├── src
    ├── templates
    │   ├── message.html
    │   └── index.html
    ├── tutorial.py
    └── static
    │   └── js
    │       ├── tutorial.js
    │       └── jquery-1.11.0.min.js
├── requirements.txt
├── .gitignore
├── README.md
├── LICENSE
└── tools.md


/src/templates/message.html:
--------------------------------------------------------------------------------
1 | <div>Your message here: {{ message}}</div>


--------------------------------------------------------------------------------
/requirements.txt:
--------------------------------------------------------------------------------
 1 | Flask==0.10.1
 2 | Jinja2==2.7.3
 3 | MarkupSafe==0.23
 4 | SPARQLWrapper==1.6.4
 5 | Werkzeug==0.9.6
 6 | html5lib==0.999
 7 | isodate==0.5.1
 8 | itsdangerous==0.24
 9 | pyparsing==2.0.3
10 | rdflib==4.1.2
11 | requests==2.5.1
12 | six==1.9.0
13 | wsgiref==0.1.2
14 | 


--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
 1 | *.py[cod]
 2 | 
 3 | # C extensions
 4 | *.so
 5 | 
 6 | # Packages
 7 | *.egg
 8 | *.egg-info
 9 | dist
10 | build
11 | eggs
12 | parts
13 | bin
14 | var
15 | sdist
16 | develop-eggs
17 | .installed.cfg
18 | lib
19 | lib64
20 | __pycache__
21 | 
22 | # Installer logs
23 | pip-log.txt
24 | 
25 | # Unit test / coverage reports
26 | .coverage
27 | .tox
28 | nosetests.xml
29 | 
30 | # Translations
31 | *.mo
32 | 
33 | # Mr Developer
34 | .mr.developer.cfg
35 | .project
36 | .pydevproject
37 | 


--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
 1 | ## Tutorial for the Semantic Web course
 2 | ### @VU University Amsterdam and University of Amsterdam
 3 | #### Rinke Hoekstra (<rinke.hoekstra@vu.nl>/<hoekstra@uva.nl>)
 4 | 
 5 | This tutorial shows the basics for building a Semantic Web-based application by guiding you through some of the typical steps involved. This means:
 6 | 
 7 | * Styling your webpage using CSS
 8 | * Using client side scripting for manipulating the webpage
 9 | * Using server side scripting for mediating between your own triple store and others
10 | * Posting information to your triple store
11 | * Using reasoning facilities of your triple store
12 | 
13 | The code is documented and explains each of these steps. All server-side code is in `src/tutorial.py`. The client-side code is in `src/static/js/tutorial.js`. Feel free to reuse the code in your own projects (perhaps even fork this GitHub repository, that would be cool)
14 | 
15 | ### Preliminaries
16 | 
17 | If you are a student of the Semantic Web course at the VU, make sure to follow the steps in the the [tools document](tools.md) to make sure you have everything in place to make this code work.
18 | 
19 | It will also contain detailed steps for installing the tutorial itself.
20 | 
21 | ### General Requirements
22 | 
23 | To get this thing up and running on a local machine, you need the following:<sup>1</sup>
24 | 
25 | * Python 2.7
26 | * In a terminal window (command prompt on Windows) change dir to the root directory of this repository.
27 | * (**OPTIONAL**) Virtualenv (`pip install virtualenv`) <sup>2</sup>
28 | * (**OPTIONAL**) Setup the virtualenv in the directory of this repository (`virtualenv .`)
29 | * (**OPTIONAL**) Activate the virtualenv (`source bin/activate` on linux-like systems) <sup>3</sup>
30 | * Install the necessary packages (`pip install -r requirements.txt`)
31 | * Check the Stardog SPARQL endpoint URL in the `TUTORIAL_REPOSITORY` variable in **both** `src/tutorial.py` and `src/static/js/tutorial.js`.  
32 | * Installing Stardog:<sup>4</sup>
33 | 	* By default, the script assumes a Stardog database with the name 'tutorial' running at <http://localhost:5820/tutorial>
34 | 	* 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`.
35 | 	* The database should have reasoning enabled, and "SameAs" reasoning should be set to "Full".
36 | 	* 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`
37 | 
38 | ### Starting the Tutorial
39 | 
40 | Once everything is ready:
41 | 
42 | * change dir into the `src` directory, and
43 | * run `python tutorial.py`.
44 | 
45 | The tutorial is then running at <http://localhost:5000> .
46 | 
47 | ###### Footnotes
48 | 
49 | <sup>1</sup> This assumes you're running on a linux/mac style system. For Windows use a backslash `\` instead of a forward slash `/` for directories.
50 | 
51 | <sup>2</sup> 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.
52 | 
53 | <sup>3</sup> You need to activate the virtual environment every time you want to start your application from a new terminal session.
54 | 
55 | <sup>4</sup> For a step-by-step guide on installing Stardog and other useful tools for the course, see the [tools document](tools.md).
56 | 


--------------------------------------------------------------------------------
/src/tutorial.py:
--------------------------------------------------------------------------------
  1 | from flask import Flask, render_template, url_for, request, jsonify
  2 | from SPARQLWrapper import SPARQLWrapper, RDF, JSON
  3 | import requests
  4 | import traceback
  5 | 
  6 | 
  7 | app = Flask(__name__)
  8 | 
  9 | TUTORIAL_REPOSITORY = 'http://localhost:5820/tutorial'
 10 | 
 11 | @app.route('/')
 12 | def first_page():
 13 |     app.logger.debug('You arrived at ' + url_for('first_page'))
 14 |     return render_template('index.html')
 15 | 
 16 | @app.route('/show',methods=['GET'])
 17 | def show_message():
 18 |     app.logger.debug('You arrived at ' + url_for('show_message'))
 19 |     app.logger.debug('I received the following arguments' + str(request.args) )
 20 | 
 21 |     # Get the message from the GET request, if nothing is found, set a default message.
 22 |     message = request.args.get('message', 'No message sent!')
 23 | 
 24 |     return render_template('message.html', message=message)
 25 | 
 26 | @app.route('/sparql', methods=['GET'])
 27 | def sparql():
 28 |     app.logger.debug('You arrived at ' + url_for('sparql'))
 29 |     app.logger.debug('I received the following arguments' + str(request.args) )
 30 | 
 31 |     endpoint = request.args.get('endpoint', None)
 32 |     query = request.args.get('query', None)
 33 | 
 34 |     return_format = request.args.get('format','JSON')
 35 | 
 36 | 
 37 |     if endpoint and query :
 38 |         sparql = SPARQLWrapper(endpoint)
 39 | 
 40 |         sparql.setQuery(query)
 41 | 
 42 |         if return_format == 'RDF':
 43 |             sparql.setReturnFormat(RDF)
 44 |         else :
 45 |             sparql.setReturnFormat(JSON)
 46 |             sparql.addParameter('Accept','application/sparql-results+json')
 47 | 
 48 |         sparql.addParameter('reasoning','true')
 49 | 
 50 |         app.logger.debug('Query:\n{}'.format(query))
 51 | 
 52 |         app.logger.debug('Querying endpoint {}'.format(endpoint))
 53 | 
 54 |         try :
 55 |             response = sparql.query().convert()
 56 | 
 57 |             app.logger.debug('Results were returned, yay!')
