Switch to using Docker

This commit refactors all code in this project to make use of docker.
This has not yet been documented properly.

README.md

@@ -2,6 +2,8 @@
 
 This repository contains a factory server implementation that creates and maintains a list of Drupal Instances. 
 
+** This documentation is not yet updated to the new approach **
+
 ** This is a work in progress and nothing in this repository is ready for production use ** 
 
 ## Overview

Vagrantfile

@@ -1,67 +1,24 @@
 # -*- mode: ruby -*-
 # vi: set ft=ruby :
 
-# All Vagrant configuration is done below. The "2" in Vagrant.configure
-# configures the configuration version (we support older styles for
-# backwards compatibility). Please don't change it unless you know what
-# you're doing.
 Vagrant.configure("2") do |config|
-  # The most common configuration options are documented and commented below.
+  # use an iamge of debian, in this case buster 64
-  # For a complete reference, please see the online documentation at
-  # https://docs.vagrantup.com.
-
-  # Every Vagrant development environment requires a box. You can search for
-  # boxes at https://vagrantcloud.com/search.
   config.vm.box = "debian/buster64"
 
-  # Disable automatic box update checking. If you disable this, then
+  # forward ports 80 and 443 to the host system
-  # boxes will only be checked for updates when the user runs
+  # this will allow accessing the webserver from the real system. 
-  # `vagrant box outdated`. This is not recommended.
+  config.vm.network "forwarded_port", guest: 80, host: 80
-  # config.vm.box_check_update = false
+  config.vm.network "forwarded_port", guest: 443, host: 443
 
-  # Create a forwarded port mapping which allows access to a specific port
+  # share the factory folder in /factory/
-  # within the machine from a port on the host machine. In the example below,
+  config.vm.synced_folder "distillery/", "/distillery/"
-  # accessing "localhost:8080" will access port 80 on the guest machine.
-  # NOTE: This will enable public access to the opened port
-  # config.vm.network "forwarded_port", guest: 80, host: 8080
 
-  # Create a forwarded port mapping which allows access to a specific port
+  # for performance, we setup 4GB of memort and 2 CPUs
-  # within the machine from a port on the host machine and only allow access
-  # via 127.0.0.1 to disable public access
-  config.vm.network "forwarded_port", guest: 80, host: 8080
-
-  # Create a private network, which allows host-only access to the machine
-  # using a specific IP.
-  # config.vm.network "private_network", ip: "192.168.33.10"
-
-  # Create a public network, which generally matched to bridged network.
-  # Bridged networks make the machine appear as another physical device on
-  # your network.
-  # config.vm.network "public_network"
-
-  # Share an additional folder to the guest VM. The first argument is
-  # the path on the host to the actual folder. The second argument is
-  # the path on the guest to mount the folder. And the optional third
-  # argument is a set of non-required options.
-  config.vm.synced_folder "factory/", "/factory/"
-
-  # Provider-specific configuration so you can fine-tune various
-  # backing providers for Vagrant. These expose provider-specific options.
-  # Example for VirtualBox:
-  #
   config.vm.provider "virtualbox" do |vb|
     vb.memory = 4096
     vb.cpus = 2
   end
-  #
-  # View the documentation for the provider you are using for more
-  # information on available options.
 
-  # Enable provisioning with a shell script. Additional provisioners such as
+  # tell the user where things are. 
-  # Ansible, Chef, Docker, Puppet and Salt are also available. Please see the
+  config.vm.post_up_message = "Ready to distil and make WissKIs. Scripts can be found in /distillery/. "
-  # documentation for more information about their specific syntax and use.
-  # config.vm.provision "shell", inline: <<-SHELL
-  #   apt-get update
-  #   apt-get install -y apache2
-  # SHELL
 end

distillery/.env.sample

@@ -1,24 +1,33 @@
-# Sometimes when http(s) is enabled, it is advisable to listen on a port different from 80. 
+# All WissKi and Drupal Installations are contained within a single directory. 
-# The public port can be configured here. 
-PUBLIC_PORT=80
-
-# All WissKI and Drupal Installations are contained within a single directory. 
 # The name of each subfolder corresponds to the appropriate domain name. 
 # This variable determines the subfolder to place installations into. 
 DRUPAL_ROOT=/var/www/factory
 
+# Furthermore, several docker-compose files are created to manage global services and the system itself. 
+# These will be placed into a folder, set its' path here. 
+COMPOSER_ROOT=/var/www/deploy
+
+# The system can support setting up certificate(s) automatically. 
+# It can be enabled by setting an email for certbot certificates. 
+# This email address can be configured here. 
+CERTBOT_EMAIL=
+
 # Each Drupal instance requires a corresponding system user, database users and databases. 
 # These are also set by the appropriate domain name. 
 # To differentiate them from other users of the system, these names can be prefixed. 
 # The prefix to use can be configured here. 
 # When changing these please consider that no system user may exist that has the same name as a mysql user. 
 # This is a MariaDB restriction. 
-SYSTEM_USER_PREFIX=factory-
 MYSQL_USER_PREFIX=mysql-factory-
 MYSQL_DATABASE_PREFIX=mysql-factory-
 GRAPHDB_USER_PREFIX=graphdb-factory-
 GRAPHDB_REPO_PREFIX=graphdb-factory-
 
+# In addition to the filesystem the WissKI distillery requires a single SQL table. 
+# It uses this database to store a list of installed things
+DISTILLERY_BOOKKEEPING_DATABASE=distillery
+DISTILLERY_BOOKKEEPING_TABLE=distillery
+
 # Each created Drupal Instance corresponds to a single domain name. 
 # These domain names should either be a complete domain name or a sub-domain of a default domain. 
 # This setting configures the default domain-name to create subdomains of. 

distillery/lib/00_init.sh

@@ -43,4 +43,19 @@ function log_warn() {
 
 function log_error() {
    echo -e "\033[0;31m$1\033[0m"
-}
+}
+
+if [ -n "$DISABLE_LOG" ]; then
+   function log_info() {
+      true
+   }
+   function log_ok() {
+      true
+   }
+   function log_warn() {
+      true
+   }
+   function log_error() {
+      true
+   }
+fi

distillery/lib/10_config.sh

@@ -67,6 +67,15 @@ function is_valid_number() {
    fi;
 }
 
+# 'is_valid_email' checks if a value is a valid email address
+function is_valid_email() {
+   if [[ "$1" =~ ^[a-zA-Z0-9._%+-]+@[a-zA-Z0-9.-]+\.[a-zA-Z]{2,}$ ]]; then
+      return 0;
+   else
+      return 1;
+   fi
+}
+
 # The 'DRUPAL_ROOT' variable must be an absolute path. 
 if ! is_valid_abspath "$DRUPAL_ROOT"; then
    log_error "Variable 'DRUPAL_ROOT' is missing or not a valid path. ";
@@ -75,10 +84,11 @@ if ! is_valid_abspath "$DRUPAL_ROOT"; then
    exit 1;
 fi
 
-# The 'SYSTEM_USER_PREFIX' variable must be a valid slug. 
+# The 'COMPOSER_ROOT' variable must be an absolute path. 
-if ! is_valid_slug "$SYSTEM_USER_PREFIX"; then
+if ! is_valid_abspath "$COMPOSER_ROOT"; then
-   log_error "Variable 'SYSTEM_USER_PREFIX' is missing or not a valid slug. ";
+   log_error "Variable 'COMPOSER_ROOT' is missing or not a valid path. ";
    log_info "Please verify that it is set correctly in '.env'. ";
+   log_info "Please ensure that it does not end in '/'. ";
    exit 1;
 fi
 
@@ -96,6 +106,21 @@ if ! is_valid_slug "$MYSQL_DATABASE_PREFIX"; then
    exit 1;
 fi
 
+# The 'DISTILLERY_BOOKKEEPING_DATABASE' variable must be a valid slug. 
+if ! is_valid_slug "$DISTILLERY_BOOKKEEPING_DATABASE"; then
+   log_error "Variable 'DISTILLERY_BOOKKEEPING_DATABASE' is missing or not a valid slug. ";
+   log_info "Please verify that it is set correctly in '.env'. ";
+   exit 1;
+fi
+
+# The 'DISTILLERY_BOOKKEEPING_TABLE' variable must be a valid slug. 
+if ! is_valid_slug "$DISTILLERY_BOOKKEEPING_TABLE"; then
+   log_error "Variable 'DISTILLERY_BOOKKEEPING_TABLE' is missing or not a valid slug. ";
+   log_info "Please verify that it is set correctly in '.env'. ";
+   exit 1;
+fi
+
+
 # The 'GRAPHDB_USER_PREFIX' variable must be a valid slug. 
 if ! is_valid_slug "$GRAPHDB_USER_PREFIX"; then
    log_error "Variable 'DATABASE_PREFIX' is missing or not a valid slug. ";
@@ -110,14 +135,22 @@ if ! is_valid_slug "$GRAPHDB_REPO_PREFIX"; then
    exit 1;
 fi
 
