Leginon

Sure, will look into this. It's been a while since I did database initialization through the setup website. I have been doing it though centos(7)AutoInstallation.py mostly.

Ben, what OS, php and mysql versions are you using? Does it work when you use standard mysql port (3306)? Thanks for your time.

CentOS Linux release 7.6.1810 (Core)
PHP 5.4.16 (cli) (built: Oct 30 2018 19:30:51)
Server version: 5.5.5-10.3.5-MariaDB-10.3.5+maria~jessie mariadb.org binary distribution

I don't have a database set up on a standard port so I don't know if it works, but I assume it does.

I did not do the installation on this system, I'm just trying to help them get it working with our database service. I will contact the installer and see if I can run the centos7AutoInstaller.py script myself and maybe get it working that way.

I tried running the centos7installer.py script, but it seems to assume a database on the local host.

I dug down into the newDBsetup.php and included files and it looks to me like the mysqli code is used here, which doesn't seem to support "host:port" in the host field, but has a separate field for port.

And chance this could be changed to support an off-box database? In the Leginon documentation it talks about the database server being on a different host. I know this is different from a non-standard port, but I don't see how this script would work for a separate database server either.

That's right, centos7installer.py script installs a database on the local host.

I've looked at Database Initialization through the setup website and, indeed, there is no option to specify mysql port. If you can't run mysql on a standard port or do port forwarding, you can edit myamiweb/inc/mysql.inc and replace line 44:
$link = @mysqli_connect($host, $this->db_user, $this->db_pass);
with
$link = @mysqli_connect($host, $this->db_user, $this->db_pass, null, 12345);

There might be other places that needs changes, but I hope this get you started.

There is a hidden feature that allows you to specify port number in sinedon.cfg for the python calls. See Issue #3028