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some analysis

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Joey Hess 2024-05-31 11:47:59 -04:00
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[[!comment format=mdwn
username="joey"
subject="""comment 1"""
date="2024-05-31T14:52:17Z"
content="""
Reproduction recipe works, thanks!
Happens back to 10.20240129 at least, this is not recent breakage.
There are some interesting things in the git-annex history.
Including some git-annex:export.tree grafting, and also
a continued transition.
I made a new empty repo, initialized and annexed some files. Running the
same script but cloning that, this problem does not occur. I also tried
exporting a tree in that repo, and still the problem doesn't occur. I even
tried running `git-annex forget` in there and still can't cause the
problem.
So something about this specific repo's git-annex branch history is
triggering the problem and I don't know what. I've archived the current
state of this repo in my big repo as git-annex-test-repos/ds002144.tar.gz
to make sure I can continue to reproduce this.
The first git-annex branch commit that is missing its tree object
is a git-annex:export.tree graft commit. That is 3 commits above
the git-annex branch pulled from github:
Very interesting. Especially since the point of those export.tree graft commits
are to make sure that the exported tree objects are referenced and so don't get
gced out from under us.
"""]]

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[[!comment format=mdwn
username="joey"
subject="""comment 2"""
date="2024-05-31T15:26:26Z"
content="""
Resetting the repo's git-annex branch all the way back to the 1st commit in it
is sufficient to reproduce this bug.
joey@darkstar:~/tmp/ds002144#main>git log git-annex
commit 2e24112747f3742c5426138def93fd3219574df7 (git-annex)
Author: Git Worker <git@openneuro.org>
Date: Fri Jan 19 21:04:18 2024 +0000
new branch for transition ["forget git history"]
Hmm. That ref contains an export.log that references some tree shas.
1596548650.649001679s 2606f878-85c6-459a-8402-5f4b98720bbd:58a4efbe-8fb4-4cb3-8be3-b982a4673947 b78b723042e6d7a967c806b52258e8554caa1696 ae2937297eb1b4f6c9bfdfcf9d7a41b1adcea32e
1705698180.15617956s 2606f878-85c6-459a-8402-5f4b98720bbd:8af9d961-216f-47ec-b052-31696fc2f12d ae2937297eb1b4f6c9bfdfcf9d7a41b1adcea32e 28b655e8207f916122bbcbd22c0369d86bb4ffc1
Those seem familiar:
missing tree b78b723042e6d7a967c806b52258e8554caa1696
missing tree ae2937297eb1b4f6c9bfdfcf9d7a41b1adcea32e
So ok.. We have here a transition that forgot git history. But it kept an
export.log that referenced 2 trees in that now-forgotten git history.
Everything else seems to follow from that. Grafting those trees back into the
git-annex branch in order to not forget them is a bad move since they're
already forgotten. So it could just avoid doing that, if the tree object
is missing, I suppose.
There might be a deeper bug though: If we want to `git-annex export`, in either
the original repo with forgotten history, or in a clone, it won't be able to
refer to those tree objects. So it won't know what has been written to the
special remote. So eg, if we export a tree that deletes a file compared to one
of these trees, it wouldn't delete the file from the special remote.
I think this problem might not happen when exporting in the original repo,
because there the export database also records the same information. More likely
it will happen in a clone.
So, action items:
* When performing a transition, the trees mentioned in export.log needs to be
grafted back in, in order not to lose them. I think it already is supposed to
do that, but it clearly didn't work in this case. So I need to find a way to
reproduce the situation in commit 2e24112747f3742c5426138def93fd3219574df7 in
a new repository to find out why that didn't happen. And fix that.
* When encountering a git-annex branch with this situation in it, avoid
grafting missing trees back into the branch. And probably `git-annex export`
needs to refuse to touch the affected special remote, or warn the user
that it's lost track of what files were sent to the special remote.
"""]]

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[[!comment format=mdwn
username="joey"
subject="""comment 3"""
date="2024-05-31T15:42:17Z"
content="""
Occurs to me that one way to get a repository into this situation would be
to do a `git-annex export`, then `git-annex forget`, and then manually
reset the git-annex branch to `git-annex^^` (or similarly push
`git-annex^^` to origin).
There is a commit after the transition commit that re-grafts the exported
tree back into the git-annex branch, and a manual reset would cause exactly
this situation.
I doubt OpenNeuro is manually resetting the git-annex branch when creating
these repos, but stranger things have happened...
"""]]