-
+# The 'DEFAULT_DOMAIN' variable must be a valid domain. 
-# The 'DOMAIN' variable must be a valid domain. 
 if ! is_valid_domain "$DEFAULT_DOMAIN"; then
    log_error "Variable 'DEFAULT_DOMAIN' is missing or not a valid domain. ";
    log_info "Please verify that it is set correctly in '.env'. ";
    exit 1;
 fi
 
+# The 'CERTBOT_EMAIL' variable should either be empty or a valid email
+if [ -n "$CERTBOT_EMAIL" ]; then
+   if ! is_valid_email "$CERTBOT_EMAIL"; then
+         log_error "Variable 'CERTBOT_EMAIL' is not a valid email address. ";
+         log_info "Please verify that it is set correctly in '.env' or remove it completly. ";
+         exit 1;
+   fi;
+fi
+
 # The 'PASSWORD_LENGTH' variable must be a valid number. 
 if ! is_valid_number "$PASSWORD_LENGTH"; then
    log_error "Variable 'PASSWORD_LENGTH' is missing or not a valid number. ";
@@ -125,11 +158,11 @@ if ! is_valid_number "$PASSWORD_LENGTH"; then
    exit 1;
 fi
 
-# The 'PUBLIC_PORT' must be a valid number. 
+# paths to composer things
-if ! is_valid_number "$PUBLIC_PORT"; then
+COMPOSER_WEB_DIR="$COMPOSER_ROOT/core/web"
-   log_error "Variable 'PUBLIC_PORT' is missing or not a valid number. ";
+COMPOSER_TRIPLESTORE_DIR="$COMPOSER_ROOT/core/triplestore"
-   log_info "Please verify that it is set correctly in '.env'. ";
+COMPOSER_SQL_DIR="$COMPOSER_ROOT/core/sql"
-   exit 1;
+COMPOSER_INSTANCES_DIR="$COMPOSER_ROOT/instances"
-fi
+
 
 log_ok "Read and validated configuration file. "

distillery/lib/20_sql.sh

@@ -0,0 +1,86 @@
+#!/bin/bash
+set -e
+
+# This is a library file. 
+# It should be 'source'd only, if it is not we bail out here. 
+if [[ "$0" = "$BASH_SOURCE" ]]; then
+   echo "This file should not be executed directly, it should be 'source'd only. "
+   exit 1;
+fi
+
+###
+### General SQL functions
+###
+
+# wait_for_sql waits for the sql database to be ready
+function wait_for_sql() {
+    log_info "Waiting for database to start ..."
+    _wait_for_sql_internal
+    log_ok "Database responded to query "
+}
+
+function _wait_for_sql_internal() {
+    timeout=30
+    times=1
+    until dockerized_mysql -e 'show databases;' > /dev/null 2>&1; do
+        ((times=times+1))
+        if [ "$times" -gt $timeout ]; then
+            log_error "Database timed out after ${timeout} seconds(s). "
+        fi;
+        echo -n "."
+        sleep 1
+    done
+}
+
+# 'dockerized_mysql' runs an sql command in the sql docker container
+function dockerized_mysql() {
+    pushd "$COMPOSER_SQL_DIR" > /dev/null
+    docker exec -i `docker-compose ps -q sql` mysql "$@"
+    retval=$?
+    popd > /dev/null
+    return $retval
+}
+
+# 'dockerized_mysql' runs an sql command in the sql docker container interactively
+function dockerized_mysql_interactive() {
+    pushd "$COMPOSER_SQL_DIR" > /dev/null
+    docker exec -ti `docker-compose ps -q sql` mysql "$@"
+    retval=$?
+    popd > /dev/null
+    return $retval
+}
+
+###
+### Bookkeeping sql
+###
+
+
+# 'sql_bookkeep_exists' checks if a given site already exists
+function sql_bookkeep_exists() {
+    COUNT=$(dockerized_mysql -D "$DISTILLERY_BOOKKEEPING_DATABASE" -e "SELECT COUNT(*) FROM \`$DISTILLERY_BOOKKEEPING_TABLE\` WHERE slug=\"$1\"; "  | tail -n +2)
+    if [ "$COUNT" = "1" ]; then
+        return 0;
+    else
+        return 1;
+    fi;
+}
+
+# 'sql_bookkeep_insert' inserts a new pair of values into the sql database
+function sql_bookkeep_insert() {
+    dockerized_mysql -D "$DISTILLERY_BOOKKEEPING_DATABASE" -e "INSERT INTO \`$DISTILLERY_BOOKKEEPING_TABLE\`($1) VALUES ($2) ;"
+}
+
+# 'sql_bookkeep_delete' removes a slug into the bookeeping table
+function sql_bookeep_delete() {
+    dockerized_mysql -D "$DISTILLERY_BOOKKEEPING_DATABASE" -e "DELETE FROM \`$DISTILLERY_BOOKKEEPING_TABLE\` WHERE slug=\"$1\";"
+}
+
+# 'sql_bookkeep_load' reads from the bookkeeping table
+function sql_bookkeep_load() {
+    dockerized_mysql -D "$DISTILLERY_BOOKKEEPING_DATABASE" -e "SELECT $2 FROM \`$DISTILLERY_BOOKKEEPING_TABLE\` WHERE slug=\"$1\";"
+}
+
+# 'sql_bookkeep_list' lists all slugs from the bookkeeping table
+function sql_bookkeep_list() {
+    dockerized_mysql -D "$DISTILLERY_BOOKKEEPING_DATABASE" -e "SELECT slug FROM \`$DISTILLERY_BOOKKEEPING_TABLE\`; " | tail -n +2
+}

distillery/lib/30_slug.sh

@@ -21,8 +21,7 @@ function require_slug_argument() {
 
     log_info " => Deriving configuration for '$SLUG'. "
     echo "Domain Name:          $INSTANCE_DOMAIN"
-    echo "Base Directory:       $BASE_DIR"
+    echo "Base Directory:       $INSTANCE_BASE_DIR"
-    echo "System User:          $SYSTEM_USER"
     echo "MySQL User:           $MYSQL_USER"
     echo "MySQL Database:       $MYSQL_DATABASE"
     echo "GraphDB User:         $GRAPHDB_USER"
@@ -52,29 +51,17 @@ USERNAME_BASE="${USERNAME_BASE//_/--u}"
 USERNAME_BASE="${USERNAME_BASE//./-}"
 
 # Generate the user and database names for the various systems
-SYSTEM_USER="${SYSTEM_USER_PREFIX}${USERNAME_BASE}"
 MYSQL_USER="${MYSQL_USER_PREFIX}${USERNAME_BASE}"
 MYSQL_DATABASE="${MYSQL_DATABASE_PREFIX}${USERNAME_BASE}"
 GRAPHDB_USER="${GRAPHDB_USER_PREFIX}${USERNAME_BASE}"
 GRAPHDB_REPO="${GRAPHDB_REPO_PREFIX}${USERNAME_BASE}"
 
 # Compute the base directory for the files that will live on disk. 
-BASE_DIR="$DRUPAL_ROOT/$INSTANCE_DOMAIN"
+INSTANCE_BASE_DIR="$COMPOSER_INSTANCES_DIR/$INSTANCE_DOMAIN"
-ENV_FILE="$BASE_DIR/wisski-env"
+INSTANCE_DATA_DIR="$INSTANCE_BASE_DIR/data/"
-COMPOSER_DIR="$BASE_DIR/project"
-WEB_DIR="$COMPOSER_DIR/web"
-ONTOLOGY_DIR="$WEB_DIR/sites/default/files/ontology"
 
-# Setup aliases for drush and composer. 
+if [ -n "$CERTBOT_EMAIL" ]; then
-alias composer="sudo -u $SYSTEM_USER /usr/local/bin/composer"
+    LETSENCRYPT_HOST="$INSTANCE_DOMAIN"
-alias drush="sudo -u $SYSTEM_USER $COMPOSER_DIR/vendor/bin/drush"
+    LETSENCRYPT_EMAIL="$CERTBOT_EMAIL"
+fi;
 
