|
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 static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_HAS_SAME_TYPE_AS;
|
|
13
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ALTERNATIVE_NAME_FOR;
|
|
14
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_BASIONYM_FOR;
|
|
15
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_CONSERVED_TYPE_OF;
|
|
16
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FEMALE_PARENT_OF;
|
|
17
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_FIRST_PARENT_OF;
|
|
18
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_HOMONYM_OF;
|
|
19
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LATER_VALIDATION_OF;
|
|
20
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_LECTOTYPE_OF;
|
|
21
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_MALE_PARENT_OF;
|
|
22
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF;
|
|
23
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REJECTED_TYPE_OF;
|
|
24
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_REPLACED_SYNONYM_FOR;
|
|
25
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_SECOND_PARENT_OF;
|
|
26
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF;
|
|
27
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TYPE_OF;
|
|
28
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_VALIDATION_OF;
|
|
29
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_TYPE_NOT_DESIGNATED;
|
|
30
|
|
|
31
|
import java.lang.reflect.Method;
|
|
32
|
import java.sql.ResultSet;
|
|
33
|
import java.sql.SQLException;
|
|
34
|
import java.util.HashMap;
|
|
35
|
import java.util.HashSet;
|
|
36
|
import java.util.Map;
|
|
37
|
import java.util.Set;
|
|
38
|
|
|
39
|
import org.apache.commons.lang.StringUtils;
|
|
40
|
import org.apache.log4j.Logger;
|
|
41
|
import org.springframework.stereotype.Component;
|
|
42
|
|
|
43
|
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
|
|
44
|
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonNameRelationImportValidator;
|
|
45
|
import eu.etaxonomy.cdm.io.common.IOValidator;
|
|
46
|
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
|
|
47
|
import eu.etaxonomy.cdm.model.agent.Person;
|
|
48
|
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
|
|
49
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
50
|
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
|
|
51
|
import eu.etaxonomy.cdm.model.name.IBotanicalName;
|
|
52
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
|
53
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
|
|
54
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
55
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
56
|
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
|
|
57
|
|
|
58
|
/**
|
|
59
|
* @author a.mueller
|
|
60
|
* @created 20.03.2008
|
|
61
|
*/
|
|
62
|
@Component
|
|
63
|
public class BerlinModelTaxonNameRelationImport extends BerlinModelImportBase {
|
|
64
|
|
|
65
|
private static final long serialVersionUID = 1197601822023101796L;
|
|
66
|
private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameRelationImport.class);
|
|
67
|
|
|
68
|
private static int modCount = 5000;
|
|
69
|
private static final String pluralString = "name relations";
|
|
70
|
private static final String dbTableName = "RelName";
|
|
71
|
|
|
72
|
|
|
73
|
