¿Cómo recuperar objetos Git dañados por fallo del disco duro?

https://stackoverflow.com/questions/801577

03-07-2019
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Pregunta

Se produjo una falla en el disco duro que resultó en el daño de algunos archivos de un repositorio Git. Al ejecutar git fsck --full obtengo el siguiente resultado:

error: .git/objects/pack/pack-6863e0a0e4b4ded6090fac5d12eba6ca7346b19c.pack SHA1 checksum mismatch
error: index CRC mismatch for object 6c8cae4994b5ec7891ccb1527d30634997a978ee from .git/objects/pack/pack-6863e0a0e4b4ded6090fac5d12eba6ca7346b19c.pack at offset 97824129
error: inflate: data stream error (invalid code lengths set)
error: cannot unpack 6c8cae4994b5ec7891ccb1527d30634997a978ee from .git/objects/pack/pack-6863e0a0e4b4ded6090fac5d12eba6ca7346b19c.pack at offset 97824129
error: inflate: data stream error (invalid stored block lengths)
error: failed to read object 0dcf6723cc69cc7f91d4a7432d0f1a1f05e77eaa at offset 276988017 from .git/objects/pack/pack-6863e0a0e4b4ded6090fac5d12eba6ca7346b19c.pack
fatal: object 0dcf6723cc69cc7f91d4a7432d0f1a1f05e77eaa is corrupted

Tengo copias de seguridad del repositorio, pero la única copia de seguridad que incluye el archivo del paquete ya está dañada. Así que creo que tengo que encontrar una manera de recuperar los objetos individuales de diferentes copias de seguridad y de alguna manera ordenar a Git que produzca un nuevo paquete con solo los objetos correctos.

¿Me puede dar sugerencias sobre cómo arreglar mi repositorio?

Solución

En algunas copias de seguridad anteriores, sus objetos defectuosos pueden haber sido empaquetados en diferentes archivos o pueden ser objetos sueltos todavía. Para que tus objetos puedan ser recuperados.

Parece que hay algunos objetos defectuosos en su base de datos. Así que podrías hacerlo de forma manual.

Debido a git hash-object , git mktree y git commit-tree no escriben los objetos porque se encuentran en el paquete , entonces empieza a hacer esto:

mv .git/objects/pack/* <somewhere>
for i in <somewhere>/*.pack; do
  git unpack-objects -r < $i
done
rm <somewhere>/*

(Sus paquetes se sacan del repositorio y se descomprimen nuevamente en él; solo los objetos buenos están ahora en la base de datos)

Puedes hacer:

git cat-file -t 6c8cae4994b5ec7891ccb1527d30634997a978ee

y compruebe el tipo de objeto.

Si el tipo es blob: recupera el contenido del archivo de las copias de seguridad anteriores (con git show o git cat-file o git unpack-file ; luego puedes git hash-object -w para volver a escribir el objeto en tu repositorio actual.

Si el tipo es árbol: podría usar git ls-tree para recuperar el árbol de las copias de seguridad anteriores; luego git mktree para escribirlo de nuevo en su repositorio actual.

Si el tipo es commit: lo mismo con git show , git cat-file y git commit-tree .

Por supuesto, haría una copia de seguridad de su copia de trabajo original antes de comenzar este proceso.

También, eche un vistazo a Cómo recuperar un objeto Blob dañado .

Otros consejos

Banengusk me estaba poniendo en el camino correcto. Para futuras referencias, quiero publicar los pasos que tomé para corregir la corrupción de mi repositorio. Tuve la suerte de encontrar todos los objetos necesarios, ya sea en paquetes antiguos o en copias de seguridad del repositorio.

# Unpack last non-corrupted pack
$ mv .git/objects/pack .git/objects/pack.old
$ git unpack-objects -r < .git/objects/pack.old/pack-012066c998b2d171913aeb5bf0719fd4655fa7d0.pack
$ git log
fatal: bad object HEAD

$ cat .git/HEAD 
ref: refs/heads/master

$ ls .git/refs/heads/

$ cat .git/packed-refs 
# pack-refs with: peeled 
aa268a069add6d71e162c4e2455c1b690079c8c1 refs/heads/master

$ git fsck --full 
error: HEAD: invalid sha1 pointer aa268a069add6d71e162c4e2455c1b690079c8c1
error: refs/heads/master does not point to a valid object!
missing blob 75405ef0e6f66e48c1ff836786ff110efa33a919
missing blob 27c4611ffbc3c32712a395910a96052a3de67c9b
dangling tree 30473f109d87f4bcde612a2b9a204c3e322cb0dc

