001 /*
002 * The contents of this file are subject to the Mozilla Public
003 * License Version 1.1 (the "License"); you may not use this file
004 * except in compliance with the License. You may obtain a copy of
005 * the License at http://www.mozilla.org/MPL/
006 *
007 * Software distributed under the License is distributed on an "AS
008 * IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or
009 * implied. See the License for the specific language governing
010 * rights and limitations under the License.
011 *
012 * The Original Code is Knowtator.
013 *
014 * The Initial Developer of the Original Code is University of Colorado.
015 * Copyright (C) 2005 - 2008. All Rights Reserved.
016 *
017 * Knowtator was developed by the Center for Computational Pharmacology
018 * (http://compbio.uchcs.edu) at the University of Colorado Health
019 * Sciences Center School of Medicine with support from the National
020 * Library of Medicine.
021 *
022 * Current information about Knowtator can be obtained at
023 * http://knowtator.sourceforge.net/
024 *
025 * Contributor(s):
026 * Philip V. Ogren <philip@ogren.info> (Original Author)
027 */
028
029 package edu.uchsc.ccp.knowtator;
030
031 import java.awt.Component;
032 import java.io.File;
033 import java.io.IOException;
034 import java.util.Arrays;
035 import java.util.Collection;
036 import java.util.HashSet;
037 import java.util.Iterator;
038 import java.util.Set;
039
040 import javax.swing.JOptionPane;
041
042 import org.apache.log4j.Logger;
043
044 import edu.stanford.smi.protege.model.BrowserSlotPattern;
045 import edu.stanford.smi.protege.model.Cls;
046 import edu.stanford.smi.protege.model.Instance;
047 import edu.stanford.smi.protege.model.KnowledgeBase;
048 import edu.stanford.smi.protege.model.Project;
049 import edu.stanford.smi.protege.model.SimpleInstance;
050 import edu.stanford.smi.protege.model.Slot;
051 import edu.stanford.smi.protege.plugin.PluginUtilities;
052 import edu.stanford.smi.protege.ui.ProjectView;
053 import edu.stanford.smi.protege.util.CollectionUtilities;
054 import edu.stanford.smi.protege.util.ComponentUtilities;
055 import edu.uchsc.ccp.knowtator.util.ProjectUtil;
056
057 public class KnowtatorProjectUtil {
058 public static final String KNOWTATOR_SUPPORT_CLS_NAME = "knowtator support class";
059
060 public static final String KNOWTATOR_VERSION_CLS_NAME = "knowtator version";
061
062 public static final String ANNOTATION_CLS_NAME = "knowtator annotation";
063
064 public static final String ANNOTATED_MENTION_SLOT_NAME = "knowtator_annotated_mention";
065
066 public static final String ANNOTATION_ANNOTATOR_SLOT_NAME = "knowtator_annotation_annotator";
067
068 public static final String ANNOTATION_COMMENT_SLOT_NAME = "knowtator_annotation_comment";
069
070 public static final String ANNOTATION_CREATION_DATE_SLOT_NAME = "knowtator_annotation_creation_date";
071
072 public static final String ANNOTATION_SPAN_SLOT_NAME = "knowtator_annotation_span";
073
074 public static final String ANNOTATION_TEXT_SLOT_NAME = "knowtator_annotation_text";
075
076 public static final String ANNOTATION_TEXT_SOURCE_SLOT_NAME = "knowtator_annotation_text_source";
077
078 public static final String SET_SLOT_NAME = "knowtator_set";
079
080 public static final String MENTION_CLS_NAME = "knowtator mention";
081
082 public static final String MENTION_ANNOTATION_SLOT_NAME = "knowtator_mention_annotation";
083
084 public static final String CLASS_MENTION_CLS_NAME = "knowtator class mention";
085
086 public static final String MENTION_CLASS_SLOT_NAME = "knowtator_mention_class";
087
088 public static final String SLOT_MENTION_SLOT_NAME = "knowtator_slot_mention";
089
090 public static final String INSTANCE_MENTION_CLS_NAME = "knowtator instance mention";
091
092 public static final String MENTION_INSTANCE_SLOT_NAME = "knowtator_mention_instance";
093
094 public static final String SLOT_MENTION_CLS_NAME = "knowtator slot mention";