-# Because of a bug in Drupal we constantly have to reset the permissions of the site directory. 
-# See https://www.drupal.org/project/drupal/issues/3091285. 
-function drupal_sites_permission_workaround() {
-    chmod -R u+w "$WEB_DIR/sites/"
-}
-
-# Apache configuration paths
-APACHE_CONFIG_SITE_AVAILABLE="/etc/apache2/sites-available/${INSTANCE_DOMAIN}.conf"
-APACHE_CONFIG_SITE_ENABLED="/etc/apache2/sites-enabled/${INSTANCE_DOMAIN}.conf"

distillery/lib/40_templates.sh

@@ -8,7 +8,8 @@ if [[ "$0" = "$BASH_SOURCE" ]]; then
    exit 1;
 fi
 
-TEMPLATE_DIR="$SCRIPT_DIR/resources/templates/"
+RESOURCE_DIR="$SCRIPT_DIR/resources"
+TEMPLATE_DIR="$RESOURCE_DIR/templates/"
 
 # load_template will load a template $1 from the template directory
 # and replace ${$2} with $3, ${$4} with $5 etc. 
@@ -30,5 +31,19 @@ function load_template() {
     echo "$TEMPLATE"
 }
 
+# install_resource_dir will copy over a resource directory
+# to a destination path recursively. 
+function install_resource_dir() {
+    from="$RESOURCE_DIR/$1"
+    to=$2
+
+    # copythe template files
+    for filename in "$from"/*; do
+        dest="$to/`basename "${filename}"`"
+        echo "Writing \"$dest\""
+        cp -r "$filename"  "$dest"
+    done
+}
+
 # path where common apache files will be installed. 
 WISSKI_COMMON_PATH="/etc/apache2/conf/wisski"

distillery/lib/lib.sh

@@ -16,6 +16,7 @@ LIB_DIR="$SCRIPT_DIR/lib"
 # These contain functionality used in the various scripts. 
 source "$LIB_DIR/00_init.sh";
 source "$LIB_DIR/10_config.sh";
-source "$LIB_DIR/20_slug.sh";
+source "$LIB_DIR/20_sql.sh";
-source "$LIB_DIR/30_templates.sh";
+source "$LIB_DIR/30_slug.sh";
-source "$LIB_DIR/40_utils.sh";
+source "$LIB_DIR/40_templates.sh";
+source "$LIB_DIR/50_utils.sh";

distillery/mysql.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+set -e
+
+# disable the log
+DISABLE_LOG=1
+
+# read the lib/shared.sh
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cd "$DIR"
+source "$DIR/lib/lib.sh"
+
+# wait for sql to come up
+wait_for_sql > /dev/null
+dockerized_mysql_interactive "$@"

distillery/provision.sh

@@ -0,0 +1,107 @@
+# To install a new system:
+
+# This script will provision a new Drupal instance and make it available to apache. 
+# Usage: sudo ./provision.sh $SLUG
+# In case the installation fails, it will bail out and leave you with an incomplete installation. 
+# To delete an incomplete installation, use the ./purge.sh script, or try fixing the error manually. 
+set -e
+
+# read the lib/shared.sh and read the slug argument. 
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cd "$DIR"
+source "$DIR/lib/lib.sh"
+require_slug_argument
+
+# wait for sql to be awake
+wait_for_sql
+
+# check if the site exists
+if sql_bookkeep_exists "$SLUG"; then
+    log_error "=> Site '$SLUG' already exists in bookeeping table. "
+    echo "Refusing to work"
+    exit 1;
+fi
+
+# Randomly generate the database name and user we will configure. 
+# Use the 'randompw' alias for this. 
+log_info " => Generating new MySQL password"
+MYSQL_PASSWORD="$(randompw)"
+
+# Initialize the SQL database with those credentials. 
+log_info " => Intializing new SQL database '${MYSQL_DATABASE}' and user '$MYSQL_USER'. "
+dockerized_mysql -e "CREATE DATABASE \`${MYSQL_DATABASE}\`;"
+dockerized_mysql -e "CREATE USER \`${MYSQL_USER}\`@'%' IDENTIFIED BY '${MYSQL_PASSWORD}';"
+dockerized_mysql -e "GRANT ALL PRIVILEGES ON \`${MYSQL_DATABASE}\`.* TO \`${MYSQL_USER}\`@\`%\`;"
+dockerized_mysql -e "FLUSH PRIVILEGES;"
+
+# Create a new repository for GraphDB. 
+# Use the template for this.
+log_info " => Generating new GraphDB repository '$GRAPHDB_REPO'"
+load_template "repository/graphdb-repo.ttl" "GRAPHDB_REPO" "${GRAPHDB_REPO}" "INSTANCE_DOMAIN" "${INSTANCE_DOMAIN}" | \
+curl -X POST \
+    http://127.0.0.1:7200/rest/repositories \
+    --header 'Content-Type: multipart/form-data' \
+    -F "config=@-"
+
+# Generate a random password for the GraphDB user
+log_info " => Generating a new GraphDB password"
+GRAPHDB_PASSWORD="$(randompw)"
+
+# Create the user and grant them access to the creatd database. 
+log_info " => Creating GraphDB user '$GRAPHDB_USER'"
+load_template "repository/graphdb-user.json" "GRAPHDB_USER" "${GRAPHDB_USER}" "GRAPHDB_REPO" "${GRAPHDB_REPO}" | \
+curl -X POST \
+    "http://127.0.0.1:7200/rest/security/user/${GRAPHDB_USER}" \
+    --header 'Content-Type: application/json' \
+    --header 'Accept: text/plain' \
+    --header "X-GraphDB-Password: $GRAPHDB_PASSWORD" \
+    -d @-
+
+log_info " => Creating local directory '$INSTANCE_BASE_DIR'"
+mkdir -p "$INSTANCE_BASE_DIR"
+mkdir -p "$INSTANCE_DATA_DIR"
+mkdir -p "$INSTANCE_DATA_DIR/.composer"
+mkdir -p "$INSTANCE_DATA_DIR/data"
+
+# Generate some more random credentials, this time for drupal. 
+# We again make use of the randompw alias. 
+log_info " => Generating new drupal credentials"
+DRUPAL_USER="admin"
+DRUPAL_PASS="$(randompw)"
+
+# TODO: copy over docker-compose into the right directory
+log_info " => Creating instance directory"
+install_resource_dir "compose/runtime" "$INSTANCE_BASE_DIR"
+
+# Log all the details into the bookeeping database
+log_info "=> Storing configuration in bookkeeping table"
+sql_bookkeep_insert \
+    "slug,filesystem_base,sql_database,sql_user,sql_password,graphdb_repository,graphdb_user,graphdb_password" \
+    "\"${SLUG}\",\"${INSTANCE_BASE_DIR}\",\"${MYSQL_DATABASE}\",\"${MYSQL_USER}\",\"${MYSQL_PASSWORD}\",\"${GRAPHDB_REPO}\",\"${GRAPHDB_USER}\",\"${GRAPHDB_PASSWORD}\""
+
+log_info " => Writing configuration file"
+load_template "runtime-config/environment" \
+    "REAL_PATH" "${INSTANCE_DATA_DIR}" \
+    "VIRTUAL_HOST" "${INSTANCE_DOMAIN}" \
+    "LETSENCRYPT_HOST" "${LETSENCRYPT_HOST}" \
+    "LETSENCRYPT_EMAIL" "${LETSENCRYPT_EMAIL}" \
+    > "$INSTANCE_BASE_DIR/.env"
+
+
+log_info " => Running and building image"
+cd "$INSTANCE_BASE_DIR"
+docker-compose build --pull
+docker-compose pull
+
+log_info " => Running provision script"
+docker-compose run --rm runtime /bin/bash -c "sudo PATH=\$PATH -u www-data /bin/bash /provision_container.sh \
+    \"${INSTANCE_DOMAIN}\" \
+    \"${MYSQL_DATABASE}\" \"${MYSQL_USER}\" \"${MYSQL_PASSWORD}\" \
+    \"${GRAPHDB_REPO}\" \"${GRAPHDB_USER}\" \"${GRAPHDB_PASSWORD}\" \
+    \"${DRUPAL_USER}\" \"${DRUPAL_PASS}\" \
+    \"${USE_DRUPAL_9}\""
+
+
+log_info " => Starting container"
+docker-compose up -d
+

