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# Cannot Connect to MariaDB
## Description
GeneNetwork3 is failing to connect to mariadb with the error:
```
⋮
2024-11-05 14:49:00 Traceback (most recent call last):
2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/flask/app.py", line 1523, in full_dispatch_request
2024-11-05 14:49:00 rv = self.dispatch_request()
2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/flask/app.py", line 1509, in dispatch_request
2024-11-05 14:49:00 return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/gn3/api/menu.py", line 13, in generate_json
2024-11-05 14:49:00 with database_connection(current_app.config["SQL_URI"], logger=current_app.logger) as conn:
2024-11-05 14:49:00 File "/gnu/store/lzw93sik90d780n09svjx5la1bb8g3df-python-3.10.7/lib/python3.10/contextlib.py", line 135, in __enter__
2024-11-05 14:49:00 return next(self.gen)
2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/gn3/db_utils.py", line 34, in database_connection
2024-11-05 14:49:00 connection = mdb.connect(db=db_name,
2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/MySQLdb/__init__.py", line 121, in Connect
2024-11-05 14:49:00 return Connection(*args, **kwargs)
2024-11-05 14:49:00 File "/gnu/store/83v79izrqn36nbn0l1msbcxa126v21nz-profile/lib/python3.10/site-packages/MySQLdb/connections.py", line 195, in __init__
2024-11-05 14:49:00 super().__init__(*args, **kwargs2)
2024-11-05 14:49:00 MySQLdb.OperationalError: (2002, "Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)")
```
We have previously defined the default socket file[^1][^2] as "/run/mysqld/mysqld.sock".
## Troubleshooting Logs
### 2024-11-05
I attempted to just bind `/run/mysqld/mysqld.sock` to `/tmp/mysql.sock` by adding the following mapping in GN3's `gunicorn-app` definition:
```
(file-system-mapping
(source "/run/mysqld/mysqld.sock")
(target "/tmp/mysql.sock")
(writable? #t))
```
but that does not fix things.
I had tried to change the mysql URI to use IP addresses, i.e.
```
SQL_URI="mysql://webqtlout:webqtlout@128.169.5.119:3306/db_webqtl"
```
but that simply changes the error from the above to the one below:
```
2024-11-05 15:27:12 MySQLdb.OperationalError: (2002, "Can't connect to MySQL server on '128.169.5.119' (115)")
```
I tried with both `127.0.0.1` and `128.169.5.119`.
My hail-mary was to attempt to expose the `my.cnf` file generated by the `mysql-service-type` definition to the "pola-wrapper", but that is proving tricky, seeing as the file is generated elsewhere[^4] and we do not have a way of figuring out the actual final path of the file.
I tried:
```
(file-system-mapping
(source (mixed-text-file "my.cnf"
(string-append "[client]\n"
"socket=/run/mysqld/mysqld.sock")))
(target "/etc/mysql/my.cnf"))
```
but that did not work either.
### 2024-11-07
Start digging into how GNU Guix services are defined[^5] to try and understand why the file mapping attempt did not work.
=> http://git.savannah.gnu.org/cgit/guix.git/tree/gnu/system/file-systems.scm?id=2394a7f5fbf60dd6adc0a870366adb57166b6d8b#n575
Looking at the code linked above specifically at lines 575 to 588, and 166, it seems, to me, that the mappings attempt should have worked.
Try it again, taking care to verify that the paths are correct, with:
```
(file-system-mapping
(source (mixed-text-file "my.cnf"
(string-append "[client-server]\n"
"socket=/run/mysqld/mysqld.sock")))
(target "/etc/my.cnf"))
```
Try rebuilding on tux04: started getting `Segmentation fault` errors out of the blue for many guix commands 🤦🏿.
Try building container on local dev machine: this took a long time - quit and continue later.
### Footnotes
[^1] Lines 47 to 49 of https://git.genenetwork.org/gn-machines/tree/production.scm?id=46a1c4c8d01198799e6ac3b99998dca40d2c7094#n47
[^2] Guix's mysql-service-type configurations https://guix.gnu.org/manual/en/html_node/Database-Services.html#index-mysql_002dconfiguration
[^3] https://mariadb.com/kb/en/server-system-variables/#socket
[^4] https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/services/databases.scm?id=4c56d0cccdc44e12484b26332715f54768738c5f#n576
[^5] https://guix.gnu.org/manual/en/html_node/Defining-Services.html
|