 58 | 
 59 |             app.logger.debug(response)
 60 | 
 61 |             if return_format == 'RDF':
 62 |                 print response
 63 |                 app.logger.debug('Serializing to Turtle format')
 64 |                 return response.serialize(format='turtle')
 65 |             else:
 66 |                 app.logger.debug('Directly returning JSON format')
 67 |                 return jsonify(response)
 68 |         except Exception as e:
 69 |             app.logger.error('Something went wrong')
 70 |             traceback.print_exc()
 71 |             return jsonify({'result': 'Error'})
 72 | 
 73 | 
 74 |     else :
 75 |         return jsonify({'result': 'Error'})
 76 | 
 77 | @app.route('/store', methods=['POST'])
 78 | def store():
 79 |     app.logger.debug('You arrived at ' + url_for('store'))
 80 |     app.logger.debug('I received the following arguments' + str(request.form) )
 81 | 
 82 |     data = request.form['data'].encode('utf-8')
 83 | 
 84 | 
 85 | 
 86 | 
 87 |     transaction_begin_url = TUTORIAL_REPOSITORY + "/transaction/begin"
 88 |     app.logger.debug('Doing a POST of your data to {}'.format(transaction_begin_url))
 89 | 
 90 |     # Start the transaction, and get a transaction_id
 91 |     response = requests.post(transaction_begin_url, headers={'Accept': 'text/plain'})
 92 |     transaction_id = response.content
 93 |     app.logger.debug(response.status_code)
 94 | 
 95 |     # POST the data to the transaction
 96 |     post_url = TUTORIAL_REPOSITORY + "/" + transaction_id + "/add"
 97 |     app.logger.debug('Assuming your data is Turtle!!')
 98 |     response = requests.post(post_url, data=data, headers={'Accept': 'text/plain', 'Content-type': 'text/turtle'})
 99 |     app.logger.debug(response.status_code)
100 |     app.logger.debug(response.content)
101 |     app.logger.debug(response.headers)
102 | 
103 |     if response.status_code != 200:
104 |         return str(response.content)
105 | 
106 | 
107 |     # Close the transaction
108 |     transaction_close_url = TUTORIAL_REPOSITORY + "/transaction/commit/" + transaction_id
109 |     response = requests.post(transaction_close_url)
110 |     app.logger.debug(response.status_code)
111 |     app.logger.debug(response.content)
112 |     app.logger.debug(response.headers)
113 | 
114 |     if response.status_code != 200:
115 |         return str(response.content)
116 |     else:
117 |         return "Ok!"
118 | 
119 | 
120 | if __name__ == '__main__':
121 |     app.debug = True
122 |     app.run()
123 | 


--------------------------------------------------------------------------------
/LICENSE:
--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
/src/static/js/tutorial.js:
--------------------------------------------------------------------------------
  1 | 
  2 | /*
  3 | // #############
  4 | // CONFIGURATION
  5 | // #############
  6 | */
  7 | 
  8 | var TUTORIAL_REPOSITORY = 'http://localhost:5820/tutorial';
  9 | 
 10 | 
 11 | 
 12 | /*
 13 | // ############
 14 | //    STEP 1
 15 | // ############
 16 | */
 17 | 
 18 | // If the element with id 'link1' is clicked
 19 | $('#link1').on('click', function(e){
 20 | 	var bootstrapCSSLink = $('<link rel="stylesheet" type="text/css" href="http://netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css">');
 21 | 	var bootstrapThemeCSSLink = $('<link rel="stylesheet" type="text/css" href="http://netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap-theme.min.css">');
 22 | 	var bootstrapJavaScriptLink = $('<script type="text/javascript" src="http://netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js"></script>');
 23 | 
 24 | 	$('body').append(bootstrapCSSLink);
 25 | 	$('body').append(bootstrapThemeCSSLink);
 26 | 	$('body').append(bootstrapJavaScriptLink);
 27 | });
 28 | 
 29 | /*
 30 | // ############
 31 | //    STEP 2
 32 | // ############
 33 | */
 34 | 
 35 | 
 36 | // No JavaScript involved!
 37 | 
 38 | 
 39 | /*
 40 | // ############
 41 | //    STEP 3
 42 | // ############
 43 | */
 44 | 
 45 | // If the element with id 'link3' is clicked
 46 | $('#link3').on('click',function(e){
 47 | 	// Do a GET request on the '/show' URL, with the data payload 'Hello World'.
 48 | 	$.get('/show',data={'message': 'Hello World'}, function(data){
 49 | 		// If successful, add the data to the DOM tree under the 'linktarget3' element.
 50 | 		$('#linktarget3').html(data);
 51 | 	});
 52 | });
 53 | 
 54 | /*
 55 | // ############
 56 | //    STEP 4
 57 | // ############
 58 | */
 59 | 
 60 | // If the element with id 'link4' is clicked
 61 | $('#link4').on('click',function(e){
 62 | 
 63 | 	var message = $('#messageInput1').val();
 64 | 
 65 | 	// Do a GET request on the '/show' URL, with the data payload 'Hello World'.
 66 | 	$.get('/show',data={'message': message}, function(data){
 67 | 		// If successful, add the data to the DOM tree under the 'linktarget3' element.
 68 | 		$('#linktarget4').html(data);
 69 | 	});
 70 | });
 71 | 
 72 | /*
 73 | // ############
 74 | //    STEP 5
 75 | // ############
 76 | */
 77 | 
 78 | // If the element with id 'link5' is clicked
 79 | $('#link5').on('click',function(e){
 80 | 
 81 | 	var message = $('#messageInput2').val();
 82 | 	$('#linktarget5').html(message);
 83 | 
 84 | });
 85 | 
 86 | 
 87 | /*
 88 | // ############
 89 | //    STEP 6
 90 | // ############
 91 | */
 92 | 
 93 | // Autocompletion from Linked Life Data
 94 | 
 95 | // http://linkedlifedata.com/autocomplete.json?
 96 | // Parameters are 'q' for query and some limit.
 97 | // Note that we have to add a 'callback=?' suffix to the URI, to make sure the call is a JSONP request.
 98 | $('#messageInput3').on('input', function(e){
 99 | 	var message = $('#messageInput3').val();
100 | 
101 | 	var lld_autocomplete_url = 'http://linkedlifedata.com/autocomplete.json?callback=?';
102 | 
103 | 	var data = {'q': message, 'limit': 100};
104 | 
105 | 	$.getJSON(lld_autocomplete_url, data=data, function(json){
106 | 		var pre = $('<pre></pre>');
107 | 		pre.text(JSON.stringify(json));
108 | 		$('#linktarget6').html(pre);
109 | 	});
110 | });
111 | 
112 | 
113 | /*
114 | // ############
115 | //    STEP 7
116 | // ############
117 | */
118 | 
119 | // Autocompletion from Linked Life Data
120 | 
121 | // http://linkedlifedata.com/autocomplete.json?
122 | // Parameters are 'q' for query and some limit.
123 | // Note that we have to add a 'callback=?' suffix to the URI, to make sure the call is a JSONP request.
124 | $('#messageInput7').on('input', function(e){
125 | 	var message = $('#messageInput7').val();
126 | 
127 | 	var lld_autocomplete_url = 'http://linkedlifedata.com/autocomplete.json?callback=?';
128 | 
129 | 	var data = {'q': message, 'limit': 100};
130 | 
131 | 	$.getJSON(lld_autocomplete_url, data=data, function(json){
132 | 
133 | 		var ul = $('<ul></ul>');
134 | 		ul.addClass('list-group');
135 | 		for (var i in json.results) {
136 | 			var r = json.results[i];
137 | 
138 | 			var uri = r.uri.namespace + r.uri.localName;
139 | 			var label = r.label;
140 | 
141 | 			var li = $('<li></li>');
142 | 			li.addClass('list-group-item');
143 | 			var a = $('<a></a>');
144 | 			a.html(label);
145 | 			a.attr('href',uri);
146 | 			li.append(a);
147 | 			ul.append(li);
148 | 		}
149 | 
150 | 		$('#linktarget7').html(ul);
151 | 	});
152 | });
153 | 
154 | 
155 | /*
156 | // ############
157 | //    STEP 8
158 | // ############
159 | */
160 | 
161 | 
162 | // Autocompletion from Linked Life Data
163 | 
164 | // http://linkedlifedata.com/autocomplete.json?
