Première dockerization

.gitignore

@@ -13,4 +13,10 @@
 !.vscode/extensions.json
 *.code-workspace
 MedShakeEHR-base.zip
-secrets.yml
+secrets.yml
+config/env.sh
+config/config.yml
+
+upgrade/*
+!upgrade/base
+!upgrade/base/*

Dockerfile

@@ -0,0 +1,75 @@
+# We start from a Docker in Docker container
+FROM docker:dind
+ENV INITSYSTEM on
+
+LABEL description="MedShake EHR All-In-One container"
+LABEL maintainer="bugeaud@gmail.com"
+
+# Set some environement variables required
+ENV APP_PATH /app
+ENV MEDSHAKEEHRPATH $APP_PATH/MedShakeEHR-base/
+ENV SCREENDIR /root/ehr/screen/
+
+# Create the application directory from the local
+ADD . $MEDSHAKEEHRPATH
+#WORKDIR $MEDSHAKEEHRPATH
+
+# Create the mount point to avoid right errors
+RUN mkdir -p $SCREENDIR -m 700
+
+# Check system is fresh and clean
+RUN apk update && apk upgrade
+
+# Install OpenRC's Init & Python package manager
+#RUN apk add screen  py-pip
+RUN apk add py-pip screen
+
+# Make sure PIP is up-to-date
+RUN pip install --upgrade pip
+
+# Install docker-compose package & supervisord
+RUN pip install docker-compose supervisor
+
+#RUN pwd
+
+# Make sure the Docker is there as "service"
+#RUN rc-update add docker boot
+
+# See what is in RC Init
+#RUN rc-status --all
+
+# Then, actually, simply run it right now
+#RUN service docker start
+
+# Move to the application
+WORKDIR $MEDSHAKEEHRPATH
+
+#RUN dockerd --host=unix:///var/run/docker.sock --host=tcp://0.0.0.0:2375
+# Config docker compose as a service $$$
+RUN docker-compose config --services
+
+# Create the sub-containers
+#RUN docker-compose up --build -d
+#RUN docker-compose up --build --no-start
+
+# Create the sub-containers
+#RUN docker-compose create
+
+#COPY docker-compose-entrypoint.sh /usr/local/bin/
+#ENTRYPOINT ["docker-compose-entrypoint.sh"]
+#CMD []
+
+RUN mkdir -p /var/log/docker-compose
+COPY docker-compose-screenrc /etc/docker-compose-screenrc
+
+# Document the exposed port. Note that 443 is for future use.
+EXPOSE 80/tcp
+EXPOSE 8080/tcp
+#EXPOSE 3606/tcp
+EXPOSE 443/tcp
+
+VOLUME /root/ehr/
+#VOLUME ~/ehr/screen
+
+# Create the screen lauching a docker daemon and a docker compose from known UNIX socket location
+ENTRYPOINT ["screen", "-c", "/etc/docker-compose-screenrc"]

Dockerfile-db

@@ -0,0 +1,27 @@
+# Let's start from a mariadb config
+FROM mariadb:latest
+
+ARG MYSQL_DATABASE=medshakeehr
+
+LABEL description="MedShake EHR dockerized DB image"
+LABEL maintainer="bugeaud@gmail.com"
+
+# Set some environement variables required
+ENV APP_PATH /app
+ENV MEDSHAKEEHRPATH $APP_PATH/MedShakeEHR-base/
+
+# Create the APP directory and move to it
+ADD --chown=mysql:mysql . $MEDSHAKEEHRPATH
+WORKDIR $MEDSHAKEEHRPATH
+
+# Add any .cnf file to MariaDB configuration
+#ADD --chown=mysql:mysql config/*.cnf /etc/mysql/mariadb.conf.d/
+
+# Create the database
+RUN echo "CREATE DATABASE IF NOT EXISTS $MYSQL_DATABASE CHARACTER SET utf8 COLLATE utf8_bin" > /docker-entrypoint-initdb.d/00-create.sql
+
+# Create the schema
+ADD --chown=mysql:mysql upgrade/base/sqlInstall.sql /docker-entrypoint-initdb.d/01-init.sql
+
+# Add some more init for basic env configuration
+ADD --chown=mysql:mysql config/configuration.sql /docker-entrypoint-initdb.d/02-env.sql

