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.io.berlinModel.in;
|
11
|
|
12
|
import java.sql.ResultSet;
|
13
|
import java.sql.SQLException;
|
14
|
import java.sql.Timestamp;
|
15
|
import java.util.Map;
|
16
|
|
17
|
import org.apache.log4j.Logger;
|
18
|
import org.joda.time.DateTime;
|
19
|
|
20
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
21
|
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
|
22
|
import eu.etaxonomy.cdm.io.common.DbImportBase;
|
23
|
import eu.etaxonomy.cdm.io.common.ICdmIO;
|
24
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
|
25
|
import eu.etaxonomy.cdm.io.common.IPartitionedIO;
|
26
|
import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;
|
27
|
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
|
28
|
import eu.etaxonomy.cdm.model.common.Annotation;
|
29
|
import eu.etaxonomy.cdm.model.common.AnnotationType;
|
30
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
31
|
import eu.etaxonomy.cdm.model.common.Language;
|
32
|
import eu.etaxonomy.cdm.model.common.User;
|
33
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
34
|
import eu.etaxonomy.cdm.model.location.Country;
|
35
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
36
|
import eu.etaxonomy.cdm.model.location.NamedAreaType;
|
37
|
import eu.etaxonomy.cdm.model.name.BotanicalName;
|
38
|
import eu.etaxonomy.cdm.model.name.Rank;
|
39
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
40
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
41
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
42
|
|
43
|
/**
|
44
|
* @author a.mueller
|
45
|
* @created 20.03.2008
|
46
|
* @version 1.0
|
47
|
*/
|
48
|
public abstract class BerlinModelImportBase extends DbImportBase<BerlinModelImportState, BerlinModelImportConfigurator> implements ICdmIO<BerlinModelImportState>, IPartitionedIO<BerlinModelImportState> {
|
49
|
private static final Logger logger = Logger.getLogger(BerlinModelImportBase.class);
|
50
|
|
51
|
public BerlinModelImportBase(String tableName, String pluralString ) {
|
52
|
super(tableName, pluralString);
|
53
|
}
|
54
|
|
55
|
|
56
|
/**
|
57
|
* @return
|
58
|
*/
|
59
|
protected String getIdQuery(BerlinModelImportState state){
|
60
|
String result = " SELECT " + getTableName() + "id FROM " + getTableName();
|
61
|
return result;
|
62
|
}
|
63
|
|
64
|
|
65
|
protected boolean doIdCreatedUpdatedNotes(BerlinModelImportState state, DescriptionElementBase descriptionElement, ResultSet rs, String id, String namespace) throws SQLException{
|
66
|
boolean success = true;
|
67
|
//id
|
68
|
success &= doId(state, descriptionElement, id, namespace);
|
69
|
//createdUpdateNotes
|
70
|
success &= doCreatedUpdatedNotes(state, descriptionElement, rs);
|
71
|
return success;
|
72
|
}
|
73
|
|
74
|
protected boolean doIdCreatedUpdatedNotes(BerlinModelImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace, boolean excludeUpdated, boolean excludeNotes)
|
75
|
throws SQLException{
|
76
|
boolean success = true;
|
77
|
//id
|
78
|
success &= doId(state, identifiableEntity, id, namespace);
|
79
|
//createdUpdateNotes
|
80
|
success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, excludeUpdated, excludeNotes);
|
81
|
return success;
|
82
|
}
|
83
|
|
84
|
|
85
|
protected boolean doIdCreatedUpdatedNotes(BerlinModelImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace)
|
86
|
throws SQLException{
|
87
|
boolean excludeUpdated = false;
|
88
|
return doIdCreatedUpdatedNotes(state, identifiableEntity, rs, id, namespace, excludeUpdated, false);
|
89
|
}
|
90
|
|
91
|
protected boolean doCreatedUpdatedNotes(BerlinModelImportState state, AnnotatableEntity annotatableEntity, ResultSet rs)
|
92
|
throws SQLException{
|
93
|
boolean excludeUpdated = false;
|
94
|
return doCreatedUpdatedNotes(state, annotatableEntity, rs, excludeUpdated, false);
|
95
|
}
|
96
|
|
97
|
protected boolean doCreatedUpdatedNotes(BerlinModelImportState state, AnnotatableEntity annotatableEntity, ResultSet rs, boolean excludeUpdated, boolean excludeNotes)
|
98
|
throws SQLException{
|
99
|
|
100
|
BerlinModelImportConfigurator config = state.getConfig();
|
101
|
Object createdWhen = rs.getObject("Created_When");