165 | // Parameters are 'q' for query and some limit.
166 | // Note that we have to add a 'callback=?' suffix to the URI, to make sure the call is a JSONP request.
167 | $('#messageInput8').on('input', function(e){
168 | 	var message = $('#messageInput8').val();
169 | 
170 | 	var lld_autocomplete_url = 'http://linkedlifedata.com/autocomplete.json?callback=?';
171 | 
172 | 	var data = {'q': message, 'limit': 100};
173 | 
174 | 	$.getJSON(lld_autocomplete_url, data=data, function(json){
175 | 
176 | 		var ul = $('<ul></ul>');
177 | 		ul.addClass('list-group');
178 | 		for (var i in json.results) {
179 | 			var r = json.results[i];
180 | 
181 | 			var uri = r.uri.namespace + r.uri.localName;
182 | 			var label = r.label;
183 | 
184 | 			var li = $('<li></li>');
185 | 			li.addClass('list-group-item');
186 | 			var a = $('<a></a>');
187 | 			a.html(label);
188 | 
189 | 			a.on('click', {'uri': uri}, function(e){
190 | 				alert('You clicked '+ e.data.uri);
191 | 			});
192 | 
193 | 			li.append(a);
194 | 			ul.append(li);
195 | 		}
196 | 
197 | 		$('#linktarget8').html(ul);
198 | 	});
199 | });
200 | 
201 | 
202 | /*
203 | // ############
204 | //    STEP 9
205 | // ############
206 | */
207 | 
208 | 
209 | // Autocompletion from Linked Life Data
210 | 
211 | // http://linkedlifedata.com/autocomplete.json?
212 | // Parameters are 'q' for query and some limit.
213 | // Note that we have to add a 'callback=?' suffix to the URI, to make sure the call is a JSONP request.
214 | $('#messageInput9').on('input', function(e){
215 | 	var message = $('#messageInput9').val();
216 | 
217 | 	var lld_autocomplete_url = 'http://linkedlifedata.com/autocomplete.json?callback=?';
218 | 
219 | 	var data = {'q': message, 'limit': 100};
220 | 
221 | 	$.getJSON(lld_autocomplete_url, data=data, function(json){
222 | 
223 | 		var ul = $('<ul></ul>');
224 | 		ul.addClass('list-group');
225 | 		for (var i in json.results) {
226 | 			var r = json.results[i];
227 | 
228 | 			var uri = r.uri.namespace + r.uri.localName;
229 | 			var label = r.label;
230 | 
231 | 			var li = $('<li></li>');
232 | 			li.addClass('list-group-item');
233 | 			var a = $('<a></a>');
234 | 			a.html(label);
235 | 
236 | 			a.on('click', {'uri': uri}, function(e){
237 | 				var clicked_uri = e.data.uri;
238 | 				var query = 'DESCRIBE <'+clicked_uri+'>';
239 | 				var endpoint = 'http://linkedlifedata.com/sparql.rdf';
240 | 				var format = 'RDF';
241 | 
242 | 				$.get('/sparql',data={'endpoint': endpoint, 'query': query, 'format': format}, function(json){
243 | 					console.log(json);
244 | 					var pre = $('<pre></pre>');
245 | 					pre.text(JSON.stringify(json));
246 | 					$('#linktarget9').html(pre);
247 | 				});
248 | 
249 | 			});
250 | 
251 | 			li.append(a);
252 | 			ul.append(li);
253 | 		}
254 | 
255 | 		$('#linktarget9').html(ul);
256 | 	});
257 | });
258 | 
259 | 
260 | /*
261 | // ############
262 | //    STEP 10
263 | // ############
264 | */
265 | 
266 | 
267 | // Autocompletion from Linked Life Data
268 | 
269 | // http://linkedlifedata.com/autocomplete.json?
270 | // Parameters are 'q' for query and some limit.
271 | // Note that we have to add a 'callback=?' suffix to the URI, to make sure the call is a JSONP request.
272 | $('#messageInput10').on('input', function(e){
273 | 	var message = $('#messageInput10').val();
274 | 
275 | 	var lld_autocomplete_url = 'http://linkedlifedata.com/autocomplete.json?callback=?';
276 | 
277 | 	var data = {'q': message, 'limit': 100};
278 | 
279 | 	$.getJSON(lld_autocomplete_url, data=data, function(json){
280 | 
281 | 		var ul = $('<ul></ul>');
282 | 		ul.addClass('list-group');
283 | 		for (var i in json.results) {
284 | 			var r = json.results[i];
285 | 
286 | 			var uri = r.uri.namespace + r.uri.localName;
287 | 			var label = r.label;
288 | 
289 | 			var li = $('<li></li>');
290 | 			li.addClass('list-group-item');
291 | 			var a = $('<a></a>');
292 | 			a.html(label);
293 | 
294 | 			console.log(uri);
295 | 
296 | 			a.on('click', {'uri': uri}, function(e){
297 | 				var clicked_uri = e.data.uri;
298 | 				console.log('Clicked URI: <'+clicked_uri+'>');
299 | 				var query = 'DESCRIBE <'+clicked_uri+'>';
300 | 				var endpoint = 'http://linkedlifedata.com/sparql.rdf';
301 | 				var format = 'RDF';
302 | 
303 | 
304 | 				$('#linktarget10').html("<div>Querying endpoint...</div>");
305 | 				$.get('/sparql',data={'endpoint': endpoint, 'query': query, 'format': format}, function(data){
306 | 					console.log(data);
307 | 					var pre = $('<pre></pre>');
308 | 					pre.text(data);
309 | 					$('#linktarget10').html(pre);
310 | 
311 | 					// New, set an identifier on our <pre> tag
312 | 
313 | 					pre.attr('id','pre10');
314 | 
315 | 					// New, enable the button, and add a click handler
316 | 
317 | 					$('#link10').toggleClass('disabled');
318 | 
319 | 					$('#link10').on('click',function(e){
320 | 						var rdf_data = $('#pre10').text();
321 | 
322 | 						$.post('/store',data={'data': rdf_data}, function(data){
323 | 							var pre = $('<pre></pre>');
324 | 							pre.text(data);
325 | 							$('#linktarget10').html(pre);
326 | 							$('#link10').toggleClass('disabled');
327 | 						});
328 | 
329 | 					});
330 | 
331 | 				});
332 | 
333 | 			});
334 | 
335 | 			li.append(a);
336 | 			ul.append(li);
337 | 		}
338 | 
339 | 		$('#linktarget10').html(ul);
340 | 	});
341 | });
342 | 
343 | 
344 | /*
345 | // ############
346 | //    STEP 11
347 | // ############
348 | */
349 | 
350 | 
351 | // Autocompletion from Linked Life Data
352 | 
353 | // http://linkedlifedata.com/autocomplete.json?
354 | // Parameters are 'q' for query and some limit.
355 | // Note that we have to add a 'callback=?' suffix to the URI, to make sure the call is a JSONP request.
