Storage can not be found by name ''

Summary

Since I've updated gitlab from 11.8.10 to 12.0.9 (installed from the Debian Experimental repository), it is not possible to interact with repositories through ssh+git. It still works with https+git.

I've tried to update to the latest available version of gitlab in experimental (12.2.9) with the same result.

What is the current bug behavior?

On client-side on a project:

$ git fetch
gitaly-upload-pack: fatal: error: %v
fatal: Could not read from remote repository.

And server side (gitlab-shell.log):

time="2019-10-23T15:53:54+02:00" level=info msg="finished HTTP request" duration=0.03395727 gitaly_embedded=false method=POST pid=8834 url="http://localhost:8080/api/v4/internal/allowed"
time="2019-10-23T15:53:54+02:00" level=info msg="executing git command" command="gitaly-upload-pack unix:/run/gitlab/sockets/private/gitaly.socket
{\"repository\":{},\"gl_repository\":\"project-2\",\"gl_project_path\":\"romain/weboob\",\"gl_id\":\"key-3\",\"gl_username\":\"romain\",\"git_config_options\":[],\"git_protocol\":null}" pid=8834 user="user with id key-3"
time="2019-10-23T15:53:54+02:00" level=error msg="error: %v" error="rpc error: code = InvalidArgument desc = Storage can not be found by name ''" pid=8834

Results of GitLab environment info

Expand for output related to the GitLab application check

# gitlab-rake gitlab:env:info
Check if Gitlab is configured correctly...
fatal: not a git repository (or any of the parent directories): .git
fatal: not a git repository (or any of the parent directories): .git
/usr/share/gitlab/lib/gitlab.rb:38: warning: already initialized constant Gitlab::COM_URL
/usr/share/gitlab/lib/gitlab.rb:38: warning: previous definition of COM_URL was here
/usr/share/gitlab/lib/gitlab.rb:39: warning: already initialized constant Gitlab::APP_DIRS_PATTERN
/usr/share/gitlab/lib/gitlab.rb:39: warning: previous definition of APP_DIRS_PATTERN was here
/usr/share/gitlab/lib/gitlab.rb:40: warning: already initialized constant Gitlab::SUBDOMAIN_REGEX
/usr/share/gitlab/lib/gitlab.rb:40: warning: previous definition of SUBDOMAIN_REGEX was here
/usr/share/gitlab/lib/gitlab.rb:41: warning: already initialized constant Gitlab::VERSION
/usr/share/gitlab/lib/gitlab.rb:41: warning: previous definition of VERSION was here
/usr/share/gitlab/lib/gitlab.rb:42: warning: already initialized constant Gitlab::INSTALLATION_TYPE
/usr/share/gitlab/lib/gitlab.rb:42: warning: previous definition of INSTALLATION_TYPE was here
/usr/share/gitlab/lib/gitlab.rb:43: warning: already initialized constant Gitlab::HTTP_PROXY_ENV_VARS
/usr/share/gitlab/lib/gitlab.rb:43: warning: previous definition of HTTP_PROXY_ENV_VARS was here
/usr/share/gitlab/config/initializers/2_app.rb:6: warning: already initialized constant Gitlab::VERSION
/usr/share/gitlab/lib/gitlab.rb:41: warning: previous definition of VERSION was here
System information
System:         Debian testing
Current User:   gitlab
Using RVM:      no
Ruby Version:   2.5.7p206
Gem Version:    2.7.6.2
fatal: not a git repository (or any of the parent directories): .git
fatal: not a git repository (or any of the parent directories): .git
Bundler Version:1.17.3
Rake Version:   12.3.3
Redis Version:  5.0.6
Git Version:    2.24.0.
Sidekiq Version:5.2.7
Go Version:     unknown
GitLab information
Version:        12.2.9
Revision:       Unknown
Directory:      /usr/share/gitlab
DB Adapter:     PostgreSQL
DB Version:     9.6.10
URL:            https://localhost
HTTP Clone URL: https://localhost/some-group/some-project.git
SSH Clone URL:  gitlab@localhost:some-group/some-project.git
Using LDAP:     no
Using Omniauth: no
GitLab Shell
Version:        9.3.0
Repository storage paths:

• default: /var/lib/gitlab/repositories GitLab Shell path: /usr/share/gitlab-shell Git: /usr/bin/git