095
096 public static final String MENTION_SLOT_SLOT_NAME = "knowtator_mention_slot";
097
098 public static final String MENTION_SLOT_VALUE_SLOT_NAME = "knowtator_mention_slot_value";
099
100 public static final String MENTIONED_IN_SLOT_NAME = "knowtator_mentioned_in";
101
102 public static final String COMPLEX_SLOT_MENTION_CLS_NAME = "knowtator complex slot mention";
103
104 public static final String BOOLEAN_SLOT_MENTION_CLS_NAME = "knowtator boolean slot mention";
105
106 public static final String FLOAT_SLOT_MENTION_CLS_NAME = "knowtator float slot mention";
107
108 public static final String INTEGER_SLOT_MENTION_CLS_NAME = "knowtator integer slot mention";
109
110 public static final String STRING_SLOT_MENTION_CLS_NAME = "knowtator string slot mention";
111
112 public static final String TEXT_SOURCE_CLS_NAME = "knowtator text source";
113
114 public static final String ANNOTATOR_CLS_NAME = "knowtator annotator";
115
116 public static final String ANNOTATOR_ID_SLOT_NAME = "knowtator_annotator_id";
117
118 public static final String HUMAN_ANNOTATOR_CLS_NAME = "knowtator human annotator";
119
120 public static final String ANNOTATOR_AFFILIATION_SLOT_NAME = "knowtator_annotation_annotator_affiliation";
121
122 public static final String ANNOTATOR_FIRST_NAME_SLOT_NAME = "knowtator_annotation_annotator_firstname";
123
124 public static final String ANNOTATOR_LAST_NAME_SLOT_NAME = "knowtator_annotation_annotator_lastname";
125
126 public static final String ANNOTATOR_TEAM_CLS_NAME = "knowtator annotator team";
127
128 public static final String ANNOTATOR_TEAM_NAME_SLOT_NAME = "knowtator_annotator_team_name";
129
130 public static final String ANNOTATOR_TEAM_MEMBERS_SLOT_NAME = "knowtator_annotator_team_members";
131
132 public static final String DISPLAY_COLOR_CLS_NAME = "knowtator display color";
133
134 public static final String DISPLAY_COLOR_B_SLOT_NAME = "knowtator_display_color_B";
135
136 public static final String DISPLAY_COLOR_G_SLOT_NAME = "knowtator_display_color_G";
137
138 public static final String DISPLAY_COLOR_NAME_SLOT_NAME = "knowtator_display_color_name";
139
140 public static final String DISPLAY_COLOR_R_SLOT_NAME = "knowtator_display_color_R";
141
142 public static final String SET_CLS_NAME = "knowtator set";
143
144 public static final String SET_DESCRIPTION_SLOT_NAME = "knowtator_set_description";
145
146 public static final String SET_NAME_SLOT_NAME = "knowtator_set_name";
147
148 public static final String CONSENSUS_SET_CLS_NAME = "knowtator consensus set";
149
150 public static final String CONSENSUS_SET_INDIVIDUAL_FILTER_SLOT_NAME = "knowtator_individual_filter";
151
152 public static final String CONSENSUS_SET_CONSENSUS_FILTER_SLOT_NAME = "knowtator_consensus_filter";
153
154 public static final String CONSENSUS_SET_TEAM_ANNOTATOR_SLOT_NAME = "knowtator_team_annotator";
155
156 public static final String FILTER_CLS_NAME = "knowtator filter";
157
158 public static final String FILTER_ANNOTATOR_SLOT_NAME = "knowtator_filter_annotator";
159
160 public static final String FILTER_NAME_SLOT_NAME = "knowtator_filter_name";
161
162 public static final String FILTER_SET_SLOT_NAME = "knowtator_filter_set";
163
164 public static final String FILTER_TYPE_SLOT_NAME = "knowtator_filter_type";
165
166 public static final String CONSENSUS_FILTER_CLS_NAME = "knowtator consensus filter";
167
168 public static final String FILTER_TYPES_NOT_SELECTABLE_FROM_TEXT_VIEWER = "knowtator_types_not_selectable_from_text_viewer";
169
170 public static final String COLOR_ASSIGNMENT_CLS_NAME = "knowtator color assignment";
171
172 public static final String COLOR_CLASS_SLOT_NAME = "knowtator_color_class";
173
174 public static final String DISPLAY_COLOR_SLOT_NAME = "knowtator_display_color";
175
176 public static final String TSC_IMPLEMENTATIONS_CLS_NAME = "knowtator text source collection implementations";
177
178 public static final String TSC_IMPLEMENTATION_SLOT_NAME = "knowtator_tsc_implementation";
