Server configuration

Supervisor

The Supervisor is a standalone web application for low-level configuration of the OBM server and projects, and for maintaining 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’s creation. Furthermore, in project mode, a file manager is available to manage the contents of the project/local folder. The supervisor project mode is also available in the project administration interface for project administrators.

system_vars.php.inc

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

/etc/openbiomaps/system_vars.php.inc

# If you use OBM in a local environment without a proxy but non-standard HTTP ports, set it to true!
#define("USE_NON_STANDARD_HTTP_PORTS",false);

# Set it according to the real server address
define("OB_DOMAIN", "localhost/biomaps");

# The default is /var/lib/openbiomaps/
# define("OB_SYSDIR", "/var/lib/openbiomaps/");

define("OB_TMP", "/var/lib/openbiomaps/tmp/");

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

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", "mapserver"); // 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', '2.5');

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

// memcache type - 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