git pull && git annex get . at forked source #125
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Hi @renelabounek, thanks for reporting this issue. There are (at least) two things happening here:
You don't need to try this right now though; we'll let you know once the Amazon S3 permissions issue is fixed. |
Ok I will do step 2, when you let me know that the issue 1 is fixed. Thanks, Rene |
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Ok, I think we don't need the If that works, then you should be able to retry downloading everything: Otherwise, could you post the results of these commands please? |
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It di not pass. STDOUTs are below. I have not done the step 2 (i.e. the git config --unset commands), as you said not to do. |
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Ok, I can reproduce this problem, and I have some idea why it's happening, and a potential way to fix it (though not 100%). The problem:
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Nope, I am still not able to get the files. |
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I'm having trouble reproducing this problem on my computer. Could you tell me the output of the following commands, so that I have a better idea what's happening? Thanks. |
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Thanks for your help. Here are the STDOUTs: |
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Thanks for your patience. After trying to reproduce the problem on my computer, I think we can try to merge the information from the
If it still doesn't work I would need to know exactly which version of git-annex you have, which is in the output of the following command: |
My expected outputs started to appear different within the first set of commands. My git does not know I assume it is a git version issue. Unfortunatelly, I am not admin at the server where the database is stored. So update git can be tricky or even impossible for me. Any other possibility before I will write to server admins the update request? |
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Yes, it looks like a git version issue. Thankfully, that option is only
needed for recent versions of git to make them act like older versions of
git, so you can safely remove just that option and try again.
(Thanks for including your exact git version, that will help with fixing
things.)
…On Thu., Jul. 21, 2022, 11:19 a.m. Rene Labounek, ***@***.***> wrote:
-
Start the automatic merging process, which we expect to fail (we'll
fix this with the following commands).
git checkout git-annex
git merge --no-edit --allow-unrelated-histories upstream/git-annex
We expect this to produce lots of output, ending with:
...
Automatic merge failed; fix conflicts and then commit the result.
My expected outputs started to appear different within the first set of
commands. My git does not know allow-unrelated-histories. Should I
continue? Or do we need to fix this first?
(base) ***@***.*** data-multi-subject]$ git checkout git-annex
Switched to branch 'git-annex'
Your branch is ahead of 'upstream/git-annex' by 5 commits.
(use "git push" to publish your local commits)
(base) ***@***.*** data-multi-subject]$
(base) ***@***.*** data-multi-subject]$ git merge --no-edit --allow-unrelated-histories upstream/git-annex
error: unknown option `allow-unrelated-histories'
usage: git merge [options] [<commit>...]
or: git merge [options] <msg> HEAD <commit>
or: git merge --abort
-n do not show a diffstat at the end of the merge
--stat show a diffstat at the end of the merge
--summary (synonym to --stat)
--log[=<n>] add (at most <n>) entries from shortlog to merge commit message
--squash create a single commit instead of doing a merge
--commit perform a commit if the merge succeeds (default)
-e, --edit edit message before committing
--ff allow fast-forward (default)
--ff-only abort if fast-forward is not possible
--rerere-autoupdate update the index with reused conflict resolution if possible
--verify-signatures Verify that the named commit has a valid GPG signature
-s, --strategy <strategy>
merge strategy to use
-X, --strategy-option <option=value>
option for selected merge strategy
-m, --message <message>
merge commit message (for a non-fast-forward merge)
-v, --verbose be more verbose
-q, --quiet be more quiet
--abort abort the current in-progress merge
--progress force progress reporting
-S, --gpg-sign[=<key id>]
GPG sign commit
--overwrite-ignore update ignored files (default)
(base) ***@***.*** data-multi-subject]$
I assume it is a git version issue
<https://stackoverflow.com/questions/41356766/unknown-option-allow-unrelated-histories>.
Unfortunatelly, I am not admin at the server where the database is stored.
So update git can be tricky or even impossible for me. Any other
possibility before I will write to server admins the update request?