356 | $('#messageInput11').on('input', function(e){
357 | 	var message = $('#messageInput11').val();
358 | 
359 | 	var lld_autocomplete_url = 'http://linkedlifedata.com/autocomplete.json?callback=?';
360 | 
361 | 	var data = {'q': message, 'limit': 100};
362 | 
363 | 	$.getJSON(lld_autocomplete_url, data=data, function(json){
364 | 
365 | 		var ul = $('<ul></ul>');
366 | 		ul.addClass('list-group');
367 | 		for (var i in json.results) {
368 | 			var r = json.results[i];
369 | 
370 | 			var uri = r.uri.namespace + r.uri.localName;
371 | 			var label = r.label;
372 | 
373 | 			var li = $('<li></li>');
374 | 			li.addClass('list-group-item');
375 | 			var a = $('<a></a>');
376 | 			a.html(label);
377 | 
378 | 			a.on('click', {'label': label}, function(e){
379 | 				var label = e.data.label;
380 | 				var query = 'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n\nCONSTRUCT {	?s rdfs:label "'+label+'" .\n ?s ?p1 ?o1 . ?o1 ?p2 ?o2 . } WHERE { ?s rdfs:label "'+label+'"@en;\n ?p1 ?o1 .\n ?o1 ?p2 ?o2 .}';
381 | 				var endpoint = 'http://live.dbpedia.org/sparql';
382 | 				var format = 'RDF';
383 | 
384 | 				$.get('/sparql',data={'endpoint': endpoint, 'query': query, 'format': format}, function(data){
385 | 					var pre = $('<pre></pre>');
386 | 					pre.text(data);
387 | 					$('#linktarget11').html(pre);
388 | 
389 | 					// New, set an identifier on our <pre> tag
390 | 
391 | 					pre.attr('id','pre11');
392 | 
393 | 					// New, enable the button, and add a click handler
394 | 
395 | 					$('#link11').toggleClass('disabled');
396 | 
397 | 					$('#link11').on('click',function(e){
398 | 						var rdf_data = $('#pre11').text();
399 | 
400 | 						$.post('/store',data={'data': rdf_data}, function(data){
401 | 							var pre = $('<pre></pre>');
402 | 							pre.text(data);
403 | 							$('#linktarget11').html(pre);
404 | 							$('#link11').toggleClass('disabled');
405 | 						});
406 | 
407 | 					});
408 | 
409 | 				});
410 | 
411 | 			});
412 | 
413 | 			li.append(a);
414 | 			ul.append(li);
415 | 		}
416 | 
417 | 		$('#linktarget11').html(ul);
418 | 	});
419 | });
420 | 
421 | /*
422 | // ############
423 | //    STEP 12
424 | // ############
425 | */
426 | 
427 | $('#link12').on('click',function(e){
428 | 	var rdf_data = $('#schema').val();
429 | 
430 | 	$.post('/store',data={'data': rdf_data}, function(data){
431 | 		var pre = $('<pre></pre>');
432 | 		pre.text(data);
433 | 		$('#linktarget12').html(pre);
434 | 	});
435 | 
436 | });
437 | 
438 | 
439 | /*
440 | // ############
441 | //    STEP 13
442 | // ############
443 | */
444 | 
445 | $('#link13').on('click', function(e){
446 | 
447 | 	var query = $('#query13').text();
448 | 	var endpoint = TUTORIAL_REPOSITORY + '/query';
449 | 	var format = 'JSON';
450 | 
451 | 	$.get('/sparql',data={'endpoint': endpoint, 'query': query, 'format': format}, function(json){
452 | 		var pre = $('<pre></pre>');
453 | 		pre.text(JSON.stringify(json));
454 | 		$('#linktarget13').html(pre);
455 | 	});
456 | 
457 | });
458 | 
459 | 
460 | /*
461 | // ############
462 | //    STEP 14
463 | // ############
464 | */
465 | 
466 | $('#link14').on('click', function(e){
467 | 
468 | 	var query = $('#query14').val();
469 | 	var endpoint = TUTORIAL_REPOSITORY + '/query';
470 | 	var format = 'JSON';
471 | 
472 | 	$.get('/sparql',data={'endpoint': endpoint, 'query': query, 'format': format}, function(json){
473 | 		console.log(json);
474 | 
475 | 		try {
476 | 			var vars = json.head.vars;
477 | 
478 | 			var ul = $('<ul></ul>');
479 | 			ul.addClass('list-group');
480 | 
481 | 			$.each(json.results.bindings, function(index,value){
482 | 				var li = $('<li></li>');
483 | 				li.addClass('list-group-item');
484 | 
485 | 				$.each(vars, function(index, v){
486 | 					var v_type = value[v]['type'];
487 | 					var v_value = value[v]['value'];
488 | 
489 | 					li.append('<strong>'+v+'</strong><br/>');
490 | 
491 | 					// If the value is a URI, create a hyperlink
492 | 					if (v_type == 'uri') {
493 | 						var a = $('<a></a>');
494 | 						a.attr('href',v_value);
495 | 						a.text(v_value);
496 | 						li.append(a);
497 | 					// Else we're just showing the value.
498 | 					} else {
499 | 						li.append(v_value);
500 | 					}
501 | 					li.append('<br/>');
502 | 
503 | 				});
504 | 				ul.append(li);
505 | 
506 | 			});
507 | 
508 | 			$('#linktarget14').html(ul);
509 | 		} catch(err) {
510 | 			$('#linktarget14').html('Something went wrong!');
511 | 		}
512 | 
513 | 
514 | 
515 | 	});
516 | 
517 | });
518 | 


--------------------------------------------------------------------------------
/src/templates/index.html:
--------------------------------------------------------------------------------
  1 | <!DOCTYPE html>
  2 | <html>
  3 | 	<head>
  4 | 		<title>SW2015 Tutorial</title>
  5 | 	</head>
  6 | 
  7 | 	<body>
  8 | 		<div class="container">
  9 | 			<div class='row'>
 10 | 				<div class='col-lg-12'>
 11 | 					<h1>Welcome to the KR on the Web Tutorial Server</h1>
 12 | 					<p>Our server is running at <code>{{ url_for('first_page', _external=True) }}</code></p>
 13 | 				</div>
 14 | 			</div>
 15 | 			<div class='row'>
 16 | 				<div class='col-lg-12'>
 17 | 					<h3>Step 1 <small>Dynamic loading of CSS and Javascript</small></h3>
 18 | 					<p>Click the link to make this page look a bit nicer</p>
 19 | 					<div><a id="link1" class='btn btn-primary'>link</a></div>
 20 | 				</div>
 21 | 			</div>
 22 | 			<div class='row'>
 23 | 				<div class='col-lg-12'>
 24 | 					<h3>Step 2 <small>Sending information to the server</small></h3>
 25 | 					<p>Click the link to send the message 'Hello World' to the server</p>
 26 | 					<div><a id="link2" class='btn btn-primary' href="/show?message=Hello World">link</a></div>
 27 | 				</div>
 28 | 			</div>
 29 | 			<div class='row'>
 30 | 				<div class='col-lg-6'>
 31 | 					<h3>Step 3 <small>Sending information via an AJAX call</small></h3>
 32 | 					<p>Click the link to send the message 'Hello World' to the server, and show the output in a <code>&lt;div&gt;</code> element</p>
 33 | 					<div><a id="link3" class='btn btn-primary'>link</a></div>
 34 | 				</div>
 35 | 				<div class='col-lg-6'>
 36 | 					<h3>Output</h3>
 37 | 					<div id="linktarget3" class='well'>This is where the message will appear.</div>
 38 | 				</div>
 39 | 			</div>
 40 | 			<div class='row'>
 41 | 				<div class='col-lg-6'>
 42 | 					<h3>Step 4 <small>Gathering user input</small></h3>
 43 | 					<p>Click the link to send your own text to the server, and show the output in a <code>&lt;div&gt;</code> element</p>
 44 | 					<form role='form'>
 45 | 						<div class='form-group'>
 46 | 							<label for='messageInput1'>Write a message</label>
 47 | 							<input type='text' class='form-control' id='messageInput1' placeholder='Type some nifty message'>
 48 | 						</div>
 49 | 					</form>
 50 | 					<div><a id="link4" class='btn btn-primary'>link</a></div>
 51 | 				</div>
 52 | 				<div class='col-lg-6'>
 53 | 					<h3>Output</h3>
 54 | 					<div id="linktarget4" class='well'>This is where your message will appear.</div>
 55 | 				</div>
 56 | 			</div>
 57 | 			<div class='row'>
 58 | 				<div class='col-lg-6'>
 59 | 					<h3>Step 5 <small>Fully client side</small></h3>
 60 | 					<p>Click the link to directly copy your message to a <code>&lt;div&gt;</code> element</p>
