04:00
Joey Hess
ef8ddaa713
attoparsec parser for presence logs 2019-01-03 15:27:29 -04:00
Joey Hess
bfc9039ead
convert git-annex branch access to ByteStrings and Builders
Most of the individual logs are not converted yet, only presense logs
have an efficient ByteString Builder implemented so far. The rest
convert to and from String.
2019-01-03 13:21:48 -04:00
Joey Hess
7d51b0c109
import Utility.FileSystemEncoding in Common 2019-01-03 11:37:02 -04:00
Joey Hess
894716512d
add a UUIDDesc type containing a ByteString
Groundwork for handling uuid.log using ByteString
2019-01-01 16:17:54 -04:00
Joey Hess
9cc6d5549b
convert UUID from String to ByteString
This should make == comparison of UUIDs somewhat faster, and perhaps a
few other operations around maps of UUIDs etc.

FromUUID/ToUUID are used to convert String, which is still used for all
IO of UUIDs. Eventually the hope is those instances can be removed,
and all git-annex branch log files etc use ByteString throughout, for a
real speed improvement.

Note the use of fromRawFilePath / toRawFilePath -- while a UUID usually
contains only alphanumerics and so could be treated as ascii, it's
conceivable that some git-annex repository has been initialized using
a UUID that is not only not a canonical UUID, but contains high unicode
or invalid unicode. Using the filesystem encoding avoids any problems
with such a thing. However, a NUL in a UUID seems extremely unlikely,
so I didn't use encodeBS / decodeBS to avoid their extra overhead in
handling NULs.

The Read/Show instance for UUID luckily serializes the same way for
ByteString as it did for String.
2019-01-01 14:45:33 -04:00
Joey Hess
9127fe4821
add DebugLocks build flag
Using the method described in
https://www.fpcomplete.com/blog/2018/05/pinpointing-deadlocks-in-haskell
but my own code to implement it, and with callstacks added.

This work is supported by the NIH-funded NICEMAN (ReproNim TR&D3) project.
2018-11-19 15:02:43 -04:00
Joey Hess
2e9f128dea
moved module and relicensed 2018-10-29 23:13:36 -04:00
Joey Hess
917a2c6095
defer updating unlocked files until after smudge filter
The smuge filter no longer provides git with annexed file content, to
avoid a git memory leak, and because that did not honor annex.thin.

git annex smudge --update has to be run after a checkout to update
unlocked files in the working tree with annexed file contents.

No hooks yet to run it.

This commit was sponsored by Nick Piper on Patreon.
2018-10-25 15:08:20 -04:00
Joey Hess
451171b7c1
clean up url removal presence update
* 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.
2018-10-04 17:35:49 -04:00
Joey Hess
0a7c5a9982
dropdead per-remote metadata
Had to refactor pure code into separate modules so it is accessible
inside Annex.Branch.Transitions.

This commit was sponsored by Peter on Patreon.
2018-09-05 13:52:46 -04:00
Joey Hess
b3d42283ad
use per-remote metadata storage for S3 version ID
Since the same key can be stored in a versioned S3 bucket multiple times
with different version IDs, this allows tracking them all. Not currently
needed, but if we ever want to drop from a versioned S3 bucket, we'll
need to know them all.

This commit was supported by the NSF-funded DataLad project.
2018-08-31 13:27:29 -04:00
Joey Hess
5c99f6247e
per-remote metadata storage
Actually very straightforward reuse of the metadata log file code.
Although I had to add a todo item as git-annex forget won't clean up
dead remote's metadata yet.

This would be worth adding to the external special remote interface
sometime. Have not opened a todo though, guess I'll wait until something
needs it.

This commit was supported by the NSF-funded DataLad project.
2018-08-31 12:23:22 -04:00
Joey Hess
358178fbfb
don't untrust appendonly exports
Make exporttree=yes remotes that are appendonly not be untrusted, and not force
verification of content, since the usual concerns about losing data when an
export is updated by someone else don't apply.