|
102
|
String createdWho = rs.getString("Created_Who");
|
103
|
createdWho = handleHieraciumPilosella(createdWho);
|
104
|
Object updatedWhen = null;
|
105
|
String updatedWho = null;
|
106
|
if (excludeUpdated == false){
|
107
|
try {
|
108
|
updatedWhen = rs.getObject("Updated_When");
|
109
|
updatedWho = rs.getString("Updated_who");
|
110
|
} catch (SQLException e) {
|
111
|
//Table "Name" has no updated when/who
|
112
|
}
|
113
|
}
|
114
|
String notes = rs.getString("notes");
|
115
|
|
116
|
boolean success = true;
|
117
|
|
118
|
//Created When, Who, Updated When Who
|
119
|
if (config.getEditor() == null || config.getEditor().equals(EDITOR.NO_EDITORS)){
|
120
|
//do nothing
|
121
|
}else if (config.getEditor().equals(EDITOR.EDITOR_AS_ANNOTATION)){
|
122
|
String createdAnnotationString = "Berlin Model record was created By: " + String.valueOf(createdWho) + " (" + String.valueOf(createdWhen) + ") ";
|
123
|
if (updatedWhen != null && updatedWho != null){
|
124
|
createdAnnotationString += " and updated By: " + String.valueOf(updatedWho) + " (" + String.valueOf(updatedWhen) + ")";
|
125
|
}
|
126
|
Annotation annotation = Annotation.NewInstance(createdAnnotationString, Language.DEFAULT());
|
127
|
annotation.setCommentator(config.getCommentator());
|
128
|
annotation.setAnnotationType(AnnotationType.TECHNICAL());
|
129
|
annotatableEntity.addAnnotation(annotation);
|
130
|
}else if (config.getEditor().equals(EDITOR.EDITOR_AS_EDITOR)){
|
131
|
User creator = getUser(state, createdWho);
|
132
|
User updator = getUser(state, updatedWho);
|
133
|
DateTime created = getDateTime(createdWhen);
|
134
|
DateTime updated = getDateTime(updatedWhen);
|
135
|
annotatableEntity.setCreatedBy(creator);
|
136
|
annotatableEntity.setUpdatedBy(updator);
|
137
|
annotatableEntity.setCreated(created);
|
138
|
annotatableEntity.setUpdated(updated);
|
139
|
}else {
|
140
|
logger.warn("Editor type not yet implemented: " + config.getEditor());
|
141
|
}
|
142
|
|
143
|
|
144
|
//notes
|
145
|
if (! excludeNotes){
|
146
|
doNotes(annotatableEntity, notes);
|
147
|
}
|
148
|
return success;
|
149
|
}
|
150
|
|
151
|
/**
|
152
|
* Special usecase for EDITWP6 import where in the createdWho field the original ID is stored
|
153
|
* @param createdWho
|
154
|
* @return
|
155
|
*/
|
156
|
private String handleHieraciumPilosella(String createdWho) {
|
157
|
String result = createdWho;
|
158
|
if (result == null){
|
159
|
return null;
|
160
|
}else if (result.startsWith("Hieracium_Pilosella import from EM")){
|
161
|
return "Hieracium_Pilosella import from EM";
|
162
|
}else{
|
163
|
return result;
|
164
|
}
|
165
|
}
|
166
|
|
167
|
private DateTime getDateTime(Object timeString){
|
168
|
if (timeString == null){
|
169
|
return null;
|
170
|
}
|
171
|
DateTime dateTime = null;
|
172
|
if (timeString instanceof Timestamp){
|
173
|
Timestamp timestamp = (Timestamp)timeString;
|
174
|
dateTime = new DateTime(timestamp);
|
175
|
}else{
|
176
|
logger.warn("time ("+timeString+") is not a timestamp. Datetime set to current date. ");
|
177
|
dateTime = new DateTime();
|
178
|
}
|
179
|
return dateTime;
|
180
|
}
|
181
|
|
182
|
/**
|
183
|
* @param state
|
184
|
* @param newTaxonId
|
185
|
* @param taxonMap
|
186
|
* @param factId
|
187
|
* @return
|
188
|
*/
|
189
|
protected Taxon getTaxon(BerlinModelImportState state, int taxonId, Map<String, TaxonBase> taxonMap, int factId) {
|
190
|
TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId));
|
191
|
|
192
|
//TODO for testing
|
193
|
if (taxonBase == null && ! state.getConfig().isDoTaxa()){
|
194
|
taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);
|
195
|
}
|
196
|
|
197
|
Taxon taxon;
|
198
|
if ( taxonBase instanceof Taxon ) {
|
199
|
taxon = (Taxon) taxonBase;
|
200
|
} else if (taxonBase != null) {
|
201
|
logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
|
202
|
return null;
|
203
|
} else {
|
204
|
logger.warn("TaxonBase (" + taxonId + ") for Fact(Specimen) with factId " + factId + " is null.");
|
205
|
return null;
|
206
|
}
|
207
|
return taxon;
|
208
|
}
|
209
|
|
210
|
|
211
|
/**
|
212
|
* Searches first in the detail maps then in the ref maps for a reference.
