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Recommended Tools

1. Introduction

This handout is meant as a guide for installing some of the tools that we will use during the course.

Warnings
  • If you copy & paste from this document, make sure that the pasted text is exactly the same as the copied one (sometimes quote marks are changed)
  • The only exception is when you see the text YOURUSERNAME: be sure to replace it with your actual user name!
  • If you change any settings in Windows, you need to restart your command prompt (CMD) for the changes to take effect

2. Important Stuff

2.1 A Programming Editor

A good programming editor, such as Atom, Sublime, TextMate (Mac only), Notepad++ (Windows only) or one of your own choice, is essential. It helps if it supports syntax highlighting for Turtle and/or SPARQL.

2.2 Java

Make sure that you have Java, and your Java version is up to date.

Install JDK version 8u101 for your platform from:

http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

Running java -version in your terminal/command prompt should give:

java version "1.8.0_101"
Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)

2.3 Python

A working version of Python, preferably somewhat close to 2.7.12 (but not 2.6 or 3.x) for your platform of choice.

  • Check what version you have by running python --version in a terminal (or command prompt) window

NB: if you are an Anaconda user, and you're happy with it (are you?), you should replace all occurrences of pip below with the corresponding conda command.

If needed:

  • Conda users can install Python 2.7 by running conda install python=2.7 in the Terminal.
  • Windows users can go to https://www.python.org to download it.
    NB: make sure to enable the 'Add Python.exe to path' option during installation.
  • Linux users should use the package manager of their system (e.g. sudo apt-get install python)
  • MacOS comes with a pre-installed version, but you may consider using Homebrew to install a clean and up-to-date version.
    • Start the Terminal application
    • Run ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" from the terminal
    • Then run brew update and brew doctor
    • Run brew install python

2.4 Programming Libraries

(For the lab session you may want to skip to section 3)

It is not usually a good idea to create and manipulate machine-interpretable files by hand. A good programming library for Linked Data is a real benefit.

Depending on your preferred programming language, examples are:

3. The Protégé Ontology Editor

There are several RDF and OWL editors that you could use (apart from your favourite text-based editor). The main contenders are Protégé and TopBraid Composer.

We advise you to use Protégé for the assignments in Week 3.

  • Protégé is a stand-alone editor that is very much tailored towards OWL ontology editing.
  • It allows you to define OWL axioms using an abstract syntax (Manchester Syntax),
  • but it is less transparent if you're interested in knowing what the syntactic RDF representation looks like. This may lead to confusing situations where it is unclear e.g. in what namespace you have defined your classes, instances, etc.
  • Protégé does support all major OWL2 DL reasoners (Fact++, Hermit and Pellet) and is thus quite powerful with respect to inferencing.

Installing Protégé

  • Download the the 5.0.0 version from GitHub: https://github.com/protegeproject/protege-distribution/releases/tag/protege-5.0.0
  • Install the Pellet plugin from within Protege, but if that doesn't work...
    • Download the Pellet reasoner from https://github.com/Complexible/pellet/archive/master.zip and place the com.clarkparsia.protege.plugin.pellet.jar file (from pellet/protege/plugin/) in the plugins directory of your Protégé installation.
      • On MacOS, you should right-click (ctrl-click) Protégé.app, and select "Show Package Contents". You should put the Pellet jar file in the Contents/Java/plugins folder.
  • To run it:
    • The Windows installer should produce an icon for you, otherwise you will need to run the run.bat (or similar) script in the Protégé directory.
    • On Linux, you should run the run.sh script in the Protégé directory
    • On MacOS, you should run the Protégé.app application in the Protégé directory
  • Make sure that the Pellet reasoner can be seen in the Reasoner menu of the Protégé application window.

4 The Stardog triple store (version 4 or higher):

Stardog is a reasoning-enabled database for Linked Data and ontologies.

  • Apply for Community Edition license at http://stardog.com (or a 30-day evaluation)
  • You will receive an email with a link to the download, and a license file.
  • NB: Stardog may require a Java JDK to be installed on your system (not just a JRE, otherwise it will probably not work). Try getting it working without first installing Java. If it complains about it, install a recent JDK from Java.com

Official installation instructions can be found at http://docs.stardog.com/#_quick_start_guide

4.1 Windows

One way to get it running:

  • Move or copy the unzipped directory stardog-4.1.3 to your Documents folder. You now have a directory called C:\Users\YOURUSERNAME\Documents\stardog-4.1.3 (where YOURUSERNAME is your actual user name!)
  • Create a data directory inside it, this is now C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\data
  • Copy the stardog-license.bin file to C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\data
  • Go to the Control Panel, and search for environment variables.
    • Create a system-wide variable called STARDOG_HOME and give it the value C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\data.
    • Update the system-wide PATH variable by adding C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\bin
  • Start the Command Prompt, and type stardog-admin.bat server start --disable-security to start Stardog (you need to do this every time you have rebooted your system. If you want to manually stop the service, type stardog-admin.bat server stop)
  • Open your browser, and go to http://localhost:5820 the login details are admin and admin
  • Whee!