 61 | 					<form role='form'>
 62 | 						<div class='form-group'>
 63 | 							<label for='messageInput2'>Write a message</label>
 64 | 							<input type='text' class='form-control' id='messageInput2' placeholder='Type some nifty message'>
 65 | 						</div>
 66 | 					</form>
 67 | 					<div><a id="link5" class='btn btn-primary'>link</a></div>
 68 | 				</div>
 69 | 				<div class='col-lg-6'>
 70 | 					<h3>Output</h3>
 71 | 					<div id="linktarget5" class='well'>This is where your message will be copied to.</div>
 72 | 				</div>
 73 | 			</div>
 74 | 			<div class='row'>
 75 | 				<div class='col-lg-6'>
 76 | 					<h3>Step 6 <small>Third-party Service</small></h3>
 77 | 					<p>Start typing to copy the server response to a <code>&lt;div&gt;</code> element</p>
 78 | 					<p>We will use the <em>autocomplete</em> service of the <a href="http://linkedlifedata.com" target="_new">LinkedLifeData.com</a> website.</p>
 79 | 					<form role='form'>
 80 | 						<div class='form-group'>
 81 | 							<label for='messageInput3'>Write a message</label>
 82 | 							<input type='text' class='form-control' id='messageInput3' placeholder='Type some nifty message'>
 83 | 						</div>
 84 | 					</form>
 85 | 					<!-- <div><a id="link5" class='btn btn-primary'>link</a></div> -->
 86 | 				</div>
 87 | 				<div class='col-lg-6'>
 88 | 					<h3>Output</h3>
 89 | 					<div id="linktarget6" class='well' style='scroll: both; overflow: auto; height: 10em;'>This is where the server response will appear.</div>
 90 | 				</div>
 91 | 			</div>
 92 | 			<div class='row'>
 93 | 				<div class='col-lg-6'>
 94 | 					<h3>Step 7 <small>Parse results</small></h3>
 95 | 					<p>Start typing to copy a parsed server response to a <code>&lt;div&gt;</code> element</p>
 96 | 					<p>We will use the <em>autocomplete</em> service of the <a href="http://linkedlifedata.com" target="_new">LinkedLifeData.com</a> website.</p>
 97 | 					<form role='form'>
 98 | 						<div class='form-group'>
 99 | 							<label for='messageInput7'>Write a message</label>
100 | 							<input type='text' class='form-control' id='messageInput7' placeholder='Type some nifty message'>
101 | 						</div>
102 | 					</form>
103 | 					<!-- <div><a id="link5" class='btn btn-primary'>link</a></div> -->
104 | 				</div>
105 | 				<div class='col-lg-6'>
106 | 					<h3>Output</h3>
107 | 					<div id="linktarget7" class='well' style='scroll: both; overflow: auto; height: 10em;'>This is where the server response will appear.</div>
108 | 				</div>
109 | 			</div>
110 | 			<div class='row'>
111 | 				<div class='col-lg-6'>
112 | 					<h3>Step 8 <small>Add click handlers</small></h3>
113 | 					<p>Start typing to copy a parsed server response to a <code>&lt;div&gt;</code> element. We add custom handlers for the click events.</p>
114 | 					<p>We will use the <em>autocomplete</em> service of the <a href="http://linkedlifedata.com" target="_new">LinkedLifeData.com</a> website.</p>
115 | 					<form role='form'>
116 | 						<div class='form-group'>
117 | 							<label for='messageInput8'>Write a message</label>
118 | 							<input type='text' class='form-control' id='messageInput8' placeholder='Type some nifty message'>
119 | 						</div>
120 | 					</form>
121 | 					<!-- <div><a id="link5" class='btn btn-primary'>link</a></div> -->
122 | 				</div>
123 | 				<div class='col-lg-6'>
124 | 					<h3>Output</h3>
125 | 					<div id="linktarget8" class='well' style='scroll: both; overflow: auto; height: 10em;'>This is where the server response will appear.</div>
126 | 				</div>
127 | 			</div>
128 | 			<div class='row'>
129 | 				<div class='col-lg-6'>
130 | 					<h3>Step 9 <small>Fire SPARQL DESCRIBE</small></h3>
131 | 					<p>Start typing to copy a parsed server response to a <code>&lt;div&gt;</code> element. The click events now use the URI returned by the autocompletion to fire a SPARQL DESCRIBE query, e.g:</p>
132 | 					<pre class='sparql'>DESCRIBE &lt;http://linkedlifedata.com/resource/umls/id/C0000970&gt;</pre>
133 | 					<p>We will use the <em>autocomplete</em> service of the <a href="http://linkedlifedata.com" target="_new">LinkedLifeData.com</a> website. And fire the SPARQL query to the endpoint at <a href="http://linkedlifedata.com/sparql">http://linkedlifedata.com/sparql</a>. However, the problem is that not all SPARQL endpoints properly handle JSONP/CORS so we wrap it in a server side function <code>{{ url_for('sparql') }}</code></p>
134 | 					<form role='form'>
135 | 						<div class='form-group'>
136 | 							<label for='messageInput9'>Write a message</label>
137 | 							<input type='text' class='form-control' id='messageInput9' placeholder='Type some nifty message'>
138 | 						</div>
139 | 					</form>
140 | 					<!-- <div><a id="link5" class='btn btn-primary'>link</a></div> -->
141 | 				</div>
142 | 				<div class='col-lg-6'>
143 | 					<h3>Output</h3>
144 | 					<div id="linktarget9" class='well' style='scroll: both; overflow: auto; height: 15em;'>This is where the server response will appear.</div>
145 | 				</div>
146 | 			</div>
147 | 			<div class='row'>
148 | 				<div class='col-lg-6'>
149 | 					<h3>Step 10 <small>Store results</small></h3>
150 | 					<p>Start typing to copy a parsed server response to a <code>&lt;div&gt;</code> element. The click events now use the URI returned by the autocompletion to fire a SPARQL DESCRIBE query, e.g:</p>
151 | 					<pre class='sparql'>DESCRIBE &lt;http://linkedlifedata.com/resource/umls/id/C0000970&gt;</pre>
152 | 					<p>We will use the <em>autocomplete</em> service of the <a href="http://linkedlifedata.com" target="_new">LinkedLifeData.com</a> website. And fire the SPARQL query to the endpoint at <a href="http://linkedlifedata.com/sparql">http://linkedlifedata.com/sparql</a>. However, the problem is that not all SPARQL endpoints properly handle JSONP/CORS so we wrap it in a server side function <code>{{ url_for('sparql') }}</code> (that will come in handy later anyway)</p>
153 | 					<p>We also specify a link button that allows us to <em>post</em> the response to our own triple store. Again, we will wrap this call in a server side function <code>{{ url_for('store') }}</code></p>
154 | 					<form role='form'>
155 | 						<div class='form-group'>
156 | 							<label for='messageInput10'>Write a message</label>
157 | 							<input type='text' class='form-control' id='messageInput10' placeholder='Type some nifty message'>
158 | 						</div>
159 | 					</form>
160 | 
161 | 					<div><a id="link10" class='btn btn-primary disabled'>link</a></div>
162 | 				</div>
163 | 				<div class='col-lg-6'>
164 | 					<h3>Output</h3>
165 | 					<div id="linktarget10" class='well' style='scroll: both; overflow: auto; height: 15em;'>This is where the server response will appear.</div>
166 | 				</div>
167 | 			</div>
168 | 			<div class='row'>
169 | 				<div class='col-lg-6'>
170 | 					<h3>Step 11 <small>Query DBPedia</small></h3>
171 | 					<p>Start typing to copy a parsed server response to a <code>&lt;div&gt;</code> element. The click events now use the <strong>label</strong> returned by the autocompletion to fire a SPARQL CONSTRUCT query, e.g:</p>
172 | 					<pre class='sparql'>
173 | PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
174 | 
175 | CONSTRUCT {
176 | 	?s rdfs:label "Aspirin" .
