galaxyproject
History import deletes history archive
Describe the bug
I imported a history from the user_library_import_dir and was surprised that the archive is deleted.
Galaxy Version and/or server at which you observed the bug Galaxy Version: 24.2
Expected behavior Galaxy should warn that the file will be deleted or not delete the file.
Galaxy should warn that the file will be deleted or not delete the file.
I think that Galaxy shouldn't delete the file, this is just a bug.
@bernt-matthias, just to verify:
I can import files from the user_library_import_dir, but I can't seem to be able to export a history to it because it is not "writeable". Anyway, I manually placed a history archive in the user_library_import_dir, and the history archive does not get deleted from there.
So, I guess you are then using ftp_upload_dir instead to export your history (which is writeable), and, in that case, If you import it back it will be deleted because the default for ftp_upload_purge is True in the config, which sets delete_on_realize to True in the underlying PosixFileSource.
I'm not sure what the fix would be here... the behavior is exactly as documented in the config. I guess the Upload FTP is not a "long term" storage unless you set ftp_upload_purge to False.
Indeed I have set both (pointing to the same directory). I'm actually "abusing" ftp_upload_dir here, since I have not setup any FTP, but my users copy via scp to our cluster.