|
213
|
* Returns the reference as soon as it finds it in one of the map, according
|
214
|
* to the order of the map.
|
215
|
* If nomRefDetailFk is <code>null</code> no search on detail maps is performed.
|
216
|
* If one of the maps is <code>null</code> no search on the according map is
|
217
|
* performed. <BR>
|
218
|
* You may define the order of search by the order you pass the maps but
|
219
|
* make sure to always pass the detail maps first.
|
220
|
* @param firstDetailMap
|
221
|
* @param secondDetailMap
|
222
|
* @param firstRefMap
|
223
|
* @param secondRefMap
|
224
|
* @param nomRefDetailFk
|
225
|
* @param nomRefFk
|
226
|
* @return
|
227
|
*/
|
228
|
protected Reference<?> getReferenceFromMaps(
|
229
|
Map<String, Reference> detailMap,
|
230
|
Map<String, Reference> refMap,
|
231
|
String nomRefDetailFk,
|
232
|
String nomRefFk) {
|
233
|
Reference<?> ref = null;
|
234
|
if (detailMap != null){
|
235
|
ref = detailMap.get(nomRefDetailFk);
|
236
|
}
|
237
|
if (ref == null){
|
238
|
ref = refMap.get(nomRefFk);
|
239
|
}
|
240
|
return ref;
|
241
|
}
|
242
|
|
243
|
|
244
|
/**
|
245
|
* Searches for a reference in the first detail map. If it does not exist it
|
246
|
* searches in the second detail map. Returns null if it does not exist in any map.
|
247
|
* A map may be <code>null</code> to avoid search on this map.
|
248
|
* @param secondDetailMap
|
249
|
* @param firstDetailMap
|
250
|
* @param nomRefDetailFk
|
251
|
* @return
|
252
|
*/
|
253
|
private Reference getReferenceDetailFromMaps(Map<String, Reference> firstDetailMap, Map<String, Reference> secondDetailMap, String nomRefDetailFk) {
|
254
|
Reference<?> result = null;
|
255
|
if (nomRefDetailFk != null){
|
256
|
//get ref
|
257
|
if (firstDetailMap != null){
|
258
|
result = firstDetailMap.get(nomRefDetailFk);
|
259
|
}
|
260
|
if (result == null && secondDetailMap != null){
|
261
|
result = secondDetailMap.get(nomRefDetailFk);
|
262
|
}
|
263
|
}
|
264
|
return result;
|
265
|
}
|
266
|
|
267
|
protected NamedArea getOtherAreas(BerlinModelImportState state, String emCodeString, String tdwgCodeString) {
|
268
|
String em = CdmUtils.Nz(emCodeString).trim();
|
269
|
String tdwg = CdmUtils.Nz(tdwgCodeString).trim();
|
270
|
//Cichorieae + E+M
|
271
|
if ("EM".equals(em)){
|
272
|
return getNamedArea(state, BerlinModelTransformer.euroMedUuid, "Euro+Med", "Euro+Med area", "EM", null, null);
|
273
|
}else if("Rf".equals(em)){
|
274
|
return Country.RUSSIANFEDERATION();
|
275
|
|
276
|
}else if("KRY-OO;UKR-UK".equals(tdwg)){
|
277
|
return Country.UKRAINE();
|
278
|
|
279
|
}else if("TCS-AZ;TCS-NA".equals(tdwg)){
|
280
|
return Country.AZERBAIJANREPUBLICOF();
|
281
|
}else if("TCS-AB;TCS-AD;TCS-GR".equals(tdwg)){
|
282
|
return Country.GEORGIA();
|
283
|
|
284
|
|
285
|
}else if("Cc".equals(em)){
|
286
|
