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_TYPE_OF;
|
27
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_VALIDATION_OF;
|
28
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_TYPE_NOT_DESIGNATED;
|
29
|
import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF;
|
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.BotanicalName;
|
51
|
import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
|
52
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
53
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
|
54
|
import eu.etaxonomy.cdm.model.name.NonViralName;
|
55
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
56
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
57
|
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
|
58
|
|
59
|
/**
|
60
|
* @author a.mueller
|
61
|
* @created 20.03.2008
|
62
|
* @version 1.0
|
63
|
*/
|
64
|
@Component
|
65
|
public class BerlinModelTaxonNameRelationImport extends BerlinModelImportBase {
|
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
|
|
79
|
@Override
|
80
|
protected String getIdQuery(BerlinModelImportState state) {
|
81
|
if (StringUtils.isNotBlank(state.getConfig().getNameIdTable())){
|
82
|
String result = super.getIdQuery(state);
|
83
|
result += " WHERE nameFk1 IN (SELECT NameId FROM %s) OR ";
|
84
|
result += " nameFk2 IN (SELECT NameId FROM %s)";
|
85
|
result = String.format(result, state.getConfig().getNameIdTable(),state.getConfig().getNameIdTable() );
|
86
|
return result;
|
87
|
}else{
|
88
|
return super.getIdQuery(state);
|
89
|
}
|
90
|
}
|
91
|
|
92
|
|
93
|
/* (non-Javadoc)
|
94
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
|
95
|
*/
|
96
|
@Override
|
97
|
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
98
|
String strQuery =
|
99
|
" SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id, RefDetail.Details " +
|
100
|
" FROM Name as FromName INNER JOIN " +
|
101
|
" RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
|
102
|
" Name AS ToName ON RelName.NameFk2 = ToName.NameId LEFT OUTER JOIN "+
|
103
|
" RefDetail ON RelName.RefDetailFK = RefDetail.RefDetailId " +
|
104
|
" WHERE (RelNameId IN ("+ID_LIST_TOKEN +"))";
|
105
|
return strQuery;
|
106
|
}
|
107
|
|
108
|
/* (non-Javadoc)
|
109
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
|
110
|
*/
|
111
|
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
|
112
|
boolean success = true ;
|
113
|
BerlinModelImportConfigurator config = state.getConfig();
|
114
|
Set<TaxonNameBase> nameToSave = new HashSet<TaxonNameBase>();
|
115
|
Map<String, TaxonNameBase> nameMap = (Map<String, TaxonNameBase>) partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
|
116
|
Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
|
117
|
|
118
|
ResultSet rs = partitioner.getResultSet();
|
119
|
try {
|
120
|
|
121
|
int i = 0;
|
122
|
//for each name relation
|
123
|
while (rs.next()){
|
124
|
|
125
|
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelName handled: " + (i-1));}
|
126
|
|
127
|
int relNameId = rs.getInt("RelNameId");
|
128
|
int name1Id = rs.getInt("name1Id");
|
129
|
int name2Id = rs.getInt("name2Id");
|
130
|
Object relRefFkObj = rs.getObject("refFk");
|
131
|
String details = rs.getString("details");
|
132
|
int relQualifierFk = rs.getInt("relNameQualifierFk");
|
133
|
String notes = rs.getString("notes");
|
134
|
|
135
|
TaxonNameBase<?,?> nameFrom = nameMap.get(String.valueOf(name1Id));
|
136
|
TaxonNameBase<?,?> nameTo = nameMap.get(String.valueOf(name2Id));
|
137
|
|
138
|
|
139
|
Reference<?> citation = null;
|
140
|
if (relRefFkObj != null){
|
141
|
String relRefFk = String.valueOf(relRefFkObj);
|
142
|
//get nomRef
|
143
|
citation = refMap.get(relRefFk);
|
144
|
}
|
145
|
|
146
|
//TODO (preliminaryFlag = true testen
|
147
|
String microcitation = details;
|
148
|
String rule = null;
|
149
|
|
150
|
if (nameFrom != null && nameTo != null){
|
151
|
success = handleNameRelationship(success, config, name1Id, name2Id, relQualifierFk,
|
152
|
notes, nameFrom, nameTo, citation, microcitation, rule);
|
153
|
|
154
|
if (! nameFrom.isProtectedTitleCache()){
|
155
|
nameFrom.setTitleCache(null);
|
156
|
nameFrom.getTitleCache();
|
157
|
}
|
158
|
if (! nameTo.isProtectedTitleCache()){
|
159
|
nameTo.setTitleCache(null);
|
160
|
nameTo.getTitleCache();
|
161
|
}
|
162
|
nameToSave.add(nameFrom);
|
163
|
|
164
|
//TODO
|
165
|
//ID
|
166
|
//etc.
