1 /*
2 * Copyright 2013-2023 Medical Information Systems Research Group (https://medical.zcu.cz),
3 * Department of Computer Science and Engineering, University of West Bohemia.
4 * Address: Univerzitni 8, 306 14 Plzen, Czech Republic.
5 *
6 * This file is part of Sparkle project.
7 *
8 * Sparkle is free software: you can redistribute it and/or modify
9 * it under the terms of the GNU General Public License as published by
10 * the Free Software Foundation, either version 3 of the License.
11 *
12 * Sparkle is distributed in the hope that it will be useful,
13 * but WITHOUT ANY WARRANTY; without even the implied warranty of
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 * GNU General Public License for more details.
16 *
17 * You should have received a copy of the GNU General Public License
18 * along with Sparkle. If not, see <http://www.gnu.org/licenses/>.
19 */
20 package cz.zcu.mre.sparkle.data.resourceStorage;
21
22 import cz.zcu.mre.sparkle.data.AbstractTermsStorage;
23 import cz.zcu.mre.sparkle.data.BuiltInVocabulary;
24 import cz.zcu.mre.sparkle.data.DataAgent;
25 import cz.zcu.mre.sparkle.data.PrefixesStorage;
26 import cz.zcu.mre.sparkle.tools.Changeable;
27 import javafx.beans.InvalidationListener;
28 import javafx.beans.Observable;
29 import javafx.beans.value.ObservableBooleanValue;
30 import javafx.collections.ObservableList;
31 import javafx.stage.Stage;
32 import org.apache.jena.rdf.model.Resource;
33 import java.io.File;
34 import java.io.IOException;
35 import java.io.Serializable;
36 import java.lang.reflect.Field;
37 import java.util.HashSet;
38 import java.util.List;
39 import java.util.Set;
40 import java.util.logging.Level;
41 import java.util.logging.Logger;
42
43 /**
44 * Třída pro skladování ostatních RDF zdrojů.
45 *
46 * @author Jan Smucr
47 * @author Klara Hlavacova
48 * @author Petr Vcelak (vcelak@kiv.zcu.cz)
49 * @see AbstractTermsStorage
50 */
51 public final class ResourcesStorage
52 extends AbstractTermsStorage<ResourceStorageEntry>
53 implements Observable, Changeable, Serializable {
54
55 private static final Logger LOG = Logger.getLogger(ResourcesStorage.class.getName());
56
57 private final Set<InvalidationListener> observers = new HashSet<>();
58
59 private static final long serialVersionUID = 5882457314144281288L;
60 private static final String XML_ELEMENT_NAME = "Resources"; //$NON-NLS-2$
61
62 public ResourcesStorage(final DataAgent dataAgent, final PrefixesStorage prefixesStorage) {
63 super(dataAgent, prefixesStorage);
64 }
65
66 /**
67 * Deserializace objektu
68 *
69 * @param in vstupni proud
70 *
71 * @throws IOException IO exception.
72 * @throws ClassNotFoundException Class not found exception.
73 */
74 private void readObject(java.io.ObjectInputStream in) throws IOException, ClassNotFoundException {
75 in.defaultReadObject();
76 }
77
78 /**
79 * Vrátí instanci {@link ResourcesStorage} obsahující vestavěné pojmy.
80 *
81 * @param dataAgent Instance {@link DataAgent}.
82 * @param prefixesStorage Instance {@link PrefixesStorage}.
83 *
84 * @return Instance {@link ResourcesStorage}.
85 */
86 public static final ResourcesStorage getBuiltIn(final DataAgent dataAgent, final PrefixesStorage prefixesStorage) {
87
88 final ResourcesStorage result = new ResourcesStorage(dataAgent, prefixesStorage);
89 BuiltInVocabulary builtInNamespaces = new BuiltInVocabulary();
90
91 builtInNamespaces.getBuiltInNamespaces().forEach((entry) -> {
92 result.loadVocabulary(entry.getVocabularyClass());
93 });
94
95 return result;
96 }
97
98 /**
99 * Načte pojmy z Java třídy reprezentující slovník. Pojmy jsou očekávány v
100 * podobě statických konstant typu {@link Resource}.
101 *
102 * @param vocabularyClass Třída slovníku.
