[Insight-developers] Git corruption help

[Bradley Lowekamp]

Hello,


My SimpleITK git repo, is a little messed up. When I first noticed I made a new backup. 

I began getting the following error when building SimpleITK:

$ cmake  .
CMake Error: File /nfs/Users/blowekamp/src/SimpleITK/.git/refs/heads/next does not exist.
CMake Error at /scratch/blowekamp/build/SimpleITK/SimpleITK-build/CMakeFiles/git-data/grabRef.cmake:23 (configure_file):
  configure_file Problem configuring file
Call Stack (most recent call first):
  CMake/GetGitRevisionDescription.cmake:58 (include)
  Version.cmake:7 (get_git_head_revision)
  CMakeLists.txt:129 (include)


Looking at that directory I don't see much ( my other repos have all the local branches there ):

$ ls -l .git/refs/heads/
total 16
drwxr-xr-x  2 blowekamp  users  2048 Aug 31  2011 stage

When I do a git branch, I see all my branches. 

the head under log appears like what I would expect.

$ ls -l .git/logs/refs/heads/
total 400
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 AddImageConstructorForVector
-rw-r--r--  1 blowekamp  users   183 Jun 14 08:30 AddSomeFilters
-rw-r--r--  1 blowekamp  users   367 Jun 14 08:30 AddVirtualDestructorToFilterExecuteBase
-rw-r--r--  1 blowekamp  users   591 Jun 14 08:30 AddingGradientFilters
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 Enable64BitIntegers
-rw-r--r--  1 blowekamp  users   173 Jun 14 08:30 MergeREnhancements
-rw-r--r--  1 blowekamp  users   173 Jun 14 08:30 SIMPLEITK-103_RemoveMacroToken
-rw-r--r--  1 blowekamp  users   146 Jun 14 08:30 SIMPLEITK-122_AddImageSeriesWriter
-rw-r--r--  1 blowekamp  users  1501 Jun 14 08:30 SIMPLEITK-167-CompareITKandSITKfilters
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 SIMPLEITK-182_FixFFTConvolutionExample
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 SIMPLEITK-1_AddImageRegistration
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 SIMPLEITK-1_registration
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 SIMPLEITK-205_AddingCorrelationFilters
-rw-r--r--  1 blowekamp  users   167 Jun 14 08:30 SIMPLEITK-224_AddVectorSupportGetBuffer_bak
-rw-r--r--  1 blowekamp  users  1239 Jun 14 08:30 SIMPLEITK-246_NativeSugarForR
-rw-r--r--  1 blowekamp  users   189 Jun 14 08:30 SIMPLEITK-264_AddTransformations
-rw-r--r--  1 blowekamp  users  2090 Jun 14 08:30 SIMPLEITK-279_AddComposeImageFilter
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 SIMPLEITK-286_AddNumpySupportForVectorImages
-rw-r--r--  1 blowekamp  users   968 Jun 14 08:30 SIMPLEITK-292_AddImageSources
-rw-r--r--  1 blowekamp  users   360 Jun 14 08:30 SIMPLEITK-295_AddGradientFilter
-rw-r--r--  1 blowekamp  users   167 Jun 14 08:30 SIMPLEITK-296_Clang-requires-explicit-Disambiguation
-rw-r--r--  1 blowekamp  users   400 Jun 14 08:30 SIMPLEITK-297_UpdateITKTowardsITK4.2
-rw-r--r--  1 blowekamp  users  1428 Jun 14 08:30 SIMPLEITK-74_AutomaticallyComputeTimeStep
-rw-r--r--  1 blowekamp  users   784 Jun 14 08:30 SIMPLEITK-AddNumpySupportForVectorImages
-rw-r--r--  1 blowekamp  users     0 Jun 14 08:30 SugarForR
-rw-r--r--  1 blowekamp  users   372 Jun 14 08:30 UpdateDataSubmodule
-rw-r--r--  1 blowekamp  users  1111 Jun 14 08:30 VectorConfidenceConnected
-rw-r--r--  1 blowekamp  users  2654 Jun 14 08:30 master
-rw-r--r--  1 blowekamp  users  8619 Jun 14 08:30 next
-rw-r--r--  1 blowekamp  users   401 Jun 14 08:30 release
drwxr-xr-x  2 blowekamp  users  2048 Aug 31  2011 stage
-rw-r--r--  1 blowekamp  users   373 Jun 14 08:30 temp

$ git fsck --full 
dangling commit 976620baf25b05208035785ebbf0195dffcbcc56
dangling commit 4197609c3895b2769b2e0f14e66583b543047efe
dangling commit 0a9b502b2953eb12310488e8fae47315867775c8
dangling commit 93bfe0cc0767af6bf66fbe1ef6ed28a0d698de67
dangling commit 5ceb60e695a9a0405bfe2f88e4bea6c0c347ec44
dangling commit ce0051a19798db5071f30ca45a56beedec57a8d1
dangling commit 1f9f312bcc118de87da51ed41b3c1233f7e8f22a
dangling commit a9d8414edde4e72a994aa27dc97bfed59fd5b4a8
dangling commit 19dc61bba4ceb86f5a6faabab6f60ac134f73b92
dangling commit b8ed719fceb2d9a1c1f3a2b259471d6fb2fb5063
dangling commit ba5bc2d40c5329a1030c5df332ebee88f3e1e2ea
dangling blob.. ( a couple more )
dangling commit... ( couple dozen more )

I am looking for suggestions are recovery options. 

Is there a way to rebuild .git/refs/head?

Or ways to check if the damage is further than what I think now.

Thanks,
Brad

========================================================
Bradley Lowekamp  
Medical Science and Computing for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov



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