return getNamedArea(state, BerlinModelTransformer.uuidCaucasia, "Caucasia (Ab + Ar + Gg + Rf(CS))", "Euro+Med area 'Caucasia (Ab + Ar + Gg + Rf(CS))'", "Cc", null, null);
|
287
|
}
|
288
|
|
289
|
//E+M
|
290
|
else if("EUR".equals(em)){
|
291
|
return TdwgAreaProvider.getAreaByTdwgAbbreviation("1");
|
292
|
}else if("14".equals(em)){
|
293
|
return TdwgAreaProvider.getAreaByTdwgAbbreviation("14");
|
294
|
}else if("21".equals(em)){
|
295
|
return TdwgAreaProvider.getAreaByTdwgAbbreviation("21"); // Macaronesia
|
296
|
}else if("33".equals(em)){
|
297
|
return TdwgAreaProvider.getAreaByTdwgAbbreviation("33");
|
298
|
|
299
|
}else if("SM".equals(em)){
|
300
|
return getNamedArea(state, BerlinModelTransformer.uuidSerbiaMontenegro, "Serbia & Montenegro", "Euro+Med area 'Serbia & Montenegro'", "SM", NamedAreaType.ADMINISTRATION_AREA(), null);
|
301
|
}else if("Sr".equals(em)){
|
302
|
return getNamedArea(state, BerlinModelTransformer.uuidSerbia, "Serbia", "Euro+Med area 'Serbia' (including Kosovo and Vojvodina)", "Sr", NamedAreaType.ADMINISTRATION_AREA(), null);
|
303
|
|
304
|
|
305
|
//see #2769
|
306
|
}else if("Rs".equals(em)){
|
307
|
return getNamedArea(state, BerlinModelTransformer.uuidUssr, "Former USSR", "Euro+Med area 'Former USSR'", "Rs", NamedAreaType.ADMINISTRATION_AREA(), null);
|
308
|
}else if("Rs(N)".equals(em)){
|
309
|
return getNamedArea(state, BerlinModelTransformer.uuidRussiaNorthern, "Russia Northern", "Euro+Med area 'Russia Northern'", "Rs(N)", null, null);
|
310
|
}else if("Rs(B)".equals(em)){
|
311
|
return getNamedArea(state, BerlinModelTransformer.uuidRussiaBaltic, "Russia Baltic", "Euro+Med area 'Russia Baltic'", "Rs(B)", null, null);
|
312
|
}else if("Rs(C)".equals(em)){
|
313
|
return getNamedArea(state, BerlinModelTransformer.uuidRussiaCentral, "Russia Central", "Euro+Med area 'Russia Central'", "Rs(C)", null, null);
|
314
|
}else if("Rs(W)".equals(em)){
|
315
|
return getNamedArea(state, BerlinModelTransformer.uuidRussiaSouthWest, "Russia Southwest", "Euro+Med area 'Russia Southwest'", "Rs(W)", null, null);
|
316
|
}else if("Rs(E)".equals(em)){
|
317
|
return getNamedArea(state, BerlinModelTransformer.uuidRussiaSouthEast, "Russia Southeast", "Euro+Med area 'Russia Southeast'", "Rs(E)", null, null);
|
318
|
|
319
|
//see #2770
|
320
|
}else if("AE".equals(em)){
|
321
|
return getNamedArea(state, BerlinModelTransformer.uuidEastAegeanIslands, "East Aegean Islands", "Euro+Med area 'East Aegean Islands'", "AE", null, null);
|
322
|
}else if("AE(T)".equals(em)){
|
323
|
return getNamedArea(state, BerlinModelTransformer.uuidTurkishEastAegeanIslands, "Turkish East Aegean Islands", "Euro+Med area 'Turkish East Aegean Islands'", "AE(T)", null, null);
|
324
|
}else if("Tu".equals(em)){
|
325
|
return getNamedArea(state, BerlinModelTransformer.uuidTurkey, "Turkey", "Euro+Med area 'Turkey' (without AE(T))", "Tu", null, null);
|
326
|
|
327
|
//TODO Azores, Canary Is.