distillery/purge.sh

@@ -0,0 +1,67 @@
+# To install a new system:
+
+# This script will provision a new Drupal instance and make it available to apache. 
+# Usage: sudo ./provision.sh $SLUG
+# In case the installation fails, it will bail out and leave you with an incomplete installation. 
+# To delete an incomplete installation, use the ./purge.sh script, or try fixing the error manually. 
+set -e
+
+# read the lib/shared.sh and read the slug argument. 
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cd "$DIR"
+source "$DIR/lib/lib.sh"
+require_slug_argument
+
+# wait for sql to be awake
+wait_for_sql
+
+while true; do
+    log_info " => I'm about to delete the '$SLUG' site from this system. "
+    read -p "This can not be undone. Please type 'y' to continue: " yn
+    case $yn in
+        [Yy]* ) break;;
+        * ) echo "Abort. "; exit 1;;
+    esac
+done
+
+# check if the site exists
+if ! sql_bookkeep_exists "$SLUG"; then
+    log_error "=> Site '$SLUG' does not exist in bookeeping table. "
+    echo "I'll try to cleanup with the current defaults. "
+    echo "This may or may not work. "
+else
+    # Read all the configuration from the database
+    log_info " => Reading components from database"
+    read -r INSTANCE_BASE_DIR MYSQL_DATABASE MYSQL_USER GRAPHDB_REPO GRAPHDB_USER <<< "$(sql_bookkeep_load "${SLUG}" "filesystem_base,sql_database,sql_user,graphdb_repository,graphdb_user" | tail -n +2)"
+fi
+
+# stop the running system container
+if [ -d "$INSTANCE_BASE_DIR" ] ; then
+    log_info "=> Stopping running system"
+    cd "$INSTANCE_BASE_DIR"
+    docker-compose down -v || true
+fi;
+
+cd
+
+# delete the mysql database. 
+log_info " => Deleting MySQL database '$MYSQL_DATABASE' and user '$MYSQL_USER'. "
+dockerized_mysql -e "DROP DATABASE IF EXISTS \`${MYSQL_DATABASE}\`;"
+dockerized_mysql -e "DROP USER IF EXISTS \`${MYSQL_USER}\`@\`%\`;"
+dockerized_mysql -e "FLUSH PRIVILEGES;"
+
+# Clear the GraphDB repository. 
+log_info " => Deleting GraphDB user '$GRAPHDB_USER'"
+curl -X DELETE http://127.0.0.1:7200/rest/security/user/$GRAPHDB_USER/
+
+log_info " => Deleting GraphDB repository '$GRAPHDB_REPO'"
+curl -X DELETE http://127.0.0.1:7200/rest/repositories/$GRAPHDB_REPO/
+
+# Delete the directory
+log_info " => Deleting '$INSTANCE_BASE_DIR'"
+rm -rf "$INSTANCE_BASE_DIR"
+
+log_info " => Clearing bookkeeping record"
+sql_bookeep_delete "$SLUG" || true
+
+log_info " => '$SLUG' has been purged. "

distillery/resources/.dockerignore

@@ -0,0 +1 @@
+data/

distillery/resources/compose/runtime/.dockerignore

@@ -0,0 +1,6 @@
+# Ignore everything
+*
+
+# allow the following files:
+!conf/*
+!scripts/*

distillery/resources/compose/runtime/.env.sample

@@ -0,0 +1,27 @@
+#######################
+# Meta Settings
+#######################
+
+# Real path for volumes to be stored
+REAL_PATH=/var/www/example.slug
+
+#######################
+### Web Server settings
+#######################
+# the hostname for the website
+VIRTUAL_HOST=example.com
+
+# optional letsencrypt support
+# when blank, ignore
+LETSENCRYPT_HOST=
+LETSENCRYPT_EMAIL=
+
+### SQL settings
+MYSQL_HOST=mysql
+MYSQL_USER=user
+MYSQL_PASS=pass
+
+### GraphDB settings
+GRAPHDB_HOST=graphdb
+GRAPHDB_USER=user
+GRAPHDB_PASS=pass

distillery/resources/compose/runtime/Dockerfile

@@ -0,0 +1,75 @@
+FROM php:7-apache-buster
+WORKDIR /var/www
+
+# install and enable the various required php extension
+RUN apt-get update && apt-get install -y \
+        libcurl4-openssl-dev curl \
+        libpng-dev \
+        libicu-dev \
+        libxml2-dev \
+        libssh2-1-dev \
+        sudo \
+        zip unzip \
+        default-mysql-client \
+    && \
+    docker-php-source extract && \
+    docker-php-ext-install \
+        curl \
+        gd \
+        intl \
+        soap \
+        mysqli \
+        opcache \
+        pdo_mysql \
+        xml \
+        xmlrpc \
+    && \
+    pecl install ssh2-1.2 && \
+    docker-php-ext-enable \
+        curl \
+        gd \
+        intl \
+        mysqli \
+        opcache \
+        pdo_mysql \
+        soap \
+        ssh2 \
+        mysqli \
+        xml \
+        xmlrpc \
+    && \
+    docker-php-source delete
+
+# enable the apache rewrite mod
+RUN a2enmod rewrite
+
+# install composer and add it to path
+RUN curl -sS https://getcomposer.org/installer | php && \
+    mv composer.phar /usr/local/bin/composer
+ENV PATH "/usr/local/bin:/var/www/data/project/vendor/bin:$PATH"
+
+# remove default configuration
+RUN rm /etc/apache2/sites-available/*.conf && \
+    rm /etc/apache2/sites-enabled/*.conf
+# Add wisski configuration
+ADD conf/ports.conf /etc/apache2/ports.conf
+ADD conf/wisski.conf /etc/apache2/sites-available/wisski.conf
+RUN a2ensite wisski
+
+# volumes for composer
+VOLUME /var/www/.composer
+VOLUME /var/www/data
+
+# increase the php memory limit to 2g
+RUN echo 'memory_limit=2G' > /usr/local/etc/php/conf.d/memory-limit.ini
+
+# Add and configure the entrypoint
+ADD scripts/entrypoint.sh /entrypoint.sh
+ENTRYPOINT [ "/entrypoint.sh" ]
+CMD ["apache2-foreground"]
+
+# Add the provision script
+ADD scripts/provision_container.sh /provision_container.sh
+
+# expose port 8080
+EXPOSE 8080

distillery/resources/compose/runtime/conf/ports.conf

@@ -0,0 +1,4 @@
+# This file configures where apache should listen. 
+# Because we are running as a limited user, we want to listen on a high port. 
+# For this we use port 8080
+Listen 8080

distillery/resources/compose/runtime/conf/wisski.conf

@@ -0,0 +1,22 @@
+<VirtualHost *:8080>
+    # the document root -- /var/www/data/project/web
+    DocumentRoot /var/www/data/project/web
+
+    <Directory /var/www/data/project/web>
+        # add types for .owl and .rdf
+        AddType application/rdf+xml .owl
+        AddType application/rdf+xml .rdf
+
+        # Rewrite the 'ontology' directory
+        ReWriteRule ^(ontology/[^/]+/).+ $1 [R=303,L]
+        ReWriteRule ^(ontology/[^/]+)/$ sites/default/files/$1.owl [L]
+
+        # Allow overrides of symlinks
+        Options Indexes FollowSymLinks
+        AllowOverride All
+        Require all granted
+    </Directory>
+
+    ErrorLog /dev/stderr
+    CustomLog /dev/stdout combined
+</VirtualHost>

distillery/resources/compose/runtime/docker-compose.yml

@@ -0,0 +1,24 @@
+version: "3.7"
+
+services:
+  runtime:
+    build: .
+    restart: always
+    environment:
+      # port and hostname for this image to use
+      VIRTUAL_HOST: ${VIRTUAL_HOST}
+      VIRTUAL_PORT: 8080
+      
+      # optional letsencrypt email
+      LETSENCRYPT_HOST: ${LETSENCRYPT_HOST}
+      LETSENCRYPT_EMAIL: ${LETSENCRYPT_EMAIL}
+    
+    # the volumes to 
+    volumes:
+      - ${REAL_PATH}/.composer:/var/www/.composer
+      - ${REAL_PATH}/data:/var/www/data
+
+networks:
+  default:
+    external:
+      name: distillery

distillery/resources/compose/runtime/scripts/entrypoint.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# This script contains 
+
+# chown the volumes to make sure they can be read and written by the limited user
+chown www-data:www-data /var/www
+chown www-data:www-data /var/www/.composer
+chown www-data:www-data /var/www/data/
+
+# run the original entrypoint
+docker-php-entrypoint "$@"

