How to recover Git objects damaged by hard disk failure

Question

I have had a hard disk failure which resulted in some files of a Git repository getting damaged  When running git fsck --full I get the following output   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   I have backups of the repository  but the only backup that includes the pack file has it already damaged  So I think that I have to find out a way to retrieve the single objects from different backups and somehow instruct Git to produce a new pack with only correct objects   Can you please give me hints how to fix my repository

User · Answer

The solution by Daniel Fanjul looked promissing. I was able to find that blob file and extracted it ("git fsck --full --no-dangling", "git cat-file -t {hash}", "git show {hash} > file.tmp") but when I tried to update pack file with "git hash-object -w file.tmp", it displayed correct hash BUT the error remained.

So I decided to try different approach. I could simply delete local repository and download everything from remote but some branches in local repository were 8 commits ahead and I did not want to lose those changes. Since that tiny, 6kb mp3 file, I decided to delete it completely. I tried many ways but the best was from here: https://itextpdf.com/en/blog/technical-notes/how-completely-remove-file-git-repository

I got the file name by running this command "git rev-list --objects --all | grep {hash}". Then I did a backup (strongly recommend to do so because I failed 3 times) and then run the command:

"java -jar bfg.jar --delete-files {filename} --no-blob-protection ."

You can get bfg.jar file from here https://rtyley.github.io/bfg-repo-cleaner/ so according to documentation I should run this command next:

"git reflog expire --expire=now --all && git gc --prune=now --aggressive"

When I did so, I got errors on last step. So I recovered everything from backup and this time, after removing file, I checkout to the branch (which was causing that error), then check out back to main and only after run the command one after each other:

"git reflog expire --expire=now --all" "git gc --prune=now --aggressive"

Then I added my file back to its location and comit. However, since many local commits were changed, I was not able to push anything to server. So I backup everything on server (in case I screw it), check out to the branch which was affected and run the command "git push --force".

What I understood from this case? GIT is great but so senstive... I should have an option to simply disregard one f... 6kb file I know what I am doing. I have no clude why "git hash-object -w" did not work either =( Lessons learnt, push all commits, do not wait, do backup of repository time to time. Also I know how to remove files from repository, if I ever need =)

I hope this saves someone's time

User · Answer

In some previous backups  your bad objects may have been packed in different files or may be loose objects yet  So your objects may be recovered   It seems there are a few bad objects in your database  So you could do it the manual way   Because of git hash-object  git mktree and git commit-tree do not write the objects because they are found in the pack  then start doing this   mv  git objects pack    lt somewhere gt  for i in  lt somewhere gt    pack  do   git unpack-objects -r  lt   i done rm  lt somewhere gt       Your packs are moved out from the repository  and unpacked again in it  only the good objects are now in the database   You can do   git cat-file -t 6c8cae4994b5ec7891ccb1527d30634997a978ee   and check the type of the object   If the type is blob  retrieve the contents of the file from previous backups  with git show or git cat-file or git unpack-file  then you may git hash-object -w to rewrite the object in your current repository   If the type is tree  you could use git ls-tree to recover the tree from previous backups  then git mktree to write it again in your current repository   If the type is commit  the same with git show  git cat-file and git commit-tree   Of course  I would backup your original working copy before starting this process   Also  take a look at How to Recover Corrupted Blob Object

User · Answer

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 gt  amp 1  gt  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   gt  dev null fsck rm corrupted popd  gt  dev null   and  unpack rm corrupted         corrupted  a      while     corrupted     do         corrupted                                               git unpack-objects -r  lt    1  2 gt  amp 1  gt  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

User · Answer

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

User · Answer

Banengusk was putting me on the right track  For further reference  I want to post the steps I took to fix my repository corruption  I was lucky enough to find all needed objects either in older packs or in repository backups     Unpack last non-corrupted pack   mv  git objects pack  git objects pack old   git unpack-objects -r  lt   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

User · Answer

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

User · Answer

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  gt  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  gt  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 gt  amp 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  lt   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    Some tricks to reconstruct blob objects in order to fix a corrupted repository  How to fix a broken repository  How to remove all broken refs from a repository  How to fix corrupted git repository   seeques  How to fix corrupted git repository   qnundrum  Error when using SourceTree with Git   Summary  failed with code 128  fatal  unable to read tree Recover A Corrupt Git Bare Repository Recovering a damaged git repository How to fix git error  object is empy   corrupt How to diagnose and fix git fatal  unable to read tree How to deal with this git error How to fix corrupted git repository  How do I   39 overwrite  39   rather than   39 merge  39   a branch on another branch in Git  How to replace master branch in git  entirely  from another branch  Git   quot Corrupt loose object quot  Git reset   fatal  unable to read tree

User · Answer

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] How to recover Git objects damaged by hard disk failure?

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