Note that all the remote operations on keys are left as usual for
appendonly export remotes, except for storing content.

This commit was supported by the NSF-funded DataLad project.
2018-08-30 11:48:04 -04:00
Joey Hess
10138056dc
v6: avoid accidental conversion when annex.largefiles is not configured
v6: When annex.largefiles is not configured for a file, running git add or
git commit, or otherwise using git to stage a file will add it to the annex
if the file was in the annex before, and to git otherwise. This is to avoid
accidental conversion.

Note that git-annex add's behavior has not changed, for reasons explained
in the added comment.

Performance: No added overhead when annex.largefiles is configured.
When not configured, there is an added call to catObjectMetaData,
which involves a round trip through git cat-file --batch.
However, the earlier catKeyFile primes the cache for it.

This commit was supported by the NSF-funded DataLad project.
2018-08-27 14:51:10 -04:00
Joey Hess
ae11394efa
added annex.commitmessage
Added annex.commitmessage config that can specify a commit message for the
git-annex branch instead of the usual "update".

This commit was supported by the NSF-funded DataLad project.
2018-08-02 14:06:06 -04:00
Joey Hess
2fc768ce72
avoid git annex info remote buffering list of keys
This leaves git annex unused --from remote still using loggedKeysFor
and buffering more than ought to be necessary, but I can't see a way to
improve that.
2018-04-26 16:13:05 -04:00
Joey Hess
bea0ad220a
avoid --all buffering list of all keys
In Annex.Branch.branch, the (++) was killing laziness.
Rewrote so it streams lazily.

filterM also kills laziness, so made loggedKeys use a Unchecked type,
and check if the key is dead in the seek loop.

Note that loggedKeysFor still buffers, so git-annex info <remote> and
git-annex unused --from remote still use more memory than necessary.

Also removed some unused functions from Annex.Journal.
2018-04-26 16:00:20 -04:00
Joey Hess
256d8f07e8
avoid insertWith' depreaction warning
Switch to Data.Map.Strict everywhere that used it.

There are still lots of lazy maps in git-annex. I think switching these
is safe. The risk is that there might be a map that is used in a way
that relies on the values not being evaluated to WHNF, and switching to
strict might result in bad performance or memory use. So, I have not
switched everything.
2018-04-22 13:28:31 -04:00
Joey Hess
f56594af9e
finish fixing inverted Ord for TrustLevel
Flipped all comparisons. When a TrustLevel list was wanted from Trusted
downwards, used Down to compare it in that order.

This commit was sponsored by mo on Patreon.
2018-04-13 15:17:54 -04:00
Joey Hess
a0e4b9678b
fix inverted Ord for TrustLevel (intermediate commit)
This commit removes the Ord and Enum instances, commenting out all code
that depends on them, to make sure that all code effected by the
inversion fix has been identified.

(Assuming no ifdefs involve TrustLevel.)

The next commit will fix up all the identified code.
2018-04-13 14:50:14 -04:00
Joey Hess
10d3b7fc62
Fix reversion introduced in 6.20171214 that caused concurrent transfers to incorrectly fail with "transfer already in progress".
Avoid creating transfer info file before transfer lock is created and
locked.

The wrong order for one thing caused transfer info to be overwritten
when a transfer was already in progress.

But worse, it caused checkTransfer to see the transfer info,
and so lock the transfer lock in order to verify the transfer was not in
progress. Which in a concurrent situation, prevented the transferrer
from locking the transfer lock, so it failed with "transfer already in
progress".

Note that the transferinfo command does not lock the transfer lock
before creating the transfer info. But, that's only run after
recvkey is running, and recvkey does lock the transfer lock, so that
seems more or less ok. (Other than being a super complicated legacy mess
that the P2P code has mostly obsoleted now.)

This commit was supported by the NSF-funded DataLad project.
2018-03-14 18:55:34 -04:00
Joey Hess
faf03ee4da
more core.sharedRepository perm fixes
Fix more places where files in .git/annex/ were written with modes that
did not take the core.sharedRepository config into account.