Dockerfile-web

@@ -0,0 +1,142 @@
+# We will go for a Ubunty Jammy
+FROM ubuntu:jammy
+LABEL description="MedShake EHR dockerized"
+LABEL maintainer="bugeaud@gmail.com"
+
+# Some environement variables to customize
+#ENV SERVER_NAME=www.example.net
+#ENV SERVER_ALIAS=
+
+# Set some environement variables required
+ENV APP_PATH /app
+ENV MEDSHAKEEHRPATH $APP_PATH/MedShakeEHR-base
+ENV MEDSHAKEEHRPUBLICPATH $APP_PATH/MedShakeEHR-base/public_html
+
+# Ensure no interractive term is used to avoid errors
+ENV DEBIAN_FRONTEND noninteractive
+
+# Create the APP directory and move to it
+ADD --chown=www-data:www-data . $MEDSHAKEEHRPATH
+WORKDIR $APP_PATH
+
+# Check system is fresh and clean
+RUN apt update && apt --assume-yes upgrade
+
+# Set the timezone
+ENV TZ 'Europe/Paris'
+RUN echo $TZ > /etc/timezone && \
+	apt install --assume-yes apt-utils tzdata locales && \
+	rm /etc/localtime && \
+	ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && \
+	dpkg-reconfigure -f noninteractive tzdata && \
+	apt clean
+
+# Install some global prerequisites
+RUN apt --assume-yes install imagemagick git dcmtk 
+# Install PhP as apache's mod
+RUN apt --assume-yes install libapache2-mod-php
+
+# Ubuntu has dropped pdftk because of gcj reliance.
+# We need to build a pdftk alternative version
+# Let's install prerequisites for the alternative pdftk 
+RUN apt --assume-yes install git openjdk-8-jdk ant libcommons-lang3-java libbcprov-java gradle
+# If gradle is used for build add : gradle
+# If latest JDK use default-jdk-headless as a JDK
+# If ANT based setup install would need : ant libcommons-lang3-java libbcprov-java
+# Get the latest alternative pdftk, build it & check if help can be displayed
+# Solution 1 : use ant
+#RUN git clone https://gitlab.com/marcvinyals/pdftk.git \
+#	&& cd pdftk \
+#	&& ant -lib /usr/share/java jar \
+#	&& java -jar build/jar/pdftk.jar --help
+# Solution 2 : use Gradle (the new default)
+#RUN git clone https://gitlab.com/pdftk-java/pdftk.git \
+#       && cd pdftk \
+#       && gradle wrapper --gradle-version 6.0.1 \
+#       && gradle shadowJar \
+#       && java -jar build/libs/pdftk-all.jar --help
+# Solution 3 : Starting from 18.10 there is a package for that :)
+RUN apt --assume-yes install pdftk
+
+WORKDIR $APP_PATH
+
+# Install curl as it is required anyway to fetch extensions 
+RUN apt --assume-yes install curl
+
+# Install PHP Composer thru bin inside latest docker image
+
+COPY --from=composer/composer:latest-bin /composer /usr/bin/composer
+
+# Test the composer & set that root exec is fine as we are in a container
+# Let's suppress the warning we are using root as we are inside Docker
+ENV COMPOSER_ALLOW_SUPERUSER=1
+RUN composer --version --no-interaction 
+
+# Fetch the PHP Extension installer for Docker
+RUN curl -sf -L -O https://github.com/docker-library/php/blob/master/docker-php-ext-install \
+	&& chmod 0774 docker-php-ext-install
+
+# Install some more PhP's dependencies
+RUN apt --assume-yes install php-gd php-dom php-mbstring php-intl php-curl php-zip php-xml php-gnupg php-imagick php-imap php-soap php-mysql php-bcmath php-yaml mariadb-client
+
+WORKDIR $MEDSHAKEEHRPATH
+
+# Ensure PHP composer has a fresh cache
+RUN composer clear-cache
+
+# Ensure updating the PHP composer dependencies
+RUN composer update
+
+# Install the MedShakeEHR Base PhP's dependencies
+#RUN composer install -d ./MedShakeEHR-base
+RUN composer install
+
+# Install MedShakeEHR's Web dependencies
+#RUN composer install -d ./MedShakeEHR-base/public_html
+RUN composer install -d ./public_html
+
+# Remove public install file
+RUN rm -f ./public_html/install.php
+
+WORKDIR $APP_PATH
+# Check which .ini files are used
+RUN php --ini
+
+# Fix the PHP ini files to ensure bigger sizes
+RUN sed -i 's/upload_max_filesize = 2M/upload_max_filesize = 20M/' /etc/php/$(php -r "echo PHP_VERSION;" | cut -c1-3)/apache2/php.ini
+RUN sed -i 's/post_max_size = 8M/post_max_size = 20M/' /etc/php/$(php -r "echo PHP_VERSION;" | cut -c1-3)/apache2/php.ini
+RUN sed -i 's/;max_input_vars = 1000/max_input_vars = 10000/' /etc/php/$(php -r "echo PHP_VERSION;" | cut -c1-3)/apache2/php.ini
+
+# Install npm
+#V2 RUN apt-get install -y -qq npm
+
+# Install bower
+#V2 RUN npm install --global bower
+
+# Allow bower to run under docker's root
+#V2 RUN echo '{ "allow_root": true }' > /root/.bowerrc
+
+# Make sure any bower module will be fixed toward wrong line end
+RUN git config --global core.autocrlf input
+
+WORKDIR $MEDSHAKEEHRPUBLICPATH
+#V2 RUN bower install -V --config.cwd ./MedShakeEHR-base/public_html/
+#RUN bower install -V
+
+# Create the Apache 2 configuration for the MedShake EHR application
+COPY medshakeehr.conf /etc/apache2/sites-available/
+
+#Enable URL rewriting
+RUN a2enmod rewrite
+
+# Activate the application
+RUN a2dissite 000-default && a2ensite medshakeehr
+
+# Run Apache 2 as foreground
+WORKDIR $APP_PATH
+#CMD apachectl -D FOREGROUND
+COPY docker-ehr-web-apache2-foreground /usr/local/bin/
+CMD docker-ehr-web-apache2-foreground
+
+EXPOSE 80/tcp
+EXPOSE 443/tcp