103 */
104 private void loadVocabulary(final Class<?> vocabularyClass) {
105 for (final Field field : vocabularyClass.getDeclaredFields()) {
106 try {
107 new ResourceStorageUpdater(this).addFromField(field);
108 } catch (IllegalArgumentException | IllegalAccessException e) {
109 LOG.log(Level.SEVERE, "Exception: ", e); //$NON-NLS-2$
110 }
111 }
112 }
113
114 /**
115 * Aktualizace termu (po nahrani dat do uloziste)
116 *
117 * @param stage Instance {@link Stage}
118 * @param files seznam souboru s daty
119 * @param namespaces seznam jmennych prostoru
120 */
121 public void updateResourceStorage(Stage stage, List<File> files, Set<String> namespaces) {
122 new ResourceStorageUpdater(this).updateResourceStorage(stage, files, namespaces);
123 }
124
125 /**
126 * Aktualizace uloziste ze souboru
127 *
128 * @param stage Instance {@link Stage}
129 * @param namespace jmenny prostor
130 * @param size pocet namespace, ktere se aktualizuje
131 * @param index index aktualizovaneho namespace
132 * @return number of the integer type.
133 */
134 public int updateResourceStorage(Stage stage, String namespace, int size, int index) {
135 return new ResourceStorageUpdater(this).updateResourceStorage(stage, namespace, size, index);
136 }
137
138 /**
139 * Přidá pojmy z uvedeného jmenného prostoru z úložiště.
140 *
141 * @param namespace Jmenný prostor.
142 * @param includeNamedIndividuals Pokud je <code>false</code>, budou
143 * filtrovány instance owl:NamedIndividual.
144 * @param cancelled Sledovatelná {@link Boolean} hodnota. Pokud je nastavena
145 * na <code>true</code>, bude požádáno o přerušení operace.
146 *
147 * @return Počet přidaných pojmů.
148 */
149 public final int addFromStorage(final String namespace, final boolean includeNamedIndividuals,
150 final ObservableBooleanValue cancelled) {
151 return new ResourceStorageUpdater(this).addFromStorage(namespace, includeNamedIndividuals, cancelled);
152 }
153
154 /**
155 * Přidá pojmy z uvedeného jmenného prostoru z úložiště.
156 *
157 * @param namespace Jmenný prostor.
158 * @param includeNamedIndividuals Pokud je <code>false</code>, budou
159 * filtrovány instance owl:NamedIndividual.
160 * @param cancelled Sledovatelná {@link Boolean} hodnota. Pokud je nastavena
161 * na <code>true</code>, bude požádáno o přerušení operace.
162 * @param dataAgent Zdroj dat.
163 *
164 * @return Počet přidaných pojmů.
165 */
166 public int addFromStorage(final String namespace, final boolean includeNamedIndividuals,
167 final ObservableBooleanValue cancelled, final DataAgent dataAgent) {
168
169 return new ResourceStorageUpdater(this).addFromStorage(namespace,
170 includeNamedIndividuals, cancelled, dataAgent);
171 }
172
173 //==============================================
174 /**
175 * Vrací seznam jmen všech známých zdrojů na základě prefixu.
176 *
177 * @param prefix Prefix.
178 * @param includePrefix Pokud je <code>true</code>, prefix bude součástí
179 * názvů ve výsledku.
180 *
181 * @return Seznam názvů zdrojů/pojmů.
182 */
183 public final ObservableList<String> getResourcesNamesByPrefix(final String prefix, final boolean includePrefix) {
184 return getTermsNamesByPrefix(prefix, includePrefix, ResourceStorageEntry.class);
185 }
186
187 /**
188 * Vrací seznam všech známých zdrojů na základě prefixu.
189 *
190 * @param prefix Prefix.
191 *
192 * @return Seznam zdrojů/pojmů.
193 */
194 public final ObservableList<Object> getResourcesByPrefix(final String prefix) {
195
196 return getTermsByPrefix(prefix, ResourceStorageEntry.class);
197 }
198
199 /**
200 * Vrací seznam jmen všech známých vlastností na základě prefixu.
201 *
202 * @param prefix Prefix.
203 * @param includePrefix Pokud je <code>true</code>, prefix bude součástí
204 * názvů ve výsledku.
205 *
206 * @return Seznam názvů vlastností.
207 */
208 public final ObservableList<String> getPropertiesNamesByPrefix(final String prefix, final boolean includePrefix) {
209
210 return getTermsNamesByPrefix(prefix, includePrefix, PropertyStorageEntry.class);
211 }
212
213 /**
214 * Vrací seznam všech známých vlastností na základě prefixu.
215 *
216 * @param prefix Prefix.
217 *
218 * @return Seznam názvů vlastností.
