1
|
/**
|
2
|
* Copyright (C) 2007 EDIT
|
3
|
* European Distributed Institute of Taxonomy
|
4
|
* http://www.e-taxonomy.eu
|
5
|
*
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
8
|
*/
|
9
|
|
10
|
package eu.etaxonomy.cdm.app.berlinModelImport;
|
11
|
|
12
|
import java.io.IOException;
|
13
|
import java.io.InputStream;
|
14
|
import java.io.InputStreamReader;
|
15
|
import java.io.Reader;
|
16
|
import java.util.Arrays;
|
17
|
import java.util.HashMap;
|
18
|
import java.util.HashSet;
|
19
|
import java.util.List;
|
20
|
import java.util.Map;
|
21
|
import java.util.Set;
|
22
|
import java.util.UUID;
|
23
|
import java.util.stream.Collectors;
|
24
|
|
25
|
import org.apache.log4j.Logger;
|
26
|
import org.springframework.security.core.GrantedAuthority;
|
27
|
import org.springframework.transaction.TransactionStatus;
|
28
|
|
29
|
import eu.etaxonomy.cdm.api.application.FirstDataInserter;
|
30
|
import eu.etaxonomy.cdm.api.application.ICdmRepository;
|
31
|
import eu.etaxonomy.cdm.api.service.IGroupService;
|
32
|
import eu.etaxonomy.cdm.api.service.description.AggregationMode;
|
33
|
import eu.etaxonomy.cdm.api.service.description.DistributionAggregation;
|
34
|
import eu.etaxonomy.cdm.api.service.description.DistributionAggregationConfiguration;
|
35
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
36
|
import eu.etaxonomy.cdm.app.common.CdmDestinations;
|
37
|
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
|
38
|
import eu.etaxonomy.cdm.database.DbSchemaValidation;
|
39
|
import eu.etaxonomy.cdm.database.ICdmDataSource;
|
40
|
import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
|
41
|
import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
|
42
|
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
|
43
|
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
|
44
|
import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
|
45
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
|
46
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
|
47
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
|
48
|
import eu.etaxonomy.cdm.io.common.Source;
|
49
|
import eu.etaxonomy.cdm.model.agent.Person;
|
50
|
import eu.etaxonomy.cdm.model.common.Language;
|
51
|
import eu.etaxonomy.cdm.model.description.Feature;
|
52
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
53
|
import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
|
54
|
import eu.etaxonomy.cdm.model.location.NamedAreaType;
|
55
|
import eu.etaxonomy.cdm.model.metadata.CdmPreference;
|
56
|
import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;
|
57
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
58
|
import eu.etaxonomy.cdm.model.name.Rank;
|
59
|
import eu.etaxonomy.cdm.model.permission.GrantedAuthorityImpl;
|
60
|
import eu.etaxonomy.cdm.model.permission.Group;
|
61
|
import eu.etaxonomy.cdm.model.permission.User;
|
62
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
63
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
64
|
import eu.etaxonomy.cdm.model.term.DefinedTermBase;
|
65
|
import eu.etaxonomy.cdm.model.term.Representation;
|
66
|
import eu.etaxonomy.cdm.model.term.TermTree;
|
67
|
import eu.etaxonomy.cdm.persistence.permission.Role;
|
68
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
69
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
70
|
|
71
|
|
72
|
/**
|
73
|
* TODO add the following to a wiki page:
|
74
|
* HINT: If you are about to import into a mysql data base running under windows and if you wish to
|
75
|
* dump and restore the resulting data bas under another operation systen
|
76
|
* you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.
|
77
|
*
|
78
|
* @author a.mueller
|
79
|
*/
|
80
|
public class EuroMedActivator {
|
81
|
private static final Logger logger = Logger.getLogger(EuroMedActivator.class);
|
82
|
|
83
|
//database validation status (create, update, validate ...)