177 | 	?s ?p1 ?o1 .
178 | 	?o1 ?p2 ?o2 .
179 | } WHERE {
180 | 	?s  rdfs:label "Aspirin"@en;
181 | 	    ?p1        ?o1 .
182 | 	?o1 ?p2        ?o2 .
183 | }</pre>
184 | 					<p>We will use the <em>autocomplete</em> service of the <a href="http://linkedlifedata.com" target="_new">LinkedLifeData.com</a> website. And fire the SPARQL query to the endpoint at <a href="http://live.dbpedia.org/sparql">http://live.dbpedia.org/sparql</a>. However, the problem is that not all SPARQL endpoints properly handle JSONP/CORS so we wrap it in a server side function <code>{{ url_for('sparql') }}</code></p>
185 | 					<p>We also specify a link button that allows us to <em>post</em> the response to our own triple store. Again, we will wrap this call in a server side function <code>{{ url_for('store') }}</code></p>
186 | 					<p>Note that the only real difference with <strong>Step 10</strong> is the SPARQL Query!</p>
187 | 					<form role='form'>
188 | 						<div class='form-group'>
189 | 							<label for='messageInput11'>Write a message</label>
190 | 							<input type='text' class='form-control' id='messageInput11' placeholder='Type some nifty message'>
191 | 						</div>
192 | 					</form>
193 | 
194 | 					<div><a id="link11" class='btn btn-primary disabled'>link</a></div>
195 | 				</div>
196 | 				<div class='col-lg-6'>
197 | 					<h3>Output</h3>
198 | 					<div id="linktarget11" class='well' style='height: 15em; scroll: both; overflow: auto;'>This is where the server response will appear.</div>
199 | 				</div>
200 | 			</div>
201 | 			<div class='row'>
202 | 				<div class='col-lg-6'>
203 | 					<h3>Step 12 <small>Add some Schema</small></h3>
204 | 					<p>Let's add some schema information to our repository:</p>
205 | 					<textarea class="form-control" id="schema" class='turtle' style='width: 100%' rows='10'>
206 | @prefix owl:  &lt;http://www.w3.org/2002/07/owl#&gt; .
207 | @prefix dbo: &lt;http://dbpedia.org/ontology/&gt; .
208 | @prefix umls-semnetwork: &lt;http://linkedlifedata.com/resource/semanticnetwork/id/&gt; .
209 | 
210 | # Let's say that the class of DBPedia 'Drug's is equivalent
211 | # to the 'Pharmacological Substance' class in LLD
212 | dbo:Drug owl:equivalentClass umls-semnetwork:T121 .
213 | </textarea>
214 | 					<p>Click the link button to <em>POST</em> the schema to our own triple store. Again, we will wrap this call in a server side function <code>{{ url_for('store') }}</code></p>
215 | 					<div><a id="link12" class='btn btn-primary'>link</a></div>
216 | 				</div>
217 | 				<div class='col-lg-6'>
218 | 					<h3>Output</h3>
219 | 					<div id="linktarget12" class='well' style='height: 15em; scroll: both; overflow: auto;'>This is where the server response will appear.</div>
220 | 				</div>
221 | 			</div>
222 | 			<div class='row'>
223 | 				<div class='col-lg-6'>
224 | 					<h3>Step 13 <small>Query for <code>rdf:type</code> relations</small></h3>
225 | 					<p>Let's run the following query against the repository and show the results in the <code>div</code> :</p>
226 | 					<pre id='query13' class='sparql' style='width: 100%' rows='10'>
227 | PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
228 | PREFIX dbo: &lt;http://dbpedia.org/ontology/&gt;
229 | 
230 | SELECT ?x WHERE {
231 |   ?x a dbo:Drug .
232 | }
233 | </pre>
234 | 					<p>Click the link button to <em>GET</em> the query to our triple store. Again, we will wrap this call in a server side function <code>{{ url_for('sparql') }}</code></p>
235 | 					<div><a id="link13" class='btn btn-primary'>link</a></div>
236 | 				</div>
237 | 				<div class='col-lg-6'>
238 | 					<h3>Output</h3>
239 | 					<div id="linktarget13" class='well' style='height: 15em; scroll: both; overflow: auto;'>This is where the server response will appear.</div>
240 | 				</div>
241 | 			</div>
242 | 			<div class='row'>
243 | 				<div class='col-lg-6'>
244 | 					<h3>Step 14 <small>Parsing query results</small></h3>
245 | 					<p>Just because some people dislike the number 13, let's run a query against the repository, do some client-side parsing of the JSON results, and show them in the <code>div</code>:</p>
246 | 					<textarea id='query14' class='sparql' style='width: 100%' rows='10'>
247 | PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
248 | PREFIX dbo: &lt;http://dbpedia.org/ontology/&gt;
249 | 
250 | SELECT ?x WHERE {
251 |   ?x a dbo:Drug .
252 | }
253 | </textarea>
254 | 					<p>Click the link button to <em>GET</em> the query to our triple store. Again, we will wrap this call in a server side function <code>{{ url_for('sparql') }}</code></p>
255 | 					<div><a id="link14" class='btn btn-primary'>link</a></div>
256 | 				</div>
257 | 				<div class='col-lg-6'>
258 | 					<h3>Output</h3>
259 | 					<div id="linktarget14" class='well' style='height: 15em; scroll: both; overflow: auto;'>This is where the server response will appear.</div>
260 | 				</div>
261 | 			</div>
262 | 
263 | 		</div>
264 | 
265 | 		<script src='{{ url_for("static", filename="js/jquery-1.11.0.min.js") }}' type='text/javascript'></script>
266 | 		<script src='{{ url_for("static", filename="js/tutorial.js") }}' type='text/javascript'></script>
267 | 
268 | 
269 | 	</body>
270 | </head>
271 | 


--------------------------------------------------------------------------------
/tools.md:
--------------------------------------------------------------------------------
  1 | # Recommended Tools
  2 | 
  3 | ## 1. Introduction
  4 | 
  5 | This handout is meant as a guide for installing some of the tools that we will use during the course.
