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Merge branch 'master' of ssh://git-annex.branchable.com

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Joey Hess 2014-10-16 12:32:52 -04:00
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doc/bugs/problems_with_enableremote_on_gcrypt_remote___40__hosted_with_gitolite__41__.mdwn Normal file
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### Please describe the problem.
cannot enable an exiting gcrypt special remote after successfully having cloned the git repository; I get this error: "git-annex: uuid mismatch ..." at the end of the enableremote command (see transcript for details)
maybe my fault but cannot understand what I'm doing wrong
### What steps will reproduce the problem?
1. cloned the encrypted repository with: "git clone gcrypt::git.myserver.net:myrepo TEST-myrepo.annex"
2. enabled the special remote with: "git annex enableremote backup type=gcrypt encryption=hybrid gitrepo=git.myserver.net:myrepo"
### What version of git-annex are you using? On what operating system?
[[!format sh """
git-annex version: 5.20140927~bpo70+2
build flags: Assistant Pairing S3 Inotify XMPP Feeds Quvi TDFA
key/value backends: SHA256E SHA1E SHA512E SHA224E SHA384E SHA256 SHA1 SHA512 SHA224 SHA384 WORM URL
remote types: git gcrypt S3 bup directory rsync web tahoe glacier ddar hook external
local repository version: 5
supported repository version: 5
upgrade supported from repository versions: 0 1 2 4
"""]]
### Please provide any additional information below.
[[!format sh """
# transcript of commands and results
(cloning)
g@renaissance:~$ git clone gcrypt::git.myserver.net:DMS-myrepo TEST-myrepo.annex
Cloning into 'TEST-myrepo.annex'...
gcrypt: Development version -- Repository format MAY CHANGE
gcrypt: Decrypting manifest
gpg: Signature made Thu 16 Oct 2014 12:58:33 CEST
[...]
gcrypt: Remote ID is :id:8sucFsBZIGQKXFv5ecSW
Receiving objects: 100% (3531/3531), 245.40 KiB | 0 bytes/s, done.
Resolving deltas: 100% (1382/1382), done.
[...]
Receiving objects: 100% (636/636), 66.78 KiB | 0 bytes/s, done.
Resolving deltas: 100% (209/209), done.
Checking connectivity... done.
(annex info)
g@renaissance:~/TEST-myrepo.annex$ git annex info
repository mode: indirect
trusted repositories: (merging origin/git-annex origin/synced/git-annex into git-annex...)
(Recording state in git...)
0
semitrusted repositories: 5
-- here
00000000-0000-0000-0000-000000000001 -- web
622362eb-3882-4429-829b-1ec0f299f5a7 -- [omissis]
69b848ef-dd29-43e4-ae1b-73ec6a01f2f6 -- [omissis]
ffc5c5d1-6166-4753-a2e4-88727d0f8c7b -- backup
untrusted repositories: 1
b185b2ed-c024-43ac-9049-3bc12a87dacc -- [omissis]
transfers in progress: none
available local disk space: 51.53 gigabytes (+1 megabyte reserved)
local annex keys: 0
local annex size: 0 bytes
annexed files in working tree: 212
size of annexed files in working tree: 210.56 megabytes
bloom filter size: 16 mebibytes (0% full)
backend usage:
SHA256E: 212
(list of remotes)
g@renaissance:~/TEST-myrepo.annex$ git annex enableremote
git-annex: Specify the name of the special remote to enable.
Known special remotes: backup
(enabling remote)
g@renaissance:~/TEST-myrepo.annex$ git annex enableremote backup type=gcrypt encryption=hybrid gitrepo=git.myserver.net:myrepo
enableremote backup (encryption update) (hybrid cipher with gpg key [omissis]) gcrypt: Development version -- Repository format MAY CHANGE
gcrypt: Decrypting manifest
gpg: Signature made Thu 16 Oct 2014 12:58:33 CEST
[omissis]
gcrypt: Remote ID is :id:8sucFsBZIGQKXFv5ecSW
From gcrypt::git.myserver.net:myrepo
* [new branch] synced/master -> backup/synced/master
* [new branch] master -> backup/master
* [new branch] synced/git-annex -> backup/synced/git-annex
* [new branch] git-annex -> backup/git-annex
gcrypt: Development version -- Repository format MAY CHANGE
gcrypt: Decrypting manifest
gpg: Signature made Thu 16 Oct 2014 12:58:33 CEST
[omissis]
Counting objects: 3, done.
Compressing objects: 100% (2/2), done.
Total 3 (delta 0), reused 1 (delta 0)
gcrypt: Encrypting to: -r [omissis]
gcrypt: Requesting manifest signature
gpg: [omissis]: skipped: public key already present
To gcrypt::git.myserver.net:myserver
1195dda..3254af7 git-annex -> git-annex
git-annex: uuid mismatch (UUID "78104a6f-16a9-504b-8e8a-d8a3c59351e8",Just (UUID "984e0333-3327-5f21-87a1-35d30f37f337"),":id:8sucFsBZIGQKXFv5ecSW")
# End of transcript or log.
"""]]

