Media symlink-script tries to remove files from immutable volume

[joachimtingvold]

Similar to #334, I was having problems upgrading to 11.0.19, and subsequently to 12.0.14. Getting the following error;

*** Running /etc/my_init.d/01_create_data_links.sh...
rm: cannot remove '/var/log': Directory not empty
*** Booting runit daemon...
*** Runit started as PID 20
*** Running /scripts/enterpoint.sh...
2025-08-08 21:30:14 Nginx ready
2025-08-08 21:30:14 This is an idle script (infinite loop) to keep container running.
[2025-08-08 21:30:14] Skip running setup-seafile-mysql.py because there is existing seafile-data folder.
[08/08/2025 21:30:14][upgrade]: The container was recreated, start fix the media symlinks
mv: not replacing '/shared/seafile/seahub-data/avatars/default-non-register.jpg'
mv: not replacing '/shared/seafile/seahub-data/avatars/default.png'
mv: not replacing '/shared/seafile/seahub-data/avatars/groups'
rm: cannot remove '/opt/seafile/seafile-pro-server-12.0.14/seahub/media/avatars': Directory not empty
Traceback (most recent call last):
  File "/scripts/start.py", line 94, in <module>
    main()
  File "/scripts/start.py", line 61, in main
    check_upgrade()
  File "/scripts/upgrade.py", line 120, in check_upgrade
    fix_media_symlinks()
  File "/scripts/upgrade.py", line 105, in fix_media_symlinks
    call('rm -rf %s' % avatars_dir)
  File "/scripts/utils.py", line 70, in call
    return subprocess.check_call(*a, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'rm -rf /opt/seafile/seafile-pro-server-12.0.14/seahub/media/avatars' returned non-zero exit status 1.

After looking at it, it seems this happened after I switched storage driver from fuse-overlayfs to overlay2 in Docker. I assume those volumes are immutable or something, which causes the logic to "remove" these folders to fail (since they're part of the immutable storage).

I could probably solve this by doing something along the lines below, but I feel thats a "hack". You should fix your "symlink script" to not attempt removing/altering things on the immutable storage.

services:
  seafile:
    […]
    volumes:
      - /foo/bar/baz:/opt/seafile/seafile-server-latest/seahub/media/avatars

[joachimtingvold]

After a bit back-and-forth, I managed to find a workaround (see below).

The changes from 11.x --> 12.x where MySQL database stuff MUST be defined via environmental variables is a bit stupid (and not especially clear in the upgrade notes). If you don't define them, Seafile silently fails (i.e. no useful error message) with the following:

[08/10/2025 00:08:53][upgrade]: The container was recreated, start fix the media symlinks
[08/10/2025 00:08:53][upgrade]: Done
Starting seafile server, please wait ...
Failed to start seafile server
Traceback (most recent call last):
  File "/scripts/start.py", line 94, in <module>
    main()
  File "/scripts/start.py", line 79, in main
    call('{} start'.format(get_script('seafile.sh')))
  File "/scripts/utils.py", line 70, in call
    return subprocess.check_call(*a, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/opt/seafile/seafile-pro-server-12.0.14/seafile.sh start' returned non-zero exit status 1.

Looking at the logs, it became more obvious what was happening (it was using the default database names, since I had not passed the real ones via environmental variables, even if they are in the config files).

Anyways. The workaround that worked for me (on Seafile 12.0.14):

1. Copy /scripts/upgrade.py out from the container.
2. Modify the script by commenting out the 5x call() lines in def fix_media_symlinks() (after if not islink(avatars_dir):).
3. Mount the script back to the container + add the volumes manually (see below)

The relevant part of my docker-compose.yml:

seafile:
    […]
    volumes:
      - ${STORAGE}/seafile:/shared
      - ${LIBRARIES}/seafile-data:/shared/seafile/seafile-data
      - ${STORAGE}/seafile/upgrade.py:/scripts/upgrade.py:ro
      - ${STORAGE}/seafile/seafile/seahub-media/avatars:/opt/seafile/seafile-pro-server-12.0.14/seahub/media/avatars
      - ${STORAGE}/seafile/seafile/seahub-media/custom:/opt/seafile/seafile-pro-server-12.0.14/seahub/media/custom
      - ${STORAGE}/seafile/seafile/seahub-media/thumbnail:/opt/seafile/seafile-pro-server-12.0.14/seahub/media/thumbnail