219 */
220 public final ObservableList<Object> getPropertiesByPrefix(final String prefix) {
221 return getTermsByPrefix(prefix, PropertyStorageEntry.class);
222 }
223
224 @Override
225 public final String getTermNamespace(final ResourceStorageEntry term) {
226 return term.getNamespace();
227 }
228
229 @Override
230 public final String getTermName(final ResourceStorageEntry term) {
231 return term.getLocalName();
232 }
233
234 @Override
235 public String getTermTitle(ResourceStorageEntry term) {
236 return term.getTitle();
237 }
238
239 @Override
240 public final String getXMLElementName() {
241 return XML_ELEMENT_NAME;
242 }
243
244 @Override
245 protected final ResourceStorageEntry createTerm(final String namespace, final String localName, String title) {
246 return new ResourceStorageEntry(namespace, localName, title);
247 }
248
249 @Override
250 protected final ResourceStorageEntry createTerm(final String namespace, final String localName, String title,
251 String type) {
252
253 if (type.equalsIgnoreCase(PROPERTY_STORAGE_ENTRY)) {
254 return new PropertyStorageEntry(namespace, localName, title);
255 } else {
256 return new ResourceStorageEntry(namespace, localName, title);
257 }
258 }
259
260 @Override
261 public Set<InvalidationListener> getObservers() {
262 return observers;
263 }
264
265 //=============================================
266 //=============================================
267
268 /*
269 * The method obtains values of a RDFS:LABEL predicate (including their
270 * data types).
271 *
272 * @param dataAgent Instance of {@link DataAgent}.
273 * @param originalQuery Original form of whole query.
274 * @param triplePanePart Currently edited {@link TriplePane}.
275 * @param selectedLanguage Prefered language (it's selected in {@link ComboBox}
276 * at the top right of main window).
277 * @param caretPosition Caret position in owner text field.
278 * @param cancelled Boolean variable - if it is <code>true</code> then obtaining of
279 * RDFS:LABELs is terminated.
280 *
281 * @return ObservableList of RDFS:LABEL values.
282 */
283 /* public final ObservableList<String> getLabels(final DataAgent dataAgent, final String originalQuery,
284 final String triplePanePart, final String selectedLanguage, int caretPosition,
285 final ObservableBooleanValue cancelled) {
286 final String requredPrefixName = "rdfs:label"; //$NON-NLS-1$
287 final String requredVariable = "label"; //$NON-NLS-1$
288 final ObservableList<String> results = FXCollections.observableArrayList();
289 final String queryText =
290 adjustLabelQuery(originalQuery, triplePanePart, requredPrefixName, requredVariable, caretPosition);
291 final CancellableConsumer<QuerySolution> consumer = new CancellableConsumer<QuerySolution>() {
292 @Override
293 public void accept(final QuerySolution qs) {
294 final Literal literal = getLiteralNode(qs, requredVariable);
295 if (literal != null) {
296 final String literalType = getLiteralType(prefixesStorage, literal, selectedLanguage);
297 if (literalType != null) {
298 results.add(requredPrefixName + Definitions.SPACE + Definitions.QUOTATION_MARK +
299 literal.getString() + Definitions.QUOTATION_MARK + literalType);
300 }
301 }
302 }
303 };
304 final ChangeListener<Boolean> cancellationListener = (observable, oldValue, newValue) -> {
305 if (newValue) {
306 consumer.cancel();
307 }
308 };
309
310 cancelled.addListener(cancellationListener);
311 dataAgent.select(queryText, consumer);
312 cancelled.removeListener(cancellationListener);
313 return results;
314 }
315 */
316 /*
317 * It adjusts "property path" to wanted RDFS:label.
318 *
319 * @param propertyPath The full property path.
320 * @param requiredPropertyText RDFS:LABEL.
321 * @param caretPosition Caret position in owner text field.
322 *
323 * @return The property path to wanted RDFS:label.
324 */
325 /* private StringBuilder getPropertyPathToLabel(final String propertyPath, final String requiredPropertyText,
326 final int caretPosition) {
327 StringBuilder sb = new StringBuilder();
328 int endOfPropPath = propertyPath.substring(0, caretPosition).lastIndexOf(Definitions.PROPERTY_PATH_DELIMITER);
329 if (endOfPropPath > -1) {
330 endOfPropPath++;
331 sb.append(propertyPath.substring(0, endOfPropPath));
332 }
333 sb.append(requiredPropertyText);
334 return sb;
335 }
336 */
337 /*
338 * It creates query to searching of RDFS:LABEL from whole triple.
339 *
340 * @param matcher Regex matches of triple.
341 * @param groupGraphPatternPanePart Full WHERE clause.
342 * @param triplePanePart Current form of {@link TriplePane} instance.
343 * @param indexOfTriplePane Index of <code>triplePanePart</code> in original query.
344 * @param requiredVariable "label".
345 * @param requiredPropertyText RDFS:LABEL.
346 * @param caretPosition Caret position in owner text field.
347 *
348 * @return Query to searching of RDFS:LABEL.