(base) ***@***.*** data-multi-subject]$ git --version
git version 1.8.3.1
(base) ***@***.*** data-multi-subject]$
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First two commands appears that everythin is up to date. The third command does not know flag |
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From the output of your commands, it looks like the `git-annex` branch on
your computer already contains all the information from both
`origin/git-annex` and `upstream/git-annex`, with no conflicts. So, the
first command `git merge` correctly and successfully did nothing (but I was
expecting a merge conflict); the second command also saw no conflicts and
did nothing; and the third command `git merge --continue` didn't recognize
the `--continue` flag (probably a git version issue, yes), but in this
situation that command didn't need to do anything so that's ok.
Can you try the next commands? And whether or not it succeeds, if you can
do the last command (for saving the git-annex state to your fork on
github), at least I should be able to examine the state myself to figure
out what's going on.
…On Thu., Jul. 21, 2022, 11:49 a.m. Rene Labounek, ***@***.***> wrote:
First two commands appears that everythin is up to date. The third command
does not know flag --continue. Possibly, again, version issue.
(base) ***@***.*** data-multi-subject]$ git merge --no-edit upstream/git-annex
Already up-to-date.
(base) ***@***.*** data-multi-subject]$
(base) ***@***.*** data-multi-subject]$ git -c 'mergetool.custom.cmd=(echo "$MERGED" | grep -Eq [.]log$) && cat "$LOCAL" "$REMOTE" | sort -nu > "$MERGED"' \
> -c mergetool.custom.trustExitCode \
> -c mergetool.keepBackup=false \
> mergetool --tool=custom
No files need merging
(base) ***@***.*** data-multi-subject]$
(base) ***@***.*** data-multi-subject]$ git -c core.editor=/bin/true merge --continue
error: unknown option `continue'
usage: git merge [options] [<commit>...]
or: git merge [options] <msg> HEAD <commit>
or: git merge --abort
-n do not show a diffstat at the end of the merge
--stat show a diffstat at the end of the merge
--summary (synonym to --stat)
--log[=<n>] add (at most <n>) entries from shortlog to merge commit message
--squash create a single commit instead of doing a merge
--commit perform a commit if the merge succeeds (default)
-e, --edit edit message before committing
--ff allow fast-forward (default)
--ff-only abort if fast-forward is not possible
--rerere-autoupdate update the index with reused conflict resolution if possible
--verify-signatures Verify that the named commit has a valid GPG signature
-s, --strategy <strategy>
merge strategy to use
-X, --strategy-option <option=value>
option for selected merge strategy
-m, --message <message>
merge commit message (for a non-fast-forward merge)
-v, --verbose be more verbose
-q, --quiet be more quiet
--abort abort the current in-progress merge
--progress force progress reporting
-S, --gpg-sign[=<key id>]
GPG sign commit
--overwrite-ignore update ignored files (default)
(base) ***@***.*** data-multi-subject]$
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@mguaypaq, sorry for ym delay. I was not around computer much through the weekend. File download failed again. Bellow are the outputs. |
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Ah, examining the previous output you gave me more carefully, I see that After that, I would be curious if the following command now works (and the output): If it fails, the output of the following commands could help me figure out what's going on: |
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This really helped. See outputs bellow. Sorry for the hessle. But in summary, what was generally different for the forked database when compared to the README.md method? Just to start with the |
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Great! I'm so glad it works now 🎉
I think that's the main thing, yes, just doing
Hopefully that explains this a bit! |
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A bit, yes... :-D I have the data updated, so we can close this issue. Only question remain, if my case was just too specific or if it would be worth to add the potential neccesity of the |
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Indeed! I'll open a separate issue for that. Thanks again for your patience! |
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I fetched upstream spine-generic:data-multi-subject into https://github.com/renelabounek/data-multi-subject. Then I called
and have got following errors saying me that re-defaced T1w images were not downloaded throught the git annex:
The text was updated successfully, but these errors were encountered: