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Virtual servers

Docker

It is the currently supported up-to-date virtual environment release of OpenBioMaps.

It is good for testing, developing or it can be applied in production environment after some updates.

For using docker 4 steps needed:

  1. Install docker compose

  2. Get obm-docker image

  3. Configure your docker according to host’s speciality (e.g. ssl, smtp)

  4. Start your docker environment

Prepare/Install Docker & Compose

sudo curl -L https://github.com/docker/compose/releases/download/1.29.2/docker-compose-`uname -s`-`uname -m` -o /usr/local/bin/docker-compose

sudo chmod +x /usr/local/bin/docker-compose

docker-compose --version

docker-compose version 1.29.2, build f46880fe

Visit this page for further inforamtion about installing docker:

https://docs.docker.com/compose/install/

Install / Setup OpenBioMaps an instance

It is recommended to put docker files into /srv/docker directory

mkdir -p /srv/docker/openbiomaps && cd /srv/docker/openbiomaps

git clone https://gitlab.com/openbiomaps/docker/obm-composer.git .

sudo su

groupadd -g 996 docker

adduser foo docker

docker network create obm_web

docker-compose pull

./obm_pre_install.sh

docker-compose up -d

./obm_post_install.sh

docker-compose restart

Visit your OBM app

http://YOUR_SERVER_NAME:9880/

http://YOUR_SERVER_NAME:9880/projects/sablon/

Log in your template databse using valaki@openbiomaps.org user name and abc123 password;

If you installed the docker in your local computer you can access the services above in localhost.

Database access

You can access your postgres database on the following preconfigured online database manager applications. However, it depends on your host-docker relationship.

phppgadmin

adminer

with sablon_admin username and 12345 password. You can manage your database with biomapsadmin user and abcd1234 password.

If you change these passwords, should be updated the following places:

/etc/openbiomaps/system_vars.php.inc

/var/www/html/biomaps/projects/sablon/local_vars.php.inc

/var/www/html/biomaps/projects/sablon/private/private.map

In the mapfile, the new encrypted password can be generated with the ms-access-key located in /var/lib/openbiomaps/maps/access.key

The two databases ‘biomaps’ and ‘gisdata’ have root postgres users respectively biomaps and gisdata (instead of the ususal postgres) and both password is changeMe.

Docker maintenance

This step is not obligatory, but can be useful if you need a strong web admin interface for docker management.

mkdir -p /srv/docker/portainer && cd /srv/docker/portainer

git clone https://gitlab.com/openbiomaps/docker/obm-portainer.git .

sudo su

docker-compose pull

# Genereate a strong random password for the admin user
bash ./password_gen.sh

docker-compose up -d

On the portainer interface use the "Get started" button...

Visit your docker-admin (portainer) app

http://YOUR_SERVER_NAME:9000/

Log in your app using admin user name and your password;

If you installed the docker in your local computer you can access the services above in localhost.

OBM maintenance

You can access OBM server admin interface: http://localhost:9880/supervisor.php

with supervisor username and password created by obm_post_install.sh. This password is located at /etc/openbiomaps/.htpasswd.

Updates: update application with Docker

foo@bar:~$ docker-compose pull
Pulling biomaps_db ... done
Pulling mapserver  ... done
Pulling app        ... done
Pulling phppgadmin ... done
Pulling adminer    ... done

foo@bar:~$ docker-compose up -d
Creating obm-composer_biomaps_db_1 ... done
Creating obm-composer_mapserver_1  ... done
Creating obm-composer_adminer_1    ... done
Creating obm-composer_phppgadmin_1 ... done
Creating obm-composer_app_1        ... done

Update only one container

foo@bar:~$ docker-compose up -d app

After founding a new project

You must set up a Mail server access to send mails from the app

Assuming that the new servers do not have their own domain name, the default value for sending mail is set to smtp (/etc/openbiomaps/system_vars.php.inc), which requires you to configure outgoing smtp servers and associated authentication for each projects (/var/www/html/biomaps/projects/…/local_vars.php.inc)

These config files can be edited in the supervisor interface.

Find the mail settings section and set up the smtp host and authentication if needed.