distillery/resources/compose/runtime/scripts/provision_container.sh

@@ -0,0 +1,126 @@
+#!/bin/bash
+set -e
+
+function log_info() {
+   echo -e "\033[1m$1\033[0m"
+}
+
+function log_ok() {
+   echo -e "\033[0;32m$1\033[0m"
+}
+
+log_info " => Reading configuration variables"
+
+INSTANCE_DOMAIN="$1"
+echo "INSTANCE_DOMAIN=$INSTANCE_DOMAIN"
+shift 1
+
+MYSQL_DATABASE="$1"
+echo "MYSQL_DATABASE=$MYSQL_DATABASE"
+MYSQL_USER="$2"
+echo "MYSQL_USER=$MYSQL_USER"
+MYSQL_PASSWORD="$3"
+echo "MYSQL_PASSWORD=$MYSQL_PASSWORD"
+
+shift 3
+
+GRAPHDB_REPO="$1"
+echo "GRAPHDB_REPO=$GRAPHDB_REPO"
+GRAPHDB_USER="$2"
+echo "GRAPHDB_USER=$GRAPHDB_USER"
+GRAPHDB_PASSWORD="$3"
+echo "GRAPHDB_PASSWORD=$GRAPHDB_PASSWORD"
+shift 3
+
+DRUPAL_USER="$1"
+echo "DRUPAL_USER=$DRUPAL_USER"
+DRUPAL_PASS="$2"
+echo "DRUPAL_PASS=$DRUPAL_PASS"
+shift 2
+
+USE_DRUPAL_9="$1"
+echo "USE_DRUPAL_9=$USE_DRUPAL_9"
+shift 1
+
+log_info " => Preparing installation environment"
+BASE_DIR="/var/www/data"
+COMPOSER_DIR="$BASE_DIR/project"
+WEB_DIR="$COMPOSER_DIR/web"
+ONTOLOGY_DIR="$WEB_DIR/sites/default/files/ontology"
+
+log_info " => Creating '$COMPOSER_DIR'"
+mkdir -p "$COMPOSER_DIR"
+cd "$COMPOSER_DIR"
+
+function drupal_sites_permission_workaround() {
+    chmod -R u+w "$WEB_DIR/sites/" || true
+}
+
+# Create a new composer project. 
+log_info " => Creating composer project"
+if [ -z "${USE_DRUPAL_9}" ]; then
+    composer create-project 'drupal/recommended-project:^8.9.0' .
+else
+    composer create-project 'drupal/recommended-project:^9.0.0' .
+fi
+
+# Install drush so that we can automate a lot of things
+log_info " => Installing 'drush'"
+composer require drush/drush
+
+# Use 'drush' to run the site-installation. 
+# Here we need to use the username, password and database creds we made above. 
+log_info " => Running drupal installation scripts"
+drush site-install standard --yes --site-name=${INSTANCE_DOMAIN} \
+    --account-name=$DRUPAL_USER --account-pass=$DRUPAL_PASS \
+    --db-url=mysql://${MYSQL_USER}:${MYSQL_PASSWORD}@sql/${MYSQL_DATABASE}
+drupal_sites_permission_workaround
+
+# create a directory for ontologies. 
+log_info " => Creating '$ONTOLOGY_DIR'"
+mkdir -p "$ONTOLOGY_DIR"
+
+# Install the Wisski packages. 
+log_info " => Installing Wisski packages"
+cd "$COMPOSER_DIR"
+
+# install the development version when requested
+if [ -z "${USE_DRUPAL_9}" ]; then
+    composer require 'drupal/wisski'
+else
+    composer require 'drupal/wisski:2.x-dev'
+fi
+
+drupal_sites_permission_workaround
+composer require drupal/inline_entity_form
+
+drupal_sites_permission_workaround
+composer require drupal/imagemagick
+
+drupal_sites_permission_workaround
+composer require drupal/image_effects
+
+drupal_sites_permission_workaround
+composer require drupal/colorbox
+
+log_info " => Enable Wisski modules"
+drush pm-enable --yes wisski_core wisski_linkblock wisski_pathbuilder wisski_adapter_sparql11_pb wisski_salz
+drupal_sites_permission_workaround
+
+log_info " => Provisioning is now complete. "
+log_ok "Your installation details are as follows:"
+function printdetails() {
+    echo "URL:                  http://$INSTANCE_DOMAIN"
+    echo "Username:             $DRUPAL_USER"
+    echo "Password:             $DRUPAL_PASS"
+    log_info " => Your GraphDB details (for WissKI Salz) are: "
+    echo "Read URL:             http://triplestore:7200/repositories/$GRAPHDB_REPO"
+    echo "Write URL:            http://triplestore:7200/repositories/$GRAPHDB_REPO/statements"
+    echo "Username:             $GRAPHDB_USER"
+    echo "Password:             $GRAPHDB_PASSWORD"
+    echo "Writable:             yes"
+    echo "Default Graph URI:    http://$INSTANCE_DOMAIN/#"
+    echo "Ontology Paths:       (empty)"
+    echo "SameAs property:      http://www.w3.org/2002/07/owl#sameAs"
+}
+printdetails

distillery/resources/compose/sql/docker-compose.yml

@@ -0,0 +1,32 @@
+version: "3.7"
+
+services:
+    sql:
+        image: mariadb
+        volumes:
+            - "./data/:/var/lib/mysql"
+        environment:
+            # This combination of environment variables will configure a passwordless root user
+            # that can only connect to the container from 'localhost'.
+            # This means we can only connect using 'docker-compose exec sql mysql -C '...' '. 
+            - "MYSQL_ALLOW_EMPTY_PASSWORD=yes"
+            - "MYSQL_ROOT_HOST=localhost"
+        restart: always
+    phpmyadmin:
+        image: phpmyadmin/phpmyadmin
+        environment:
+            - "PMA_HOST=sql"
+            - "HIDE_PHP_VERSION=true"
+        # phpmyadmin running on localhost:8080 so that we can easily access the system graphically. 
+        # By default no admin account is created, so initial shell access to make one is needed. 
+        ports:
+            - 127.0.0.1:8080:80
+        depends_on:
+            - sql
+        restart: always
+
+
+networks:
+    default:
+        external:
+          name: distillery

distillery/resources/compose/triplestore/docker-compose.yml

@@ -0,0 +1,17 @@
+version: "3.7"
+
+services:
+    triplestore:
+        build: .
+        ports:
+            - "127.0.0.1:7200:7200"
+        volumes:
+            - './data/data:/opt/graphdb/data'
+            - './data/work:/opt/graphdb/work'
+            - './data/logs:/opt/graphdb/logs'
+        restart: always
+
+networks:
+    default:
+        external:
+          name: distillery

distillery/resources/compose/web/docker-compose.yml

@@ -0,0 +1,45 @@
+version: "3.7"
+
+services:
+  nginx-proxy:
+    image: nginxproxy/nginx-proxy:alpine
+    ports:
+      - "80:80"
+      - "443:443"
+    volumes:
+      - "vhost:/etc/nginx/vhost.d"
+      - "htpasswd:/etc/nginx/htpasswd"
+      - "html:/usr/share/nginx/html"
+      - "/var/run/docker.sock:/tmp/docker.sock:ro"
+      - "certs:/etc/nginx/certs"
+    labels:
+      com.github.jrcs.letsencrypt_nginx_proxy_companion.nginx_proxy: true
+    restart: always
+    networks:
+      - default
+
+  letsencrypt-nginx-proxy-companion:
+    image: jrcs/letsencrypt-nginx-proxy-companion
+    volumes:
+      - "/var/run/docker.sock:/var/run/docker.sock:ro"
+      - "htpasswd:/etc/nginx/htpasswd"
+      - "vhost:/etc/nginx/vhost.d"
+      - "html:/usr/share/nginx/html"
+      - "/var/run/docker.sock:/tmp/docker.sock:ro"
+      - "certs:/etc/nginx/certs"
+    restart: always
+    networks:
+      - default
+    depends_on:
+      - nginx-proxy
+
+volumes:
+  vhost:
+  html:
+  certs:
+  htpasswd:
+
+networks:
+  default:
+    external:
+      name: distillery

distillery/resources/templates/bookkeeping/create.sql

@@ -0,0 +1,28 @@
+-- create the database if it doesn't exist yet
+CREATE DATABASE IF NOT EXISTS `${DATABASE}`;
+
+-- use the database we just created
+USE `${DATABASE}`;
+
+-- create the bookkeeping table
+CREATE TABLE IF NOT EXISTS `${TABLE}`(
+    -- automatically created fields
+    pk INT NOT NULL PRIMARY KEY AUTO_INCREMENT,
+    created DATETIME DEFAULT CURRENT_TIMESTAMP,
+    
+    -- slug of the website
+    slug TEXT NOT NULL UNIQUE,
+
+    -- local file path
+    filesystem_base TEXT NOT NULL,
+    
+    -- sql access credentials
+    sql_database TEXT NOT NULL,
+    sql_user TEXT NOT NULL,
+    sql_password TEXT NOT NULL,
+
+    -- graphdb credentials
+    graphdb_repository TEXT NOT NULL,
+    graphdb_user TEXT NOT NULL,
+    graphdb_password TEXT NOT NULL
+);