179
180 public static final String SELECTED_FILTERS_CLS_NAME = "knowtator selected filters";
181
182 public static final String SELECTED_FILTERS_SLOT_NAME = "knowtator_selected_filters";
183
184 public static final String SLOT_MATCHER_CONFIG_CLS_NAME = "knowtator slot matcher config";
185
186 public static final String COMPLEX_SLOT_MATCH_CRITERIA_CLS_NAME = "knowtator complex slot match criteria";
187
188 public static final String SIMPLE_SLOT_MATCH_CRITERIA_CLS_NAME = "knowtator simple slot match criteria";
189
190 public static final String CLASS_MATCH_CRITERIA_SLOT_NAME = "knowtator_class_match_criteria";
191
192 public static final String SLOT_MATCH_CRITERIA_SLOT_NAME = "knowtator_slot_match_criteria";
193
194 public static final String SPAN_MATCH_CRITERIA_SLOT_NAME = "knowtator_span_match_criteria";
195
196 public static final String SLOT_MATCHER_SLOT_SLOT_NAME = "knowtator_slot_matcher_slot";
197
198 public static final String SLOT_MATCHER_SIMPLE_SLOTS_SLOT_NAME = "knowtator_slot_matcher_simple_slots";
199
200 public static final String PROPOGATE_TRIVIAL_MATCH_SLOT_NAME = "knowtator_propogate_trivial_match";
201
202 Cls knowtatorSupportCls;
203
204 Cls annotationCls;
205
206 Slot annotatedMentionSlot;
207
208 Slot annotationAnnotatorSlot;
209
210 Slot annotationCommentSlot;
211
212 Slot annotationCreationDateSlot;
213
214 Slot annotationSpanSlot;
215
216 Slot annotationTextSlot;
217
218 Slot annotationTextSourceSlot;
219
220 Slot setSlot;
221
222 Cls mentionCls;
223
224 Slot mentionAnnotationSlot;
225
226 Cls classMentionCls;
227
228 Slot mentionClassSlot;
229
230 Slot slotMentionSlot;
231
232 Cls instanceMentionCls;
233
234 Slot mentionInstanceSlot;
235
236 Cls slotMentionCls;
237
238 Slot mentionSlotSlot;
239
240 Slot mentionSlotValueSlot;
241
242 Slot mentionedInSlot;
243
244 Cls complexSlotMentionCls;
245
246 Cls booleanSlotMentionCls;
247
248 Cls floatSlotMentionCls;
249
250 Cls integerSlotMentionCls;
251
252 Cls stringSlotMentionCls;
253
254 Cls textSourceCls;
255
256 Cls annotatorCls;
257
258 Slot annotatorIDSlot;
259
260 Cls humanAnnotatorCls;
261
262 Slot annotatorAffiliationSlot;
263
264 Slot annotatorFirstNameSlot;
265
266 Slot annotatorLastNameSlot;
267
268 Cls teamAnnotatorCls;
269
270 Slot annotatorTeamNameSlot;
271
272 Slot annotatorTeamMembersSlot;
273
274 Cls displayColorCls;
275
276 Slot displayColorBSlot;
277
278 Slot displayColorGSlot;
279
280 Slot displayColorNameSlot;
281
282 Slot displayColorRSlot;
283
284 Cls setCls;
285
286 Slot setDescriptionSlot;
287
288 Slot setNameSlot;
289
290 Cls consensusSetCls;
291
292 Slot consensusSetIndividualFilterSlot;
293
294 Slot consensusSetConsensusFilterSlot;
295
296 Slot consensusSetTeamAnnotatorSlot;
297
298 Cls filterCls;
299
300 Slot filterAnnotatorSlot;
301
302 Slot filterNameSlot;
303
304 Slot filterSetSlot;
305
306 Slot filterTypeSlot;
307
308 Slot filterTypesNotSelectableFromTextViewerSlot;
309
310 Cls consensusFilterCls;
311
312 Cls colorAssignmentCls;
313
314 Slot colorClassSlot;
315
316 Slot displayColorSlot;
317
318 Cls tscImplementationsCls;
319
320 Slot tscImplementationsSlot;
321
322 Cls selectedFiltersCls;
323
324 Slot selectedFiltersSlot;
325
326 Cls complexSlotMatchCriteriaCls;
327
328 Slot classMatchCriteriaSlot;
329
330 Slot propogateTrivialMatchSlot;
331
332 Slot slotMatcherSimpleSlotsSlot;
333
334 Slot slotMatcherSlotSlot;
335
336 Slot spanMatchCriteriaSlot;
337
338 Cls simpleSlotMatchCriteriaCls;
339
340 Cls slotMatcherConfigCls;
341
342 Slot slotMatchCriteriaSlot;
343
344 public static final String CONFIGURATION_CLS_NAME = "knowtator configuration";
345
346 public static final String ACTIVE_FILTERS_SLOT_NAME = "knowtator_active_filters";
347
348 public static final String COLOR_ASSIGNMENTS_SLOT_NAME = "knowtator_color_assignments";
349
350 public static final String ROOT_CLSES_SLOT_NAME = "knowtator_root_clses";
351