|
84
|
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
85
|
// static final Source berlinModelSource = BerlinModelSources.euroMed_Pub2();
|
86
|
static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();
|
87
|
// static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3();
|
88
|
//
|
89
|
static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
|
90
|
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed();
|
91
|
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed2();
|
92
|
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_euroMed();
|
93
|
// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_euromed();
|
94
|
|
95
|
//check - import
|
96
|
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
|
97
|
|
98
|
static final boolean doUser = true;
|
99
|
// //authors
|
100
|
static final boolean doAuthors = true;
|
101
|
//references
|
102
|
static final DO_REFERENCES doReferences = DO_REFERENCES.ALL;
|
103
|
//names
|
104
|
static final boolean doTaxonNames = true;
|
105
|
static final boolean doRelNames = true;
|
106
|
static final boolean doNameStatus = true;
|
107
|
static final boolean doNameFacts = true;
|
108
|
|
109
|
//taxa
|
110
|
static final boolean doTaxa = true;
|
111
|
static final boolean doFacts = true;
|
112
|
static final boolean doRelTaxa = true;
|
113
|
static final boolean doOccurrences = true;
|
114
|
static final boolean doOccurrenceSources = true;
|
115
|
static final boolean doCommonNames = true;
|
116
|
|
117
|
static final boolean doNamedAreas = true;
|
118
|
|
119
|
//serious types do not exist in E+M except for name types which are handled in name relations
|
120
|
static final boolean doTypes = false; //serious types do not exist in E+M except for name types which are handled in name relations
|
121
|
|
122
|
|
123
|
static final boolean doRunTransmissionEngine = false; // (hbm2dll == DbSchemaValidation.VALIDATE);
|
124
|
|
125
|
//etc.
|
126
|
static final boolean doMarker = false; //no relevant markers exist
|
127
|
|
128
|
boolean invers = !(hbm2dll == DbSchemaValidation.CREATE);
|
129
|
|
130
|
boolean doPreliminaryRefDetailsWithNames = true;
|
131
|
|
132
|
boolean logNotMatchingOldNames = false;
|
133
|
boolean logMatchingNotExportedOldNames = false; //true
|
134
|
boolean checkOldNameIsSynonym = false;
|
135
|
boolean includeMANsForOldNameCheck = true;
|
136
|
|
137
|
static final boolean includePesiExport = false;
|
138
|
|
139
|
static final int sourceSecId = 7000000; //500000
|
140
|
static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");
|
141
|
static final boolean useSingleClassification = true;
|
142
|
static final String classificationName = "Euro+Med 2018";
|
143
|
static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");
|
144
|
static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};
|
145
|
|
146
|
// set to zero for unlimited nameFacts
|
147
|
static final int maximumNumberOfNameFacts = 0;
|
148
|
|
149
|
static final int partitionSize = 2500;
|
150
|
|
151
|
|
152
|
//editor - import
|
153
|
static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;
|
154
|
|
155
|
//NomenclaturalCode
|
156
|
static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;
|
157
|
|
158
|
//ignore null
|
159
|
static final boolean ignoreNull = false;
|
160
|
|
161
|
static final boolean switchSpeciesGroup = true;
|
162
|
|
163
|
static boolean useClassification = true;
|
164
|
|
165
|
static boolean isSplitTdwgCodes = false;
|
166
|
static boolean useEmAreaVocabulary = true;
|
167
|
|
168
|
private final boolean removeHttpMapsAnchor = true;
|
169
|
|
170
|
|
171
|
static final String infrGenericRankAbbrev = "[unranked]";
|
172
|
static final String infrSpecificRankAbbrev = "[unranked]";
|
173
|
|
174
|
static boolean useLastScrutinyAsSec = true;
|
175
|
static boolean warnForDifferingSynonymReference = false;
|
176
|
|
177
|
|
178
|
static String taxonTable = "v_cdm_exp_taxaAll";
|
179
|
static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId;
|
180
|
static String relPTaxonIdQuery = " SELECT r.RelPTaxonId "
|
181
|
+ " FROM RelPTaxon AS r "
|
182
|
+ " INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk "
|
183
|
+ " INNER JOIN PTaxon As pt1 ON pt1.PTNameFk = r.PTNameFk1 AND pt1.PTRefFk = r.PTRefFk1 "
|
184
|
+ " WHERE r.RelPTaxonID NOT IN (1874890,1874959,1874932,1874793,1874956,1874971,1874902,1874696) " //Relations to unpublished Kew genus taxa of Bethulaceae which are not imported anymore, but Bethalaceae is still imported
|
185
|
+ " AND NOT (pt1.PTRefFk = 8000000 AND pt1.publishFlag = 0) ";
|
186
|
static String nameIdTable = " v_cdm_exp_namesAll ";
|
187
|
static String referenceIdTable = " v_cdm_exp_refAll ";
|
188
|
static String refDetailFilter = " RefDetailID IN (SELECT RefDetailID FROM v_cdm_exp_RefDetail) ";
|
189
|
static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 13, 14, 249, 251))";
|
190
|
static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
|
191
|
static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";
|
192
|
static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";
|
193
|
static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";
|
194
|
static String authorTeamFilter = " authorTeamId IN (SELECT drvTab.authorTeamId FROM (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) as drvTab) ";
|
195
|
static String authorFilter = " authorId IN (SELECT drvTab.authorId FROM (SELECT authorId FROM v_cdm_exp_authorsAll) as drvTab) ";
|
196
|
|
197
|
|
198
|
|
199
|
// **************** ALL *********************
|
200
|
|
201
|
|
202
|
public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
|
203
|
System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");
|
204
|
//make BerlinModel Source
|
205
|
|
206
|
BerlinModelImportConfigurator config = BerlinModelImportConfigurator.NewInstance(source, destination);
|
207
|
|
208
|
config.setClassificationName(classificationName);
|
209
|
|
210
|
config.setClassificationUuid(classificationUuid);
|
211
|
config.setSourceSecId(sourceSecId);
|
212
|
config.setNomenclaturalCode(nomenclaturalCode);
|
213
|
config.setIgnoreNull(ignoreNull);
|
214
|
|
215
|
config.setDoAuthors(doAuthors ^ invers);
|
216
|
config.setDoReferences(invers ? doReferences.invers() : doReferences);
|
217
|
config.setDoTaxonNames(doTaxonNames ^ invers);
|
218
|
config.setDoRelNames(doRelNames ^ invers);
|
219
|
config.setDoNameStatus(doNameStatus ^ invers);
|
220
|
config.setDoTypes(doTypes); //always false
|
221
|
config.setDoNameFacts(doNameFacts ^ invers);
|
222
|
config.setDoTaxa(doTaxa ^ invers);
|
223
|
config.setDoRelTaxa(doRelTaxa ^ invers);
|
224
|
config.setDoFacts(doFacts ^ invers);
|
225
|
config.setDoOccurrence(doOccurrences ^ invers);
|
226
|
config.setDoOccurrenceSources(doOccurrenceSources ^ invers);
|
227
|
config.setDoCommonNames(doCommonNames ^ invers);
|
228
|
config.setDoNamedAreas(doNamedAreas ^ invers);
|
229
|
|
230
|
config.setDoMarker(doMarker);
|
231
|
config.setDoUser(doUser ^ invers);
|
232
|
|
233
|
config.setEuroMed(true);
|
234
|
config.setDoSourceNumber(true);
|
235
|
|
236
|
config.setLogNotMatchingOldNames(logNotMatchingOldNames);
|
237
|
config.setLogMatchingNotExportedOldNames(logMatchingNotExportedOldNames);
|
238
|
config.setCheckOldNameIsSynonym(checkOldNameIsSynonym);
|
239
|
config.setIncludeMANsForOldNameCheck(includeMANsForOldNameCheck);
|
240
|
|
241
|
config.setUseClassification(useClassification);
|
242
|
config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);
|
243
|
config.setEditor(editor);
|
244
|
config.setDbSchemaValidation(hbm2dll);
|
245
|
config.setUseLastScrutinyAsSec(useLastScrutinyAsSec);
|
246
|
config.setWarnForDifferingSynonymReference(warnForDifferingSynonymReference);
|
247
|
|
248
|
// maximum number of name facts to import
|
249
|
config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);
|
250
|
|
251
|
config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);
|
252
|
config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);
|
253
|
config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);
|
254
|
|
255
|
config.setDoPreliminaryRefDetailsWithNames(doPreliminaryRefDetailsWithNames);
|
256
|
|
257
|
// filter
|
258
|
config.setTaxonTable(taxonTable);