distillery/resources/templates/runtime-config/environment

@@ -0,0 +1,17 @@
+#######################
+# Meta Settings
+#######################
+
+# Real path for volumes to be stored
+REAL_PATH=${REAL_PATH}
+
+#######################
+### Web Server settings
+#######################
+# the hostname for the website
+VIRTUAL_HOST=${VIRTUAL_HOST}
+
+# optional letsencrypt support
+# when blank, ignore
+LETSENCRYPT_HOST=${LETSENCRYPT_HOST}
+LETSENCRYPT_EMAIL=${LETSENCRYPT_EMAIL}

distillery/system_install.sh

@@ -0,0 +1,89 @@
+#!/bin/bash
+set -e
+
+# read the lib/shared.sh
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cd "$DIR"
+source "$DIR/lib/lib.sh"
+
+# Read the 'GRAPHDB_ZIP' argument from the command line. 
+# If it's not set, throw an error. 
+GRAPHDB_ZIP=$1
+if [ -z "$GRAPHDB_ZIP" ]; then
+    log_error "Usage: system_install.sh GRAPHDB_ZIP"
+    exit 1;
+fi;
+
+
+# print some general info on the screen
+log_info "=> Preparing system to become a WissKI Distillery"
+echo "This script will install or upgrade this system to become a WissKI distillery. "
+echo "It is idempotent and can safely be run multiple times. "
+sleep 5
+
+
+# Install default system upgrades. 
+log_info "=> Installing system updates"
+apt-get update
+apt-get upgrade -y
+
+# install docker dependencies. 
+log_info "=> Installing docker installer dependencies"
+apt-get update
+apt-get install -y curl
+
+# install docker using an automated script. 
+log_info "=> Installing docker"
+curl -fsSL https://get.docker.com -o - | /bin/sh
+
+# install docker-compose dependencies. 
+log_info "=> Install docker-compose installer dependencies"
+apt-get update
+apt-get install -y python3-pip
+
+# install docker-compose. 
+log_info "=> Installing docker-compose"
+pip3 install --upgrade docker-compose
+
+log_info "=> Creating docker-compose directories"
+mkdir -p "$COMPOSER_INSTANCES_DIR"
+mkdir -p "$COMPOSER_WEB_DIR"
+mkdir -p "$COMPOSER_TRIPLESTORE_DIR"
+mkdir -p "$COMPOSER_SQL_DIR"
+
+log_info "=> Creating 'distillery' network"
+docker network create distillery || true
+
+log_info "=> Creating 'docker-compose' files for the 'web'. "
+install_resource_dir "compose/web" "$COMPOSER_WEB_DIR"
+
+# copy over the directory
+log_info "=> Creating 'docker-compose' files for the 'triplestore'. "
+install_resource_dir "compose/triplestore" "$COMPOSER_TRIPLESTORE_DIR"
+
+# copy the graphdb.zip
+echo "Writing \"$COMPOSER_TRIPLESTORE_DIR/graphdb.zip\""
+cp "$GRAPHDB_ZIP" "$COMPOSER_TRIPLESTORE_DIR/graphdb.zip"
+
+# create data (volume) location
+mkdir -p "$COMPOSER_TRIPLESTORE_DIR/data/data/"
+mkdir -p "$COMPOSER_TRIPLESTORE_DIR/data/work/"
+mkdir -p "$COMPOSER_TRIPLESTORE_DIR/data/logs/"
+
+# copy over the sql resource directory, then ensure the data diretory for sql exists. 
+log_info "=> Creating 'docker-compose' files for the 'sql'. "
+install_resource_dir "compose/sql" "$COMPOSER_SQL_DIR"
+mkdir -p "$COMPOSER_SQL_DIR/data/"
+
+# Run all the updates via system_update.sh
+log_info " => Running 'system_update.sh'"
+bash "$SCRIPT_DIR/system_update.sh"
+
+log_info "=> Waiting for sql to come up"
+wait_for_sql
+
+log_info "=> Creating '$DISTILLERY_BOOKKEEPING_DATABASE' database and '$DISTILLERY_BOOKKEEPING_TABLE' table"
+load_template "bookkeeping/create.sql" "DATABASE" "$DISTILLERY_BOOKKEEPING_DATABASE" "TABLE" "$DISTILLERY_BOOKKEEPING_TABLE" | \
+    dockerized_mysql
+
+log_info "=> System installation finished, ready to distill. "

distillery/system_update.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+set -e
+
+# read the lib/shared.sh
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+cd "$DIR"
+source "$DIR/lib/lib.sh"
+
+# update_stack fully updates a docker-compose stack in the given location. 
+function update_stack() {
+    cd "$1"
+    docker-compose pull
+    docker-compose build --pull
+    docker-compose up -d
+}
+
+log_info "=> Rebuilding and restarting 'web' stack"
+update_stack "$COMPOSER_WEB_DIR"
+
+# build and start the triplestore
+log_info "=> Rebuilding and restarting 'triplestore' stack"
+update_stack "$COMPOSER_TRIPLESTORE_DIR"
+
+# build and start the triplestore
+log_info "=> Rebuilding and restarting 'sql' stack"
+update_stack "$COMPOSER_SQL_DIR"
+
+# TODO: Iterate over all the instance
+# and a  pull_and_update
+
+log_info "=> System up-to-date. "

