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Database access

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.

Using docker is easy! Only 3 steps needed:

  1. Install docker compose
  2. Get obm-docker image
  3. start your docker environment

Prepare/Install Docker & Compose

foo@bar:~$ sudo curl -L https://github.com/docker/compose/releases/download/1.22.0/docker-compose-`uname -s`-`uname -m` -o /usr/local/bin/docker-compose

foo@bar:~$ sudo chmod +x /usr/local/bin/docker-compose

foo@bar:~$ docker-compose --version

docker-compose version 1.22.0, build f46880fe

Visit this page for further inforamtion about installing docker https://docs.docker.com/compose/install/

OBM docker install

foo@bar:~$ git clone git@gitlab.com:openbiomaps/docker/obm-composer.git

foo@bar:~$ cd obm-composer/

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

Visit these pages on your browser

http://localhost:9880/biomaps/

http://localhost:9880/biomaps/projects/sablon/

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

You can access your postgres database at

http://localhost:9880/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

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

with supervisor username and 12345 password. This password is located at /etc/openbiomaps/.htaccess.

Updates: update application with Docker

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

foo@bar:~$ docker-compose up -d
Starting obm-composer_gisdata_1 ... done
Starting obm-composer_biomaps_1 ... done
Starting obm-composer_mapserver_1  ... done
Starting obm-composer_adminer_1    ... done
Starting obm-composer_phppgadmin_1 ... done
Recreating obm-composer_app_1      ... done

Stopping docker

foo@bar:~$ docker-compose down

Drop everything (including data and databases)

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

Shell access of web app

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

Reading logs

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

VirtualBox

  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