|
259
|
config.setClassificationQuery(classificationQuery);
|
260
|
config.setRelTaxaIdQuery(relPTaxonIdQuery);
|
261
|
config.setNameIdTable(nameIdTable);
|
262
|
config.setReferenceIdTable(referenceIdTable);
|
263
|
config.setAuthorTeamFilter(authorTeamFilter);
|
264
|
config.setAuthorFilter(authorFilter);
|
265
|
config.setFactFilter(factFilter);
|
266
|
config.setRefDetailFilter(refDetailFilter);
|
267
|
config.setCommonNameFilter(commonNameFilter);
|
268
|
config.setOccurrenceFilter(occurrenceFilter);
|
269
|
config.setOccurrenceSourceFilter(occurrenceSourceFilter);
|
270
|
config.setWebMarkerFilter(webMarkerFilter);
|
271
|
config.setUseSingleClassification(useSingleClassification);
|
272
|
|
273
|
//TDWG codes
|
274
|
config.setSplitTdwgCodes(isSplitTdwgCodes);
|
275
|
config.setUseEmAreaVocabulary(useEmAreaVocabulary);
|
276
|
|
277
|
config.setCheck(check);
|
278
|
config.setEditor(editor);
|
279
|
config.setRecordsPerTransaction(partitionSize);
|
280
|
|
281
|
config.setSwitchSpeciesGroup(switchSpeciesGroup);
|
282
|
|
283
|
// invoke import
|
284
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<>();
|
285
|
bmImport.invoke(config);
|
286
|
|
287
|
// renameRanks(config, bmImport);
|
288
|
|
289
|
createFeatureTree(config, bmImport);
|
290
|
|
291
|
changeCommonNameLabel(config, bmImport);
|
292
|
|
293
|
createUsersAndRoles(config, bmImport);
|
294
|
|
295
|
runTransmissionEngine(config, bmImport);
|
296
|
|
297
|
importShapefile(config, bmImport);
|
298
|
|
299
|
// createPreferences(config, bmImport); => manual
|
300
|
|
301
|
// markAreasAsHidden(config, bmImport); //has been moved to BM occurrence import
|
302
|
|
303
|
System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");
|
304
|
}
|
305
|
|
306
|
private void createPreferences(BerlinModelImportConfigurator config,
|
307
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
308
|
|
309
|
if (config.isDoUser() && (config.getCheck().isImport() )){
|
310
|
ICdmRepository app = bmImport.getCdmAppController();
|
311
|
|
312
|
//area vocs
|
313
|
CdmPreference preference = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, BerlinModelTransformer.uuidVocCaucasusAreas.toString()+";" + BerlinModelTransformer.uuidVocEuroMedAreas.toString());
|
314
|
preference.setAllowOverride(false);
|
315
|
app.getPreferenceService().set(preference);
|
316
|
|
317
|
//occ status list
|
318
|
String status ="42946bd6-9c22-45ad-a910-7427e8f60bfd;9eb99fe6-59e2-4445-8e6a-478365bd0fa9;c3ee7048-15b7-4be1-b687-9ce9c1a669d6;643cf9d1-a5f1-4622-9837-82ef961e880b;0c54761e-4887-4788-9dfa-7190c88746e3;83eb0aa0-1a45-495a-a3ca-bf6958b74366;aeec2947-2700-4623-8e32-9e3a430569d1;ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7;310373bf-7df4-4d02-8cb3-bcc7448805fc;5c397f7b-59ef-4c11-a33c-45691ceda91b;925662c1-bb10-459a-8c53-da5a738ac770;61cee840-801e-41d8-bead-015ad866c2f1;e191e89a-a751-4b0c-b883-7f1de70915c9";
|
319
|
CdmPreference statusListPref = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, status);
|
320
|
statusListPref.setAllowOverride(false);
|
321
|
app.getPreferenceService().set(statusListPref);
|
322
|
|
323
|
//distr. editor activated
|
324
|
CdmPreference distrEditorActive = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DistributionEditorActivated, "true");
|
325
|
statusListPref.setAllowOverride(true);
|
326
|
app.getPreferenceService().set(distrEditorActive);
|
327
|
|
328
|
// //idInVoc for areas
|
329
|
// CdmPreference distrEditorShowIdInVocForAreas = CdmPreference.NewTaxEditorInstance(PreferencePredicate.Sho.ShowIdInVocabulary, "true");
|
330
|
// distrEditorShowIdInVocForAreas.setAllowOverride(true);
|
331
|
// app.getPreferenceService().set(distrEditorShowIdInVocForAreas);
|
332
|
//
|
333
|
// //areas sort order
|
334
|
// //?? correct?
|
335
|
// CdmPreference distrEditorSorted = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AreasSortedByIdInVocabulary, "true");
|
336
|
// distrEditorSorted.setAllowOverride(true);
|
337
|
// app.getPreferenceService().set(distrEditorSorted);
|
338
|
//
|
339
|
// //distr. status uses symbol
|
340
|
// //?? correct?
