Script to solve "/etc/letsencrypt/live/.../cert.pem to be a symlink Renewal configuration file /etc/letsencrypt/renewal/...conf is broken. " certbot problem.

letsencrypt_symlink_error.py

"""
I'm not sure how and when, but certbot stopped updating my certificates because the cert files were expected but 
turned out to be actual real files. No idea how this happened.
 
This caused the annoying error:
 expected 
/etc/letsencrypt/live/.../cert.pem to be a symlink Renewal configuration file /etc/letsencrypt/renewal/...conf is 
broken. This scr… expected /etc/letsencrypt/live/.../cert.pem to be a symlink Renewal configuration file 
/etc/letsencrypt/renewal/...conf is broken. Skipping.

As I didn't feel like deleting and linking dozens of directories I've written this script to help me. Run with
-x parameter to actually delete and link files where needed. 

"""

import glob
import os
import sys

le_live_dir = "/etc/letsencrypt/live"
le_archive_dir = "/etc/letsencrypt/archive"

def find_archive_file(domain, file):
    count = 1
    archive_file = os.path.join(le_archive_dir, domain, file).replace(".pem", str(count) + ".pem")
    if not os.path.isfile(archive_file):
        raise ValueError("Could not find " + archive_file + ". Expected to at least have one file for " + file + " in " + domain + " archive dir, quitting")

    last_archive = False
    while os.path.isfile(archive_file):
        last_archive = archive_file
        count += 1
        archive_file = os.path.join(le_archive_dir, domain, file).replace(".pem", str(count) + ".pem")

    return last_archive


dry_run = len(sys.argv) < 2 or sys.argv[1] != "-x"
if dry_run:
    print("This is a dry run, please start with the -x parameter to actually delete and replace with symlinks")

livedirs = glob.glob(le_live_dir + "/*/*")
expected_links = ["fullchain.pem", "chain.pem", "privkey.pem", "cert.pem"]
for file in livedirs:
    basefile = os.path.basename(file)
    domain = file.split("/")[-2]
    if basefile in expected_links:
        if os.path.islink(file):
            print(basefile + " in domain " + domain + " is a symlink, as expected.")
        else:
            print(basefile + " in domain " + domain + " is a file, not a symlink.")
            archive_filename = find_archive_file(domain, basefile)
            print("Linking " + archive_filename + " there now")
            if dry_run:
                print("Dry run flag set: not deleting this file")
            else:
                try:
                    os.remove(file)
                    os.symlink(archive_filename, file)
                    print("Succesfully linked " + basefile + " from " + archive_filename)
                except OSError as e:
                    print("Could not delete " + e.filename + ", got error " + e.strerror)
                    print("You probably need to run this script as the root user..")
                    sys.exit(1)