352 public static final String SELECTED_ANNOTATION_SET_SLOT_NAME = "knowtator_selected_annotation_set";
353
354 public static final String SELECTED_ANNOTATOR_SLOT_NAME = "knowtator_selected_annotator";
355
356 public static final String SELECTED_FILTER_SLOT_NAME = "knowtator_selected_filter";
357
358 public static final String TOKEN_REGEX_SLOT_NAME = "knowtator_token_regex";
359
360 public static final String FADE_UNSELECTED_ANNOTATIONS = "knowtator_fade_unselected_annotations";
361
362 public static final String SUBTEXT_SLOT_SLOT_NAME = "knowtator_subtext_slot";
363
364 Cls configurationCls;
365
366 Slot activeFiltersSlot;
367
368 Slot colorAssignmentsSlot;
369
370 Slot rootClsesSlot;
371
372 Slot selectedAnnotationSetSlot;
373
374 Slot selectedAnnotatorSlot;
375
376 Slot selectedFilterSlot;
377
378 Slot tokenRegexSlot;
379
380 Slot fadeUnselectedAnnotationsSlot;
381
382 Slot subtextSlotSlot;
383
384 public static final String KNOWTATOR_SUPPORT_CLASSES_VERSION = "KNOWTATOR_SUPPORT_CLASSES_VERSION";
385
386 public static final String UNVERSIONED = "UNVERSIONED";
387
388 public static final String V001 = "V001";
389
390 public static final String V002 = "V002";
391
392 public static final String V003 = "V003";
393
394 public static final String V004 = "V004";
395
396 public static final String V005 = "V005";
397
398 public static final String V006 = "V006";
399
400 public static final String V007 = "V007";
401
402 public static final String CURRENT_VERSION = V007;
403
404 public static final String VERSION_BEING_UPDATED = "VERSION_BEING_UPDATED";
405
406 private static final Set<String> VALID_VERSIONS = new HashSet<String>();
407 static {
408 for (String version : new String[] { V001, V002, V003, V004, V005, V006, V007 })
409 VALID_VERSIONS.add(version);
410 }
411
412 KnowledgeBase kb;
413
414 String version = null;
415
416 Logger logger = Logger.getLogger(KnowtatorProjectUtil.class);
417
418 public KnowtatorProjectUtil(KnowledgeBase kb) {
419 this(kb, null);
420 }
421
422 public KnowledgeBase getKnowledgeBase() {
423 return kb;
424 }
425
426 /** Creates a new instance of KnowtatorKBUtil */
427 public KnowtatorProjectUtil(KnowledgeBase kb, Component parent) {
428 this.kb = kb;
429 version = getKnowtatorSupportClassesVersion();
430 if (!isKnowtatorSupportClassesCurrent()) {
431 logger.info("knowtator.pprj version is out of date: expected = " + CURRENT_VERSION + ", actual = "
432 + getKnowtatorSupportClassesVersion());
433 } else {
434 logger.info("knowtator.pprj version is up-to-date: " + getKnowtatorSupportClassesVersion());
435 }
436 initKnowtatorFrames();
437 initConfiguration();
438 }
439
440 private void initConfiguration() {
441 logger.debug("");
442 SimpleInstance configuration = ProjectSettings.getActiveConfiguration(kb.getProject());
443 if (configuration == null) {
444 configuration = (SimpleInstance) kb.createInstance(null, configurationCls);
445 ProjectSettings.setActiveConfiguration(kb.getProject(), configuration);
446 JOptionPane.showMessageDialog(null, "The configuration information for Knowtator has been reset.\n"
447 + "To create color assignments, set the default annotator, or \n"
448 + "specify root classes please select Menu->Knowtator->Configure.\n"
449 + "For additional help please consult the online documentation at:\n"
450 + "http://knowtator.sourceforge.net//configure.shtml", "Configuration Reset",
451 JOptionPane.INFORMATION_MESSAGE);
452 ProjectUtil.saveProject(kb.getProject());
453 logger.debug("added new configuration and saved project");
454 } else {
455 logger.debug("annotation project has an active configuration: " + configuration.getName());
456 }
457 }
458
459 public String getKnowtatorSupportClassesVersion() {
460 logger.debug("");
461 if (version != null)
462 return version;
463 else
464 return getKnowtatorSupportClassesVersion(kb);
465 }
466
467 public static String getKnowtatorSupportClassesVersion(KnowledgeBase kb) {
468 Instance versionInstance = kb.getInstance("knowtator_Instance_20002");