|
341
|
// CdmPreference distrEditorStatusUseSymbols = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSymbolForStatus, "false");
|
342
|
// distrEditorStatusUseSymbols.setAllowOverride(true);
|
343
|
// app.getPreferenceService().set(distrEditorStatusUseSymbols);
|
344
|
|
345
|
//media view
|
346
|
CdmPreference showMediaView = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowMediaView, "false");
|
347
|
showMediaView.setAllowOverride(false);
|
348
|
app.getPreferenceService().set(showMediaView);
|
349
|
|
350
|
//multi classification
|
351
|
CdmPreference multiClassification = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DisableMultiClassification, "true");
|
352
|
multiClassification.setAllowOverride(false);
|
353
|
app.getPreferenceService().set(multiClassification);
|
354
|
|
355
|
//taxon node wizard
|
356
|
CdmPreference showTaxonNodeWizard = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowTaxonNodeWizard, "false");
|
357
|
showTaxonNodeWizard.setAllowOverride(false);
|
358
|
app.getPreferenceService().set(showTaxonNodeWizard);
|
359
|
|
360
|
//import+export
|
361
|
CdmPreference showImportExportMenu = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowImportExportMenu, "false");
|
362
|
showImportExportMenu.setAllowOverride(true);
|
363
|
app.getPreferenceService().set(showImportExportMenu);
|
364
|
|
365
|
//show specimen
|
366
|
CdmPreference showSpecimen = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSpecimen, "false");
|
367
|
showSpecimen.setAllowOverride(false);
|
368
|
app.getPreferenceService().set(showSpecimen);
|
369
|
|
370
|
}
|
371
|
|
372
|
}
|
373
|
|
374
|
//Rename Ranks (still needed?)
|
375
|
private void renameRanks(BerlinModelImportConfigurator config,
|
376
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
377
|
|
378
|
if (config.isDoTaxonNames() && (config.getCheck().isImport() ) ){
|
379
|
ICdmRepository app = bmImport.getCdmAppController();
|
380
|
TransactionStatus tx = app.startTransaction();
|
381
|
try {
|
382
|
Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
|
383
|
Representation repr = sectBot.getRepresentation(Language.ENGLISH());
|
384
|
repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
|
385
|
repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
|
386
|
sectBot.setTitleCache(null, false); //to definitely update the titleCache also
|
387
|
app.getTermService().saveOrUpdate(sectBot);
|
388
|
|
389
|
Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());
|
390
|
repr = subSectBot.getRepresentation(Language.ENGLISH());
|
391
|
repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());
|
392
|
repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());
|
393
|
subSectBot.setTitleCache(null, false); //to definitely update the titleCache also
|
394
|
app.getTermService().saveOrUpdate(subSectBot);
|
395
|
app.commitTransaction(tx);
|
396
|
} catch (Exception e) {
|
397
|
e.printStackTrace();
|
398
|
logger.error("Exception in renameRanks: " + e.getMessage());
|
399
|
}
|
400
|
}
|
401
|
}
|
402
|
|
403
|
//create feature tree
|
404
|
private void createFeatureTree(BerlinModelImportConfigurator config,
|
405
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport){
|
406
|
if (config.isDoFacts() && (config.getCheck().isImport() ) ){
|
407
|
try {
|
408
|
ICdmRepository app = bmImport.getCdmAppController();
|
409
|
TransactionStatus tx = app.startTransaction();
|
410
|
|
411
|
//make feature tree
|
412
|
TermTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, config.getFeatureMap(), featureKeyList);
|
413
|
tree.setTitleCache("Euro+Med Feature Tree", true);
|
414
|
tree.getRoot().addChild(Feature.IMAGE());
|
415
|
tree.getRoot().addChild(Feature.DISTRIBUTION(), 1);
|
416
|
tree.getRoot().addChild(Feature.COMMON_NAME(), 2);
|
417
|
app.getFeatureTreeService().saveOrUpdate(tree);
|
418
|
|
419
|
app.commitTransaction(tx);
|
420
|
} catch (Exception e) {
|
421
|
e.printStackTrace();
|
422
|
logger.error("Exception in createFeatureTree: " + e.getMessage());
|
423
|
}
|
424
|
}
|
425
|
}
|
426
|
|
427
|
//Change common name label
|
428
|