public BerlinModelTaxonNameRelationImport(){
|
|
74
|
super(dbTableName, pluralString);
|
|
75
|
}
|
|
76
|
|
|
77
|
|
|
78
|
@Override
|
|
79
|
protected String getIdQuery(BerlinModelImportState state) {
|
|
80
|
if (StringUtils.isNotBlank(state.getConfig().getNameIdTable())){
|
|
81
|
String result = super.getIdQuery(state);
|
|
82
|
result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR ";
|
|
83
|
result += " nameFk2 IN (SELECT NameId FROM %s)";
|
|
84
|
result = String.format(result, state.getConfig().getNameIdTable(),state.getConfig().getNameIdTable() );
|
|
85
|
return result;
|
|
86
|
}else{
|
|
87
|
return super.getIdQuery(state);
|
|
88
|
}
|
|
89
|
}
|
|
90
|
|
|
91
|
|
|
92
|
@Override
|
|
93
|
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
|
94
|
String strQuery =
|
|
95
|
" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
|
|
96
|
" FROM Name as FromName INNER JOIN " +
|
|
97
|
" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
|
|
98
|
" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
|
|
99
|
" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
|
|
100
|
" WHERE (RelNameId IN ("+ID_LIST_TOKEN +"))";
|
|
101
|
return strQuery;
|
|
102
|
}
|
|
103
|
|
|
104
|
@Override
|
|
105
|
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
|
|
106
|
boolean success = true ;
|
|
107
|
BerlinModelImportConfigurator config = state.getConfig();
|
|
108
|
Set<TaxonName> nameToSave = new HashSet<>();
|
|
109
|
Map<String, TaxonName> nameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
|
|
110
|
Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
|
|
111
|
|
|
112
|
ResultSet rs = partitioner.getResultSet();
|
|
113
|
try {
|
|
114
|
|
|
115
|
int i = 0;
|
|
116
|
//for each name relation
|
|
117
|
while (rs.next()){
|
|
118
|
|
|
119
|
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelName handled: " + (i-1));}
|
|
120
|
|
|
121
|
int relNameId = rs.getInt("RelNameId");
|
|
122
|
int name1Id = rs.getInt("name1Id");
|
|
123
|
int name2Id = rs.getInt("name2Id");
|
|
124
|
Object relRefFkObj = rs.getObject("refFk");
|
|
125
|
String details = rs.getString("details");
|
|
126
|
int relQualifierFk = rs.getInt("relNameQualifierFk");
|
|
127
|
String notes = rs.getString("notes");
|
|
128
|
|
|
129
|
TaxonName nameFrom = nameMap.get(String.valueOf(name1Id));
|
|
130
|
TaxonName nameTo = nameMap.get(String.valueOf(name2Id));
|
|
131
|
|
|
132
|
|
|
133
|
Reference citation = null;
|
|
134
|
if (relRefFkObj != null){
|
|
135
|
String relRefFk = String.valueOf(relRefFkObj);
|
|
136
|
//get nomRef
|
|
137
|
citation = refMap.get(relRefFk);
|
|
138
|
}
|
|
139
|
|
|
140
|
//TODO (preliminaryFlag = true testen
|
|
141
|
String microcitation = details;
|
|
142
|
String rule = null;
|
|
143
|
|
|
144
|
if (nameFrom != null && nameTo != null){
|
|
145
|
success = handleNameRelationship(success, config, name1Id, name2Id, relQualifierFk,
|
|
146
|
notes, nameFrom, nameTo, citation, microcitation, rule);
|
|
147
|
|
|
148
|
if (! nameFrom.isProtectedTitleCache()){
|
|
149
|
nameFrom.setTitleCache(null);
|
|
150
|
nameFrom.getTitleCache();
|
|
151
|
}
|
|
152
|
if (! nameTo.isProtectedTitleCache()){
|
|
153
|
nameTo.setTitleCache(null);
|
|
154
|
nameTo.getTitleCache();
|
|
155
|
}
|
|
156
|
nameToSave.add(nameFrom);
|
|
157
|
|
|
158
|
//TODO
|
|
159
|
//ID
|
|
160
|
//etc.
