Getting abosl

[chambm]

For upload_from_galaxy_filesystem(preserve_dirs=False), do I understand correctly that the uploaded files should be placed in the indicated folder_id regardless of the filesystem paths that are being uploaded?

Because I'm not seeing that. I'm getting full absolute filepaths in 20.09 when using symlinks and preserve_dirs=False (which should be the default anyway.

[nsoranzo]

Sorry for the late reply! The uploaded files (or the symlinks) should be created in the indicated folder id, if I understand correctly what you are doing. If you are still experiencing this, could you provide an example call of upload_from_galaxy_filesystem(), what you get as result and what you would expect instead?