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Virtual server with Docker

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

It is good for testing, and developing, and in a production environment as well.

For using obm-docker 4 steps are needed:

  1. Install docker-compose

  2. Get the obm-docker image

  3. Configure your docker according to the 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 information about installing docker:

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

Install / Setup an OpenBioMaps instance

In one step:

curl -s https://gitlab.com/openbiomaps/docker/obm-composer/-/raw/master/install.sh > /tmp/install.sh && sudo bash /tmp/install.sh

Visit your OBM app

http://YOUR_SERVER_NAME:9080/

http://YOUR_SERVER_NAME:9080/projects/sablon/

Log in to your template database using valaki@openbiomaps.org user name and abc123 password. After the first login, please change this default 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 pre-configured online database manager applications. However, it depends on your host-docker relationship.

!PhpPgAdmin is not available currently!

*Phppgadmin: http://YOUR_SERVER_NAME:9881/*

PhpPgadmin notes:

It is a very friendly tool, but unfortunately, it is currently not maintained, so we have to create our edition or wait for someone else…

Adminer: http://YOUR_SERVER_NAME:9882/

Adminer notes:

server = openbiomaps_biomaps_db_1
db_name = biomaps | gisadmin
db_user = biomapsadmin | sablon_admin | YOUR_PROJECT_admin
password = (check the .env file for the biomapsadmin's password or the local_vars.php.inc for ..._admin's password)

You can manage the database with the biomapsadmin user. This is a superuser. Its password is generated by the system during installation and can be found in the /srv/docker/openbiomaps/.env file.

For the MapServer map file, the encrypted password for the database connection can be generated with the /var/lib/openbiomaps/maps/access.key.

OpenBioMaps creates two databases by default. The ‘biomaps’ contains the tables needed for the system to work, while the ‘gisdata’ contains the data tables of the project databases. In other words, the latter is where the data collected by users will be stored and to which users can connect. The ‘biomapsadmin’ is a superuser in both databases. Its password is generated by the system during installation and stored in the /srv/docker/openbiomaps/.env file.

Docker maintenance app

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 to 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: Supervisor

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

or

https://yourserver.com/supervisor.php

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

You can regenerate the Supervisor’s password with ./obm_post_install.sh update supervisor command

Updates: update application with Docker

These commands are safe, they do not destroy the changes made through the OpenBioMaps web interface.

foo@bar:~$ docker-compose pull
Pulling biomaps_db ... done
Pulling mapserver  ... done
Pulling app        ... done
## Pulling phppgadmin ... done -- There is no PhpPgAdmin currently
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

Email setting for projects

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

Assuming that the new server does not have its 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 project (/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 should 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 networks is enough above, I did not test 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 mail from the image to the host. The network address of obm_back must be allowed as an 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 all projects on 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 to use global parameters. The local parameters override the globals always.

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 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 the Docker shell, but from outside

foo@bar:~$ docker-compose restart app

Remove huge amounts of old, not used docker images

Do we have a lot?

docker images | grep "<none>"

Let’s 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, …

For scripts follow this repo:

https://github.com/OpenBioMaps/scripts

  • use this to set up a periodic sql dumps of important tables: archive.sh

crontab setting examples for archive.sh

#dumping normal tables from Monday to Saturday
15 04 * * 1-6 /root/archive.sh normal &
#dumping all tables and whole databases on every Sunday
15 04 * * 7 /root/archive.sh full &

Example settings in obm_archive_settings.sh

#path of table list
table_list="${HOME}/.archive_list.txt"

#postgres parameters
project_database="gisdata"
system_database="biomaps"
admin_user="gisadmin"
archive_path="/home/archives"
pgport="5432"
pg_dump="pg_dump -p $pgport"
psql="psql -p $pgport"

#FOR DOCKER based OBM systems
#docker="/usr/bin/docker-compose -f /path/to/docker-compose.yml exec -T"
#pg_dump="$docker biomaps_db pg_dump -p $pgport"
#psql="$docker biomaps_db psql -p $pgport"

#table dayof_week dayofmonth month
#foo at every day
#foo * * *
#bar every Monday
#bar 1 * *
#casbla at every 1st day of every June
#casbla * 1 6

Dumping table from the database using docker

docker-compose exec -T biomaps_db bash -c “pg_dump -U biomapsadmin –table public.YOUR_TABLE gisdata” > YOUR_TABLE.sql

Not docker: VirtualBox (outdated!!!)

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 next steps: http://openbiomaps.org/downloads/virtual-image/README