factory/provision.sh

@@ -1,212 +0,0 @@
-#!/bin/bash
-
-# This script will provision a new Drupal instance and make it available to apache. 
-# Usage: sudo ./provision.sh $SLUG
-# In case the installation fails, it will bail out and leave you with an incomplete installation. 
-# To delete an incomplete installation, use the ./purge.sh script, or try fixing the error manually. 
-set -e
-
-# read the lib/shared.sh and read the slug argument. 
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-cd "$DIR"
-source "$DIR/lib/lib.sh"
-require_slug_argument
-
-
-# A global flag 'USE_DRUPAL_9' can be set to enable drupal 9 support. 
-# We print out the value of the flag here
-if [ -z "${USE_DRUPAL_9}" ]; then
-    log_info " => Will install stable Drupal 8 (Use 'USE_DRUPAL_9=1' for Drupal 9). "
-else
-    log_info " => Will install experimental Drupal 9 version ('USE_DRUPAL_9' was set)"
-fi
-
-log_info " => Validing configuration"
-
-# If the base directory already exists, we might have accidentally picked a name that already exists. 
-# In that case we bail out for safety reasons. 
-if [ -d "$BASE_DIR" ]; then
-    echo "'$BASE_DIR' already exists. "
-    echo "Aborting provisioning, please make sure you picked a unique name. "
-    exit 1
-fi
-
-# Check that the apache2 config is correct. 
-# This is a sanity test so that we don't randomly fail later because of bad config. 
-log_info " => Checking apache configuration"
-apache2ctl configtest > /dev/null
-
-# Create a system user and group
-log_info " => Creating system user and group '$SYSTEM_USER'"
-addgroup --system "$SYSTEM_USER"
-adduser --home "$BASE_DIR" --system --disabled-password --disabled-login --ingroup "$SYSTEM_USER" "$SYSTEM_USER"
-
-# Make directory for the composer project to live in
-log_info " => Making composer directory '$COMPOSER_DIR'"
-sudo -u "$SYSTEM_USER" mkdir -p "$COMPOSER_DIR"
-cd "$COMPOSER_DIR"
-
-# Write out a new apache configuration file into /etc/apache2/sites-available. 
-# We will need to substitute in some configuration directories. 
-log_info " => Writing new apache configuration file"
-load_template "wisski-site.conf" \
-    "PUBLIC_PORT" "${PUBLIC_PORT}" \
-    "WEB_DIR" "${WEB_DIR}" \
-    "INSTANCE_DOMAIN" "${INSTANCE_DOMAIN}" \
-    "SYSTEM_USER" "${SYSTEM_USER}" \
-    "WISSKI_COMMON_PATH" "${WISSKI_COMMON_PATH}" \
-    > "${APACHE_CONFIG_SITE_AVAILABLE}"
-
-# Create a new composer project. 
-log_info " => Creating composer project"
-if [ -z "${USE_DRUPAL_9}" ]; then
-    composer create-project 'drupal/recommended-project:^8.9.0' .
-else
-    composer create-project 'drupal/recommended-project:^9.0.0' .
-fi
-composer require drush/drush
-
-# Randomly generate the database name and user we will configure. 
-# Use the 'randompw' alias for this. 
-log_info " => Generating new MySQL password"
-MYSQL_PASSWORD="$(randompw)"
-
-# Initialize the SQL database with those credentials. 
-log_info " => Intializing new SQL database '${MYSQL_DATABASE}' and user '$MYSQL_USER'. "
-mysql -e "CREATE DATABASE \`${MYSQL_DATABASE}\`;"
-mysql -e "CREATE USER \`${MYSQL_USER}\`@localhost IDENTIFIED BY '${MYSQL_PASSWORD}';"
-mysql -e "GRANT ALL PRIVILEGES ON \`${MYSQL_DATABASE}\`.* TO \`${MYSQL_USER}\`@localhost;"
-mysql -e "FLUSH PRIVILEGES;"
-
-# Generate some more random credentials, this time for drupal. 
-# We again make use of the randompw alias. 
-log_info " => Generating new drupal credentials"
-DRUPAL_USER="admin"
-DRUPAL_PASS="$(randompw)"
-
-# Use 'drush' to run the site-installation. 
-# Here we need to use the username, password and database creds we made above. 
-log_info " => Running drupal installation scripts"
-drush site-install standard --yes --site-name=${INSTANCE_DOMAIN} \
-    --account-name=$DRUPAL_USER --account-pass=$DRUPAL_PASS \
-    --db-url=mysql://${MYSQL_USER}:${MYSQL_PASSWORD}@localhost/${MYSQL_DATABASE}
-
-drupal_sites_permission_workaround
-
-# Create a new repository for GraphDB. 
-# Use the template for this.
-log_info " => Generating new GraphDB repository '$GRAPHDB_REPO'"
-load_template "graphdb-repo.ttl" "GRAPHDB_REPO" "${GRAPHDB_REPO}" "INSTANCE_DOMAIN" "${INSTANCE_DOMAIN}" | \
-curl -X POST \
-    http://127.0.0.1:7200/rest/repositories \
-    --header 'Content-Type: multipart/form-data' \
-    -F "config=@-"
-
-# Generate a random password for the GraphDB user
-log_info " => Generating a new GraphDB password"
-GRAPHDB_PASSWORD="$(randompw)"
-
-# Create the user and grant them access to the creatd database. 
-log_info " => Creating GraphDB user '$GRAPHDB_USER'"
-load_template "graphdb-user.json" "GRAPHDB_USER" "${GRAPHDB_USER}" "GRAPHDB_REPO" "${GRAPHDB_REPO}" | \
-curl -X POST \
-    "http://127.0.0.1:7200/rest/security/user/${GRAPHDB_USER}" \
-    --header 'Content-Type: application/json' \
-    --header 'Accept: text/plain' \
-    --header "X-GraphDB-Password: $GRAPHDB_PASSWORD" \
-    -d @-
-
-# create a directory for ontologies. 
-log_info " => Creating '$ONTOLOGY_DIR'"
-mkdir -p "$ONTOLOGY_DIR"
-
-# Install the Wisski packages. 
-log_info " => Installing Wisski packages"
-cd "$COMPOSER_DIR"
-
-drupal_sites_permission_workaround
-
-# install the development version when requested
-if [ -z "${USE_DRUPAL_9}" ]; then
-    composer require 'drupal/wisski'
-else
-    composer require 'drupal/wisski:2.x-dev'
-fi
-
-drupal_sites_permission_workaround
-composer require drupal/inline_entity_form
-
-drupal_sites_permission_workaround
-composer require drupal/imagemagick
-
-drupal_sites_permission_workaround
-composer require drupal/image_effects
-
-drupal_sites_permission_workaround
-composer require drupal/colorbox
-
-log_info " => Installation is now technically complete. "
-log_ok "Some things below may fail. If that is the case, run: "
-log_ok "$ a2ensite \"${INSTANCE_DOMAIN}\""
-log_ok "$ systemctl reload apache2"
-log_ok "$ $SCRIPT_DIR/shell.sh $SLUG"
-log_ok "Your installation details are as follows:"
-function printdetails() {
-    echo "URL:                  http://$INSTANCE_DOMAIN"
-    echo "Username:             $DRUPAL_USER"
-    echo "Password:             $DRUPAL_PASS"
-    log_info " => Your GraphDB details (for WissKI Salz) are: "
-    echo "Read URL:             http://127.0.0.1:7200/repositories/$GRAPHDB_REPO"
-    echo "Write URL:            http://127.0.0.1:7200/repositories/$GRAPHDB_REPO/statements"
-    echo "Writable:             yes"
-    echo "Default Graph URI:    http://$INSTANCE_DOMAIN/#"
-    echo "Ontology Paths:       (empty)"
-    echo "SameAs property:      http://www.w3.org/2002/07/owl#sameAs"
-}
-printdetails
-
-function alldetails() {
-    echo "# Automatically generated WissKi details"
-    echo "# generated $(date -u +"%Y-%m-%dT%H:%M:%SZ")"
-    echo "SLUG=$SLUG"
-    echo "INSTANCE_DOMAIN=$INSTANCE_DOMAIN"
-    echo "# System"
-    echo "SYSTEM_USER=$SYSTEM_USER"
-    echo "# Drupal"
-    echo "DRUPAL_USER=$DRUPAL_USER"
-    echo "DRUPAL_PASSWORD=$DRUPAL_PASSWORD"
-    echo "# MySQL"
-    echo "MYSQL_USER=$MYSQL_USER"
-    echo "MYSQL_PASSWORD=$MYSQL_PASSWORD"
-    echo "MYSQL_DATABASE=$MYSQL_DATABASE"
-    echo "# GraphDB"
-    echo "GRAPHDB_USER=$GRAPHDB_USER"
-    echo "GRAPHDB_PASSWORD=$GRAPHDB_PASSWORD"
-    echo "GRAPHDB_REPO=$GRAPHDB_REPO"
-}
-
-# put installation details in ENV_FILE
-log_info " => Storing installation details in $ENV_FILE"
-alldetails > "$ENV_FILE"
-chown "$SYSTEM_USER:$SYSTEM_USER" "$ENV_FILE"
-chmod o-r "$ENV_FILE"
-
-# Enable the WissKI modules. 
-log_info " => Enable Wisski modules"
-drush pm-enable --yes wisski_core wisski_linkblock wisski_pathbuilder wisski_adapter_sparql11_pb wisski_salz
-drupal_sites_permission_workaround
-
-# Because of a regresssion in EasyRDF and Tomcat, we need to manually patch EasyRDF
-EASYRDF_RESPONSE="$COMPOSER_DIR/vendor/easyrdf/easyrdf/lib/EasyRdf/Http/Response.php"
-log_info " => Patching '$EASYRDF_RESPONSE'"
-load_template "easyrdf.patch" | patch "$EASYRDF_RESPONSE"
-
-# Finally enable the apache2 config. 
-# And then reload to start serving it. 
-log_info " => Enabling and reloading apache configuration"
-a2ensite "${INSTANCE_DOMAIN}"
-systemctl reload apache2
-
-# and done!
-log_info " => Finished, your Drupal details are: "
-printdetails

factory/purge.sh

@@ -1,44 +0,0 @@
-#!/bin/bash
-set -e
-
-# TODO: Delete system user
-
-# read the lib/shared.sh and read the slug argument. 
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-cd "$DIR"
-source "$DIR/lib/lib.sh"
-require_slug_argument
-
-# Delete the apache configuration files first. 
-# This prevents drupal from being served. 
-log_info " => Removing apache configuration files"
-rm "$APACHE_CONFIG_SITE_ENABLED" || true
-rm "$APACHE_CONFIG_SITE_AVAILABLE" || true
-
-# Reload apache to apply the configuration. 
-log_info " => Reloading apache"
-systemctl reload apache2
-
-# Delete the MySQL database next. 
-log_info " => Deleting MySQL database '$MYSQL_DATABASE' and user '$MYSQL_USER'. "
-mysql -e "DROP DATABASE IF EXISTS \`${MYSQL_DATABASE}\`;" || true
-mysql -e "DROP USER IF EXISTS \`${MYSQL_USER}\`@localhost;"  || true
-mysql -e "FLUSH PRIVILEGES;"
-
-# Clear the GraphDB repository. 
-log_info " => Deleting GraphDB repository '$GRAPHDB_REPO'"
-curl -X DELETE http://127.0.0.1:7200/rest/repositories/$GRAPHDB_REPO/
-
-log_info " => Deleting GraphDB user '$GRAPHDB_USER'"
-curl -X DELETE http://127.0.0.1:7200/rest/security/user/$GRAPHDB_USER/
-
-
-log_info " => Deleting system user and group '$SYSTEM_USER'"
-deluser "$SYSTEM_USER" || true
-delgroup "$SYSTEM_USER" || true
-
-# Finally remove any trace of the repository by removing the base directory. 
-log_info " => Removing directory '$BASE_DIR'"
-rm -rf "$BASE_DIR"
-
-log_info " => Finished, '$INSTANCE_DOMAIN' has been purged. "