If there is an external smtp server here you are an example:

// Mail settings
define('SMTP_AUTH',true); # true
define('SMTP_HOST','mail.my-mail-server.com');
define('SMTP_USERNAME','my-name@my-mail-server.com');
define('SMTP_PASSWORD','something');
define('SMTP_SECURE','tls'); # Or starttls
define('SMTP_PORT','587'); # 465
define('SMTP_SENDER','openbiomaps@my-mail-server.com');

If SMTP_SENDER is not set, the SMTP_USERNAME will be the sender. Sending mails with google, with these simple settings is not possible, because google uses xoauth layer to authenticate! It is possible to include that layer here!

If the host system will be the smtp server:

 // Mail settings
define('SMTP_AUTH',false);
define('SMTP_HOST','172.17.0.1');
define('SMTP_PORT','25');
define('SMTP_SENDER','info@you-smtp-server');

For the ip address above check host “ip addr | grep docker0”

On the host depending on what MTA you have here you some examples:

Exim4

In the /etc/exim4/update-exim4.conf file

dc_relay_nets=‘172.21.0.0/16’ dc_local_interfaces=‘127.0.0.1 ; ::1 ; 172.17.0.1’

these lines shoud be updated, but depending on your exim config maybe something else as well.

In the /etc/exim4/exim4.config file

“hostlist relay_from_hosts…” line, you should extend with the obm_back network e.g.

hostlist relay_from_hosts = localhost :172.20.0.0/16 :172.17.0.0/16 :172.21.0.0/16

Comment: “Maybe one of the three network is enough above, I did not tested yet”

Postfix

inet_interfaces = 172.17.0.1

mynetworks = 172.21.0.4 172.20.0.6

Here’s how to find out docker networks and ip addresses:

docker container ls

search for obm-composer_app_1

docker inspect xxxxx_obm-composer_app_1

Search for obm_back and obm_web interfaces: obm-composer_obm_back {

… “IPAddress”: “172.20.0.6”,

} obm-composer_obm_web {

… “IPAddress”: “172.21.0.4”,

}

Firewall

You may also need to update your firewall to enable incoming mails from image to host. The network address of obm_back must be allowed as incoming network for the firewall. E.g.

ufw allow from 172.20.0.0/16 proto tcp to any port 25

Global smtp settings

Most probably you want to use the same smtp settings for your all project in your server. In this case use the

  • SMTP_GLOBAL_HOST

  • SMTP_GLOBAL_AUTH

  • SMTP_GLOBAL_USERNAME

  • SMTP_GLOBAL_PASSWORD

  • SMTP_GLOBAL_SECURE

  • SMTP_GLOBAL_PORT

  • SMTP_GLOBAL_SENDER

    parameters in the sytem_vars.php.inc. At least the SMTP_GLOBAL_HOST should be set if you want use global params. The local params override the globals allways.

Docker maintenance

Stopping docker

foo@bar:~$ docker-compose down

Drop everything (including data and databases)

foo@bar:~$ docker-compose down -v

Shell access of the system in the the container image

foo@bar:~$ docker-compose exec app bash

Here we accessed the app service. See service names in docker-compose.yml file.

Reading logs

foo@bar:~$ docker-compose logs -f app

Using pgtop

docker-compose exec -u postgres pg_top

Restart app

Do not restart apache from docker shell, but from outside

foo@bar:~$ docker-compose restart app

Remove huge amount of old, not used docker images

Do we have a lot?

docker images | grep "<none>"

Let drop them….

docker images | grep "<none>" | awk '{print $3}' | sed -e 's/^/docker rmi /' | bash

You may need to edit the traefik2.0/traefik.yml, traefik2.0/docker-compose.yml and traefik2.0/acme.json files

Archive tables, data, …

https://github.com/OpenBioMaps/scripts

Not docker: VirtualBox

The VirtualBox edition currently is outdated, not recommended to use it!

  1. Download virtualbox from https://www.virtualbox.org/wiki/Downloads

  2. Download the latest .ova image from http://openbiomaps.org/downloads

  3. Read this readme for the the next steps: http://openbiomaps.org/downloads/virtual-image/README