diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/genenetwork/cannot-connect-to-mariadb.gmi | 76 | ||||
| -rw-r--r-- | issues/genenetwork/containerising-production-issues.gmi | 1 |
2 files changed, 77 insertions, 0 deletions
diff --git a/issues/genenetwork/cannot-connect-to-mariadb.gmi b/issues/genenetwork/cannot-connect-to-mariadb.gmi new file mode 100644 index 0000000..16a5ebb --- /dev/null +++ b/issues/genenetwork/cannot-connect-to-mariadb.gmi @@ -0,0 +1,76 @@ +# 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 Log + +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. + +### 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 diff --git a/issues/genenetwork/containerising-production-issues.gmi b/issues/genenetwork/containerising-production-issues.gmi index 6648554..6478b8a 100644 --- a/issues/genenetwork/containerising-production-issues.gmi +++ b/issues/genenetwork/containerising-production-issues.gmi @@ -30,3 +30,4 @@ The link above documents the various services that make up the GeneNetwork servi => ./setup-mailing-on-tux04 [x] Setting up email service on Tux04 => ./virtuoso-shutdown-clears-data [x] Virtuoso seems to lose data on restart => ./python-requests-error-in-container [ ] Fix python's requests library certificates error +=> ./cannot-connect-to-mariadb [ ] GN3 cannot connect to mariadb server |