|
167
|
}else{
|
168
|
//TODO
|
169
|
if (nameFrom == null){
|
170
|
logger.warn("from TaxonName " + name1Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + ") does not exist in store. ToName is: " + (nameTo == null ? "" : nameTo.getTitleCache()));
|
171
|
}
|
172
|
if (nameTo == null){
|
173
|
logger.warn("to TaxonName " + name2Id + " for RelName (" + relNameId + " , type: " + relQualifierFk + ") does not exist in store. FromName is: " + (nameFrom == null ? "" : nameFrom.getTitleCache()));
|
174
|
}
|
175
|
success = false;
|
176
|
}
|
177
|
}
|
178
|
|
179
|
|
180
|
partitioner.startDoSave();
|
181
|
getNameService().save(nameToSave);
|
182
|
|
183
|
return success;
|
184
|
} catch (SQLException e) {
|
185
|
logger.error("SQLException:" + e);
|
186
|
return false;
|
187
|
}
|
188
|
}
|
189
|
|
190
|
/**
|
191
|
* @param success
|
192
|
* @param config
|
193
|
* @param name1Id
|
194
|
* @param name2Id
|
195
|
* @param relQualifierFk
|
196
|
* @param notes
|
197
|
* @param nameFrom
|
198
|
* @param nameTo
|
199
|
* @param citation
|
200
|
* @param microcitation
|
201
|
* @param rule
|
202
|
* @return
|
203
|
*/
|
204
|
private boolean handleNameRelationship(boolean success,
|
205
|
BerlinModelImportConfigurator config, int name1Id, int name2Id,
|
206
|
int relQualifierFk, String notes, TaxonNameBase nameFrom,
|
207
|
TaxonNameBase nameTo, Reference<?> citation,
|
208
|
String microcitation, String rule) {
|
209
|
AnnotatableEntity nameRelationship = null;
|
210
|
if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
|
211
|
nameRelationship = nameTo.addBasionym(nameFrom, citation, microcitation, rule);
|
212
|
}else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
|
213
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
|
214
|
}else if (relQualifierFk == NAME_REL_IS_TREATED_AS_LATER_HOMONYM_OF){
|
215
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), citation, microcitation, rule) ;
|
216
|
}else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
|
217
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, rule) ;
|
218
|
}else if (relQualifierFk == NAME_REL_HAS_SAME_TYPE_AS){
|
219
|
nameTo.getHomotypicalGroup().merge(nameFrom.getHomotypicalGroup());
|
220
|
}else if (relQualifierFk == NAME_REL_IS_VALIDATION_OF){
|
221
|
nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.VALIDATED_BY_NAME(), citation, microcitation, rule) ;
|
222
|
}else if (relQualifierFk == NAME_REL_IS_LATER_VALIDATION_OF){
|
223
|
nameRelationship = nameTo.addRelationshipToName(nameFrom, NameRelationshipType.LATER_VALIDATED_BY_NAME(), citation, microcitation, rule) ;
|
224
|
}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 ){
|
225
|
boolean isRejectedType = (relQualifierFk == NAME_REL_IS_REJECTED_TYPE_OF);
|
226
|
boolean isConservedType = (relQualifierFk == NAME_REL_IS_CONSERVED_TYPE_OF);
|
227
|
boolean isLectoType = (relQualifierFk == NAME_REL_IS_LECTOTYPE_OF);
|
228
|
boolean isNotDesignated = (relQualifierFk == NAME_REL_TYPE_NOT_DESIGNATED);
|
229
|
|
230
|
NameTypeDesignationStatus status = null;
|
231
|
String originalNameString = null;
|
232
|
//TODO addToAllNames true or false?