This commit was sponsored by Jeff Goeke-Smith on Patreon.
2018-01-04 14:46:58 -04:00
Joey Hess
24df95f0f6
Fix several places where files in .git/annex/ were written with modes that did not take the core.sharedRepository config into account.
git grep writeFile finds some more that might also be problems, but
for now I've concentrated on .git/annex/ log files. There are certianly
cases where writeFile is not a problem too.

This commit was sponsored by mo on Patreon.
2018-01-02 17:25:25 -04:00
Joey Hess
edd25f04d9
unused: Write .git/annex/unused etc files with appropriate permissions for the core.sharedRepository config.
This commit was sponsored by an anonymous bitcoin donor.
2018-01-02 16:25:27 -04:00
Joey Hess
4e38c4f57f
Allow exporttree remotes to be marked as dead.
Union with max so that DeadTrusted wins over UnTrusted.

This commit was sponsored by Trenton Cronholm on Patreon.
2017-12-05 13:46:55 -04:00
Joey Hess
3febb79c8f
wip 2017-11-28 17:17:40 -04:00
Joey Hess
7ad1d3210f
remove dead code 2017-11-07 14:18:10 -04:00
Joey Hess
e1ac299ad0
better dup key with -J fix
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.
2017-10-17 18:48:53 -04:00
Joey Hess
68a49adcda
Improve behavior when -J transfers multiple files that point to the same key
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.
2017-10-17 17:10:50 -04:00
Joey Hess
099bfc2daf
remove redundant definition of lck 2017-10-03 13:23:10 -04:00
Joey Hess
3cd47f9978
info: Improve cleanup of stale transfer info files.
In my git-annex repos, I found some stale transfer info files
without lock files.

Pass a mode to tryLockExclusive, so it will create the lock file if
not present, and so not fail to clean up such transfer info files.

Normally, transfer info files are accompanied by a lock file.
But, when alwaysRunTransfer is used, the locking can fail
and it will still write the transfer info file. Perhaps there are other
cases too? Note that mkProgressUpdater's meter
writes to the transfer info file too, and it might be possible for
that meter to fire after runTransfer has cleaned up.

This commit was sponsored by andrea rota.
2017-10-02 13:55:26 -04:00
Joey Hess
4d0e522b72
Warn when metadata is inherited from a previous version of a file
to avoid the user being surprised in cases where that behavior is not desired or expected

This commit was supported by the NSF-funded DataLad project.
2017-09-28 12:56:35 -04:00
Joey Hess
b31d682539
cleanup imports 2017-09-13 12:53:19 -04:00
Joey Hess
f8fd66d3f8
fix compaction of export.log
It was not getting old lines removed, because the tree graft confused
the updater, so it union merged from the previous git-annex branch,
which still contained the old lines. Fixed by carefully using setIndexSha.

This commit was supported by the NSF-funded DataLad project.
2017-09-12 18:30:36 -04:00
Joey Hess
c8ed941a26
change export.log format to support multiple export remotes
This breaks backwards compatibility, but only with unreleased versions of
git-annex, which I think is acceptable.

This commit was supported by the NSF-funded DataLad project.
2017-09-12 17:45:52 -04:00
Joey Hess
9c3622882b
export: cache connections for S3 and webdav 2017-09-12 16:59:04 -04:00
Joey Hess
8de516ad2c
leave export logged as incomplete if initial renames fail
This way, the temp files that might be left due to failure will be
cleaned up next time.

Also, nub the list of incomplete exports to avoid repeatedly adding the
same tree to it when running export repeatedly when it's failing.

This commit was supported by the NSF-funded DataLad project.
2017-09-12 14:21:15 -04:00
Joey Hess
16eb2f976c
prevent exporttree=yes on remotes that don't support exports
Don't allow "exporttree=yes" to be set when the special remote
does not support exports. That would be confusing since the user would
set up a special remote for exports, but `git annex export` to it would
later fail.

This commit was supported by the NSF-funded DataLad project.
2017-09-07 13:48:44 -04:00
Joey Hess
0fa948b402
record incomplete exports in export.log
Not yet used, but essential for resuming cleanly.

