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nfdi4plants / ARCCommander

Tool to manage your ARCs
MIT License
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[BUG] git-lfs related Smudge error downloading arc-added lfs #105

Closed Brilator closed 2 years ago

Brilator commented 2 years ago

Describe the bug Indirectly related to arcCommander! Same error occurs with git only, but the referenced arc was init and synced via arccommander.

I'm having troubles cloning via arc get: ../20220201_macos_DB/arc get -r ssh://git@gitlab.nfdi4plants.de:/brilator/samplearc_metabolomics.git

Error message: 

Start processing command with the arguments:
        BranchName:Field ""
        RepositoryAddress:Field "ssh://git@gitlab.nfdi4plants.de:/brilator/samplearc_metabolomics.git"

Start Arc Get 
Cloning into 'samplearc_metabolomics'...
remote: Enumerating objects: 494, done.
remote: Counting objects: 100% (465/465), done.
remote: Compressing objects: 100% (446/446), done.
remote: Total 494 (delta 35), reused 433 (delta 19), pack-reused 29
Receiving objects: 100% (494/494), 185.19 KiB | 1.49 MiB/s, done.
Resolving deltas: 100% (38/38), done.
Downloading assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin (76 KB)
Error downloading object: assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin (2cf3723): Smudge error: Error downloading assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin (2cf37230ab009bb3c82e35052c3542ccfd5a5cb982afa712c97d4a14dcbe8905): batch request: missing protocol: "<unknown>"

Errors logged to /Users/dominikbrilhaus/Library/CloudStorage/OneDrive-SharedLibraries-DataPLANT/Tools - arcCommander/arcCommander_testing/20220209_tests_DB/samplearc_metabolomics/.git/lfs/logs/20220209T105413.96276.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin: smudge filter lfs failed
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

ERROR: Git command could not be run. 
Done processing command.

OS and framework information (please complete the following information):

Brilator commented 2 years ago

TLDR: Can someone comment, wether arc get -r ssh://git@gitlab.nfdi4plants.de:/brilator/samplearc_metabolomics.git is running on your system.

HLWeil commented 2 years ago

arc get -r ssh://git@gitlab.nfdi4plants.de:/brilator/samplearc_metabolomics.git

Start processing command with the arguments: BranchName:Field "" RepositoryAddress:Field "ssh://git@gitlab.nfdi4plants.de:/brilator/samplearc_metabolomics.git"

Start Arc Get ERROR: Cloning into 'samplearc_metabolomics'... ERROR: Host key verification failed. ERROR: fatal: Could not read from remote repository. ERROR: ERROR: Please make sure you have the correct access rights ERROR: and the repository exists. Done processing command.

I'm not sure about the syntax you used for the repo address. I tried: arc get -r https://gitlab.nfdi4plants.de/brilator/samplearc_metabolomics an that worked fine

HLWeil commented 2 years ago

But that doesn't seem to be the problem anyways judging from your error message.

Btw my git and git-lfs versions are the same

Martin-Kuhl commented 2 years ago

I also get an error using arc get -r ssh://git@gitlab.nfdi4plants.de:/brilator/samplearc_metabolomics.git

remote: Enumerating objects: 494, done. remote: Counting objects: 100% (465/465), done. remote: Compressing objects: 100% (446/446), done. remote: Total 494 (delta 35), reused 433 (delta 19), pack-reused 29R Receiving objects: 100% (494/494), 185.19 KiB | 3.14 MiB/s, done. Resolving deltas: 100% (38/38), done. Downloading assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin (76 KB) Error downloading object: assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin (2cf3723): Smudge error: Error downloading assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin (2cf37230ab009bb3c82e35052c3542ccfd5a5cb982afa712c97d4a14dcbe8905): batch request: missing protocol: "" Errors logged to C:\Users\Martin\Desktop\test\samplearc_metabolomics.git\lfs\logs\20220209T113728.1721495.log Use git lfs logs last to view the log. error: external filter 'git-lfs filter-process' failed fatal: assays/Talinum_GCMS_minimal/dataset/150112_03.D/AcqData/71_82_EC5_2GHz_Fiensplitless_wo_sugar.ei.M/7890Method.bin: smudge filter lfs failed warning: Clone succeeded, but checkout failed. You can inspect what was checked out with 'git status' and retry with 'git restore --source=HEAD :/' ERROR: Git command could not be run. Done processing command.

Seems to work for arc get -r https://gitlab.nfdi4plants.de/brilator/samplearc_metabolomics. At least it's still running...

Edit: worked

HLWeil commented 2 years ago

Might be an authentication problem? If I remember correctly, authentication to the GitLab instance and the git lfs storage behind it are separately handled. Maybe using your approach somehow the ssh key is handed to GitLab but not to git lfs?

Brilator commented 2 years ago

see my note 4: This arc get -r ssh://git@gitlab.nfdi4plants.de:27005/brilator/emptyarc.git works.

HLWeil commented 2 years ago

Ah didn't catch that. But I guess that supports my theory

Brilator commented 2 years ago

And as I said (note 2), there's some stupid Mac issue with cloning via https. However, this is not the case for cloning from GitHub. arc get -r https://github.com/nfdi4plants/ARC.gitworks.

Brilator commented 2 years ago

Might be an authentication problem? If I remember correctly, authentication to the GitLab instance and the git lfs storage behind it are separately handled. Maybe using your approach somehow the ssh key is handed to GitLab but not to git lfs?

Nope, that's not it. Cloning another arc, from gitlab, with lfs files, via ssh, works fine:

arc get -r ssh://git@gitlab.nfdi4plants.de:27005/martinkuhl/samplearc_rnaseq.git

So there's something particularly iffy about the samplearc_metabolomics with ssh and git lfs.

HLWeil commented 2 years ago

Could you clear out your issues?

Because of Note 3, we can assume that this is not an issue with the ArcCommander, but with the git <-> GitLab interaction. Therefore, I think this would actually rather fall within the scope of tasks of the guys maintaining this GitLab instance.

Brilator commented 2 years ago

Yes. I pushed the repository to the .org gitlab (https://git.nfdi4plants.org/brilator/samplearc_metabolomics.git) and was able to arc get -r from there.