README.md

@@ -23,3 +23,134 @@ MedShakeEHR-base constitue le coeur commun du logiciel. Il peut être accompagn
 MedShakeEHR fonctionne sur un serveur xAMP.  
 
 L'installation et la configuration complète du logiciel sont documentées sur le site [www.logiciel-cabinet-medical.fr](http://www.logiciel-cabinet-medical.fr/) à la rubrique [Documentation technique](http://www.logiciel-cabinet-medical.fr/documentation-technique/).
+
+## Docker Image Build / Construction d'image Docker
+
+WARNING : The docker configuration requires various environment variables to be set (server name, password ...). If you decided not to follow the procedure, make sure to set the expected environement variables (cf. the docker-compose.yml)
+ATTENTION : La configuration Docker requiert le positionnement de variables d'environements (nom de serveur, mot de passe ...). Si vous décidez de ne pas suivre la procédure, assurez-vous de positionner ces variables (cf. docker-compose.yml).
+
+1- Install Git and Docker as per their documentation for your platform. For instance on Ubuntu :
+1- Installer GIT & Docker selon les instruction de votre plateforme. Par exemple sous Ubuntu :
+
+>sudo apt install git docker.io docker-compose
+
+NOTE : The version on the Ubuntu repository are usually a bit old. If you experience issues, check with the latest release.
+NB: Les version disponibles danes les dépots Ubuntu sont souvent anciens. Si vous rencontrez des difficutlés, vérifiez avec des versions plus récentes.
+
+2- Fetch/clone the desired version of EHR that is Docker compatible (here the latest):
+2- Récupérer la version souhaitée de EHR qui soit compatible Docker (ici la dernière):
+
+>git clone https://github.com/MedShake/MedShakeEHR-base.git
+
+Until the pull request #32 is not done, you shall get instead :
+Tant que la demande d'intégration #32 n'est pas actée, vous devez effectuer à la place :
+
+>git clone https://github.com/bugeaud/MedShakeEHR-base.git
+
+3- Enter the folder
+3- Entrer dans le répertoire
+
+>cd MedShakeEHR-base
+
+4- Define (export) the required environement variables. Only EHR_SERVER_NAME is mandatory to be set as the real FQDN for the hostname.
+4- Definir (export) les variables d'environement requises. Seul EHR_SERVER_NAME doit obligatoirement être positionée.
+
+  - EHR_SERVER_NAME  : Nom du server / Name of the server
+  - EHR_SERVER_ALIAS : Alias web / Web alias
+  - EHR_DBMS_NAME : Nom de la base / Name of the database
+  - EHR_DBMS_ROOT_PASSWORD : Mot de passe root de la base / Root password for the database
+  - EHR_DBMS_USER_NAME :  Nom de l'utilisateur applicatif de la base / Database application user name
+  - EHR_DBMS_USER_PASSWORD : Mot de passe de l'utilisateur applicatif de la base / Database application user name's password
+  - EHR_DBMS_VAR : Some random data used at the dbms level
+  - EHR_FINGERPRINT : Some random data used at the web level
+
+5- Prepare the local filesystem to store the user data
+5- Prepare le système de fichier local pour le stocker des données utilisateurs
+
+> ./docker-ehr-prepare.sh
+
+6- Initialize legacy configuration files with environement variables set :
+6- Initialiser les fichiers de configuration historique à l'aide des valeur des variables d'environement positionnés :
+
+> . docker-ehr-config.sh
+