private void changeCommonNameLabel(BerlinModelImportConfigurator config,
|
429
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
430
|
if (config.isDoFacts() && (config.getCheck().isImport() ) ){
|
431
|
try {
|
432
|
ICdmRepository app = bmImport.getCdmAppController();
|
433
|
TransactionStatus tx = app.startTransaction();
|
434
|
|
435
|
DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());
|
436
|
commonNameFeature.setLabel("Common Names", Language.ENGLISH());
|
437
|
commonNameFeature.setTitleCache(null, false); //to definitely update the titleCache also
|
438
|
app.getTermService().saveOrUpdate(commonNameFeature);
|
439
|
|
440
|
app.commitTransaction(tx);
|
441
|
} catch (Exception e) {
|
442
|
e.printStackTrace();
|
443
|
logger.error("Exception in changeCommonNameLabel: " + e.getMessage());
|
444
|
}
|
445
|
}
|
446
|
}
|
447
|
|
448
|
//1. run transmission engine #3979
|
449
|
private void runTransmissionEngine(BerlinModelImportConfigurator config,
|
450
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
451
|
|
452
|
if (doRunTransmissionEngine && (config.getCheck().isImport() ) ){
|
453
|
try {
|
454
|
ICdmRepository app = bmImport.getCdmAppController();
|
455
|
|
456
|
final List<String> term_init_strategy = Arrays.asList(new String []{
|
457
|
"representations"
|
458
|
});
|
459
|
|
460
|
UUID uuidSuperAreaLevel = BerlinModelTransformer.uuidEuroMedAreaLevelFirst;
|
461
|
NamedAreaLevel euroMedLevel1 = (NamedAreaLevel)app.getTermService().find(uuidSuperAreaLevel);
|
462
|
|
463
|
Pager<NamedArea> areaPager = app.getTermService().list(
|
464
|
euroMedLevel1,
|
465
|
(NamedAreaType) null,
|
466
|
null,
|
467
|
null,
|
468
|
(List<OrderHint>) null,
|
469
|
term_init_strategy);
|
470
|
DistributionAggregation distributionAggregation = new DistributionAggregation();
|
471
|
|
472
|
Set<UUID> classificationUuids = new HashSet<>();
|
473
|
TaxonNodeFilter filter = TaxonNodeFilter.NewInstance(classificationUuids, null, null, null, null,
|
474
|
null, Rank.uuidGenus);
|
475
|
|
476
|
DistributionAggregationConfiguration aggregationConfig = DistributionAggregationConfiguration
|
477
|
.NewInstance(
|
478
|
AggregationMode.byAreasAndRanks(),
|
479
|
areaPager.getRecords().stream().map(area->area.getUuid()).collect(Collectors.toList()),
|
480
|
filter,
|
481
|
DefaultProgressMonitor.NewInstance());
|
482
|
distributionAggregation.invoke(aggregationConfig, app);
|
483
|
} catch (Exception e) {
|
484
|
e.printStackTrace();
|
485
|
logger.error("Exception in markAreasAsHidden: " + e.getMessage());
|
486
|
}
|
487
|
}
|
488
|
}
|
489
|
|
490
|
// //5.Mark areas to be hidden #3979 .5
|
491
|
// private void markAreasAsHidden(BerlinModelImportConfigurator config,
|
492
|
// CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
493
|
//
|
494
|
// if (config.isDoOccurrence() && (config.getCheck().isImport())){
|
495
|
// try {
|
496
|
// ICdmRepository app = bmImport.getCdmAppController();
|
497
|
// TransactionStatus tx = app.startTransaction();
|
498
|
//
|
499
|
// MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);
|
500
|
// hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);
|
501
|
// @SuppressWarnings("unchecked")
|
502
|
// TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);
|
503
|
// if (vocUserDefinedMarkerTypes == null){
|
504
|
// String message = "Marker type vocabulary could not be found. Hidden areas not added.";
|
505
|
// logger.error(message);
|
506
|
// System.out.println(message);
|
507
|
// }else{
|
508
|
// vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);
|
509
|
// app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);
|
510
|
//
|
511
|
// //Add hidden area marker to Rs(C) and Rs(N)
|
512
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);
|
513
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);
|
514
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);
|
515
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);
|
516
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);
|
517
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);
|
518
|
// hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);