  6 | 
  7 | ##### Warnings
  8 | * 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)
  9 | * The only exception is when you see the text `YOURUSERNAME`: be sure to replace it with your actual user name!
 10 | * If you change any settings in Windows, you need to restart your command prompt (CMD) for the changes to take effect
 11 | 
 12 | 
 13 | ## 2. Important Stuff
 14 | ### 2.1 A Programming Editor
 15 | A good **programming editor**, such as [Atom](http://atom.io), [Sublime](http://sublimetext.com), [TextMate](http://macromates.com) (Mac only), [Notepad++](https://notepad-plus-plus.org) (Windows only) or one of your own choice, is essential. It helps if it supports syntax highlighting for **Turtle** and/or **SPARQL**.
 16 | 
 17 | ### 2.2 Java
 18 | Make sure that you have Java, and your Java version is up to date.
 19 | 
 20 | Install JDK version 8u101 for your platform from:
 21 | 
 22 | <http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html>
 23 | 
 24 | Running `java -version` in your terminal/command prompt should give:
 25 | 
 26 | ```
 27 | java version "1.8.0_101"
 28 | Java(TM) SE Runtime Environment (build 1.8.0_101-b13)
 29 | Java HotSpot(TM) 64-Bit Server VM (build 25.101-b13, mixed mode)
 30 | ```
 31 | 
 32 | ### 2.3 Python
 33 | A working version of **Python**, preferably somewhat close to 2.7.12 (but not 2.6 or 3.x) for your platform of choice.
 34 | 
 35 | * Check what version you have by running `python --version` in a terminal (or command prompt) window
 36 | 
 37 | **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. 
 38 | 
 39 | If needed:
 40 | * Conda users can install Python 2.7 by running `conda install python=2.7` in the Terminal.
 41 | * Windows users can go to <https://www.python.org> to download it.  
 42 |   **NB**: make sure to enable the 'Add Python.exe to path' option during installation.
 43 | * Linux users should use the package manager of their system (e.g. `sudo apt-get install python`)
 44 | * MacOS comes with a pre-installed version, but you may consider using [Homebrew](http://brew.sh) to install a clean and up-to-date version.
 45 |   - Start the Terminal application
 46 |   - Run `ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"` from the terminal
 47 |   - Then run `brew update` and `brew doctor`
 48 |   - Run `brew install python`
 49 | 
 50 | ### 2.4 Programming Libraries
 51 | (For the lab session you may want to skip to section 3)
 52 | 
 53 | 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.
 54 | 
 55 | Depending on your preferred programming language, examples are:
 56 | 
 57 | * [RDFLib](https://rdflib.readthedocs.io/en/stable/), for Python. Simply `pip install rdflib`
 58 | * [Jena](http://jena.apache.org) for Java.
 59 | * [EasyRDF](http://www.easyrdf.org) for PHP (but don't, oh, please)
 60 | * [rdflib.js](https://github.com/linkeddata/rdflib.js) for JavaScript
 61 | * [Redland](http://librdf.org) for C
 62 | 
 63 | ## 3. The **Protégé** Ontology Editor
 64 | 
 65 | There are several RDF and OWL editors that you could use (apart from your favourite text-based editor). The main contenders are [Protégé](http://protege.stanford.edu) and [TopBraid Composer](http://www.topquadrant.com/downloads/topbraid-composer-install/).
 66 | 
 67 | We advise you to use Protégé for the assignments in Week 3.
 68 | 
 69 | * **Protégé** is a stand-alone editor that is very much tailored towards OWL ontology editing.
 70 | * It allows you to define OWL axioms using an abstract syntax (Manchester Syntax),
 71 | * 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.  
 72 | * Protégé does support all major OWL2 DL reasoners (Fact++, Hermit and Pellet) and is thus quite powerful with respect to inferencing.
 73 | 
 74 | ### Installing Protégé
 75 | 
 76 | * Download the the 5.0.0 version from GitHub: <https://github.com/protegeproject/protege-distribution/releases/tag/protege-5.0.0> 
 77 | * Install the Pellet plugin from within Protege, but if that doesn't work...
 78 |   * 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.
 79 |     * 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.
 80 | * To run it:
 81 |   * 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.
 82 |   * On Linux, you should run the `run.sh` script in the Protégé directory
 83 |   * On MacOS, you should run the `Protégé.app` application in the Protégé directory
 84 | * Make sure that the **Pellet** reasoner can be seen in the **Reasoner** menu of the Protégé application window.
 85 | 
 86 | 
 87 | 
 88 | ## 4 The **Stardog** triple store (version 4 or higher):
 89 | 
 90 | Stardog is a reasoning-enabled database for Linked Data and ontologies.
 91 | 
 92 | * Apply for Community Edition license at <http://stardog.com> (or a 30-day evaluation)
 93 | * You will receive an email with a link to the download, and a license file.
 94 | * **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
 95 | 
 96 | Official installation instructions can be found at <http://docs.stardog.com/#_quick_start_guide>
 97 | 
 98 | #### 4.1 Windows
 99 | One way to get it running:
100 | 
101 | * 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!)
102 | * Create a `data` directory inside it, this is now `C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\data`
103 | * Copy the `stardog-license.bin` file to `C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\data`
104 | * Go to the Control Panel, and search for `environment variables`.
105 | 	* Create a system-wide variable called `STARDOG_HOME` and give it the value `C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\data`.
106 | 	* Update the system-wide `PATH` variable by adding `C:\Users\YOURUSERNAME\Documents\stardog-4.1.3\bin`
107 | * 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`)
108 | * Open your browser, and go to <http://localhost:5820> the login details are `admin` and `admin`
109 | * Whee!
110 | 
111 | Follow the next steps under **4.3**
112 | 
113 | Alternative installation instructions can be found at <http://docs.stardog.com/#_quick_start_guide>
114 | 
115 | #### 4.2 Linux/Mac
116 | One way to get it running:
117 | 
118 | * 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`
119 | * Create a `data` directory inside it, this is now `/Users/YOURUSERNAME/Documents/stardog-4.1.3/data`
120 | * Copy the `stardog-license.bin` to `/Users/YOURUSERNAME/Documents/stardog-4.1.3/data`
121 | * Open up a Terminal window, and type `open ~/.bash_profile`, this opens a TextEdit window on mac. Linux users will know what to do.
122 | * Add the following lines anywhere in the file:
123 | 
124 | ```
125 | export STARDOG_HOME=/Users/YOURUSERNAME/Documents/stardog-4.1.3/data
126 | export PATH=$PATH:/Users/YOURUSERNAME/Documents/stardog-4.1.3/bin
127 | ```
128 | * Close the Terminal window, and open a new one
129 | * 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`)
130 | * Open your browser, and go to <http://localhost:5820> the login details are `admin` and `admin`
131 | * Whee!
132 | 
133 | Follow the next steps under **4.3**
134 | 
135 | #### 4.3 Starting and Stopping Stardog
136 | 
137 | To start: ``stardog-admin server start --disable-security`` (`stardog-admin.bat` on Windows)
138 | 
139 | To stop: ``stardog-admin server stop`` (`stardog-admin.bat` on Windows)
140 | 
141 | #### 4.3 All Platforms
142 | * Go to <http://localhost:5820>, create a new Database called `tutorial` (you may need to login using *admin*/*admin*)
143 | * Make sure to set reasoning to `SL` and "SameAs reasoning" to `FULL` otherwise leave the settings unchanged.