469 if (versionInstance == null) {
470 Cls knowtatorVersionCls = kb.getCls(KNOWTATOR_VERSION_CLS_NAME);
471 if (knowtatorVersionCls != null) {
472 Collection versionInstances = kb.getInstances();
473 if (versionInstances != null && versionInstances.size() > 0) {
474 versionInstance = (SimpleInstance) CollectionUtilities.getFirstItem(versionInstances);
475 }
476 }
477 }
478 if (versionInstance != null) {
479 String version = (String) versionInstance.getDirectOwnSlotValue(kb.getSlot("version"));
480 if (VALID_VERSIONS.contains(version)) {
481 return version;
482 }
483 }
484 return UNVERSIONED;
485 }
486
487
488 public boolean isKnowtatorSupportClassesCurrent() {
489 String version = getKnowtatorSupportClassesVersion();
490 return version.equals(CURRENT_VERSION);
491 }
492
493 public static boolean isKnowtatorSupportClassesCurrent(KnowledgeBase kb) {
494 String version = getKnowtatorSupportClassesVersion(kb);
495 return version.equals(CURRENT_VERSION);
496 }
497
498 public static void updateKnowtatorProject(Project project) throws IOException {
499 KnowledgeBase kb = project.getKnowledgeBase();
500 String oldVersion = getKnowtatorSupportClassesVersion(kb);
501
502 // this code is needed to get from V002 to V003 of knowtator.pprj
503 // is safe to keep in here for any upgrade
504 Cls knowtatorSelectedFilters = kb.getCls("knowtator selected filters");
505 if (knowtatorSelectedFilters != null) {
506 Collection selectedFiltersInstances = kb.getInstances(knowtatorSelectedFilters);
507 for (Iterator it = selectedFiltersInstances.iterator(); it.hasNext();) {
508 Instance instance = (Instance) it.next();
509 kb.deleteInstance(instance);
510 }
511 }
512
513 Slot knowtatorTextSourceAnnotationSlot = kb.getSlot("knowtator_text_source_annotation");
514 if (knowtatorTextSourceAnnotationSlot != null) {
515 kb.deleteSlot(knowtatorTextSourceAnnotationSlot);
516 }
517
518 // this code is needed to remove any color assignments created with
519 // colors that have been removed in
520 // version V003 (and replaced with 141 new colors)
521 if (oldVersion.equals(V003) || oldVersion.equals(V002) || oldVersion.equals(V001) || oldVersion.equals(V001)
522 || oldVersion.equals(UNVERSIONED)) {
523 Cls colorAssignmentCls = kb.getCls("knowtator color assignment");
524 if (colorAssignmentCls != null) {
525 Collection colorAssignments = kb.getInstances(colorAssignmentCls);
526 for (Iterator it = colorAssignments.iterator(); it.hasNext();) {
527 Instance instance = (Instance) it.next();
528 kb.deleteInstance(instance);
529 }
530 }
531 }
532 ProjectUtil.saveProjectAs(kb.getProject(), new File(kb.getProject().getProjectURI()));
533
534 }
535
536 public void displayAnnotationAuthor() {
537 Cls annotationCls = getAnnotationCls();
538 BrowserSlotPattern pattern = new BrowserSlotPattern(Arrays.asList(new Object[] { getAnnotationTextSlot(), " [",
539 getAnnotationAnnotatorSlot(), " : ", getSetSlot(), "]" }));
540 annotationCls.setDirectBrowserSlotPattern(pattern);
541 }
542
543 public SimpleInstance getShowAllFilter() {
544 SimpleInstance showAllFilter = kb.getSimpleInstance("knowtator_Instance_0");
545 return showAllFilter;
546 }
547
548 public SimpleInstance getShowNoneFilter() {
549 SimpleInstance showAllFilter = kb.getSimpleInstance("knowtator_Instance_20000");
550 return showAllFilter;
551 }
552
553 private void initKnowtatorFrames() {
554 annotationCls = kb.getCls(ANNOTATION_CLS_NAME);
555 annotatedMentionSlot = kb.getSlot(ANNOTATED_MENTION_SLOT_NAME);
556 annotationAnnotatorSlot = kb.getSlot(ANNOTATION_ANNOTATOR_SLOT_NAME);
557 annotationCommentSlot = kb.getSlot(ANNOTATION_COMMENT_SLOT_NAME);
558 annotationCreationDateSlot = kb.getSlot(ANNOTATION_CREATION_DATE_SLOT_NAME);
559 annotationSpanSlot = kb.getSlot(ANNOTATION_SPAN_SLOT_NAME);
560 annotationTextSlot = kb.getSlot(ANNOTATION_TEXT_SLOT_NAME);
561 annotationTextSourceSlot = kb.getSlot(ANNOTATION_TEXT_SOURCE_SLOT_NAME);
562 setSlot = kb.getSlot(SET_SLOT_NAME);
