DOCKER-FILO-SCIENCE

• Presentation
• Docker installation
  • Debian, Ubuntu or Raspbian
  • Windows
• Installation of containers
  • launch the web application
    • Docker is installed in the computer that is used to access the application
    • Docker is installed in a Raspberry
  • Some useful docker commands
  • Database backup
  • Update the application
    • Make a backup of the database
    • Update the database
    • Update the application
• Using a Raspberry Pi
  • Installation of Raspbian
  • ssh connection
  • Install Docker and the software
  • Change the rights for the database backup
  • Create a wifi network to connect terminals directly
• Acknowledgements
• License

This file is translated from REAMDE-FR.md with www.DeepL.com/Translator

The softwareFilo-Science allows you to enter information from electric fish fisheries, as well as information on the tracking of animals equipped with tags. If it is designed to operate in web mode, its use in offline mode may sometimes be necessary, especially at the edge of watercourses.

To do this, the software must be able to be embedded on a field computer (Windows or Linux laptop or tablet, or Raspberry Pi). The technology chosen is the one based on Docker containers, to be able to install a Postgresql database and an Apache2 Web server to host the PHP code.

The scripts provided allow you to install two Docker containers, one to host the database and the other for the web server.

This solution can also be used to run Filo-Science on any other OS (CentOS, Windows, etc.), while ensuring that it runs in the Debian environment.

    sudo -s
    apt-get update
    apt-get install curl
    curl -fsSL https://get.docker.com/ | sh
    apt-get install docker-compose
    systemctl enable docker
    service docker start
    groupadd docker
    usermod -aG docker $USER

Follow the instructions described here: https://docs.docker.com/docker-for-windows/install/.

Also install the Windows PowerShell program, which will allow you to open a terminal and launch manual commands.

The commands are given for Linux. Remember to adapt the approach to Windows (manual download from a browser, decompression with Windows, etc.).

Download the code of this deposit in a folder on your computer:

sudo apt-get install wget unzip
wget https://github.com/inrae/filo-docker/archive/master.zip
unzip master.zip
cd filo-docker-master

Create a Docker volume to host the Postgresql database:

docker volume create --name filopgdata -d local

Create the two images and the associated containers:

docker-compose up --build

If all goes well, you will find the following images:

docker images
REPOSITORY                 TAG                 IMAGE ID            CREATED             SIZE
filo-docker_filo-web       latest              834d8fd9f504        18 hours ago        782MB
filo-docker_filo-db        latest              78d95ff5fea4        19 hours ago        888MB

And the containers:

docker container ls
CONTAINER ID        IMAGE                  COMMAND                  CREATED             STATUS              PORTS                                      NAMES
125eafce92ac        filo-docker_filo-web   "/bin/sh -c /start.sh"   56 seconds ago      Up 54 seconds       0.0.0.0:80->80/tcp, 0.0.0.0:443->443/tcp   filo-docker_filo-web_1
4f6b43a1261a        filo-docker_filo-db    "su - postgres -c 'P…"   17 hours ago        Up 10 minutes       0.0.0.0:5433->5432/tcp                     filo-docker_filo-db_1

**Caution: **the web server exposes ports 80 and 443. If you already have a web server running on your computer, you will need to shut down your local web server before starting the containers.

If you have installed the Postgresql client on your computer, the postgresql server will be accessible from port 5433, at localhost :

psql -U filo -h localhost -p 5433
filo user password: filoPassword

This is the case with a Windows or Linux laptop. First, retrieve the IP address of the web server:

docker exec filo-docker_filo-web_1 ifconfig
eth0: flags=4163<UP,BROADCAST,RUNNING,MULTICAST> mtu 1500
        inet 172.19.0.3 netmask 255.255.0.0.0 broadcast 172.19.255.255.255

Here, the container has been assigned the IP address 172.19.0.3.

Add a line in your /etc/hosts (Linux) or c:\Windows\System32\drivers\etc\hosts (Windows) file:

172.19.0.3 filo-docker filo-docker.local

In your browser, go to the site: https://filo-docker.local. Accept the security exception: you should access the application.

You can connect with the login admin, password password: this is a default installation. Then remember to delete the admin account or change the password when you are working in production (except for local access only).

Refer to the corresponding documentation in the chapterUsing a Raspberry Pi.

The docker-compose commands must be executed from the filo-docker-master folder.

• docker images: displays the list of available images
• docker container ls: displays the list of containers
• docker stop filo-docker-master_filo-web_1 : stops the container containing the filo-web image
• docker start filo-docker-master_filo-web_1 &! starts the previously stopped container
• docker-compose up -d: starts the filo-web and filo-db in their respective containers, recreating them
• docker exec -ti filo-docker-master_filo-web_1 /bin/bash: connects to the container and allows to execute commands
• docker rmi filo-docker_filo-web --force: suddenly deletes the filo-web image
• docker-compose up --build: recreates both images. Warning: the database will be recreated!
• docker update --restart=no filo-docker_filo-web_1 : disables the automatic start of the container
• docker inspect filo-docker_filo-web_1: displays the current container settings
• docker system prune -a : deletes all images, to reset docker

The filo-db image includes an automatic database backup, which is triggered every day at 13:00. You will find it in your computer, in the folder Personal folder/filopgbackup. Remember to move it to another location on the network, to avoid losing everything in the event of a computer crash or theft.

