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Jena Fuseki for SDBM triples

Configuration, instructions, and helper script for running SDBM triples under Jena Fuseki using TDB2 and Fuseki2.

Install and configure Jena and Jena Fuseki

Skip to the Usage section if you've already completed the installation and configuration steps.

If you don't already have it, install the Java runtime environment (JRE) on your computer:

You must have Java 11 to run this version of Jena (4.5.0).

Note: I'm assuming the JRE will work. If it does not you may need to install the Java Development Kit (JDK).

Confirm that you have Java installed by running the java command.

$ java --version
java 11.0.2 2019-01-15 LTS
Java(TM) SE Runtime Environment 18.9 (build 11.0.2+9-LTS)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.2+9-LTS, mixed mode)

Your output will differ depending on the Java version you have install. If you get an error, refer to the Java website installation instructions for your operating system.

Create a folder on your Linux/MacOS computer home directory called Java.

$ mkdir $HOME/Java

This will create a folder like /home/<YOUR_USER>/Java or /Users/<YOUR_USER>/Java.

Download and unzip the these files in the new Java directory:

NOTE: You can use a more recent version of Jena and Jena-Fuseki, but you'll need to adjust the FUSEKI_HOME AND JENA_HOME variables described below for your environment.

Configure your system to use Jena 4.5

Copy the sample configuration file, sample.sdbmjfrc, to .sdbmjfrc.

cp sample.sdbmjfrc .sdbmjfrc

This will be used to create the FUSEKI_HOME and JENA_HOME environment variables and add Jena and Fuseki commands to your PATH. Its contents are:

export FUSEKI_HOME=$HOME/Java/apache-jena-fuseki-4.5.0
export JENA_HOME=$HOME/Java/apache-jena-4.5.0

PATH=$PATH:$FUSEKI_HOME
PATH=$PATH:$FUSEKI_HOME/bin
PATH=$PATH:$JENA_HOME/bin

export PATH

You will need to adjust this file if Jena and Fuseki are installed at different locations from the one recommended here, or if you're using a version other than 4.5.0.

You can add these lines to your $HOME/.bashrc file or, if you're running ZSH (the default on MacOS) to $HOME/.zshrc.

Test the setup

There are two steps here:

  1. Load the test data into Jena
  2. Query the data using Fuseki

Load the test data into Jena

Make sure the FUSEKI_HOME, JENA_HOME and PATH values are set in your environment either by adding the lines in the .sdbmjfrc to $HOME/.bashrc or $HOME/.zshrc, or by sourcing the .sdbmjfrc:

source .sdbmjfrc

If you already have a folder called TDB2, delete it and reload the ttl file data. If you're loading the data, you must delete the TDB2 folder to avoid loading the data twice.

rm -rf TDB2
the following creates the `TDB2` folder
tdb2.tdbloader --verbose --loc TDB2 test/test.ttl

Run the script start-fuseki.sh:

./start-fuseki.sh

You should see something something like the following.

[2022-07-27 16:05:54] Server     INFO  Apache Jena Fuseki 4.5.0
[2022-07-27 16:05:54] Config     INFO  FUSEKI_HOME=/Users/emeryr/Java/apache-jena-fuseki-4.5.0
[2022-07-27 16:05:54] Config     INFO  FUSEKI_BASE=/Users/emeryr/code/GIT/sdbm-jena-fuseki/run
[2022-07-27 16:05:54] Config     INFO  Shiro file: file:///Users/emeryr/code/GIT/sdbm-jena-fuseki/run/shiro.ini
[2022-07-27 16:05:55] Server     INFO  Path = /tdb2-database
[2022-07-27 16:05:55] Server     INFO  System
[2022-07-27 16:05:55] Server     INFO    Memory: 1.2 GiB
[2022-07-27 16:05:55] Server     INFO    Java:   11.0.2
[2022-07-27 16:05:55] Server     INFO    OS:     Mac OS X 10.16 x86_64
[2022-07-27 16:05:55] Server     INFO    PID:    8101
[2022-07-27 16:05:55] Server     INFO  Started 2022/07/27 16:05:55 EDT on port 3030

Go to http://localhost:3030/#/. Click on the "Query" action for the dataset, '/sdbm', and run the default query.

Use the Control-C key combination to stop the server.

Usage

In this project folder, create a folder called data if it doesn't already exist.

cd path/to/sdbm-jena-fuseki
mkdir data

From the SDBM downloads page, download the lasted version of the SDBM TTL file to the data folder and unzip it, using the correct name of the TTL file.

gunzip data/output-20220727T050002-UTC.ttl.gz

Warning: The unzipped file is very large, ~1 GB. It will take a long time to load, and once loaded, you will probably want to re-compress it when it's been loaded.

Make sure the FUSEKI_HOME, JENA_HOME and PATH values are set in your environment either by adding the lines in the .sdbmjfrc to $HOME/.bashrc or $HOME/.zshrc, or by sourcing the .sdbmjfrc:

# if you've just added the lines to .bashrc
source $HOME/.bashrc

# if you've just added the lines to .zshrc
source $HOME/.zshrc

# if you've haven't already run, source .sdbmjfrc in this shell session
source .sdbmjfrc

Remove the TDB2 directory and load the data into Jena.

Note: The SDBM TTL file is very large (over 1GB), and the load will take several minutes.

rm -rf TDB2
# the following creates the `TDB2` folder
# substute `output-20220727T050002-UTC.ttl` with the correct file name
tdb2.tdbloader --verbose --loc TDB2 data/output-20220727T050002-UTC.ttl

Start Fuseki:

./start-fuseki.sh

Use the Control-C key combination to stop the server.

Go to http://localhost:3030/#/. Click on the "Query" action for the dataset, '/sdbm', and run the default query.

Clean up

As noted above the TTL is quite large. After loader process has finished, be sure to zip the TTL file in the data folder. Don't delete it, as it may be needed again.