|
519
|
// }
|
520
|
// app.commitTransaction(tx);
|
521
|
// } catch (Exception e) {
|
522
|
// e.printStackTrace();
|
523
|
// logger.error("Exception in markAreasAsHidden: " + e.getMessage());
|
524
|
// }
|
525
|
// }
|
526
|
// }
|
527
|
//
|
528
|
// private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {
|
529
|
// NamedArea area = (NamedArea)app.getTermService().find(areaUuid);
|
530
|
// area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));
|
531
|
// app.getTermService().saveOrUpdate(area);
|
532
|
// }
|
533
|
|
534
|
//2. import shapefile attributes #3979 .2
|
535
|
private void importShapefile(BerlinModelImportConfigurator config,
|
536
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
537
|
|
538
|
if (config.isDoOccurrence() && (config.getCheck().isImport())){
|
539
|
|
540
|
try {
|
541
|
UUID areaVocabularyUuid = BerlinModelTransformer.uuidVocEuroMedAreas;
|
542
|
List<String> idSearchFields = Arrays.asList(new String[]{"EMAREA","PARENT"});
|
543
|
String wmsLayerName = "euromed_2013";
|
544
|
Set<UUID> areaUuidSet = null;
|
545
|
|
546
|
ICdmRepository app = bmImport.getCdmAppController();
|
547
|
IEditGeoService geoService = (IEditGeoService)app.getBean("editGeoService");
|
548
|
|
549
|
Map<NamedArea, String> resultMap;
|
550
|
try {
|
551
|
InputStream in = EuroMedActivator.class.getResourceAsStream("/euromed/euromed_2013.csv");
|
552
|
Reader reader = new InputStreamReader(in, "UTF-8");
|
553
|
|
554
|
resultMap = geoService.mapShapeFileToNamedAreas(
|
555
|
reader, idSearchFields , wmsLayerName , areaVocabularyUuid, areaUuidSet);
|
556
|
Map<String, String> flatResultMap = new HashMap<>(resultMap.size());
|
557
|
for(NamedArea area : resultMap.keySet()){
|
558
|
flatResultMap.put(area.getTitleCache() + " [" + area.getUuid() + "]", resultMap.get(area));
|
559
|
}
|
560
|
} catch (IOException e) {
|
561
|
String message = "IOException when reading from mapping file or creating result map.";
|
562
|
logger.error(message);
|
563
|
System.out.println(message);
|
564
|
}
|
565
|
} catch (Exception e) {
|
566
|
e.printStackTrace();
|
567
|
logger.error("Exception in importShapefile: " + e.getMessage());
|
568
|
}
|
569
|
}
|
570
|
}
|
571
|
|
572
|
//4. Create users and assign roles #3979
|
573
|
private void createUsersAndRoles(BerlinModelImportConfigurator config,
|
574
|
CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {
|
575
|
|
576
|
try {
|
577
|
if (config.isDoRelTaxa() && (config.getCheck().isImport())){
|
578
|
ICdmRepository app = bmImport.getCdmAppController();
|
579
|
TransactionStatus tx = app.startTransaction();
|
580
|
|
581
|
//eraabstraube
|
582
|
String eraabstraube = "e.raabstraube";
|
583
|
List<User> users = app.getUserService().listByUsername(eraabstraube, MatchMode.EXACT, null, null, null, null, null);
|
584
|
User userEraabStraube;
|
585
|
if (users.isEmpty()){
|
586
|
userEraabStraube = User.NewInstance(eraabstraube, eraabstraube);
|
587
|
}else{
|
588
|
userEraabStraube = users.get(0);
|
589
|
}
|
590
|
if (userEraabStraube.getPerson() == null){
|
591
|
Person eckhard = Person.NewInstance();
|
592
|
eckhard.setFamilyName("von Raab-Straube");
|
593
|
eckhard.setGivenName("Eckhard");
|
594
|
eckhard.setPrefix("Dr.");
|
595
|
userEraabStraube.setPerson(eckhard);
|
596
|
}
|
597
|
app.getUserService().saveOrUpdate(userEraabStraube);
|
598
|
|
599
|
//groups
|
600
|
Group groupEditor = app.getGroupService().load(Group.GROUP_EDITOR_UUID);
|
601
|
groupEditor.addMember(userEraabStraube);
|
602
|
app.getGroupService().saveOrUpdate(groupEditor);
|
603
|
|
604
|
Group groupProjectManager = app.getGroupService().load(Group.GROUP_PROJECT_MANAGER_UUID);
|
605
|
groupProjectManager.addMember(userEraabStraube);
|
606
|
app.getGroupService().saveOrUpdate(groupProjectManager);
|
607
|
|
608
|
String[] publishRoles = new String[]{Role.ROLE_PUBLISH.toString()};
|
609
|
Group groupPublisher = checkGroup(app.getGroupService(), Group.GROUP_PUBLISHER_UUID, "Publisher", publishRoles);
|
610
|
groupPublisher.addMember(userEraabStraube);
|
611
|
app.getGroupService().saveOrUpdate(groupPublisher);