|
|
161
|
}else{
|
|
162
|
//TODO
|
|
163
|
if (nameFrom == null){
|
|
164
|
if ( ! (config.isUseEmAreaVocabulary() && relNameId == 28159 )) {
|
|
165
|
logger.warn("from TaxonName " + name1Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + " , toName: " + name2Id+ ") does not exist in store. ToName is: " + (nameTo == null ? "" : nameTo.getTitleCache()));
|
|
166
|
}
|
|
167
|
}
|
|
168
|
if (nameTo == null){
|
|
169
|
logger.warn("to TaxonName " + name2Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + " , fromName: " + name1Id + ") does not exist in store. FromName is: " + (nameFrom == null ? "" : nameFrom.getTitleCache()));
|
|
170
|
}
|
|
171
|
success = false;
|
|
172
|
}
|
|
173
|
}
|
|
174
|
|
|
175
|
|
|
176
|
partitioner.startDoSave();
|
|
177
|
getNameService().save(nameToSave);
|
|
178
|
|
|
179
|
return success;
|
|
180
|
} catch (SQLException e) {
|
|
181
|
logger.error("SQLException:" + e);
|
|
182
|
return false;
|
|
183
|
}
|
|
184
|
}
|
|
185
|
|
|
186
|
/**
|
|
187
|
* @param success
|
|
188
|
* @param config
|
|
189
|
* @param name1Id
|
|
190
|
* @param name2Id
|
|
191
|
* @param relQualifierFk
|
|
192
|
* @param notes
|
|
193
|
* @param nameFrom
|
|
194
|
* @param nameTo
|
|
195
|
* @param citation
|
|
196
|
* @param microcitation
|
|
197
|
* @param rule
|
|
198
|
* @return
|
|
199
|
*/
|
|
200
|
private boolean handleNameRelationship(boolean success,
|
|
201
|
BerlinModelImportConfigurator config, int name1Id, int name2Id,
|
|
202
|
int relQualifierFk, String notes, TaxonName nameFrom,
|
|
203
|
TaxonName nameTo, Reference citation,
|
|
204
|
String microcitation, String rule) {
|
|
205
|
AnnotatableEntity nameRelationship = null;
|
|
206
|
if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
|
|
207
|
nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule);
|
|
208
|
}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
|
|
209
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
|
|
210
|
}else if (relQualifierFk == NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF){
|
|
211
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
|
|
212
|
}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
|
|
213
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule) ;
|
|
214
|
}else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
|
|
215
|
nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());
|
|
216
|
}else if (relQualifierFk == NAME_REL_IS_VALIDATION_OF){
|
|
217
|
nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.VALIDATED_BY_NAME(), citation, microcitation, rule) ;
|
|
218
|
}else if (relQualifierFk == NAME_REL_IS_LATER_VALIDATION_OF){
|
|
219
|
nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.LATER_VALIDATED_BY_NAME(), citation, microcitation, rule) ;
|
|
220
|
}else if (relQualifierFk == NAME_REL_IS_TYPE_OF || relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF || relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF || relQualifierFk == NAME_REL_IS_LECTOTYPE_OF || relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED ){
|
|
221
|
boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF);
|
|
222
|
boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF);
|
|
223
|
boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF);
|
|
224
|
boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED);
|
|
225
|
|
|
226
|
NameTypeDesignationStatus status = null;
|
|
227
|
String originalNameString = null;
|
|
228
|
//TODO addToAllNames true or false?
|
|
229
|
boolean addToAllNames = false;
|
|
230
|
if (config.getNameTypeDesignationStatusMethod() != null){
|
|
231
|
Method method = config.getNameTypeDesignationStatusMethod();
|
|
232
|
method.setAccessible(true);
|
|
233
|
try {
|
|
234
|
status = (NameTypeDesignationStatus)method.invoke(null, notes);
|
|
235
|
nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames);
|
|
236
|
} catch (Exception e) {
|
|
237
|
throw new RuntimeException(e);
|
|
238
|
}
|
|
239
|
}else{
|
|
240
|
if (isLectoType){
|
|
241
|
status = NameTypeDesignationStatus.LECTOTYPE();