The update of the application will be done in two steps:

• on the one hand, by updating the database, if necessary;
• on the other hand, by recreating the image filo-web.

For download the code, you must connected to Internet: use a Ethernet cable if your software is installed in a Raspberry-Pi.

docker exec -ti filo-docker-master_filo-db_1 bash
su - postgres -c /var/lib/postgresql/backup.sh

You should find your backup files in the /filopgbackup folder on your computer ( corresponds to your default folder).

Retrieve the version number of the current database version:

docker exec -ti filo-docker-master_filo-db_1 bash
su postgres -c 'psql filo -c "select dbversion_number from filo.dbversion order by dbversion_date desc limit 1"'

Check the Github repository for a database modification script (inhttps://github.com/inrae/filo-science/tree/master/install/pgsql). The script is in the form:

alter-1.1-1.2.sql

where 1.1 is the current version of your database, and 1.2 is the version to be reached.

In your Docker container, download the script:

su - postgres
wget https://github.com/inrae/filo-science/raw/master/install/pgsql/alter-1.1-1.2.sql

and execute this script:

psql -U filo filo -h localhost -f alter-1.2-1.3.sql

The default password is: filoPassword

If you are a few versions late, you will have to run the scripts successively to get to the current version level.

Quit the container with ctrl-D ctrl-D.

Save the configuration files:

mkdir param
docker cp filo-docker-master_filo-web_1:/var/www/filo-science/filo-science/param/param.inc.php param/
docker cp filo-docker-master_filo-web_1:/var/www/filo-science/filo-science/param/id_filo-science param/
docker cp filo-docker-master_filo-web_1:/var/www/filo-science/filo-science/param/id_filo-science.pub param/

Stop the container, and recreate the image:

docker stop filo-docker-master_filo-web_1
cd filo-docker-master
docker-compose up --build filo-web &!

Docker will recreate the image by loading the new version of the application. Once the container is started, reintegrate the previously saved configuration files:

cd ..
docker cp param/param.inc.php filo-docker-master_filo-web_1:/var/www/filo-science/filo-science/param/
docker cp param/id_filo-science filo-docker-master_filo-web_1:/var/www/filo-science/filo-science/param/
docker cp param/id_filo-science.pub filo-docker-master_filo-web_1:/var/www/filo-science/filo-science/param/
docker exec -ti filo-docker-master_filo-web_1 bash
cd /var/www/filo-science/filo-science/param
chgrp www-data id_filo-science*
chmod g+r id_filo-science*

Quit the container with Ctrl+D

Warning: if you recreate the container, you will have to restart the copy of the configuration files.

For the installation of Raspbian, refer to theRaspberry installation documentation.

Remember to enable access via ssh, and disable the graphical user interface at startup, which consumes resources and is irrelevant in the context of Filo-Science.

To connect to your Raspberry, use the command :

ssh pi@adresse_ip

Once connected, type the command:

sudo -s

If you have to work with the root login.

Review the detailed instructions at the beginning of the document.

By being connected with the pi account:

cd /home/pi
sudo chown pi:pi filopgbackup
chmod 777 filopgbackup

Follow the instructions defined in the first chapter of this document: https://www.raspberrypi.org/documentation/configuration/wireless/access-point.md (Setting up a Raspberry Pi as an access point in a standalone network (NAT)).

Adapt the content of the file /etc/hostapd/hostapd.conf, and in particular :

• ssid=filo-docker
• wpa_passphrase=votre_mot_de_passe

Then edit the file /etc/dnsmasq.conf, and add these lines:

server=8.8.8.8
address=/filo-docker.local/192.168.4.1

The server line corresponds to Google's web address server (DNS). If you want to use another DNS, for example your organization's, change this line.

Restart the Raspberry, and connect to the wifi network filo-docker. Test the communication with the application, by entering the following address in a browser: https://filo-docker.local. You must access the home page. In case of access problems (address not recognized), you can also connect directly to the IP address: https://192.168.4.1.

This configuration allows you to load the Openstreetmap tiles before leaving for the field:

• at the office, connect the Raspberry to the local network with an Ethernet cable
• connect your tablet to the Raspberry via wifi
• Launch the application at https://192.168.4.1.
• Open the module Parameters>Map Caching, and download the tiles you will need in the field
• stop the Raspberry, disconnect the Ethernet cable, close the browser from your tablet
• Restart the Raspberry, reconnect the tablet to the wifi, and reopen the application: the tiles are accessible without you being connected to the Internet.

The scripts are based on those developed by Julien Ancelin and Christine Plumejeaud-Perreau for the distribution via Docker of the applicationCollec-Science, and distributed inGithub. We would like to thank them for their work.

The scripts are released under MIT license.