Follow the next steps under 4.3

Alternative installation instructions can be found at http://docs.stardog.com/#_quick_start_guide

4.2 Linux/Mac

One way to get it running:

  • Move or copy the unzipped directory stardog-4.1.3 to your Documents folder. You now have a directory called /Users/YOURUSERNAME/Documents/stardog-4.1.3
  • Create a data directory inside it, this is now /Users/YOURUSERNAME/Documents/stardog-4.1.3/data
  • Copy the stardog-license.bin to /Users/YOURUSERNAME/Documents/stardog-4.1.3/data
  • Open up a Terminal window, and type open ~/.bash_profile, this opens a TextEdit window on mac. Linux users will know what to do.
  • Add the following lines anywhere in the file:
export STARDOG_HOME=/Users/YOURUSERNAME/Documents/stardog-4.1.3/data
export PATH=$PATH:/Users/YOURUSERNAME/Documents/stardog-4.1.3/bin
  • Close the Terminal window, and open a new one
  • Run the Stardog server via stardog-admin server start --disable-security (you need to do this every time you have rebooted your system. If you want to manually stop the service, type stardog-admin server stop)
  • Open your browser, and go to http://localhost:5820 the login details are admin and admin
  • Whee!

Follow the next steps under 4.3

4.3 Starting and Stopping Stardog

To start: stardog-admin server start --disable-security (stardog-admin.bat on Windows)

To stop: stardog-admin server stop (stardog-admin.bat on Windows)

4.3 All Platforms

  • Go to http://localhost:5820, create a new Database called tutorial (you may need to login using admin/admin)
  • Make sure to set reasoning to SL and "SameAs reasoning" to FULL otherwise leave the settings unchanged.
  • Done!

5. The Semantic Web Tutorial

Once you have Python, Java and Stardog in place, you can try out the Semantic Web tutorial.

  • Open up a Terminal or a Command Prompt window
  • Change directory to e.g. your Documents directory (on Mac/Linux: cd ~/Documents, on Windows cd C:\Users\YOURUSERNAME\Documents)
  • If you have GIT, you can "clone" the source code from Github. Type: git clone https://github.com/RinkeHoekstra/semanticweb-web-application-tutorial.git web-application to clone it into a folder called web-application
  • Otherwise, download the zip file from https://github.com/RinkeHoekstra/semanticweb-web-application-tutorial/archive/master.zip and unzip to a folder called web-application
  • Change directory to the newly created folder: cd web-application
  • (OPTIONAL) Setup the virtualenv in the directory of this repository (virtualenv .)
  • (OPTIONAL) Activate the virtualenv (source bin/activate on linux-like systems)
  • Install the necessary packages (pip install -r requirements.txt)
  • Check the Stardog SPARQL endpoint URL in the TUTORIAL_REPOSITORY variable in both src/tutorial.py and src/static/js/tutorial.js.
  • If you haven't done so, install Stardog and make sure it is running.
    • By default, the script assumes a Stardog database with the name 'tutorial' running at http://localhost:5820/tutorial.
    • The database should have reasoning set to SLand "SameAs reasoning" toFULL`.
      • Start your Stardog server with stardog-admin server start --disable-security (don't forget the --disable-security flag!). To stop Stardog, run stardog-admin server stop.
      • If you want to use a different name or location (i.e. not running on localhost, port 5820) you need to set the TUTORIAL_REPOSITORY variable in src/tutorial.py, and make appropriate modifications to the Stardog configuration.
  • Run the tutorial from within the src directory by running python tutorial.py

Other information on how to run the tutorial can be found in the readme file on the GitHub page of the tutorial: https://github.com/RinkeHoekstra/semantic-web-application-tutorial.

The Ultimate Test: does it work?

Go to http://localhost:5000 in your browser.

  • In step 10,
    • type Aspirin, (this retrieves all matches for Aspirin from Linked Life Data)
    • select the link Aspirin,
    • and press the "Link" button. This pushes the RDF representation of LLD Aspirin to your Stardog instance.
    • Output should be 'Ok!'
  • In step 11,
    • also type Aspirin (this will retrieve all matches for Aspirin from DBPedia),
    • select the link Aspirin,
    • and press the "Link" button.
    • Output should be 'Ok!'
  • In step 12,
    • just press the "Link" button.
    • Output should be 'Ok!'
  • Skip step 13
  • In step 14,
    • just press the "Link" button.
    • Output should have two results, one from Linked Life Data, and one from DBPedia.

6. Optional but Recommended Tools

6.1 brwsr

brwsr is a lightweight Linked Data browser, implemented in Python, that can be run as interface on top of a SPARQL endpoint, or just a list of files.

It supports:

  • Rendering of all triples in which a resource plays a role (po, sp, and so)
  • It is named-graph aware, allowing you to see what graph a triple belongs to
  • It supports content negotiation for RDF clients
  • It can browse external URIs, provided that they are published as Cool URIs (dereferencable URIs)
  • It retrieves standard labels for URIs from preflabel.org

To install it, download the zip file or, clone it to a directory of your choice.