|
|
242
|
}
|
|
243
|
nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, /*isLectoType,*/ isNotDesignated, addToAllNames);
|
|
244
|
}
|
|
245
|
|
|
246
|
}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
|
|
247
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule) ;
|
|
248
|
}else if (relQualifierFk == NAME_REL_IS_ALTERNATIVE_NAME_FOR){
|
|
249
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ALTERNATIVE_NAME(), citation, microcitation, rule) ;
|
|
250
|
}else if (relQualifierFk == NAME_REL_IS_FIRST_PARENT_OF || relQualifierFk == NAME_REL_IS_SECOND_PARENT_OF || relQualifierFk == NAME_REL_IS_FEMALE_PARENT_OF || relQualifierFk == NAME_REL_IS_MALE_PARENT_OF){
|
|
251
|
//HybridRelationships
|
|
252
|
try {
|
|
253
|
HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk);
|
|
254
|
IBotanicalName parent = nameFrom;
|
|
255
|
IBotanicalName child = nameTo;
|
|
256
|
|
|
257
|
nameRelationship = parent.addHybridChild(child, hybridRelType, rule);
|
|
258
|
|
|
259
|
} catch (UnknownCdmTypeException e) {
|
|
260
|
logger.warn(e);
|
|
261
|
success = false;
|
|
262
|
}
|
|
263
|
}else {
|
|
264
|
//TODO
|
|
265
|
Method method = config.getNamerelationshipTypeMethod();
|
|
266
|
if (method != null){
|
|
267
|
try {
|
|
268
|
method.invoke(null, relQualifierFk, nameTo, nameFrom);
|
|
269
|
} catch (Exception e) {
|
|
270
|
logger.error(e.getMessage());
|
|
271
|
logger.warn("NameRelationship could not be imported");
|
|
272
|
success = false;
|
|
273
|
}
|
|
274
|
}else{
|
|
275
|
logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
|
|
276
|
success = false;
|
|
277
|
}
|
|
278
|
}
|
|
279
|
doNotes(nameRelationship, notes);
|
|
280
|
return success;
|
|
281
|
}
|
|
282
|
|
|
283
|
@Override
|
|
284
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
|
285
|
String nameSpace;
|
|
286
|
Class<?> cdmClass;
|
|
287
|
Set<String> idSet;
|
|
288
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
289
|
|
|
290
|
try{
|
|
291
|
Set<String> nameIdSet = new HashSet<String>();
|
|
292
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
293
|
Set<String> refDetailIdSet = new HashSet<String>();
|
|
294
|
while (rs.next()){
|
|
295
|
handleForeignKey(rs, nameIdSet, "name1Id");
|
|
296
|
handleForeignKey(rs, nameIdSet, "name2Id");
|
|
297
|
handleForeignKey(rs, referenceIdSet, "RefFk");
|
|
298
|
handleForeignKey(rs, refDetailIdSet, "RefDetailFk");
|
|
299
|
}
|
|
300
|
|
|
301
|
//name map
|
|
302
|
nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
|
|
303
|
cdmClass = TaxonName.class;
|
|
304
|
idSet = nameIdSet;
|
|
305
|
Map<String, Person> objectMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
306
|
result.put(nameSpace, objectMap);
|
|
307
|
|
|
308
|
//reference map
|
|
309
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
310
|
cdmClass = Reference.class;
|
|
311
|
idSet = referenceIdSet;
|
|
312
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
313
|
result.put(nameSpace, referenceMap);
|
|
314
|
|
|
315
|
//refDetail map
|
|
316
|
nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
|
|
317
|
cdmClass = Reference.class;
|
|
318
|
idSet = refDetailIdSet;
|
|
319
|
Map<String, Reference> refDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
320
|
result.put(nameSpace, refDetailMap);
|
|
321
|
|
|
322
|
} catch (SQLException e) {
|
|
323
|
throw new RuntimeException(e);
|
|
324
|
}
|
|
325
|
return result;
|
|
326
|
}
|
|
327
|
|
|
328
|
/* (non-Javadoc)
|
|
329
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
330
|
*/
|
|
331
|
@Override
|
|
332
|
protected boolean doCheck(BerlinModelImportState state){
|
|
333
|
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator();
|
|
334
|
return validator.validate(state);
|
|
335
|
}
|
|
336
|
|
|
337
|
/* (non-Javadoc)
|
|
338
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
339
|
*/
|
|
340
|
@Override
|
|
341
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
342
|
return ! state.getConfig().isDoRelNames();
|
|
343
|
}
|
|
344
|
|
|
345
|
|
|
346
|
}
|