Note that, in normmal operation, only one commit is made to export.log
during an export; the incomplete version only gets to the journal and
is then overwritten.

This commit was supported by the NSF-funded DataLad project.
2017-09-06 13:45:03 -04:00
Joey Hess
662f2a5ee7
git annex get from exports
Straightforward enough, except for the needed belt-and-suspenders sanity
checks to avoid foot shooting due to exports not being key/value stores.

* Even when annex.verify=false, always verify from exports.
* Only get files from exports that use a backend that supports
  checksum verification.
* Never trust exports, even if the user says to, because then
  `git annex drop` would drop content if the export seemed to contain
  a copy.

This commit was supported by the NSF-funded DataLad project.
2017-09-04 16:39:56 -04:00
Joey Hess
5483ea90ec
graft exported tree into git-annex branch
So it will be available later and elsewhere, even after GC.

I first though to use git update-index to do this, but feeding it a line
with a tree object seems to always cause it to generate a git subtree
merge. So, fell back to using the Git.Tree interface to maniupulate the
trees, and not involving the git-annex branch index file at all.

This commit was sponsored by Andreas Karlsson.
2017-08-31 18:06:49 -04:00
Joey Hess
978885247e
implement export.log and resolve export conflicts
Incremental export updates work now too.

This commit was sponsored by Anthony DeRobertis on Patreon.
2017-08-31 15:47:23 -04:00
Joey Hess
0b307f43e1
avoid accidental Show of VectorClock
Removed its Show instance.
2017-08-14 14:51:54 -04:00
Joey Hess
2cecc8d2a3
Added GIT_ANNEX_VECTOR_CLOCK environment variable
Can be used to override the default timestamps used in log files in the
git-annex branch. This is a dangerous environment variable; use with
caution.

Note that this only affects writing to the logs on the git-annex branch.
It is not used for metadata in git commits (other env vars can be set for
that).

There are many other places where timestamps are still used, that don't
get committed to git, but do touch disk. Including regular timestamps
of files, and timestamps embedded in some files in .git/annex/, including
the last fsck timestamp and timestamps in transfer log files.

A good way to find such things in git-annex is to get for getPOSIXTime and
getCurrentTime, although some of the results are of course false positives
that never hit disk (unless git-annex gets swapped out..)

So this commit does NOT necessarily make git-annex comply with some HIPPA
privacy regulations; it's up to the user to determine if they can use it in
a way compliant with such regulations.

Benchmarking: It takes 0.00114 milliseconds to call getEnv
"GIT_ANNEX_VECTOR_CLOCK" when that env var is not set. So, 100 thousand log
files can be written with an added overhead of only 0.114 seconds. That
should be by far swamped by the actual overhead of writing the log files
and making the commit containing them.

This commit was supported by the NSF-funded DataLad project.
2017-08-14 14:19:58 -04:00
Joey Hess
bcf276655c
Keys marked as dead are now skipped by --all.
fsck already special-cased dead keys to make --all not report errors with
them, and it makes sense to also expand that to whereis. I think it makes
sense for dead keys to be skipped by all uses of --all, so mistakes can be
completely forgotten about and not come back to haunt us.

The speed impact of testing if the key is dead is negligible for fsck and
whereis, since they use the location log anyway and it gets cached.
This does slow down a few commands that support --all, in particular
metadata --all runs around 2x as slow. I don't think metadata
--all is often used though. It might slow down copy/move/mirror
--all and get --all.
log --all is not affected (does not use the normal --all machinery).

Dead keys will still be processed by --incomplete, --branch,
--failed, and --key. Although it would be unlikely for a dead key to
ave in incomplete or failed transfer. It seems to make perfect sense for
--branch to process keys on the branch, even if dead.

(fsck's special-casing of dead keys was left in, so if one of these options
causes a dead key to be fscked, there will be a nice message.)