563
564 mentionCls = kb.getCls(MENTION_CLS_NAME);
565 mentionAnnotationSlot = kb.getSlot(MENTION_ANNOTATION_SLOT_NAME);
566 classMentionCls = kb.getCls(CLASS_MENTION_CLS_NAME);
567 mentionClassSlot = kb.getSlot(MENTION_CLASS_SLOT_NAME);
568 slotMentionSlot = kb.getSlot(SLOT_MENTION_SLOT_NAME);
569 instanceMentionCls = kb.getCls(INSTANCE_MENTION_CLS_NAME);
570 mentionInstanceSlot = kb.getSlot(MENTION_INSTANCE_SLOT_NAME);
571 slotMentionCls = kb.getCls(SLOT_MENTION_CLS_NAME);
572 mentionSlotSlot = kb.getSlot(MENTION_SLOT_SLOT_NAME);
573 mentionSlotValueSlot = kb.getSlot(MENTION_SLOT_VALUE_SLOT_NAME);
574 mentionedInSlot = kb.getSlot(MENTIONED_IN_SLOT_NAME);
575 complexSlotMentionCls = kb.getCls(COMPLEX_SLOT_MENTION_CLS_NAME);
576 booleanSlotMentionCls = kb.getCls(BOOLEAN_SLOT_MENTION_CLS_NAME);
577 floatSlotMentionCls = kb.getCls(FLOAT_SLOT_MENTION_CLS_NAME);
578 integerSlotMentionCls = kb.getCls(INTEGER_SLOT_MENTION_CLS_NAME);
579 stringSlotMentionCls = kb.getCls(STRING_SLOT_MENTION_CLS_NAME);
580
581 textSourceCls = kb.getCls(TEXT_SOURCE_CLS_NAME);
582
583 annotatorCls = kb.getCls(ANNOTATOR_CLS_NAME);
584 annotatorIDSlot = kb.getSlot(ANNOTATOR_ID_SLOT_NAME);
585 humanAnnotatorCls = kb.getCls(HUMAN_ANNOTATOR_CLS_NAME);
586 annotatorAffiliationSlot = kb.getSlot(ANNOTATOR_AFFILIATION_SLOT_NAME);
587 annotatorFirstNameSlot = kb.getSlot(ANNOTATOR_FIRST_NAME_SLOT_NAME);
588 annotatorLastNameSlot = kb.getSlot(ANNOTATOR_LAST_NAME_SLOT_NAME);
589 teamAnnotatorCls = kb.getCls(ANNOTATOR_TEAM_CLS_NAME);
590 annotatorTeamNameSlot = kb.getSlot(ANNOTATOR_TEAM_NAME_SLOT_NAME);
591 annotatorTeamMembersSlot = kb.getSlot(ANNOTATOR_TEAM_MEMBERS_SLOT_NAME);
592
593 displayColorCls = kb.getCls(DISPLAY_COLOR_CLS_NAME);
594 displayColorBSlot = kb.getSlot(DISPLAY_COLOR_B_SLOT_NAME);
595 displayColorGSlot = kb.getSlot(DISPLAY_COLOR_G_SLOT_NAME);
596 displayColorNameSlot = kb.getSlot(DISPLAY_COLOR_NAME_SLOT_NAME);
597 displayColorRSlot = kb.getSlot(DISPLAY_COLOR_R_SLOT_NAME);
598
599 setCls = kb.getCls(SET_CLS_NAME);
600 setDescriptionSlot = kb.getSlot(SET_DESCRIPTION_SLOT_NAME);
601 setNameSlot = kb.getSlot(SET_NAME_SLOT_NAME);
602 consensusSetCls = kb.getCls(CONSENSUS_SET_CLS_NAME);
603 consensusSetIndividualFilterSlot = kb.getSlot(CONSENSUS_SET_INDIVIDUAL_FILTER_SLOT_NAME);
604 consensusSetConsensusFilterSlot = kb.getSlot(CONSENSUS_SET_CONSENSUS_FILTER_SLOT_NAME);
605 consensusSetTeamAnnotatorSlot = kb.getSlot(CONSENSUS_SET_TEAM_ANNOTATOR_SLOT_NAME);
606
607 filterCls = kb.getCls(FILTER_CLS_NAME);
608 filterAnnotatorSlot = kb.getSlot(FILTER_ANNOTATOR_SLOT_NAME);
609 filterNameSlot = kb.getSlot(FILTER_NAME_SLOT_NAME);
610 filterSetSlot = kb.getSlot(FILTER_SET_SLOT_NAME);
611 filterTypeSlot = kb.getSlot(FILTER_TYPE_SLOT_NAME);
612 filterTypesNotSelectableFromTextViewerSlot = kb.getSlot(FILTER_TYPES_NOT_SELECTABLE_FROM_TEXT_VIEWER);
613 consensusFilterCls = kb.getCls(CONSENSUS_FILTER_CLS_NAME);
614
615 colorAssignmentCls = kb.getCls(COLOR_ASSIGNMENT_CLS_NAME);
616 colorClassSlot = kb.getSlot(COLOR_CLASS_SLOT_NAME);
617 displayColorSlot = kb.getSlot(DISPLAY_COLOR_SLOT_NAME);
618
619 tscImplementationsCls = kb.getCls(TSC_IMPLEMENTATIONS_CLS_NAME);
620 tscImplementationsSlot = kb.getSlot(TSC_IMPLEMENTATION_SLOT_NAME);
621
622 selectedFiltersCls = kb.getCls(SELECTED_FILTERS_CLS_NAME);
623 selectedFiltersSlot = kb.getSlot(SELECTED_FILTERS_SLOT_NAME);
624
625 complexSlotMatchCriteriaCls = kb.getCls(COMPLEX_SLOT_MATCH_CRITERIA_CLS_NAME);
626 classMatchCriteriaSlot = kb.getSlot(CLASS_MATCH_CRITERIA_SLOT_NAME);
627 propogateTrivialMatchSlot = kb.getSlot(PROPOGATE_TRIVIAL_MATCH_SLOT_NAME);
628 slotMatcherSimpleSlotsSlot = kb.getSlot(SLOT_MATCHER_SIMPLE_SLOTS_SLOT_NAME);
629 slotMatcherSlotSlot = kb.getSlot(SLOT_MATCHER_SLOT_SLOT_NAME);
630 spanMatchCriteriaSlot = kb.getSlot(SPAN_MATCH_CRITERIA_SLOT_NAME);
631 simpleSlotMatchCriteriaCls = kb.getCls(SIMPLE_SLOT_MATCH_CRITERIA_CLS_NAME);