# Copy HEAD object from backup of repository
$ cp repobackup/.git/objects/aa/268a069add6d71e162c4e2455c1b690079c8c1 .git/objects/aa
# Now copy all missing objects from backup of repository and run "git fsck --full" afterwards
# Repeat until git fsck --full only reports dangling objects

# Now garbage collect repo
$ git gc
warning: reflog of 'HEAD' references pruned commits
warning: reflog of 'refs/heads/master' references pruned commits
Counting objects: 3992, done.
Delta compression using 2 threads.
fatal: object bf1c4953c0ea4a045bf0975a916b53d247e7ca94 inconsistent object length (6093 vs 415232)
error: failed to run repack

# Check reflogs...
$ git reflog

# ...then clean
$ git reflog expire --expire=0 --all

# Now garbage collect again
$ git gc       
Counting objects: 3992, done.
Delta compression using 2 threads.
Compressing objects: 100% (3970/3970), done.
Writing objects: 100% (3992/3992), done.
Total 3992 (delta 2060), reused 0 (delta 0)
Removing duplicate objects: 100% (256/256), done.
# Done!

Try the following commands at first (re-run again if needed):

$ git fsck --full
$ git gc
$ git gc --prune=today
$ git fetch --all
$ git pull --rebase

And then you you still have the problems, try can:

remove all the corrupt objects, e.g.

fatal: loose object 91c5...51e5 (stored in .git/objects/06/91c5...51e5) is corrupt
$ rm -v .git/objects/06/91c5...51e5

remove all the empty objects, e.g.

error: object file .git/objects/06/91c5...51e5 is empty
$ find .git/objects/ -size 0 -exec rm -vf "{}" \;

check a "broken link" message by:
```
git ls-tree 2d9263c6d23595e7cb2a21e5ebbb53655278dff8
```
This will tells you what file the corrupt blob came from!
to recover file, you might be really lucky, and it may be the version that you already have checked out in your working tree:
```
git hash-object -w my-magic-file
```
again, and if it outputs the missing SHA1 (4b945..) you're now all done!
assuming that it was some older version that was broken, the easiest way to do it is to do:
```
git log --raw --all --full-history -- subdirectory/my-magic-file
```
and that will show you the whole log for that file (please realize that the tree you had may not be the top-level tree, so you need to figure out which subdirectory it was in on your own), then you can now recreate the missing object with hash-object again.
to get a list of all refs with missing commits, trees or blobs:
```
$ git for-each-ref --format='%(refname)' | while read ref; do git rev-list --objects $ref >/dev/null || echo "in $ref"; done
```
It may not be possible to remove some of those refs using the regular branch -d or tag -d commands, since they will die if git notices the corruption. So use the plumbing command git update-ref -d $ref instead. Note that in case of local branches, this command may leave stale branch configuration behind in .git/config. It can be deleted manually (look for the [branch "$ref"] section).
After all refs are clean, there may still be broken commits in the reflog. You can clear all reflogs using git reflog expire --expire=now --all. If you do not want to lose all of your reflogs, you can search the individual refs for broken reflogs:
```
$ (echo HEAD; git for-each-ref --format='%(refname)') | while read ref; do git rev-list -g --objects $ref >/dev/null || echo "in $ref"; done
```
(Note the added -g option to git rev-list.) Then, use git reflog expire --expire=now $ref on each of those. When all broken refs and reflogs are gone, run git fsck --full in order to check that the repository is clean. Dangling objects are Ok.

Below you can find advanced usage of commands which potentially can cause lost of your data in your git repository if not used wisely, so make a backup before you accidentally do further damages to your git. Try on your own risk if you know what you're doing.

To pull the current branch on top of the upstream branch after fetching:

$ git pull --rebase

You also may try to checkout new branch and delete the old one:

$ git checkout -b new_master origin/master

To find the corrupted object in git for removal, try the following command:

while [ true ]; do f=`git fsck --full 2>&1|awk '{print $3}'|sed -r 's/(^..)(.*)/objects\/\1\/\2/'`; if [ ! -f "$f" ]; then break; fi; echo delete $f; rm -f "$f"; done

For OSX, use sed -E instead of sed -r.

Other idea is to unpack all objects from pack files to regenerate all objects inside .git/objects, so try to run the following commands within your repository:

$ cp -fr .git/objects/pack .git/objects/pack.bak
$ for i in .git/objects/pack.bak/*.pack; do git unpack-objects -r < $i; done
$ rm -frv .git/objects/pack.bak

If above doesn't help, you may try to rsync or copy the git objects from another repo, e.g.