|
612
|
|
613
|
UUID uuidEuroMedPlantBaseGroup = UUID.fromString("91be42ea-ad04-4458-9836-389277e773db");
|
614
|
String[] emPlantBaseRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]"};
|
615
|
Group euroMedPlantbase = checkGroup(app.getGroupService(), uuidEuroMedPlantBaseGroup, "Euro+Med Plantbase", emPlantBaseRoles);
|
616
|
euroMedPlantbase.addMember(userEraabStraube);
|
617
|
app.getGroupService().saveOrUpdate(euroMedPlantbase);
|
618
|
|
619
|
//cichorieae-editor
|
620
|
String cichorieaeEditor = "cichorieae-editor";
|
621
|
app.getUserService().listByUsername(cichorieaeEditor, MatchMode.EXACT, null, null, null, null, null);
|
622
|
User userCichEditor;
|
623
|
if (users.isEmpty()){
|
624
|
userCichEditor = User.NewInstance(cichorieaeEditor, cichorieaeEditor);
|
625
|
}else{
|
626
|
userCichEditor = users.get(0);
|
627
|
}
|
628
|
app.getUserService().saveOrUpdate(userCichEditor);
|
629
|
|
630
|
//groups
|
631
|
groupEditor.addMember(userCichEditor);
|
632
|
app.getGroupService().saveOrUpdate(groupEditor);
|
633
|
|
634
|
UUID uuidCichorieaeSubtree = null;
|
635
|
UUID uuidCichorieae = UUID.fromString("63c7dbeb-b9a2-48b8-a75f-e3fe5e161f7c");
|
636
|
Taxon cich = (Taxon)app.getTaxonService().find(uuidCichorieae);
|
637
|
if (cich != null){
|
638
|
if (!cich.getTaxonNodes().isEmpty()){
|
639
|
TaxonNode cichNode = cich.getTaxonNodes().iterator().next();
|
640
|
uuidCichorieaeSubtree = cichNode.getUuid();
|
641
|
}
|
642
|
}
|
643
|
|
644
|
String[] cichorieaeRoles = new String[]{};
|
645
|
if (uuidCichorieaeSubtree != null){
|
646
|
cichorieaeRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]{"+uuidCichorieaeSubtree.toString()+"}"};
|
647
|
}else{
|
648
|
String message = "Cichorieae node could not be found for cichorieae-editor role";
|
649
|
logger.warn(message);
|
650
|
System.out.println(message);
|
651
|
}
|
652
|
UUID uuidCichorieaeGroup = UUID.fromString("a630938d-dd4f-48c2-9406-91def487b11e");
|
653
|
String cichorieaeGroupName = "Cichorieae";
|
654
|
Group cichorieaeGroup = checkGroup(app.getGroupService(), uuidCichorieaeGroup, cichorieaeGroupName, cichorieaeRoles);
|
655
|
cichorieaeGroup.addMember(userCichEditor);
|
656
|
app.getGroupService().saveOrUpdate(cichorieaeGroup);
|
657
|
|
658
|
app.commitTransaction(tx);
|
659
|
}
|
660
|
} catch (Exception e) {
|
661
|
e.printStackTrace();
|
662
|
logger.error("Exception in createUsersAndRoles: " + e.getMessage());
|
663
|
}
|
664
|
}
|
665
|
|
666
|
/**
|
667
|
* copied from {@link FirstDataInserter#checkGroup}
|
668
|
*/
|
669
|
private Group checkGroup(IGroupService groupService, UUID groupUuid, String groupName, String[] requiredAuthorities) {
|
670
|
Group group = groupService.load(groupUuid);
|
671
|
if(group == null){
|
672
|
group = Group.NewInstance();
|
673
|
group.setUuid(groupUuid);
|
674
|
logger.info("New Group '" + groupName + "' created");
|
675
|
}
|
676
|
group.setName(groupName); // force name
|
677
|
|
678
|
Set<GrantedAuthority> grantedAuthorities = group.getGrantedAuthorities();
|
679
|
|
680
|
for(String a : requiredAuthorities){
|
681
|
boolean isMissing = true;
|
682
|
for(GrantedAuthority ga : grantedAuthorities){
|
683
|
if(a.equals(ga.getAuthority())){
|
684
|
isMissing = false;
|
685
|
break;
|
686
|
}
|
687
|
}
|
688
|
if(isMissing){
|
689
|
GrantedAuthorityImpl newGa = GrantedAuthorityImpl.NewInstance(a);
|
690
|
group.addGrantedAuthority(newGa);
|
691
|
logger.info("New GrantedAuthority '" + a + "' added to '" + groupName + "'");
|
692
|
}
|
693
|
}
|
694
|
groupService.saveOrUpdate(group);
|
695
|
logger.info("Check of group '" + groupName + "' done");
|
696
|
return group;
|
697
|
}
|
698
|
|
699
|
|
700
|
/**
|
701
|
* @param args
|
702
|
*/
|
703
|
public static void main(String[] args) {
|
704
|
EuroMedActivator importActivator = new EuroMedActivator();
|
705
|
Source source = berlinModelSource;
|
706
|
ICdmDataSource cdmRepository = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
|
707
|
|
708
|
importActivator.importEm2CDM(source, cdmRepository, hbm2dll);
|
709
|
System.exit(0);
|
710
|
}
|
711
|
|
712
|
}
|