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Install OpenSILEX in production

Using the ready to use Docker

Before reading this document, you can check the docker container for OpenSILEX This docker container allows you to install and configure OpenSILEX and all required databases (RDF4J and MongoDB) within only a few steps.

If you prefer a fine tuned control on the installed databases or if you prefer a custom installation, you are at the right place !

Pre-requisites

Operating System

OpenSILEX should work on any system where the required pieces of software are available, but we recommend using Linux for a production installation.

The commands in this document should work on any Debian-like distribution (configured with sudo) but can be easily adapted for any Linux distribution.

Java

You need at least Java JDK 11+ installed on the server.

You can install it on Linux with the following command:

sudo apt install openjdk-11-jdk openjdk-11-jre

You can check Java installation and version with the following command:

java --version

Set up MongoDB

Please follow MongoDB's official install documentation specific to your operating system.

Install MongoDB 4.2+

/!\ CAUTION /!\

You must start a MongoDB Replica Set to allow transaction usage with MongoDB. This requires the use of a MongoDB server with a version >= 4.2. To do so you need to start the MongoDB daemon with the option --replSet opensilex. opensilex stands for your replica set name and can be modified at your own will. Look at this documentation for more information about replica set.

We recommend the use of this MongoDB Docker image. More documentation for this image here

Linux example command

docker network create mongoCluster
docker run -d --rm -p 27017:27017 --name mongo_opensilex --network mongoCluster mongo:5 mongod --replSet opensilex --bind_ip localhost,mongo_opensilex
  • The MongoDB exposed port is 27017
  • A replica set named opensilex is created
  • The docker container name is mongo_opensilex
  • The docker container uses a network called mongoCluster

Set up a triplestore

You can use RDF4J 5.X or GraphDB for storing semantic data.

You can find a quick comparison of both triplestore engines here.

Please refer to their websites for more information.

RDF4J

For RDF4J you first need to set up and configure a Servlet Container server like Tomcat. And then follow RDF4J's documentation .

You can also use this docker image: eclipse/rdf4j-workbench

Linux example command

sudo docker run -d -p 8080:8080 -e JAVA_OPTS="-Xms4g -Xmx4g" \
	-v data:/var/rdf4j -v logs:/usr/local/tomcat/logs eclipse/rdf4j-workbench:5.0.3
  • The RDF4J exposed port is 8080
  • RDF4J data will be stored in /var/rdf4j in the docker host
  • Tomcat server logs in /usr/local/tomcat/logs in the docker host
  • 4GB of RAM memory are allocated for the JVM's heap

GraphDB

A free version of GraphDB is available and can be used as an alternative to RDF4J.

Please follow their documentation to install it.

You can also use this docker image: ontotext/graphdb

Linux example command:

sudo docker run -d ontotext/graphdb

Installation

All directories and usernames in this installation procedure can be changed, but you need to change the configuration accordingly in order to make it work.

Set up a user

Create a user with its home directory:

sudo useradd -s /bin/bash -d /home/opensilex/ -m opensilex

Set up a password for your new user:

sudo passwd opensilex

Give sudo permissions to this user :

sudo usermod -a -G sudo opensilex

Connect with this username and the defined password:

su - opensilex

Create directories

Directory for OpenSILEX binaries:

mkdir -p /home/opensilex/bin

Directory for OpenSILEX configuration file:

mkdir -p /home/opensilex/config

Directory for OpenSILEX data file storage:

mkdir -p /home/opensilex/data

Directory for OpenSILEX file logs:

mkdir -p /home/opensilex/logs

Download & extract the OpenSILEX production release

Please download the OpenSILEX latest release archive on GitHub.