$ rsync -varu git_server:/path/to/git/.git local_git_repo/
$ rsync -varu /local/path/to/other-working/git/.git local_git_repo/
$ cp -frv ../other_repo/.git/objects .git/objects

To fix the broken branch when trying to checkout as follows:

$ git checkout -f master
fatal: unable to read tree 5ace24d474a9535ddd5e6a6c6a1ef480aecf2625

Try to remove it and checkout from upstream again:

$ git branch -D master
$ git checkout -b master github/master

In case if git get you into detached state, checkout the master and merge into it the detached branch.

Another idea is to rebase the existing master recursively:

$ git reset HEAD --hard
$ git rebase -s recursive -X theirs origin/master

See also:

Here are the steps I followed to recover from a corrupt blob object.

1) Identify corrupt blob

git fsck --full
  error: inflate: data stream error (incorrect data check)
  error: sha1 mismatch 241091723c324aed77b2d35f97a05e856b319efd
  error: 241091723c324aed77b2d35f97a05e856b319efd: object corrupt or missing
  ...

Corrupt blob is 241091723c324aed77b2d35f97a05e856b319efd

2) Move corrupt blob to a safe place (just in case)

mv .git/objects/24/1091723c324aed77b2d35f97a05e856b319efd ../24/

3) Get parent of corrupt blob

git fsck --full
  Checking object directories: 100% (256/256), done.
  Checking objects: 100% (70321/70321), done.
  broken link from    tree 0716831e1a6c8d3e6b2b541d21c4748cc0ce7180
              to    blob 241091723c324aed77b2d35f97a05e856b319efd

Parent hash is 0716831e1a6c8d3e6b2b541d21c4748cc0ce7180.

4) Get file name corresponding to corrupt blob

git ls-tree 0716831e1a6c8d3e6b2b541d21c4748cc0ce7180
  ...
  100644 blob 241091723c324aed77b2d35f97a05e856b319efd    dump.tar.gz
  ...

Find this particular file in a backup or in the upstream git repository (in my case it is dump.tar.gz). Then copy it somewhere inside your local repository.

5) Add previously corrupted file in the git object database

git hash-object -w dump.tar.gz

6) Celebrate!

git gc
  Counting objects: 75197, done.
  Compressing objects: 100% (21805/21805), done.
  Writing objects: 100% (75197/75197), done.
  Total 75197 (delta 52999), reused 69857 (delta 49296)

Git checkout can actually pick out individual files from a revision. Just give it the commit hash and the file name. More detailed info here.

I guess the easiest way to fix this safely is to revert to the newest uncommited backup and then selectively pick out uncorrupted files from newer commits. Good luck!

Here are two functions that may help if your backup is corrupted, or you have a few partially corrupted backups as well (this may happen if you backup the corrupted objects).

Run both in the repo you're trying to recover.

Standard warning: only use if you're really desperate and you have backed up your (corrupted) repo. This might not resolve anything, but at least should highlight the level of corruption.

fsck_rm_corrupted() {
    corrupted='a'
    while [ "$corrupted" ]; do
        corrupted=$(                                  \
        git fsck --full --no-dangling 2>&1 >/dev/null \
            | grep 'stored in'                          \
            | sed -r 's:.*(\.git/.*)\).*:\1:'           \
        )
        echo "$corrupted"
        rm -f "$corrupted"
    done
}

if [ -z "$1" ]  || [ ! -d "$1" ]; then
    echo "'$1' is not a directory. Please provide the directory of the git repo"
    exit 1
fi

pushd "$1" >/dev/null
fsck_rm_corrupted
popd >/dev/null

and

unpack_rm_corrupted() {
    corrupted='a'
    while [ "$corrupted" ]; do
        corrupted=$(                                  \
        git unpack-objects -r < "$1" 2>&1 >/dev/null \
            | grep 'stored in'                          \
            | sed -r 's:.*(\.git/.*)\).*:\1:'           \
        )
        echo "$corrupted"
        rm -f "$corrupted"
    done
}

if [ -z "$1" ]  || [ ! -d "$1" ]; then
    echo "'$1' is not a directory. Please provide the directory of the git repo"
    exit 1
fi

for p in $1/objects/pack/pack-*.pack; do
    echo "$p"
    unpack_rm_corrupted "$p"
done

I have resolved this problem to add some change like git add -A and git commit again.

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