Results of GitLab application Check

Expand for output related to the GitLab application check

gitlab-rake gitlab:check SANITIZE=true
Check if Gitlab is configured correctly...
fatal: not a git repository (or any of the parent directories): .git
fatal: not a git repository (or any of the parent directories): .git
/usr/share/gitlab/lib/gitlab.rb:38: warning: already initialized constant Gitlab::COM_URL
/usr/share/gitlab/lib/gitlab.rb:38: warning: previous definition of COM_URL was here
/usr/share/gitlab/lib/gitlab.rb:39: warning: already initialized constant Gitlab::APP_DIRS_PATTERN
/usr/share/gitlab/lib/gitlab.rb:39: warning: previous definition of APP_DIRS_PATTERN was here
/usr/share/gitlab/lib/gitlab.rb:40: warning: already initialized constant Gitlab::SUBDOMAIN_REGEX
/usr/share/gitlab/lib/gitlab.rb:40: warning: previous definition of SUBDOMAIN_REGEX was here
/usr/share/gitlab/lib/gitlab.rb:41: warning: already initialized constant Gitlab::VERSION
/usr/share/gitlab/lib/gitlab.rb:41: warning: previous definition of VERSION was here
/usr/share/gitlab/lib/gitlab.rb:42: warning: already initialized constant Gitlab::INSTALLATION_TYPE
/usr/share/gitlab/lib/gitlab.rb:42: warning: previous definition of INSTALLATION_TYPE was here
/usr/share/gitlab/lib/gitlab.rb:43: warning: already initialized constant Gitlab::HTTP_PROXY_ENV_VARS
/usr/share/gitlab/lib/gitlab.rb:43: warning: previous definition of HTTP_PROXY_ENV_VARS was here
/usr/share/gitlab/config/initializers/2_app.rb:6: warning: already initialized constant Gitlab::VERSION
/usr/share/gitlab/lib/gitlab.rb:41: warning: previous definition of VERSION was here
Checking GitLab subtasks ...
Checking GitLab Shell ...
GitLab Shell: ... GitLab Shell version >= 9.3.0 ? ... OK (9.3.0)
Running /usr/share/gitlab-shell/bin/check
fatal: not a git repository (or any of the parent directories): .git
fatal: not a git repository (or any of the parent directories): .git
Check GitLab API access: OK
Redis available via internal API: OK
Access to /usr/share/gitlab/.ssh/authorized_keys: fatal: not a git repository (or any of the parent directories): .git
fatal: not a git repository (or any of the parent directories): .git
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: ... LDAP is disabled in config/gitlab.yml
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? ... yes

Init script up-to-date? ... yes

Projects have namespace: ...

weboob / weboob ... yes

Romain Bignon / weboob ... yes

weboob / modules ... yes

weboob / stable ... yes

Laurent Bachelier / weboob ... yes

weboob / website ... yes

weboob / association ... yes

weboob / debian ... yes

ntome / devel ... yes

ZeHiro / devel ... yes
Bezleputh / devel ... yes
Jonathan SCHMIDT / devel ... yes
weboob / weboob-ci ... yes

Matthieu Weber / devel ... yes

Damien Cassou / website ... yes

Kitof / devel ... yes

Florent Fourcot / devel ... yes
Philipp Schmitt / devel ... yes

François Revol / devel ... yes
ntome / website ... yes

Alexis de Lattre / devel ... yes

glundy35 / devel ... yes
Jerome / modules ... yes

alkino / devel ... yes
Guillaume Seznec / devel ... yes

Mickaël Thomas / devel ... yes
Guyzmo / git-repo ... yes
JEAN Sébastien / weboob ... yes
Geoffrey R. / devel ... yes
Kremer / devel ... yes
Benjamin Bouvier / devel ... yes
Adrien / weboob ... yes
Laurent Bachelier / scrapoob ... yes
gagbo / devel ... yes
Guicar / devel ... yes

Rémi - Filament / devel ... yes

dohseven / devel ... yes
Jerome / devel ... yes

Damien Espitallier / devel ... yes
Nicolas Frandeboeuf / devel ... yes
Caram Dache / devel ... yes
Rémi - Filament / stable ... yes

Julien Juke Hebert / devel ... yes
Bruno Chabrier / devel ... yes

Julien Veyssier / devel ... yes
Manoj / devel ... yes
ntome / debian ... yes
ntome / test zzz ... yes

Anthony Martinet / devel ... yes
Sebastien Marie / devel ... yes
ahuillet / devel ... yes
Redis version >= 2.8.0? ... yes

Ruby version >= 2.3.3 ? ... yes (2.5.7)
Git version >= 2.22.0 ? ... yes (2.24.0)
Git user has default SSH configuration? ... yes

Active users: ... 1920
Checking GitLab App ... Finished
Checking GitLab subtasks ... Finished