This commit was supported by the NSF-funded DataLad project.
2017-05-09 12:55:21 -04:00
Joey Hess
c3970f6c1a
multicast: New command, uses uftp to multicast annexed files, for eg a classroom setting.
This commit was supported by the NSF-funded DataLad project.
2017-03-30 19:35:30 -04:00
Joey Hess
1c4e5f65fc
Drop support for building with old versions of directory, feed, and http-types. 2017-03-10 15:57:41 -04:00
Joey Hess
c8e1e3dada
AssociatedFile newtype
To prevent any further mistakes like 301aff34c4

This commit was sponsored by Francois Marier on Patreon.
2017-03-10 13:35:31 -04:00
Joey Hess
27eca014be
fix up Read instance incompatability caused by recent commit
9c4650358c changed the Read instance for
Key.

I've checked all uses of that instance (by removing it and seeing what
breaks), and they're all limited to the webapp, except one.
That is GitAnnexDistribution's Read instance.

So, 9c4650358c would have broken upgrades
of git-annex from downloads.kitenet.net. Once the .info files there got
updated for a new release, old releases would have failed to parse them
and never upgraded.

To fix this, I found a way to make the .info files that contain
GitAnnexDistribution values be readable by the old version of git-annex.

This commit was sponsored by Ewen McNeill.
2017-02-24 18:59:12 -04:00
Joey Hess
ed56dba868
annex.autocommit can be configured via git-annex config
... 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.
2017-02-03 13:58:53 -04:00
Joey Hess
9eb10caa27
Some optimisations to string splitting code.
Turns out that Data.List.Utils.split is slow and makes a lot of
allocations. Here's a much simpler single character splitter that behaves
the same (even in wacky corner cases) while running in half the time and
75% the allocations.

As well as being an optimisation, this helps move toward eliminating use of
missingh.

(Data.List.Split.splitOn is nearly as slow as Data.List.Utils.split and
allocates even more.)

I have not benchmarked the effect on git-annex, but would not be surprised
to see some parsing of eg, large streams from git commands run twice as
fast, and possibly in less memory.

This commit was sponsored by Boyd Stephen Smith Jr. on Patreon.
2017-01-31 19:06:22 -04:00
Joey Hess
5676d267b5
forgot to add this new source file 2017-01-30 17:36:45 -04:00
Joey Hess
26d23e38f1
vicfg: Include the numcopies configuation.
Docs say vicfg can configure everything from git-annex branch,
so it ought to configure numcopies.

Note that commenting out existing numcopies does not unset it.

This commit was sponsored by Thom May on Patreon.
2017-01-30 15:27:25 -04:00
Joey Hess
8484c0c197
Always use filesystem encoding for all file and handle reads and writes.
This is a big scary change. I have convinced myself it should be safe. I
hope!
2016-12-24 14:46:31 -04:00
Joey Hess
0a4479b8ec
Avoid backtraces on expected failures when built with ghc 8; only use backtraces for unexpected errors.
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.
2016-11-15 21:29:54 -04:00
Joey Hess
7cae6c746c
Optimised git-annex branch log file timestamp parsing. 10% speedup
This sped up git annex find --not --in web from 6.64s to 5.69s.
The optimised parser is probably more like 50% faster than the general one
it replaced.
2016-09-29 14:04:53 -04:00
Joey Hess
c9082cf0e4
move Arbitrary instance to new Types.Transfer module
Avoid orphan instance warning
2016-09-05 14:52:06 -04:00
Joey Hess
d17f08afdc
avoid warning about orphan Arbirary instance 2016-09-05 14:51:07 -04:00
Joey Hess
1a0e2c9901
get, move, copy, mirror: Added --failed switch which retries failed copies/moves
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/
2016-08-03 12:37:12 -04:00
Joey Hess
c4d011bf3e
log: Added --all option. 2016-07-17 15:15:08 -04:00
Joey Hess
176cd98293
remove \r from Arbitrary for log tests 2016-05-27 12:04:49 -04:00
Joey Hess
eba68572dc
Split lines in the git-annex branch on \r as well as \n, to deal with \r\n terminated lines written by some versions of git-annex on Windows.
This fixes strange displays in some cases, including whereis showing
many duplicate locations, and showing more total copies than actually
exist.