Open up a terminal, and change into that directory:

  • create and activate a virtualenv if you so desire
  • run pip install -r requirements.txt
  • rename or copy config-template.py to config.py
  • make appropriate settings in the file (documentation is inline)
  • Start it with python run.py from within the src directory.

6.2 curl

curl is a simple command line utility for (amongst others) sending HTTP requests. You may need it for testing e.g. whether content negotiation works for your dataset.

You can also use an online service such as http://hurl.it.

  • Windows users can download curl directly from http://dl.uxnr.de/mirror/curl/curl-7.33.0-win64-ssl-sspi.zip.
    NB: curl is an executable (.exe file) that you should explicitly call on the command prompt. Double clicking in an explorer window will just briefly flash a command prompt window.
    • Create a folder called 'curl' in the C:\Program Files directory,
    • copy curl.exe from the unzipped file to the C:\Program Files\curl directory,
    • then add the C:\Program Files\curl directory to the PATH system environment variable (in Control Panel, search for environment variable).
    • Edit the variable value, different directory names should be separated by a semicolon (;)
    • Start the Command Prompt (in Win 8/10 use the search) and type curl.exe to see whether it does anything.
  • Linux typically comes shipped with curl, but you may need to use the package manager of their distribution (e.g. sudo apt-get install curl)
  • MacOS comes shipped with curl

You can test whether it works by going to a Terminal window, or to the Command Prompt and executing: curl -L -H "Accept: text/turtle" "http://dbpedia.org/resource/Inside_Out_(2015_film)"

Did you see any triples?

6.3 IPython Notebook (Jupyter)

Interactive notebooks are simple and effective tools for testing small bits of your code before you integrate it in a larger application.

Run pip install jupyter in a Terminal or the Command Prompt.

Jupyter documentation is here: http://jupyter.readthedocs.org.

6.4 Virtualenv

If you don't yet have it, it may be a good idea to install the virtualenv package. The advantage of using virtualenv is that this creates a nicely self-contained Python environment in which you can install the packages needed for your application. This way your global environment does not get clogged, and you avoid potential incompatibilities between different Python projects.

Run pip install virtualenv in a Terminal or the Command Prompt.

Have a look at the virtualenv page at the Hitchhikers Guide to Python for a good description of how you should work with virtual environments.

  • pip is shipped with Python. If Windows complains that it cannot find it, you should add the folder C:\Python27\Scripts to the system wide PATH environment variable, see above.
  • If, when installing virtualenv, your system complains that a directory is not writable, try running sudo pip install virtualenv (on Windows: right click the Command Prompt icon, and select Run as Administrator, then run pip install virtualenv)

6.5 Git

The git version control system for your platform of choice. Version control is very important when collaboratively developing code. You could also use Dropbox or equivalent, but these systems do not prevent conflicting copies. Git is the most modern version control mechanism that is currently in use by millions of developers, and GitHub is the online cloud service of choice.

Try and learn here why and how you should use it.

  • Windows users can go to https://git-scm.com to download it
  • Linux users should use the package manager of their system (e.g. sudo apt-get install git)
  • MacOS users can most easily install it with Homebrew (brew install git) or download it from https://git-scm.com
  • Note: it makes sense to also install a UI-based application, such as SourceTree.

6.6 TopBraid Composer

  • Download TopBraid Free Edition from http://www.topquadrant.com/downloads/topbraid-composer-install/.
  • The Standard and Maestro Editions can be evaluated for a limited period.
  • Unzip the downloaded file, and move the folder it creates to a location of your choice (e.g. /Applications on MacOS, or C:\Program Files on Windows systems).
  • To run it: double click the TopBraid Composer executable file inside the folder.
  • It will ask you for a 'Workspace' directory: this should be an existing directory which will be the parent directory of any RDF/OWL projects you are planning to start.
  • After TopBraid has started, you can get started by creating a new project by right-clicking in the "Navigator" panel (bottom right, by default).
  • Make sure to synchronise the workspace after you make any changes to the files inside your project form outside of the Eclipse environment.

6.7 A Standalone Reasoner

You can use the Stardog triple store for running inverences (see below), but sometimes it is useful to be able to run a classifier against a local ontology/RDF file. We have a Pellet build avialable on Dropbox that you can use. Pellet is by the same developers as Stardog. See https://github.com/Complexible/pellet for licensing information.

After downloading, unzip the file, and move the resulting directory to a location of your choice.

You can run Pellet from your Terminal or Command Prompt window by running ./pellet.sh or pellet.bat (on Windows). On Mac/Linux systems make sure to set the permissions to executable on this file: chmod u+x pellet.sh.

Running ./pellet.sh help will give you basic usage information. There's also a readme.

6.8 Linked Data Reactor (LD-R) Framework

LD-R is a framework for building reactive component-based Linked Data Applications. LD-R utilizes Facebook's ReactJS components, Flux architecture and Yahoo!'s Fluxible framework for implementing isomorphic Semantic Web applications. Follow this quick tutorial to install and use LD-R.