factory/resources/templates/easyrdf.patch

@@ -1,4 +0,0 @@
-281c281
-<         if (preg_match("|^HTTP/([\d\.x]+) (\d+) ([^\r\n]+)|", $status, $m)) {
----
->         if(preg_match("|^HTTP/([\d\.x]+) (\d+) ([^\r\n]*)|", $status, $m)) {

factory/resources/templates/graphdb.service

@@ -1,17 +0,0 @@
-# This file contains a systemd service for GraphDB.
-# It was tailed to a WissKI service and may or may not work in general. 
-
-[Unit]
-Description=GraphDB
-
-[Service]
-Type=simple
-# use the special graphdb user and group, so that other users can not just access this system. 
-User=graphdb
-Group=graphdb
-
-# The options here make it listen only on 127.0.0.1; this prevents external users from attempting access.  
-ExecStart=/opt/graphdb/bin/graphdb –Xmx6g -Dgraphdb.connector.address=127.0.0.1
-
-[Install]
-WantedBy=multi-user.target

factory/resources/templates/wisski-site.conf

@@ -1,16 +0,0 @@
-# This file was generated automatically. 
-# It contains configuration for the WissKI site:
-#   ${INSTANCE_DOMAIN}
-# Do not edit unless you know exactly what you are doing.
-
-<VirtualHost *:${PUBLIC_PORT}>
-    DocumentRoot ${WEB_DIR}
-    ServerName ${INSTANCE_DOMAIN}
-    AssignUserId ${SYSTEM_USER} ${SYSTEM_USER}
-
-    <Directory ${WEB_DIR}>
-        include "${WISSKI_COMMON_PATH}/wisski-common-dir.conf"
-    </Directory>
-
-    include "${WISSKI_COMMON_PATH}/wisski-common.conf"
-</VirtualHost>

factory/resources/wisski-apache-common/wisski-common-dir.conf

@@ -1,14 +0,0 @@
-# This file is included inside the 'directory' configuration of all WissKI sites. 
-
-# add types for .owl and .rdf
-AddType application/rdf+xml .owl
-AddType application/rdf+xml .rdf
-
-# Rewrites the ontology directory
-ReWriteRule ^(ontology/[^/]+/).+ $1 [R=303,L]
-ReWriteRule ^(ontology/[^/]+)/$ sites/default/files/$1.owl [L]
-
-# Allow overrides of symlinks
-Options Indexes FollowSymLinks
-AllowOverride All
-Require all granted

factory/resources/wisski-apache-common/wisski-common.conf

@@ -1,4 +0,0 @@
-# This file is included inside the 'virtualhost' of a WissKI site. 
-
-ErrorLog ${APACHE_LOG_DIR}/error.log
-CustomLog ${APACHE_LOG_DIR}/access.log combined

factory/shell.sh

@@ -1,17 +0,0 @@
-#!/bin/bash
-set -e
-
-# read the lib/shared.sh and lib/slug.sh
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-cd "$DIR"
-source "$DIR/lib/lib.sh"
-require_slug_argument
-
-log_info " => Opening shell in '$COMPOSER_DIR'"
-
-# cd into the right directory. 
-cd "$COMPOSER_DIR"
-
-# add /usr/local/bin (for composer) and the vendor bin (for drush) to path
-# and open a bash shell as www-data there. 
-sudo -u "$SYSTEM_USER" PATH="$COMPOSER_DIR/vendor/bin:/usr/local/bin:$PATH" /bin/bash

factory/system_install.sh

@@ -1,108 +0,0 @@
-#!/bin/bash
-set -e
-
-# read the lib/shared.sh
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-cd "$DIR"
-source "$DIR/lib/lib.sh"
-
-# This script will prepare a server to become a factory for Drupal Instances. 
-# Even though it assumes a clean server, it *should* be idempotent. 
-log_info "=> Preparing system to serve as a factory. "
-
-# Read the 'GRAPHDB_ZIP' argument from the command line. 
-# If it's not set, throw an error. 
-GRAPHDB_ZIP=$1
-if [ -z "$GRAPHDB_ZIP" ]; then
-    log_error "Usage: system_install.sh GRAPHDB_ZIP"
-    exit 1;
-fi;
-
-# Make a temporary directory to use for various tasks during this script. 
-log_info " => Making temporary directory"
-tmpdir="$(mktemp -d)"
-log_ok "Made $tmpdir"
-
-# fetch new package versions, then upgrade everything we already have. 
-# This isn't technically neccessary, but it means it'll work on an otherwise untouched system. 
-log_info " => Installing package updates ..."
-apt-get update
-apt-get dist-upgrade -y
-
-# Install composer, by downloading it using curl and then run it with php to install it in /usr/local/bin. 
-log_info " => Installing composer"
-apt-get install -y curl php-cli php-mbstring git unzip
-curl -sS https://getcomposer.org/installer -o "$tmpdir/composer-setup.php"
-php $tmpdir/composer-setup.php --install-dir=/usr/local/bin --filename=composer
-
-# Install required php extensions for Drupal and WissKI. 
-log_info " => Installing required php extensions"
-apt-get install -y php-xml php-gd php-mysql php-common php-xmlrpc php-soap php-gd php-intl php-mysql php-zip php-curl php-ssh2
-
-# Install the mariadb kernel. 
-log_info " => Installing mariadb"
-apt-get -y install mariadb-server
-
-# Install apache and required php extensions. 
-log_info " => Installing apache2, php and auth modules"
-apt-get install -y apache2 libapache2-mod-php libapache2-mpm-itk
-
-# Install apache and required php extensions. 
-log_info " => Enabling apache 'rewrite' module"
-a2enmod rewrite
-
-# Copy over the wisski templates
-log_info " => Copying over Apache Templates"
-mkdir -p "$WISSKI_COMMON_PATH"
-cp -v $SCRIPT_DIR/resources/wisski-apache-common/* "$WISSKI_COMMON_PATH"
-
-# Make the directory for all drupal instances to live in. 
-log_info " => Making root directory for Drupal Installations"
-mkdir -p "$DRUPAL_ROOT"
-
-# Install java for GraphDB. 
-# We use the 'headless' package to prevent installing anything graphical on a headless server. 
-log_info " => Installing java"
-apt-get install -y default-jre-headless
-
-
-# Next we have to check if we need to install graphdb. 
-# If '/opt/graphdb' exists, assume that the installation has already been performed. 
-if [ -d "/opt/graphdb" ]; then
-    log_info " => 'opt/graphdb' exists, skipping setup step. ";
-else
-
-    # Unzip the GraphDB sources into a temporary directory. 
-    echo " => Unzipping GraphDB into temporary directory"
-    unzip "$GRAPHDB_ZIP" -d "$tmpdir/graphdb"
-
-    # Then move them into /opt/graphdb.
-    # Here we need to make sure that the first subdirectoy is renamed appropriately during the move. 
-    echo " => Moving GraphDB into /opt/graphdb"
-    mv "$tmpdir/graphdb"/* /opt/graphdb
-fi
-
-# Next make a system group 'graphdb' and system user 'graphdb'. 
-# And also chown the /opt/graphdb directory to that user. 
-# As the user might already exist, we surpress errors of the commands. 
-log_info " => Making GraphDB group and user"
-addgroup --system graphdb || true
-adduser --home "/opt/graphdb" --system --no-create-home --disabled-password --disabled-login --ingroup graphdb graphdb || true
-chown -R graphdb:graphdb /opt/graphdb
-
-# Create a service file to use graphdb with systemd. 
-# This file uses the users created above, and also hard-codes listening address and maximum memory. 
-# This avoids having to write the config file using bash hacks. 
-log_info " => Making 'graphdb.service'"
-load_template 'graphdb.service' > /etc/systemd/system/graphdb.service
-
-# We just created a service, so now start it and put it into autostart mode. 
-log_info " => Starting and enabling graphdb.service"
-systemctl enable graphdb
-systemctl start graphdb
-
-# Finally remove the temporary directory we created above. 
-log_info " => Removing temporary directory"
-rm -rf "$tmpdir"
-
-log_info " => Server is now ready to become a factory. "

factory/update.sh

@@ -1,14 +0,0 @@
-#!/bin/bash
-set -e
-
-# read the lib/shared.sh and lib/slug.sh
-DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-cd "$DIR"
-source "$DIR/lib/lib.sh"
-require_slug_argument
-
-# TODO: Figure out if this is enough. 
-echo " => Running 'composer update'"
-cd "$COMPOSER_DIR"
-drupal_sites_permission_workaround
-composer update