It's unknown if that lead to data loss when eg, dropping. At the moment,
it seems unlikely it could, since the UUID with \r's appended is not the
same as a UUID without, and so no remote matches it.

It's also unknown if \r's can leak in on windows, perhaps when merging the
git-annex branch.
2016-05-27 11:45:13 -04:00
Joey Hess
823c28d2dc
nub transitionList to avoid ugly message after repeated transitions, and avoid redundant work for repeated ForgetDeadRemotes transitions 2016-05-18 12:26:38 -04:00
Joey Hess
8ab27235ea
reinject: Added new mode which can reinject known files into the annex.
For example: git-annex reinject --known /mnt/backup/*
2016-04-22 13:49:32 -04:00
Joey Hess
403b56fb91
Limit annex.largefiles parsing to the subset of preferred content expressions that make sense in its context.
So, not "standard" or "lackingcopies", etc.
2016-02-03 15:04:42 -04:00
Joey Hess
cdf5977053
simplify 2016-02-03 13:23:34 -04:00
Joey Hess
737e45156e
remove 163 lines of code without changing anything except imports 2016-01-20 16:36:33 -04:00
Joey Hess
1f3358512a
refactor 2016-01-19 15:55:32 -04:00
Joey Hess
983c1894eb
avoid unnecessary reading of git-annex branch data when matching on annex.largefiles
This makes git annex clean not look at the git-annex branch at all,
and so speeds it up by 50% or more.
2015-12-04 15:06:41 -04:00
Joey Hess
b0626230b7
fix use of hifalutin terminology 2015-11-16 14:37:31 -04:00
Joey Hess
aaf1ef268d
convert from Utility.LockPool to Annex.LockPool everywhere 2015-11-12 18:13:37 -04:00
Joey Hess
f9adb905fc
Avoid unncessary write to the location log when a file is unlocked and then added back with unchanged content.
Implemented with no additional overhead of compares etc.

This is safe to do for presence logs because of their locality of change;
a given repo's presence logs are only ever changed in that repo, or in a
repo that has just been actively changing the content of that repo.

So, we don't need to worry about a split-brain situation where there'd
be disagreement about the location of a key in a repo. And so, it's ok to
not update the timestamp when that's the only change that would be made
due to logging presence info.
2015-10-12 14:46:47 -04:00
Joey Hess
6fbabfcf16 oops, didn't mean to commit this debug 2015-10-06 17:28:20 -04:00
Joey Hess
ba7ecf68c0 analysis 2015-10-06 17:11:52 -04:00
Joey Hess
16947ef654 Fix bug in combination of preferred and required content settings. When one was set to the empty string and the other set to some expression, this bug caused all files to be wanted, instead of only files matching the expression.
Avoid: MAny `MOr` otherexpression
Which matches anything.
2015-09-15 12:50:14 -04:00
Joey Hess
6e829939e9 add test case that all standard group preferred content expressions parse 2015-06-17 13:44:19 -04:00
Joey Hess
5c960601aa 4 ns optimisation of repeated calls to hasDifference on the same Differences
I want this as fast as possible, so it can be added to code paths without
slowing them down.

Avoid the set lookup, and rely on laziness,
drops runtime from 14.37 ns to 11.03 ns according to this criterion benchmark:

import Criterion.Main
import qualified Types.Difference as New
import qualified Types.DifferenceOld as Old

main :: IO ()
main = defaultMain
	[ bgroup "hasDifference"
		[ bench "new" $ whnf (New.hasDifference New.OneLevelObjectHash) new
		, bench "old" $ whnf (Old.hasDifference Old.OneLevelObjectHash) old
		]
	]
  where
	s = "fromList [ObjectHashLower, OneLevelObjectHash, OneLevelBranchHash]"
	new = New.readDifferences s
	old = Old.readDifferences s