In this paragraph, <X.Y.Z> corresponds to the specific OpenSILEX release version. Extract the downloaded ZIP file into /home/opensilex/bin

Linux example commands:

cd /home/opensilex/bin
wget https://github.com/OpenSILEX/opensilex/releases/download/X.Y.Z/opensilex-X.Y.Z.zip
unzip opensilex-X.Y.Z.zip

For the latest version - go to Latest version

Example with version 1.1.1:

cd /home/opensilex/bin
wget https://github.com/OpenSILEX/opensilex/releases/download/1.1.1/opensilex-release-1.1.1.zip
unzip opensilex-release-1.1.1.zip

You should get the following directory structure:

/home/opensilex/
+-- bin/
    +-- <X.Y.Z>/
        +-- opensilex.jar
        +-- logback.xml
        +-- modules/
            +-- opensilex-core.jar
            +-- opensilex-front.jar
            +-- opensilex-fs.jar
            +-- opensilex-nosql.jar
            +-- opensilex-security.jar
            +-- opensilex-sparql.jar
            +-- opensilex-phis.jar
+-- config/
+-- data/
+-- logs/

Configuration

Create main configuration file

Create a YML file in /home/opensilex/config named opensilex.yml for example. If you want to work with multiple configurations you can name this file differently.

Here is a minimal configuration example, containing all values which must be adapted to your setup:

ontologies:
  baseURI: http://www.opensilex.org/
  baseURIAlias: os
  sparql:
    config:
      serverURI: http://localhost:8080/rdf4j-server/
      repository: opensilex

file-system:
  fs:
    config:
      basePath: /home/opensilex/data

big-data:
  mongodb:
    config:
      host: localhost
      port: 27017
      database: opensilex

N.B. The ontologies OESO and OEEV are stored in opensilex-core/src/main/resources/ontologies. Other specific ontologies can be stored in each module.

Configure logging

Edit the file /home/opensilex/bin/<X.Y.Z>/logback.xml

Set the path property to reflect your installation:

<property name="log.path" value="/home/opensilex/logs"/>

For Logging we use the Java Logback library in our application. Please read their documentation to tailor its configuration to your needs.

By default, the logs will be printed to the console output and written into a rotating daily log file stored for 30 days.

Initialize database and check configuration

Create a script to access instructions

  • Create
nano /home/opensilex/bin/<X.Y.Z>/opensilex.sh
  • Content
#!/bin/bash

SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"

CONFIG_FILE="/home/opensilex/config/opensilex.yml"

cd $SCRIPT_DIR

java -jar $SCRIPT_DIR/opensilex.jar --BASE_DIRECTORY=$SCRIPT_DIR --CONFIG_FILE=$CONFIG_FILE "$@"
  • Activation
chmod +x /home/opensilex/bin/<X.Y.Z>/opensilex.sh

Add an alias

  • Edit
nano ~/.bash_aliases
  • Content
alias opensilex="/home/opensilex/bin/<X.Y.Z>/opensilex.sh"
  • Activation
source  ~/.bashrc
  • Verification
opensilex help

Initialize your triplestore

opensilex system install

This instruction creates the repository (with the name defined in the configuration file). It also creates the default administrator and imports the ontologies.

GraphDB

If you want to use GraphDB, you have to manually creates the repository in your graphdb instance and update your OpenSILEX config by using the graphdb server/repository likes following :

ontologies:
  baseURI: http://opensilex.dev/
  baseURIAlias: os
  sparql:
    config:
      serverURI: http://localhost:7200
      repository: opensilex

Now you can run

opensilex system install

Import ontologies

opensilex sparql reset-ontologies

Create default administrator

This instruction creates a user "admin@opensilex.org" with the password "admin"

opensilex user add --admin

More information about the command

opensilex user add --help

Start openSilex

opensilex server start --host=192.168.178.31 --port=8081 --adminPort=4081

Stop openSilex

opensilex server stop --host=192.168.178.31 --adminPort=4081

Add a Reverse Proxy Nginx to redirect the application on port 80

  • Instructions
sudo apt install nginx
sudo nano /etc/nginx/sites-enabled/default
  • Content
        location / {
                #comment the following line to avoid an error and enable proxy
                #try_files $uri $uri/ =404;
                #add proxy settings
                include proxy_params;
                proxy_pass http://127.0.0.1:8081;
        }
  • Activation
sudo systemctl restart nginx