632 slotMatcherConfigCls = kb.getCls(SLOT_MATCHER_CONFIG_CLS_NAME);
633 slotMatchCriteriaSlot = kb.getSlot(SLOT_MATCH_CRITERIA_SLOT_NAME);
634
635 configurationCls = kb.getCls(CONFIGURATION_CLS_NAME);
636 activeFiltersSlot = kb.getSlot(ACTIVE_FILTERS_SLOT_NAME);
637 colorAssignmentsSlot = kb.getSlot(COLOR_ASSIGNMENTS_SLOT_NAME);
638 rootClsesSlot = kb.getSlot(ROOT_CLSES_SLOT_NAME);
639 selectedAnnotationSetSlot = kb.getSlot(SELECTED_ANNOTATION_SET_SLOT_NAME);
640 selectedAnnotatorSlot = kb.getSlot(SELECTED_ANNOTATOR_SLOT_NAME);
641 selectedFilterSlot = kb.getSlot(SELECTED_FILTER_SLOT_NAME);
642 tokenRegexSlot = kb.getSlot(TOKEN_REGEX_SLOT_NAME);
643 fadeUnselectedAnnotationsSlot = kb.getSlot(FADE_UNSELECTED_ANNOTATIONS);
644 subtextSlotSlot = kb.getSlot(SUBTEXT_SLOT_SLOT_NAME);
645 }
646
647 public Cls getAnnotationCls() {
648 return this.annotationCls;
649 }
650
651 public Slot getAnnotatedMentionSlot() {
652 return this.annotatedMentionSlot;
653 }
654
655 public Slot getAnnotationAnnotatorSlot() {
656 return this.annotationAnnotatorSlot;
657 }
658
659 public Slot getAnnotationCommentSlot() {
660 return this.annotationCommentSlot;
661 }
662
663 public Slot getAnnotationCreationDateSlot() {
664 return this.annotationCreationDateSlot;
665 }
666
667 public Slot getAnnotationSpanSlot() {
668 return this.annotationSpanSlot;
669 }
670
671 public Slot getAnnotationTextSlot() {
672 return this.annotationTextSlot;
673 }
674
675 public Slot getAnnotationTextSourceSlot() {
676 return this.annotationTextSourceSlot;
677 }
678
679 public Slot getSetSlot() {
680 return this.setSlot;
681 }
682
683 public Cls getMentionCls() {
684 return this.mentionCls;
685 }
686
687 public Slot getMentionAnnotationSlot() {
688 return this.mentionAnnotationSlot;
689 }
690
691 public Cls getClassMentionCls() {
692 return this.classMentionCls;
693 }
694
695 public Slot getMentionClassSlot() {
696 return this.mentionClassSlot;
697 }
698
699 public Slot getSlotMentionSlot() {
700 return this.slotMentionSlot;
701 }
702
703 public Cls getInstanceMentionCls() {
704 return this.instanceMentionCls;
705 }
706
707 public Slot getMentionInstanceSlot() {
708 return this.mentionInstanceSlot;
709 }
710
711 public Cls getSlotMentionCls() {
712 return this.slotMentionCls;
713 }
714
715 public Slot getMentionSlotSlot() {
716 return this.mentionSlotSlot;
717 }
718
719 public Slot getMentionSlotValueSlot() {
720 return this.mentionSlotValueSlot;
721 }
722
723 public Slot getMentionedInSlot() {
724 return this.mentionedInSlot;
725 }
726
727 public Cls getComplexSlotMentionCls() {
728 return this.complexSlotMentionCls;
729 }
730
731 public Cls getBooleanSlotMentionCls() {
732 return this.booleanSlotMentionCls;
733 }
734
735 public Cls getFloatSlotMentionCls() {
736 return this.floatSlotMentionCls;
737 }
738
739 public Cls getIntegerSlotMentionCls() {
740 return this.integerSlotMentionCls;
741 }
742
743 public Cls getStringSlotMentionCls() {
744 return this.stringSlotMentionCls;
745 }
746
747 public Cls getTextSourceCls() {
748 return this.textSourceCls;
749 }
750
751 public Cls getAnnotatorCls() {
752 return this.annotatorCls;
753 }
754
755 public Cls getHumanAnnotatorCls() {
756 return humanAnnotatorCls;
757 }
758
759 public Cls getTeamAnnotatorCls() {
760 return teamAnnotatorCls;
761 }
762
763 public Slot getAnnotatorTeamMembersSlot() {
764 return annotatorTeamMembersSlot;
765 }
766
767 public Slot getAnnotatorTeamNameSlot() {
768 return annotatorTeamNameSlot;
769 }
770
771 public Cls getDisplayColorCls() {
772 return this.displayColorCls;
773 }
774
775 public Slot getDisplayColorBSlot() {
776 return this.displayColorBSlot;
777 }
778
779 public Slot getDisplayColorGSlot() {
780 return this.displayColorGSlot;
781 }
782
783 public Slot getDisplayColorNameSlot() {
784 return this.displayColorNameSlot;
785 }
786
787 public Slot getDisplayColorRSlot() {
788 return this.displayColorRSlot;
789 }
790
791 public Cls getSetCls() {