A little bit of added boilerplate, but I suppose it's worth it to not
need to worry about set lookup overhead. Note that adding more differences
would slow down the old implementation; the new implementation will run
the same speed.
2015-06-11 16:34:35 -04:00
Joey Hess
f8ab3bc449 dead --key: Can be used to mark a key as dead. 2015-06-09 14:52:05 -04:00
Joey Hess
6eefc5db65 fsck: Ignore keys that are known to be dead when running in --all mode or a in a bare repo. Otherwise, still reports files with lost contents, even if the content is dead. 2015-06-09 14:08:57 -04:00
Joey Hess
53ede1a10e parse X in location log file as indicating a dead key
A dead key is both not present at the location that thinks it has a copy,
and also is assumed to probably not be present anywhere else. Although
there may be lurking disconnected repos that somehow still have a copy.

Suprisingly few changes needed for this! This is because the presence log
code only really concerns itself with keys that are present, and dead keys
are not present.

Note that both the location and web log can be parsed as having a dead key.
I don't see any value to having keys listed as dead in the web log, but
since it doesn't change any behavior, there was no point in not parsing it.
2015-06-09 13:28:30 -04:00
Joey Hess
6383d22ffa remove back-compat code for old version of containers
Already b-d on a newer version.
2015-06-06 15:23:53 -04:00
Joey Hess
87f28bb2ea ignore failure to clean up stale transfer lock file
Perhaps due to permissions problem, or perhaps a race with another process
also cleaning up.
2015-05-19 23:46:42 -04:00
Joey Hess
9de5cd2966 fix crash in stale transfer lockfile cleanup code
Need to differentiate between the lockfile not being locked, and it not
existing.
2015-05-19 23:35:24 -04:00
Joey Hess
ecb0d5c087 use lock pools throughout git-annex
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.
2015-05-19 14:09:52 -04:00
Joey Hess
6915b71c57 lock pools to work around non-concurrency/composition safety of POSIX fcntl 2015-05-18 15:57:17 -04:00
Joey Hess
7ebf234616 Stale transfer lock and info files will be cleaned up automatically when get/unused/info commands are run.
Deleting lock files is tricky, tricky stuff. I think I got it right!
2015-05-12 20:11:23 -04:00
Joey Hess
643b233860 an optimization that also fixes a reversion
This is a little optimisation; avoid loading the info file for the
download of the current key when checking for other downloads.

The reversion it fixes is sorta strange.
a812d598ef broke checking for transfers
that were already in progress. Indeed, the transfer lock was not held
after getTransfers was called.

Why? I think it's magic in ghc's handling of getLock and setLock,
although it's hard to tell since those functions are almost entirely
undocumented as to their semantics.

Something, either the RTS (or maybe it's linux?) notices that the
same process has taken a lock and is now calling getLock on a FD attached
to the same file. So, it drops the lock.

So, this optimisation avoids that problematic behavior.
2015-05-12 18:34:49 -04:00
Joey Hess
a812d598ef Take space that will be used by running downloads into account when checking annex.diskreserve. 2015-05-12 15:20:22 -04:00
Joey Hess
03667a162a couple of AMP warnings I missed before 2015-05-10 16:51:03 -04:00
Joey Hess
ec267aa1ea rejigger imports for clean build with ghc 7.10's AMP changes
The explict import Prelude after import Control.Applicative is a trick
to avoid a warning.
2015-05-10 16:20:30 -04:00
Joey Hess
6c2d5b5e41 more time-1.5 fixes 2015-05-10 15:36:58 -04:00
Joey Hess
33a2264546 fix build warning with time 1.5 2015-05-10 15:28:23 -04:00
Joey Hess
a5a53ca011 forgot to add new module 2015-05-10 15:23:38 -04:00
Joey Hess
6cf62a9bde support time-1.5.0
This no longer uses old-locale's defaultTimeLocale, but provides one
of its own.