144 | * Done!
145 | 
146 | ## 5. The **Semantic Web** Tutorial
147 | 
148 | Once you have Python, Java and Stardog in place, you can try out the Semantic Web tutorial.
149 | 
150 | * Open up a Terminal or a Command Prompt window
151 | * Change directory to e.g. your Documents directory (on Mac/Linux: `cd ~/Documents`, on Windows `cd C:\Users\YOURUSERNAME\Documents`)
152 | * 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`
153 | * 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`
154 | * Change directory to the newly created folder: `cd web-application`
155 | * (**OPTIONAL**) Setup the virtualenv in the directory of this repository (`virtualenv .`)
156 | * (**OPTIONAL**) Activate the virtualenv (`source bin/activate` on linux-like systems)
157 | * Install the necessary packages (`pip install -r requirements.txt`)
158 | * Check the Stardog SPARQL endpoint URL in the `TUTORIAL_REPOSITORY` variable in **both** `src/tutorial.py` and `src/static/js/tutorial.js`.  
159 | * If you haven't done so, install **Stardog** and make sure it is running.
160 |   * By default, the script assumes a Stardog database with the name 'tutorial' running at <http://localhost:5820/tutorial>.
161 |   * The database should have `reasoning set to `SL` and "SameAs reasoning" to `FULL`.
162 | 	* 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`.
163 | 	* 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.
164 | * Run the tutorial from within the `src` directory by running `python tutorial.py`
165 | 
166 | 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>.
167 | 
168 | #### The Ultimate Test: does it work?
169 | 
170 | Go to <http://localhost:5000> in your browser.
171 | 
172 | * In step 10,
173 |   * type `Aspirin`, (this retrieves all matches for Aspirin from Linked Life Data)
174 |   * select the link `Aspirin`,
175 |   * and press the "Link" button. This pushes the RDF representation of LLD Aspirin to your Stardog instance.
176 |   * Output should be 'Ok!'
177 | * In step 11,
178 |   * also type `Aspirin` (this will retrieve all matches for Aspirin from DBPedia),
179 |   * select the link `Aspirin`,
180 |   * and press the "Link" button.
181 |   * Output should be 'Ok!'
182 | * In step 12,
183 |   * just press the "Link" button.
184 |   * Output should be 'Ok!'
185 | * Skip step 13
186 | * In step 14,
187 |    * just press the "Link" button.
188 |    * Output should have two results, one from Linked Life Data, and one from DBPedia.
189 | 
190 | ## 6. Optional but Recommended Tools
191 | 
192 | ### 6.1 brwsr
193 | 
194 | [brwsr](https://github.com/Data2Semantics/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.
195 | 
196 | It supports:
197 | * Rendering of all triples in which a resource plays a role (po, sp, and so)
198 | * It is named-graph aware, allowing you to see what graph a triple belongs to
199 | * It supports content negotiation for RDF clients
200 | * It can browse external URIs, provided that they are published as Cool URIs (dereferencable URIs)
201 | * It retrieves standard labels for URIs from preflabel.org
202 | 
203 | To install it, download the zip file or, clone it to a directory of your choice.
204 | 
205 | Open up a terminal, and change into that directory:
206 | 
207 | * create and activate a `virtualenv` if you so desire
208 | * run `pip install -r requirements.txt`
209 | * rename or copy `config-template.py` to `config.py`
210 | * make appropriate settings in the file (documentation is inline)
211 | * Start it with `python run.py` from within the `src` directory.
212 | 
213 | ### 6.2 curl
214 | `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.
215 | 
216 | You can also use an online service such as <http://hurl.it>.
217 | 
218 | * Windows users can download `curl` directly from <http://dl.uxnr.de/mirror/curl/curl-7.33.0-win64-ssl-sspi.zip>.  
219 |   **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.  
220 |   * Create a folder called 'curl' in the `C:\Program Files` directory,
221 |   * copy `curl.exe` from the unzipped file to the `C:\Program Files\curl` directory,
222 |   * then add the `C:\Program Files\curl` directory to the `PATH` system environment variable (in Control Panel, search for `environment variable`).
223 |   * Edit the variable value, different directory names should be separated by a semicolon (`;`)
224 |   * Start the Command Prompt (in Win 8/10 use the search) and type `curl.exe` to see whether it does anything.
225 | * 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`)
226 | * MacOS comes shipped with `curl`
227 | 
228 | 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)"`
229 | 
230 | Did you see any triples?
231 | 
232 | 
233 | ### 6.3 IPython Notebook (Jupyter)
234 | 
235 | Interactive notebooks are simple and effective tools for testing small bits of your code before you integrate it in a larger application.
236 | 
237 | Run `pip install jupyter` in a Terminal or the Command Prompt.
238 | 
239 | Jupyter documentation is here:  <http://jupyter.readthedocs.org>.
240 | 
241 | ### 6.4 Virtualenv
242 | 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.
243 | 
244 | Run `pip install virtualenv` in a Terminal or the Command Prompt.
245 | 
246 | Have a look at the `virtualenv` page at the [Hitchhikers Guide to Python](http://docs.python-guide.org/en/latest/dev/virtualenvs/) for a good description of how you should work with virtual environments.
247 | 
248 | * `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.
249 | * 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`)
250 | 
251 | ### 6.5 Git
252 | 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](http://github.com) is the online cloud service of choice.
253 | 
254 | Try and learn [here](http://try.github.io) why and how you should use it.
255 | 
256 | * Windows users can go to <https://git-scm.com> to download it
257 | * Linux users should use the package manager of their system (e.g. `sudo apt-get install git`)
258 | * MacOS users can most easily install it with Homebrew (`brew install git`) or download it from <https://git-scm.com>
259 | * Note: it makes sense to also install a UI-based application, such as [SourceTree](https://www.sourcetreeapp.com).
260 | 
261 | ### 6.6 TopBraid Composer
262 | 
263 | * Download TopBraid Free Edition from <http://www.topquadrant.com/downloads/topbraid-composer-install/>.
264 | * The Standard and Maestro Editions can be evaluated for a limited period.
265 | * 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).
266 | * To run it: double click the `TopBraid Composer` executable file inside the folder.
267 | * 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.
268 | * After TopBraid has started, you can get started by creating a new project by right-clicking in the "Navigator" panel (bottom right, by default).
269 | * Make sure to synchronise the workspace after you make any changes to the files inside your project form outside of the Eclipse environment.
270 | 
271 | ### 6.7 A Standalone Reasoner
272 | 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](https://www.dropbox.com/s/sugzmjq91ggsney/pellet.tar.gz?dl=0) that you can use. Pellet is by the same developers as Stardog. See <https://github.com/Complexible/pellet> for licensing information.
273 | 
274 | After downloading, unzip the file, and move the resulting directory to a location of your choice.
275 | 
276 | 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`.
277 | 
278 | Running `./pellet.sh help` will give you basic usage information. There's also a readme.
279 | 
280 | ### 6.8 Linked Data Reactor (LD-R) Framework
281 | [LD-R](http://ld-r.org) is a framework for building reactive component-based Linked Data Applications.
282 | LD-R utilizes Facebook's ReactJS components, Flux architecture and Yahoo!'s Fluxible framework for implementing isomorphic Semantic Web applications.
283 | Follow [this quick tutorial](http://ld-r.org/docs/basicTutorial.html) to install and use LD-R.
284 | 


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5 | 


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