Unable to renew letsencrypt certificate anymore
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### Summary
I can't renew letsencrypt certificate anymore while it was working fine for several months.
I'm running Omnibus, starter edition.
### Steps to reproduce
I'm running omnibus on my own company server, I was using GitLab 12.5.0 and I wanted to upgrade to 12.5.3 when I figured out this issue.
As suggested by the error message during the upgrade attempt, I ran `sudo gitlab-ctl reconfigure` to try to fix the issue but then I had this letsencrypt error message.
### Example Project
Not sure I can provide anything to help here...
### What is the current *bug* behavior?
When running `gitlab-ctl reconfigure` or `gitlab-ctl renew-le-certs`, I'm having the following error:
```shell
Acme::Client::Error::Malformed
------------------------------
acme_certificate[staging] (/opt/gitlab/embedded/cookbooks/cache/cookbooks/letsencrypt/resources/certificate.rb line 25) had an error: Acme::Client::Error::Malformed: Method not allowed
```
The full log is attached: [sudo_gitlab-ctl_renew-le-certs.log](/uploads/927de42da1c16b91ed50884b5b701122/sudo_gitlab-ctl_renew-le-certs.log)
**Please note that:**
* the tcp port 80 and 443 are open to the internet (tested with telnet)
* I have tried to shutdown the firewall of the host running gitlab: no change
* this worked fine during several months
* I've run through a lot of similar issues but no one had the exact same error message and all the working fixes (mainly about not open ports and wrong gitlab.rb configuration...) didn't work on my side
* my gitlab.rb contains the following:
```ruby
# nginx['enable'] = true
# nginx['client_max_body_size'] = '250m'
nginx['redirect_http_to_https'] = true
nginx['redirect_http_to_https_port'] = 80
...
letsencrypt['enable'] = true
# letsencrypt['contact_emails'] = # This should be an array of email addresses to add as contacts
# letsencrypt['group'] = 'root'
# letsencrypt['key_size'] = 2048
# letsencrypt['owner'] = 'root'
# letsencrypt['wwwroot'] = '/var/opt/gitlab/nginx/www'
# See http://docs.gitlab.com/omnibus/settings/ssl.html#automatic-renewal for more on these sesttings
letsencrypt['auto_renew'] = true
letsencrypt['auto_renew_hour'] = "2"
# letsencrypt['auto_renew_minute'] = nil # Should be a number or cron expression, if specified.
letsencrypt['auto_renew_day_of_month'] = "*/20"
```
### What is the expected *correct* behavior?
`gitlab-ctl reconfigure` should run successfully...
### Relevant logs and/or screenshots
see above.
### Output of checks
(If you are reporting a bug on GitLab.com, write: This bug happens on GitLab.com)
#### Results of GitLab environment info
<details>
<summary>Expand for output related to GitLab environment info</summary>
<pre>
System information
System:
Proxy: no
Current User: git
Using RVM: no
Ruby Version: 2.6.3p62
Gem Version: 2.7.9
Bundler Version:1.17.3
Rake Version: 12.3.3
Redis Version: 3.2.12
Git Version: 2.22.0
Sidekiq Version:5.2.7
Go Version: unknown
GitLab information
Version: 12.5.3-ee
Revision: 63955893276
Directory: /opt/gitlab/embedded/service/gitlab-rails
DB Adapter: PostgreSQL
DB Version: 10.9
URL: https://gitlab-server-name.company.com
HTTP Clone URL: https://gitlab-server-name.company.com/some-group/some-project.git
SSH Clone URL: git@gitlab-server-name.company.com:some-group/some-project.git
Elasticsearch: no
Geo: no
Using LDAP: yes
Using Omniauth: yes
Omniauth Providers:
GitLab Shell
Version: 10.2.0
Repository storage paths:
- default: /var/opt/gitlab/git-data/repositories
GitLab Shell path: /opt/gitlab/embedded/service/gitlab-shell
Git: /opt/gitlab/embedded/bin/git
</pre>
</details>
#### Results of GitLab application Check
<details>
<summary>Expand for output related to the GitLab application check</summary>
<pre>
Checking GitLab subtasks ...
Checking GitLab Shell ...
GitLab Shell: ... GitLab Shell version >= 10.2.0 ? ... OK (10.2.0)
Running /opt/gitlab/embedded/service/gitlab-shell/bin/check
Internal API available: OK
Redis available via internal API: OK
gitlab-shell self-check successful
Checking GitLab Shell ... Finished
Checking Gitaly ...
Gitaly: ... default ... OK
Checking Gitaly ... Finished
Checking Sidekiq ...
Sidekiq: ... Running? ... yes
Number of Sidekiq processes ... 1
Checking Sidekiq ... Finished
Checking Incoming Email ...
Incoming Email: ... Reply by email is disabled in config/gitlab.yml
Checking Incoming Email ... Finished
Checking LDAP ...
LDAP: ... Server: ldapmain
LDAP authentication... Success
LDAP users with access to your GitLab server (only showing the first 100 results)
User output sanitized. Found 7 users of 100 limit.
Checking LDAP ... Finished
Checking GitLab App ...
Git configured correctly? ... yes
Database config exists? ... yes
All migrations up? ... yes
Database contains orphaned GroupMembers? ... no
GitLab config exists? ... yes
GitLab config up to date? ... yes
Log directory writable? ... yes
Tmp directory writable? ... yes
Uploads directory exists? ... yes
Uploads directory has correct permissions? ... yes
Uploads directory tmp has correct permissions? ... yes
Init script exists? ... skipped (omnibus-gitlab has no init script)
Init script up-to-date? ... skipped (omnibus-gitlab has no init script)
Projects have namespace: ...
19/1 ... yes
3/4 ... yes
3/5 ... yes
7/10 ... yes
3/11 ... yes
3/13 ... yes
3/14 ... yes
3/15 ... yes
2/17 ... yes
13/19 ... yes
3/21 ... yes
17/23 ... yes
2/24 ... yes
19/25 ... yes
19/26 ... yes
19/28 ... yes
19/29 ... yes
21/30 ... yes
21/31 ... yes
21/32 ... yes
21/33 ... yes
Redis version >= 2.8.0? ... yes
Ruby version >= 2.5.3 ? ... yes (2.6.3)
Git version >= 2.22.0 ? ... yes (2.22.0)
Git user has default SSH configuration? ... yes
Active users: ... 8
Is authorized keys file accessible? ... yes
Elasticsearch version 5.6 - 6.x? ... skipped (elasticsearch is disabled)
Checking GitLab App ... Finished
Checking GitLab subtasks ... Finished
</pre>
</details>
### Possible fixes
(If you can, link to the line of code that might be responsible for the problem)
issue