792 return this.setCls;
793 }
794
795 public Slot getSetDescriptionSlot() {
796 return this.setDescriptionSlot;
797 }
798
799 public Slot getSetNameSlot() {
800 return this.setNameSlot;
801 }
802
803 public Cls getConsensusSetCls() {
804 return this.consensusSetCls;
805 }
806
807 public Slot getConsensusSetConsensusFilterSlot() {
808 return this.consensusSetConsensusFilterSlot;
809 }
810
811 public Slot getConsensusSetIndividualFilterSlot() {
812 return this.consensusSetIndividualFilterSlot;
813 }
814
815 public Slot getConsensusSetTeamAnnotatorSlot() {
816 return this.consensusSetTeamAnnotatorSlot;
817 }
818
819 public Cls getFilterCls() {
820 return this.filterCls;
821 }
822
823 public Slot getFilterAnnotatorSlot() {
824 return this.filterAnnotatorSlot;
825 }
826
827 public Slot getFilterNameSlot() {
828 return this.filterNameSlot;
829 }
830
831 public Slot getFilterSetSlot() {
832 return this.filterSetSlot;
833 }
834
835 public Slot getFilterTypeSlot() {
836 return this.filterTypeSlot;
837 }
838
839 public Cls getConsensusFilterCls() {
840 return this.consensusFilterCls;
841 }
842
843 public Cls getColorAssignmentCls() {
844 return this.colorAssignmentCls;
845 }
846
847 public Slot getColorClassSlot() {
848 return this.colorClassSlot;
849 }
850
851 public Slot getDisplayColorSlot() {
852 return this.displayColorSlot;
853 }
854
855 public Slot getClassMatchCriteriaSlot() {
856 return classMatchCriteriaSlot;
857 }
858
859 public Cls getComplexSlotMatchCriteriaCls() {
860 return complexSlotMatchCriteriaCls;
861 }
862
863 public Slot getPropogateTrivialMatchSlot() {
864 return propogateTrivialMatchSlot;
865 }
866
867 public Cls getSimpleSlotMatchCriteriaCls() {
868 return simpleSlotMatchCriteriaCls;
869 }
870
871 public Slot getSlotMatchCriteriaSlot() {
872 return slotMatchCriteriaSlot;
873 }
874
875 public Cls getSlotMatcherConfigCls() {
876 return slotMatcherConfigCls;
877 }
878
879 public Slot getSlotMatcherSimpleSlotsSlot() {
880 return slotMatcherSimpleSlotsSlot;
881 }
882
883 public Slot getSlotMatcherSlotSlot() {
884 return slotMatcherSlotSlot;
885 }
886
887 public Slot getSpanMatchCriteriaSlot() {
888 return spanMatchCriteriaSlot;
889 }
890
891 public Slot getActiveFiltersSlot() {
892 return activeFiltersSlot;
893 }
894
895 public Slot getAnnotatorAffiliationSlot() {
896 return annotatorAffiliationSlot;
897 }
898
899 public Slot getAnnotatorFirstNameSlot() {
900 return annotatorFirstNameSlot;
901 }
902
903 public Slot getAnnotatorIDSlot() {
904 return annotatorIDSlot;
905 }
906
907 public Slot getAnnotatorLastNameSlot() {
908 return annotatorLastNameSlot;
909 }
910
911 public Slot getColorAssignmentsSlot() {
912 return colorAssignmentsSlot;
913 }
914
915 public Cls getConfigurationCls() {
916 return configurationCls;
917 }
918
919 public Cls getKnowtatorSupportCls() {
920 return knowtatorSupportCls;
921 }
922
923 public Slot getRootClsesSlot() {
924 return rootClsesSlot;
925 }
926
927 public Slot getSelectedAnnotationSetSlot() {
928 return selectedAnnotationSetSlot;
929 }
930
931 public Slot getSelectedAnnotatorSlot() {
932 return selectedAnnotatorSlot;
933 }
934
935 public Cls getSelectedFiltersCls() {
936 return selectedFiltersCls;
937 }
938
939 public Slot getSelectedFilterSlot() {
940 return selectedFilterSlot;
941 }
942
943 public Slot getSelectedFiltersSlot() {
944 return selectedFiltersSlot;
945 }
946
947 public Slot getTokenRegexSlot() {
948 return tokenRegexSlot;
949 }
950
951 public Cls getTscImplementationsCls() {
952 return tscImplementationsCls;
953 }
954
955 public Slot getTscImplementationsSlot() {
956 return tscImplementationsSlot;
957 }
958
959 public Slot getFilterTypesNotSelectableFromTextViewerSlot() {
960 return filterTypesNotSelectableFromTextViewerSlot;
961 }
962
963 public Slot getFadeUnselectedAnnotationsSlot() {
964 return fadeUnselectedAnnotationsSlot;
965 }
966
967 public Slot getSubtextSlotSlot() {
968 return subtextSlotSlot;
969 }
970
971 }