+NOTE : The dot and space before the command are mandatory to enable the spreading of the environement variables. Please save all the generated data at a proper location
+NB: Le point et l'espace avant la commande sont obligatoires pour permettre la bonne propagation des variables d'environements. Veuillez sauvegarder toutes les données générées
+
+7- Build the required EHR images :
+7- Construire les images de EHR :
+
+> ./docker-ehr-build.sh
+
+8- Set the EHR environment variables
+8- Positioner les variables d'environement EHR
+
+> . ~/ehr/env.sh
+
+9- Launch the application (create + start)
+9- Lancer l'application (create + start)
+
+> ~/ehr/ehr-up.sh
+
+10- An EHR instance is ready :
+10- Vous avez une instance de EHR de disponible :
+
+>http://$EHR_SERVER_NAME/
+
+Follow the instructions there ...
+Y suivre les instructions ...
+
+## Docker Compose
+
+A ready to use Docker Compose setup is proposed with the following containers :
+Une configuration Docker Compose prête à l'emploi est proposée qui dispose des conteneurs suivants :
+- db : the DBMS for EHR / le SGBD de EHR
+- web : the web front / le frontal web
+
+An additional myadmin container can be enabled to perform some database maintenance duty.
+Un conteneur myadmin additionel peut être activé pour effectuer des tâches de maintenances sur la base.
+
+To create/start the containers
+Pour créer/démarrer les conteneurs
+
+> ~/ehr/ehr-up.sh
+
+To stop the containers (this will not remove ~/ehr/data)
+Pour arrêter les conteneurs (ne supprime pas ~/ehr/data)
+
+> ~/ehr/ehr-down.sh
+
+To list the containers :
+Pour lister les conteneurs :
+
+> docker-compose ps
+
+From another terminal, from the EHR directory (~/ehr/), access a shell from the EHR desired container (here the "web" container) :
+Depuis un autre terminal, depuis le répertoire EHR (~/ehr/), accèder à l'invite du conteneurEHR  désiré (ici le conteneur "web") :
+
+>  docker exec -it $(docker-compose ps -q web) "/bin/bash"
+
+Or you might  use from the docker-ehr-shell script provided in the EHR base source code : 
+Ou vous pourriez aussi utiliser le script docker-ehr-shell fourni dans les sources de EHR base :
+> .../MedShakeEHR-base/utils/docker-ehr-shell.sh web
+
+NOTE : most changes on files will not be retained if starting a new container fresh from the image.
+NB : la plus part des changements sur des fichiers ne seront pas concervés si un nouveau conteneur est créé à partir de l'image.
+
+## Single container Install / Installation dans un conteneur unique
+
+There is also an alpha Docker-in-Docker (dind) single container configuration existing thru the Dockerfile file.
+Il existe également une installation Docker-in-Docker (dind) de disponible via le fichier Dockerfile.
+
+To use it follow the docker compose procedure, but at step 6 to build, use :
+Pour l'utiliser, suivre la procédure pour docker, mais à l'étape 6 pour construire, utiliser  :
+
+> ./docker-ehr-single-build.sh
+
+Then, instead of th you can run the dind setup :
+Ensuite, vous pouvez lancer la configuration dind :
+
+> ./docker-ehr-single-run.sh
+
+This would launch a GNU screen with multiple screen : 1 for the dind's docker daemon, 1 for building  & docker-compose and 2 more for shells available for you.
+Ceci lancera un GNU screen avec de multiples écrans : 1 pour le service docker de dind, 1 pour la construction & docker-compose et 2 extra comme invites disponibles pour vous.