[BUG] Datalad on WSL 2 - "datalad save" not always working

[jhpb7]

Current behavior

I’m currently working my way through the handbook and while most of it works, there is one error occurring. When trying to save the books (pdfs in folder books) in section 1.2, using datalad save -m "add books on Python and Unix to read later"

the following error occurs: add(ok): somedataset (file) add(ok): .gitmodules (file)

[ERROR ] git-annex: .git/annex/othertmp/TLCL.pdf.0/TLCL.pdf: rename: permission denied (Permission denied) [add(/mnt/c/Users/++USERNAME++/Documents/datalab/test/DataLad-101/books/TLCL.pdf)] add(error): books/TLCL.pdf (file) [git-annex: .git/annex/othertmp/TLCL.pdf.0/TLCL.pdf: rename: permission denied (Permission denied)] [ERROR ] git-annex: .git/annex/othertmp/byte-of-python.pdf.0/byte-of-python.pdf: rename: permission denied (Permission denied) [add(/mnt/c/Users/++USERNAME++/Documents/datalab/test/DataLad-101/books/byte-of-python.pdf)] add(error): books/byte-of-python.pdf (file) [git-annex: .git/annex/othertmp/byte-of-python.pdf.0/byte-of-python.pdf: rename: permission denied (Permission denied)] save(ok): . (dataset) action summary: add (error: 2, ok: 2) save (ok: 1)

After that everything works fine until at section 5.3, I tried to use the “write your own procedures” and then again saving the python code yields this permission denied error. Between all this, saving (e.g. to the notes.txt) works fine.

Operating system

• Windows 10 Version 21H1 (Build 19043.1586)

DataLad information

WTF

configuration <SENSITIVE, report disabled by configuration>

datalad

• full_version: 0.12.4
• version: 0.12.4

  dependencies

• appdirs: 1.4.3
• boto: 2.49.0
• cmd:7z: 16.02
• cmd:annex: 8.20200226
• cmd:bundled-git: 2.25.1
• cmd:git: 2.25.1
• cmd:system-git: 2.25.1
• cmd:system-ssh: 8.2p1
• exifread: 2.1.2
• git: 3.0.7
• gitdb: 2.0.6
• humanize: 1.0.0
• iso8601: 0.1.12
• keyring: 18.0.1
• keyrings.alt: 3.4.0
• msgpack: 0.6.2
• mutagen: 1.44.0
• requests: 2.22.0
• wrapt: 1.11.2

  environment

• GIT_PYTHON_GIT_EXECUTABLE: /usr/bin/git
• LANG: C.UTF-8
• PATH: /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0/:/mnt/c/Windows/System32/OpenSSH/:/mnt/c/Program Files/Microsoft SQL Server/130/Tools/Binn/:/mnt/c/Program Files/SCIPOptSuite 8.0.0/bin:/mnt/c/Users/++USERNAME++/Anaconda3:/mnt/c/Users/++USERNAME++/Anaconda3/Library/mingw-w64/bin:/mnt/c/Users/++USERNAME++/Anaconda3/Library/usr/bin:/mnt/c/Users/++USERNAME++/Anaconda3/Library/bin:/mnt/c/Users/++USERNAME++/Anaconda3/Scripts:/mnt/c/Users/++USERNAME++/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/++USERNAME++/AppData/Local/Programs/Microsoft VS Code/bin:/mnt/c/Users/++USERNAME++/AppData/Local/Programs/Git/cmd:/snap/bin

  extensions

  git-annex

• 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: -....
• operating system: linux x86_64
• remote types:
  • git
  • gcrypt
  • p2p
  • S3
  • bup
  • directory
  • rsync
  • web
  • bittorrent
  • webdav
  • adb
  • tahoe
  • glacier
  • ddar
  • git-lfs
  • hook
  • external
• supported repository versions:
  • 8
• upgrade supported from repository versions:
  • 0
  • 1
  • 2
  • 3
  • 4
  • 5
  • 6
  • 7
• version: 8.20200226

  location

• path: /mnt/c/Users/++USERNAME++/Documents/test
• type: directory

  metadata_extractors

• annex:
  • load_error: None
  • module: datalad.metadata.extractors.annex
  • version: None
• audio:
  • load_error: None
  • module: datalad.metadata.extractors.audio
  • version: None
• datacite:
  • load_error: None
  • module: datalad.metadata.extractors.datacite
  • version: None
• datalad_core:
  • load_error: None
  • module: datalad.metadata.extractors.datalad_core
  • version: None
• datalad_rfc822:
  • load_error: None
  • module: datalad.metadata.extractors.datalad_rfc822
  • version: None
• exif:
  • load_error: None
  • module: datalad.metadata.extractors.exif
  • version: None
• frictionless_datapackage:
  • load_error: None
  • module: datalad.metadata.extractors.frictionless_datapackage
  • version: None
• image:
  • load_error: None
  • module: datalad.metadata.extractors.image
  • version: None
• xmp:
  • load_error: No module named 'libxmp' [xmp.py::20]
  • module: datalad.metadata.extractors.xmp

    python

• implementation: CPython
• version: 3.8.2

  system

• distribution: ubuntu/20.04/focal
• encoding:
  • default: utf-8
  • filesystem: utf-8
  • locale.prefered: UTF-8
• max_path_length: 290
• name: Linux
• release: 5.10.102.1-microsoft-standard-WSL2
• type: posix
• version: #1 SMP Wed Mar 2 00:30:59 UTC 2022

Browser

No response

Additional context

• using VS Code and starting WSL in cmd line (wsl.exe)
• WSL 2 with Ubuntu 20.04 LTS
• working on a Windows folder, thus "/mnt/c/Users/++USERNAME++/Documents/datalab"

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[adswa]

Hi @jhpb7 , thanks for the detailed report! I can't help much right away, I'm on vacation with limited internet access. There are two things I recommend doing: Can you update datalad and git-annex and check if the problem persists? Both of your versions are more 2 years old, and more recent versions have seen improvements that may at least produce more informative errors. Try to get versions along the lines of datalad 0.15.x and git-annex 10.xxx. If this doesn't help, could you open an issue in github.com/datalad/datalad and link your report?

[jhpb7]

Hi @adswa, thanks for your quick reply! I updated to datalad 0.15.x but was not able to find a proper git-annex version > 8.20. However, you were right about a more insightful message. I reported an issue here. I would keep the issue open here until it is fixed, ok? Thank you + have a nice vacation :)

[jhpb7]

Issue is closed due to a workaround posted here.