349 */
350 /* private StringBuilder createQueryFromTriple(final Matcher matcher, final String groupGraphPatternPanePart,
351 final String triplePanePart, final int indexOfTriplePane, final String requiredVariable,
352 final String requiredPropertyText, final int caretPosition) {
353 final StringBuilder sb = new StringBuilder(" SELECT ?"); //$NON-NLS-1$
354 sb.append(requiredVariable).append(" WHERE ") //$NON-NLS-2$
355 .append(groupGraphPatternPanePart
356 .substring(0, indexOfTriplePane)).
357 append(matcher.group(1))
358 .append(Definitions.SPACE).
359 append(getPropertyPathToLabel(
360 matcher.group(2),
361 requiredPropertyText,
362 caretPosition))
363 .append(" ?").append(requiredVariable)
364 .append(" . "). //$NON-NLS-1$ //$NON-NLS-2$
365 append(
366 groupGraphPatternPanePart.substring(indexOfTriplePane + triplePanePart.length()));
367 return sb;
368 }*/
369
370 /*
371 * It creates query to searching of RDFS:LABEL from subtriple.
372 *
373 * @param matcher Regex matches of triple.
374 * @param groupGraphPatternPanePart Full WHERE clause.
375 * @param triplePanePart Current form of {@link TriplePane} instance.
376 * @param indexOfTriplePane Index of <code>triplePanePart</code> in original query.
377 * @param requiredVariable "label".
378 * @param requiredPropertyText RDFS:LABEL.
379 * @param caretPosition Caret position in owner text field.
380 *
381 * @return Query to searching of RDFS:LABEL.
382 */
383 /* private StringBuilder createQueryFromSubTriple(final Matcher matcher, final String groupGraphPatternPanePart,
384 final String triplePanePart, final int indexOfTriplePane, final String requiredVariable,
385 final String requiredPropertyText, final int caretPosition) {
386 final StringBuilder sb = new StringBuilder(" SELECT ?"); //$NON-NLS-1$
387 sb.append(requiredVariable).append(" WHERE ") //$NON-NLS-2$
388 .append(groupGraphPatternPanePart
389 .substring(0, indexOfTriplePane)). //$NON-NLS-1$
390 append(
391 getPropertyPathToLabel(matcher.group(1), requiredPropertyText, caretPosition)).append(" ?")
392 .append(requiredVariable). //$NON-NLS-1$
393 append(
394 groupGraphPatternPanePart.substring(indexOfTriplePane + triplePanePart.length() - 1));
395 return sb;
396 }*/
397
398 /*
399 * The method forms a final query that is used to obtain RDFS:LABEL values.
400 *
401 * @param originalQuery Original form of obtained query.
402 * @param triplePanePart Current form of {@link TriplePane} instance.
403 * @param requiredPropertyText RDFS:LABEL.
404 * @param requiredVariable "label".
405 * @param caretPosition Caret position in owner text field.
406 *
407 * @return Final form of query.
408 */
409 /* private String adjustLabelQuery(final String originalQuery, final String triplePanePart,
410 final String requiredPropertyText, final String requiredVariable, final int caretPosition) {
411
412 final String groupGraphPatternPanePart = getGroupGraphPattPaneFromQuery(originalQuery, triplePanePart);
413 final int indexOfTriplePane = groupGraphPatternPanePart.indexOf(triplePanePart);
414 StringBuilder sb = new StringBuilder();
415 Matcher m = TRIPLE_PANE.matcher(triplePanePart);
416 if (m.matches()) {
417 sb.append(createQueryFromTriple(m, groupGraphPatternPanePart, triplePanePart, indexOfTriplePane,
418 requiredVariable, requiredPropertyText, caretPosition));
419 } else {
420 m = SUB_TRIPLE_PANE.matcher(triplePanePart);
421 if (m.matches()) {
422 sb.append(createQueryFromSubTriple(m, groupGraphPatternPanePart, triplePanePart, indexOfTriplePane,
423 requiredVariable, requiredPropertyText, caretPosition));
424 }
425 }
426 if (sb.length() > 0) {
427 sb.insert(0,
428 getUsedQueryPrefixes(getQueryPrefixesStorage().getNsPrefixMap(), sb.toString())); // Adding of prefixes
429 return sb.toString();
430 }
431 return null;
432 }*/
433
434 /*
435 * It obtains a literal record from QuerySolution (result of SELECT query).
436 *
437 * @param qs Result of SELECT query.
438 * @param varName Name of required variable.
439 *
440 * @return A RDF literal record.
441 */
442 /* private Literal getLiteralNode(final QuerySolution qs, final String varName) {
443 if (!qs.contains(varName)) {
444 return null;
445 }
446
447 final RDFNode node = qs.get(varName);
448 if (!node.isLiteral()) {
449 return null;
450 }
451
452 return node.asLiteral();
453 }
454 */
455 }