Server configuration

Supervisor

The Supervisor is a standalone web application to perform low-level configuration of OBM server and projects and to maintain updates. Supervisor is also installed during the OBM server installation and can be accessed from its root URL, e.g. yourserver.com/supervisor/ or yourserver.com/supervisor.php

The Supervisor login password can be regenerated by running the obm_post_install.sh command:

/srv/docker/openbiomaps# /obm_post_install.sh update supervisor

Supervisor has two modes of operation, system and project. In system mode, system level updates are available and system_vars.php.inc can be modified. In project mode, project updates are available and local_vars.php.inc can be modified, as well as database level modifications related to the project that are related to the project creation. Furthermore, in project mode, a file manager is available to manage the contents of the project/local folder. Supervisor project mode is also available from the project administration interface for project administrators.

system_vars.php.inc

The system settings for OpenBioMaps can be found in the system_vars.php.inc file. This can be modified via the Supervisor.

/etc/openbiomaps/system_vars.php.inc

define("OB_DOMAIN",".../biomaps");

define("OB_SYSDIR","/mnt/data/");

define("OB_TMP","/mnt/data/tmp/");

define("OB_ROOT","/var/www/html/biomaps/");

define("OB_ROOT_SITE","/var/www/html/biomaps/root-site/");

define("POSTGRES_PORT","5432");

define("GISDB_HOST",'localhost');     // for creating new project

define("MAPSERVER_HOST",'localhost'); // for creating new project

define("OB_RESOURCES","/var/www/html/biomaps/resources/");

define('biomapsdb_user','...');

define('biomapsdb_pass','...');

define('biomapsdb_name','...');

define('biomapsdb_host','localhost');

// Postgis version - not necessary to set, it only has historical value
define('POSTGIS_V','2.1');

// Default sendmail opetion, can be override in project level in local_vars.php.inc
define('SENDMAIL','smtp'); # sendmail | smtp

// memcache tpye - choose this
define('CACHE','memcache');

// R-Shiny Server ports, for the projects where R shiny server should be enabled
define('RSERVER_PORT_someproject',7982);

// Supported languages
define('LANGUAGES','en,hu,ro');

// bug report system can be activated by put AUTO_BUGREPORT_ADDRESS constant
// ask the issue-key from the gitlab-repo mainteners
define('AUTO_BUGREPORT_ADDRESS','incoming+openbiomaps...');

// mandatory constant for web auth. The same value should be set in the database: biomaps->oauth_clients->web->oauth_secret
define('WEB_CLIENT_SECRET','...');

apache server

  • cgi-bin settings

mapserver

  • fastcgi settings

  • mapcache settings

PHP

  • memcache settings

cron

There are some recommended cron jobs to set up (examples):

# m h  dom mon dow   command
0 4,16 * * * /srv/docker/openbiomaps/auto_update.sh > /srv/docker/openbiomaps/system_update_job.log

# m h  dom mon dow   command
0 2 * * *  /path_to/obm_archive.sh normal
15 2 * * * /path_to/obm_archive.sh system
15 3 1 * * /path_to/obm_archive.sh full
0 5 * * *  /path_to/obm_archive.sh clean
# remote servers
0 4 * * *  /path_to/obm_archive.sh sync remote_user@remote-server.com /remote_path_to_archives

On Docker use the instructions at the end of obm_archive_settings.sh

  • jobs runner

# m h  dom mon dow   command
*/5 * * * * /path_to/docker-compose -f /srv/docker/openbiomaps/docker-compose.yml exec -u www-data -T app php /var/www/html/biomaps/root-site/projects/PROJECTTABLE/jobs.php