Factored out a Logs.TimeStamp.
2015-05-10 15:21:35 -04:00
Joey Hess
06211738c1 Fix activity log parsing.
I had some cargo culting in there that used the wrong type, so it failed
to parse old logs, and overwrote them with the new log.
2015-04-09 21:02:38 -04:00
Joey Hess
9445556c97 rethought distributed fsck; instead add activity.log and expire command
This is much more space efficient!
2015-04-05 12:50:02 -04:00
Joey Hess
656fc1c881 fsck: Added --distributed and --expire options, for distributed fsck. 2015-04-01 17:53:16 -04:00
Joey Hess
9e25cbde20 importfeed: Avoid downloading a redundant item from a feed whose guid has been downloaded before, even when the url has changed.
To support this, always store itemid in metadata; before this was only done
when annex.genmetadata was set.
2015-03-31 13:30:13 -04:00
Joey Hess
f0195b2a43 Fix GETURLS in external special remote protocol to strip downloader prefix from logged url info before checking for the specified prefix.
This doesn't change what GETURLS returns, but only whether it matches
any prefix that the external special remote asked for.
2015-03-27 18:49:03 -04:00
Joey Hess
6045406deb Added SETURIPRESENT and SETURIMISSING to external special remote protocol
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.
2015-03-05 13:50:15 -04:00
Joey Hess
b0575c621f implement annex.tune.branchhash1
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.
2015-01-28 17:17:26 -04:00
Joey Hess
e8c376e0ad import Data.Default in Common 2015-01-28 16:11:28 -04:00
Joey Hess
037d86e046 refactor 2015-01-28 13:56:38 -04:00
Joey Hess
ba3825441c rework Differences data type
Eliminated complexity and future proofed. The most important change is that
all functions over Difference are now total; any Difference that can be
expressed should be handled. Avoids needs for sanity checking of inputs,
and version skew with the future.

Also, the difference.log now serializes a [Difference], not a Differences.
This saves space and keeps it simpler.

Note that [Difference] might contain conflicting differences (eg,
[Version5, Version6]. In this case, one of them needs to consistently win
over the others, probably based on Ord.
2015-01-28 13:50:02 -04:00
Joey Hess
70736d2b41 Repository tuning parameters can now be passed when initializing a repository for the first time.
* 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.
2015-01-27 17:38:06 -04:00
Joey Hess
afc5153157 update my email address and homepage url 2015-01-21 12:50:09 -04:00
Joey Hess
3bab5dfb1d revert parentDir change
Reverts 965e106f24

Unfortunately, this caused breakage on Windows, and possibly elsewhere,
because parentDir and takeDirectory do not behave the same when there is a
trailing directory separator.
2015-01-09 13:11:56 -04:00
Joey Hess
965e106f24 made parentDir return a Maybe FilePath; removed most uses of it
parentDir is less safe than takeDirectory, especially when working
with relative FilePaths. It's really only useful in loops that
want to terminate at /

This commit was sponsored by Audric SCHILTKNECHT.
2015-01-06 18:55:56 -04:00
Joey Hess
43dc7f678f setpresentkey: A new plumbing-level command. 2014-12-29 15:16:40 -04:00
Joey Hess
589a048a7d fix addurl behavior when location and url logs are inconsistent
The url log could have an url for a key, while the location log thinks it's
not present in the web. In this case, addurl --file url would not do
anything. Fixed it to re-add the web as a location.

I don't know how this situation could arise, but I saw it in the wild in
the conference_proceedings repo, affecting key
URL-s17806003--http://mirror.linux.org.au/pub/linux.conf.au/2014/Wednesday/53-Building_Effective_Alliances_around_the_Trans-Pacific_Partnershi-c0505b631127ccc67e38e637344d988e
Investigating the presence log, it looked like that key
was originally listed as present in the web, then in commit
56abf9e9f3e691ed9d83513037d4019313321ca3 someone else's git-annex
set it and some other things to not present in the web. It would be
interesting to know what that user did, but I doubt I'll be able to find
out. All I can tell from this investigation is that the inconsistency was
not introduced when originally addurl-ing the url.
2014-12-29 14:22:47 -04:00