|
328
|
}else if("Md(D)".equals(em)){
|
329
|
return getNamedArea(state, BerlinModelTransformer.uuidDesertas, "Desertas", "Euro+Med area 'Desertas'", "Md(D)", null, null);
|
330
|
}else if("Md(M)".equals(em)){
|
331
|
return getNamedArea(state, BerlinModelTransformer.uuidMadeira, "Madeira", "Euro+Med area 'Madeira'", "Md(M)", null, null);
|
332
|
}else if("Md(P)".equals(em)){
|
333
|
return getNamedArea(state, BerlinModelTransformer.uuidPortoSanto, "Porto Santo", "Euro+Med area 'Porto Santo'", "Md(P)", null, null);
|
334
|
//Azores
|
335
|
}else if("Az(L)".equals(em)){
|
336
|
return getNamedArea(state, BerlinModelTransformer.uuidFlores, "Flores", "Euro+Med area 'Flores'", "Az(L)", null, null);
|
337
|
}else if("Az(C)".equals(em)){
|
338
|
return getNamedArea(state, BerlinModelTransformer.uuidCorvo, "Corvo", "Euro+Med area 'Corvo'", "Az(C)", null, null);
|
339
|
}else if("Az(F)".equals(em)){
|
340
|
return getNamedArea(state, BerlinModelTransformer.uuidFaial, "Faial", "Euro+Med area 'Faial'", "Az(F)", null, null);
|
341
|
}else if("Az(G)".equals(em)){
|
342
|
return getNamedArea(state, BerlinModelTransformer.uuidGraciosa, "Graciosa", "Euro+Med area 'Graciosa'", "Az(G)", null, null);
|
343
|
}else if("Az(J)".equals(em)){
|
344
|
return getNamedArea(state, BerlinModelTransformer.uuidSaoJorge, "S\u00E3o Jorge", "Euro+Med area 'S\u00E3o Jorge'", "Az(J)", null, null);
|
345
|
}else if("Az(M)".equals(em)){
|
346
|
return getNamedArea(state, BerlinModelTransformer.uuidSaoMiguel, "S\u00E3o Miguel", "Euro+Med area 'S\u00E3o Miguel'", "Az(M)", null, null);
|
347
|
}else if("Az(P)".equals(em)){
|
348
|
return getNamedArea(state, BerlinModelTransformer.uuidPico, "Pico", "Euro+Med area 'Pico'", "Az(P)", null, null);
|
349
|
}else if("Az(S)".equals(em)){
|
350
|
return getNamedArea(state, BerlinModelTransformer.uuidSantaMaria, "Santa Maria", "Euro+Med area 'Santa Maria'", "Az(S)", null, null);
|
351
|
}else if("Az(T)".equals(em)){
|
352
|
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Terceira", "Euro+Med area 'Terceira'", "Az(T)", null, null);
|
353
|
//Canary Islands
|
354
|
}else if("Ca(C)".equals(em)){
|
355
|
return getNamedArea(state, BerlinModelTransformer.uuidGranCanaria, "Gran Canaria", "Euro+Med area 'Gran Canaria'", "Ca(C)", null, null);
|
356
|
}else if("Ca(F)".equals(em)){
|
357
|
return getNamedArea(state, BerlinModelTransformer.uuidFuerteventura, "Fuerteventura with Lobos", "Euro+Med area 'Fuerteventura with Lobos'", "Ca(F)", null, null);
|
358
|
}else if("Ca(G)".equals(em)){
|
359
|
return getNamedArea(state, BerlinModelTransformer.uuidGomera, "Gomera", "Euro+Med area 'Gomera'", "Ca(G)", null, null);
|
360
|
}else if("Ca(H)".equals(em)){
|
361
|
return getNamedArea(state, BerlinModelTransformer.uuidHierro, "Hierro", "Euro+Med area 'Hierro'", "Ca(H)", null, null);
|
362
|
}else if("Ca(L)".equals(em)){
|
363
|
return getNamedArea(state, BerlinModelTransformer.uuidLanzaroteWithGraciosa, "Lanzarote with Graciosa", "Euro+Med area 'Lanzarote with Graciosa'", "Ca(L)", null, null);
|
364
|
}else if("Ca(P)".equals(em)){
|
365
|
return getNamedArea(state, BerlinModelTransformer.uuidLaPalma, "La Palma", "Euro+Med area 'La Palma'", "Ca(P)", null, null);
|
366
|
}else if("Ca(T)".equals(em)){
|
367
|
return getNamedArea(state, BerlinModelTransformer.uuidTenerife, "Tenerife", "Euro+Med area 'Tenerife'", "Ca(T)", null, null);
|
368
|
//Baleares
|
369
|
}else if("Bl(I)".equals(em)){
|
370
|
return getNamedArea(state, BerlinModelTransformer.uuidIbizaWithFormentera, "Ibiza with Formentera", "Euro+Med area 'Ibiza with Formentera'", "Bl(I)", null, null);
|
371
|
}else if("Bl(M)".equals(em)){
|
372
|
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Mallorca", "Euro+Med area 'Mallorca'", "Bl(M)", null, null);
|
373
|
}else if("Bl(N)".equals(em)){
|
374
|
return getNamedArea(state, BerlinModelTransformer.uuidTerceira, "Menorca", "Euro+Med area 'Menorca'", "Bl(N)", null, null);
|
375
|
}
|
376
|
|
377
|
logger.warn("Area(em: '" + em + "', tdwg: '" + tdwg +"') could not be found for occurrence import");
|
378
|
|
379
|
return null;
|
380
|
}
|
381
|
|
382
|
|
383
|
}
|