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Failure to clone on Windows - slow file system?  #337

@adswa

Description

@adswa

I tried the JülichData tutorial on Windows, and found that the cloning of the example dataset was seemingly stuck. A possible hint was visible when I git clone'ed and interrupted the hanging process:

C:\Users\mih\TMP\my-dataset>git clone "datalad-annex::?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC" testingk
12:13:36.900291 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/bin
12:13:36.900291 git.c:479               trace: built-in: git clone 'datalad-annex::?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC' testingk
Cloning into 'testingk'...
12:13:36.938082 run-command.c:667       trace: run_command: git remote-datalad-annex origin '?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC'
12:13:36.938082 run-command.c:928       trace: start_command: git remote-datalad-annex origin '?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC'
12:13:36.953730 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
12:13:36.969355 git.c:783               trace: exec: git-remote-datalad-annex origin '?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC'
12:13:36.969355 run-command.c:667       trace: run_command: git-remote-datalad-annex origin '?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC'
12:13:36.969355 run-command.c:928       trace: start_command: git-remote-datalad-annex origin '?type=external&externaltype=dataverse&encryption=none&exporttree=yes&url=https://demo.dataverse.org/&doi=doi:10.70122/FK2/KXGHCC'
[INFO] 12:13:39.210060 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.213056 git.c:783               trace: exec: git-annex init -c annex.dotfiles=true
[INFO] 12:13:39.213056 run-command.c:667       trace: run_command: git-annex init -c annex.dotfiles=true
| 12:13:39.213056 run-command.c:928       trace: start_command: git-annex init -c annex.dotfiles=true
[INFO] 12:13:39.278087 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.282087 git.c:479               trace: built-in: git config --null --list
[INFO] 12:13:39.333964 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.336968 git.c:479               trace: built-in: git show-ref --hash refs/heads/git-annex
[INFO] 12:13:39.350967 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.352966 git.c:479               trace: built-in: git show-ref --verify -q refs/remotes/origin/git-annex
[INFO] 12:13:39.367974 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.370977 git.c:479               trace: built-in: git update-index -z --index-info
[INFO] 12:13:39.384972 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.386970 git.c:479               trace: built-in: git write-tree
[INFO] 12:13:39.406918 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.408921 git.c:479               trace: built-in: git commit-tree 4b825dc642cb6eb9a060e54bf8d69288fbee4904 --no-gpg-sign -m 'branch created'
[INFO] 12:13:39.424862 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.426862 git.c:479               trace: built-in: git update-ref refs/heads/git-annex 80c539149f3e30a05c3c163dd59b98e952ba5789
[INFO] 12:13:39.449864 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.451871 git.c:479               trace: built-in: git config annex.uuid 244e03d6-d211-4d83-81fe-263ed5f29570
[INFO] 12:13:39.467865 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.469866 git.c:479               trace: built-in: git config --null --list
[INFO] Detected a filesystem without fifo support.
[INFO] Disabling ssh connection caching.
[INFO] 12:13:39.484863 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.486864 git.c:479               trace: built-in: git config annex.sshcaching false
[INFO] 12:13:39.500867 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.503864 git.c:479               trace: built-in: git config --null --list
[INFO] Detected a crippled filesystem.
[INFO] 12:13:39.518867 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.520863 git.c:479               trace: built-in: git config annex.crippledfilesystem true
[INFO] 12:13:39.535869 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.539862 git.c:479               trace: built-in: git config --null --list
[INFO] 12:13:39.553861 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.555873 git.c:479               trace: built-in: git show-ref git-annex
[INFO] 12:13:39.568860 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.570861 git.c:479               trace: built-in: git show-ref --hash refs/heads/git-annex
[INFO] 12:13:39.584861 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.587868 git.c:479               trace: built-in: git log refs/heads/git-annex..80c539149f3e30a05c3c163dd59b98e952ba5789 '--pretty=%H' -n1
[INFO] 12:13:39.610876 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.612865 git.c:479               trace: built-in: git hash-object -w --no-filters --stdin-paths
[INFO] 12:13:39.619872 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.622868 git.c:479               trace: built-in: git cat-file --batch
[INFO] 12:13:39.623868 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.627863 git.c:479               trace: built-in: git update-index -z --index-info
[INFO] 12:13:39.632869 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.635862 git.c:479               trace: built-in: git diff-index --raw -z -r --no-renames -l0 --cached refs/heads/git-annex --
[INFO] 12:13:39.661867 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.663872 git.c:479               trace: built-in: git config annex.version 10
[INFO] 12:13:39.683872 exec-cmd.c:266          trace: resolved executable dir: C:/Program Files/Git/mingw64/libexec/git-core
[INFO] 12:13:39.688863 git.c:479               trace: built-in: git config --null --list
Deletion of directory 'testingk/.git/dl-repoannex/origin/repoannex' failed. Should I try again? (y/n) Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Scripts\git-remote-datalad-annex.exe\__main__.py", line 7, in <module>
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad_next\gitremotes\datalad_annex.py", line 1311, in main
    remote.communicate()
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad_next\gitremotes\datalad_annex.py", line 765, in communicate
    self.get_remote_refs(raise_on_error=True)
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad_next\gitremotes\datalad_annex.py", line 992, in get_remote_refs
    ra = self.repoannex
         ^^^^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad_next\gitremotes\datalad_annex.py", line 522, in repoannex
    ra.call_annex(
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\support\annexrepo.py", line 1318, in call_annex
    return self._call_annex(
           ^^^^^^^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\support\annexrepo.py", line 997, in _call_annex
    return runner.run(
           ^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\runner\runner.py", line 225, in run
    results_or_iterator = threaded_runner.run()
                          ^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\runner\nonasyncrunner.py", line 347, in run
    return self._locked_run()
           ^^^^^^^^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\runner\nonasyncrunner.py", line 520, in _locked_run
    return self.process_loop()
           ^^^^^^^^^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\runner\nonasyncrunner.py", line 527, in process_loop
    self.process_queue()
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\site-packages\datalad\runner\nonasyncrunner.py", line 641, in process_queue
    file_number, state, data = self.output_queue.get(
                               ^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\queue.py", line 180, in get
    self.not_empty.wait(remaining)
  File "C:\Users\mih\AppData\Local\Programs\Python\Python312\Lib\threading.py", line 338, in wait
    gotit = waiter.acquire(True, timeout)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyboardInterrupt
Deletion of directory 'testingk/.git/dl-repoannex/origin/repoannex' failed. Should I try again? (y/n)

I'm investigating why the deletion failed. It could be that some process still has the directory or that Windows is so slow that it thinks thats the case, or maybe a permission issue...

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