Open mariehbourget opened 3 years ago
kousu
commented
3 years ago This sounds suspiciously similar to #137. At least, it overlaps with it.
It sounds like your local annex somehow corrupted itself. Can you please mv /home/mhbourget/dataset/data_axondeepseg_tem/ /home/mhbourget/dataset/data_axondeepseg_tem-corrupted and try redownloading everything?
mariehbourget
commented
3 years ago Can you please
mv /home/mhbourget/dataset/data_axondeepseg_tem/ /home/mhbourget/dataset/data_axondeepseg_tem-corruptedand try redownloading everything?
I already tried that a couple of times in the last few weeks, with branch reviews for corrections on the tem dataset.
So each time I renamed the "corrupted" dataset and re-cloned/downloaded from scratch.
The same "corrupted" behavior happens every time when I try to switch branch i.e. if I run git annex get . once, the local repo is stuck on the branch as described above.
kousu
commented
3 years ago Okay thanks @mariehbourget, I'll reproduce it and try to figure it out.
To honest though this just motivates me to push for #68 even more. I have a long list of similar problems with git-annex: https://github.com/neuropoly/data-management/labels/git-annex%20bugs
mariehbourget
commented
3 years ago I am working in Ubuntu 20.04 in WSL1 if that changes anything.
kousu
commented
3 years ago I wasn't able to reproduce this on Linux:
Are you working on a Mac? And what version of git-annex do you have? This is a working version:
u108545@joplin:~/data_axondeepseg_tem$ git annex version
git-annex version: 8.20200226
build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.20 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.6.5 http-client-0.5.14 persistent-sqlite-2.9.3 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs hook external
operating system: linux x86_64
supported repository versions: 8
upgrade supported from repository versions: 0 1 2 3 4 5 6 7
local repository version: 8
u108545@joplin:~/data_axondeepseg_tem$ git version
git version 2.25.1
u108545@joplin:~/data_axondeepseg_tem$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.3 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.3 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal
jcohenadad
commented
3 years ago To honest though this just motivates me to push for #68 even more. I have a long list of similar problems with git-annex: https://github.com/neuropoly/data-management/labels/git-annex%20bugs
😊
mariehbourget
commented
3 years ago I am on Ubuntu 20.04 in WSL1.
Same version for git-annex and git. Slightly different for OS..
mhb@LAPTOP:~$ git annex version
git-annex version: 8.20200226
build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.20 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.6.5 http-client-0.5.14 persistent-sqlite-2.9.3 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs hook external
operating system: linux x86_64
supported repository versions: 8
upgrade supported from repository versions: 0 1 2 3 4 5 6 7
mhb@LAPTOP:~$ git version
git version 2.25.1
mhb@LAPTOP:~$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focalI will probably use rosenberg in the near future, so I'll test there as well and keep you posted.
Question: I will need another key for that, right?
kousu
commented
3 years ago I am working in Ubuntu 20.04 in WSL1 if that changes anything.
Ah WSL. I don't have WSL easily at hand.
Question: I will need another key for that, right?
Yep, but you can set it up yourself: https://github.com/neuropoly/data-management/blob/master/internal-server.md#add-extra-devices
You would just do:
ssh rosenberg.neuro.polymtl.ca
ssh-keygen # i.e. this should be run *on* rosenberg
exit
ssh rosenberg cat .ssh/id_rsa.pub | ssh git@data.neuro.polymtl.ca keys add maboudb@rosenberg # this needs to be run *from WSL*EDIT: I forgot, you need to authorize your new key using your old key, of course, so you need to run the last command from WSL.
mariehbourget
commented
2 years ago Hi @kousu, I was able to set up my key for rosenberg following the instructions in https://github.com/neuropoly/data-management/blob/master/internal-server.md#add-extra-devices.
The command ssh rosenberg cat .ssh/id_rsa.pub | ssh git@data.neuro.polymtl.ca keys add maboudb@rosenberg you suggested above was not working with error ssh: Could not resolve hostname rosenberg: Name or service not known.
I tried ssh rosenberg.neuro.polymtl.ca cat .ssh/id_rsa.pub | ssh git@data.neuro.polymtl.ca keys add maboudb@rosenberg instead, it was asking me my passphrase for the key and then to answer yes or no (without a question) and I was confused.
So I'm all set anyway, but I wanted to let you know.
kousu
commented
2 years ago Ah! I quoted a raccourci I have set up on my system. I'm glad you managed to get it working despite my confusing suggestion :) :sweat_smile:
I have an issue when trying to switch branch in a git-annex repo for reviewing PRs.
After cloning and running the
git annex get .command and after all files are downloaded, I get this repeated error and I have to kill the process (Ctrl+C) to go back to the prompt.Then if I try to
checkoutanother branch, I get:I assume it is because of the previously "killed" process. If I removed the
.git/index.lockfile and re-try thecheckoutI get:git statusindicates that all files have changed.git restore .seems to run normally but again at the end I get the same error as my first one that I have to kill:So I'm stuck in a loop and I have to clone and download the files again each time I want to do a review.
I'm following instructions here for download and here for checkout, but I think I am missing something.
Thank you for your help!