Usage of pathlib.Path.resolve() breaks symlink trees / forests

[EricCousineau-TRI]

Description

Unfortunate case of spacebar heating 😅

We have some bazel code which runs notebooks.
Bazel works by creating a "runfiles" directory, which contains a series of symlinks from files that may not come from the same directories.

#415 introduced the following logic:

jupyter_server/jupyter_server/serverapp.py

Lines 2542 to 2545 in 55d9f68

	rootdir_abspath = pathlib.Path(self.root_dir).resolve()
	file_rawpath = pathlib.Path(self.file_to_run)
	combined_path = (rootdir_abspath / file_rawpath).resolve()
	is_child = str(combined_path).startswith(str(rootdir_abspath))

However (as a surprise to me), pathlib.Path.resolve() will not only make a path absolute, but it will resolve against symlinks.

This is an internal project, but similar code was hoisted to one of our public projects:
https://github.com/RobotLocomotion/drake/tree/v1.0.0/tools/jupyter

Reproduce

No direct repro script yet; however, I confirmed this will break Bazel out of sandboxes.
If I inject some print statements in this area, I get the following:

$ bazel run //:my_jupyter_notebook
...
file_rawpath: /path/to/project/bazel-bin/my_notebook.runfiles/project/my_notebook.ipynb
rootdir_abspath: /bazel/cache/execroot/anzu/bazel-out/k8-opt/bin/my_notebook.runfiles/project
combined_path: /path/to/project/my_notebook.ipynb
...
`root_dir` and `file_to_run` are incompatible. They don't share the same subtrees. Make sure `file_to_run` is on the same path as `root_dir`.

Expected behavior

It should only get absolute path, not the real path, and it should work fine.

Possible workarounds:

• In our own setup, use os.path.realpath on the notebook
  • Feasible, may do this, but would still like to keep the option of using runfiles
• File PR and wait - better
• Copy all files to the physically same directory - eww
• Monkey patch serverapp.py to use os.path.abspath() - meh

Context

• Operating System and version: Ubuntu 20.04
• Browser and version: Firefox 97.0.2
• Jupyter Server version: 1.13.5

Troubleshoot Output

$ bazel run //tools/jupyter:jupyter troubleshoot
...
$PATH:
        {effective venv}
        /usr/local/sbin
        /usr/local/bin
        /usr/sbin
        /usr/bin
        /sbin
        /bin
        /usr/games
        /usr/local/games
        /snap/bin
sys.path:

{effective venv}

/usr/lib/python38.zip

/usr/lib/python3.8

/usr/lib/python3.8/lib-dynload

/usr/local/lib/python3.8/dist-packages

/usr/lib/python3/dist-packages
sys.executable:

/usr/bin/python3.8
sys.version:

3.8.10 (default, Nov 26 2021, 20:14:08)

[GCC 9.3.0]
platform.platform():

Linux-5.13.0-30-generic-x86_64-with-glibc2.29
which -a jupyter:

/bazel/cache/execroot/project/bazel-out/k8-opt/bin/external/pip_deps/data/python3.8/bin/jupyter

/path/to/project/wip/project/bazel-bin/tools/jupyter/jupyter.runfiles/pip_deps/data/python3.8/bin/jupyter

/usr/bin/jupyter

/bin/jupyter
pip list:

Package                  Version

------------------------ --------------------

...

jupyter                  1.0.0

jupyter-client           7.1.2

jupyter-console          6.4.3

jupyter-core             4.9.2

jupyter-packaging        0.11.1

jupyter-server           1.13.5

jupyterlab               3.3.0

jupyterlab-pygments      0.1.2

jupyterlab-server        2.10.3

jupyterlab-widgets       1.0.2

...

Command Line Output

N/A (I believe)

Browser Output

N/A

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[davidbrochart]

Thanks for reporting @EricCousineau-TRI.
It looks like using .absolute() instead of .resolve() would work.

[EricCousineau-TRI]

Nice! Didn't see .absolute() in the Python docs for some reason, so I guess that's another bug 😿
Tested in our local setup, and it worked perfectly!

See #712

[EricCousineau-TRI]

Ah, was about to file bug report for Python, but looks like it's already fixed in newer (dev) docs:
https://docs.python.org/3.11/library/pathlib.html#id5