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[[!comment format=mdwn
username="https://www.google.com/accounts/o8/id?id=AItOawlZ-6dtxJY4cP7shhvV8E6YyuV0Rak8it4"
nickname="Giovanni"
subject="I messed up that repo"
date="2014-10-16T13:31:15Z"
content="""
I'm sure I messed up the repository at some point
the remote repository have a duplicated (I hope just duplicated and not triplicated) UUID: both ffc5c5d1-6166-4753-a2e4-88727d0f8c7b and 984e0333-3327-5f21-87a1-35d30f37f337
on one of my working remotes I already used \"git annex dead 984e0333-3327-5f21-87a1-35d30f37f337\" and synced the special (bare) remote **but** trying to make a new clone and adding the remote special with enableremote i always get the same \"UUID mismatch\" error, listing the (marked) dead UUID
please is there a way to get rid of the mess I did?!? :-)
I'm tempted to manually add \"annex-uuid = ffc5c5d1-6166-4753-a2e4-88727d0f8c7b\" to the repo \".git/config\" but I fear I'm going to further mess things
sorry for reportng this as a bug... actually it was my fault
best regards
Giovanni
"""]]

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I have been trying to uninit a very large directory and ran into problems.
`git annex unannex` seems to be completely infeasible because of how long it takes, also it seemed to grow the directory enormously, probably because it copies large files and then waits to delete them?
I tried unannexing with the following commands instead:
`git annex get --from=backup`
`git annex unannex --fast`
`git annex uninit`
This does what it is supposed to it seems, it hard links all copies of files. However, the unint step gives the following message:
git-annex: Not fully uninitialized
Some annexed data is still left in /science/carlo/GR_Coverage_Manuscript_Revisions_140616/.git/annex/objects/
This may include deleted files, or old versions of modified files.
If you don't care about preserving the data, just delete the
directory.
Or, you can move it to another location, in case it turns out
something in there is important.
Or, you can run `git annex unused` followed by `git annex dropunused`
to remove data that is not used by any tag or branch, which might
take care of all the data.
Then run `git annex uninit` again to finish.
However, running `git annex unused` returns nothing.
When I run `du -l -h --max-depth=1` I get the following output:
646G ./01-Collate_New_Species_Data
6.3G ./02-Prep_Annotations
1.8T ./03-Map_Riboprofiling_Data
111G ./04-Generate_Preprocessed_Files
94G ./05-Det_Codon_Specfic_Occupancy
3.6T ./.git
6.2T .
The .git/annex/objects directory remains 3.5TB in size, while the root directory, minus the contents of .git is only 2.7TB.
I want to delete the .git folder to free up space, but I am very nervous now, because it looks like there is extra data in git annex that isn't present in the main directory. I don't want that to be lost, that would be a complete disaster.
I tried the exact same process on a test directory, and it seemed to work completely, but losing this data would be an absolute disaster, so I don't want to risk it.
Any thoughts?