|
233
|
boolean addToAllNames = false;
|
234
|
if (config.getNameTypeDesignationStatusMethod() != null){
|
235
|
Method method = config.getNameTypeDesignationStatusMethod();
|
236
|
method.setAccessible(true);
|
237
|
try {
|
238
|
status = (NameTypeDesignationStatus)method.invoke(null, notes);
|
239
|
nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, addToAllNames);
|
240
|
} catch (Exception e) {
|
241
|
throw new RuntimeException(e);
|
242
|
}
|
243
|
}else{
|
244
|
if (isLectoType){
|
245
|
status = NameTypeDesignationStatus.LECTOTYPE();
|
246
|
}
|
247
|
nameRelationship = nameTo.addNameTypeDesignation(nameFrom, citation, microcitation, originalNameString, status, isRejectedType, isConservedType, /*isLectoType,*/ isNotDesignated, addToAllNames);
|
248
|
}
|
249
|
|
250
|
}else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
|
251
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), citation, microcitation, rule) ;
|
252
|
}else if (relQualifierFk == NAME_REL_IS_ALTERNATIVE_NAME_FOR){
|
253
|
nameRelationship = nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ALTERNATIVE_NAME(), citation, microcitation, rule) ;
|
254
|
}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){
|
255
|
//HybridRelationships
|
256
|
if (! (nameTo instanceof NonViralName ) || ! (nameFrom instanceof NonViralName)){
|
257
|
logger.warn("HybridrelationshipNames ("+name1Id +"," + name2Id +") must be of type NonViralNameName but are not");
|
258
|
success = false;
|
259
|
}
|
260
|
try {
|
261
|
HybridRelationshipType hybridRelType = BerlinModelTransformer.relNameId2HybridRel(relQualifierFk);
|
262
|
BotanicalName parent = (BotanicalName)nameFrom;
|
263
|
BotanicalName child = (BotanicalName)nameTo;
|
264
|
|
265
|
nameRelationship = parent.addHybridChild(child, hybridRelType, rule);
|
266
|
|
267
|
} catch (UnknownCdmTypeException e) {
|
268
|
logger.warn(e);
|
269
|
success = false;
|
270
|
}
|
271
|
}else {
|
272
|
//TODO
|
273
|
Method method = config.getNamerelationshipTypeMethod();
|
274
|
if (method != null){
|
275
|
try {
|
276
|
method.invoke(null, relQualifierFk, nameTo, nameFrom);
|
277
|
} catch (Exception e) {
|
278
|
logger.error(e.getMessage());
|
279
|
logger.warn("NameRelationship could not be imported");
|
280
|
success = false;
|
281
|
}
|
282
|
}else{
|
283
|
logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
|
284
|
success = false;
|
285
|
}
|
286
|
}
|
287
|
doNotes(nameRelationship, notes);
|
288
|
return success;
|
289
|
}
|
290
|
|
291
|
@Override
|
292
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
293
|
String nameSpace;
|
294
|
Class<?> cdmClass;
|
295
|
Set<String> idSet;
|
296
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
297
|
|
298
|
try{
|
299
|
Set<String> nameIdSet = new HashSet<String>();
|
300
|
Set<String> referenceIdSet = new HashSet<String>();
|
301
|
Set<String> refDetailIdSet = new HashSet<String>();
|
302
|
while (rs.next()){
|
303
|
handleForeignKey(rs, nameIdSet, "name1Id");
|
304
|
handleForeignKey(rs, nameIdSet, "name2Id");
|
305
|
handleForeignKey(rs, referenceIdSet, "RefFk");
|
306
|
handleForeignKey(rs, refDetailIdSet, "RefDetailFk");
|
307
|
}
|
308
|
|
309
|
//name map
|
310
|
nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
|
311
|
cdmClass = TaxonNameBase.class;
|
312
|
idSet = nameIdSet;
|
313
|
Map<String, Person> objectMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
314
|
result.put(nameSpace, objectMap);
|
315
|
|
316
|
//reference map
|
317
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
318
|
cdmClass = Reference.class;
|
319
|
idSet = referenceIdSet;
|
320
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
321
|
result.put(nameSpace, referenceMap);
|
322
|
|
323
|
//refDetail map
|
324
|
nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;
|
325
|
cdmClass = Reference.class;
|
326
|
idSet = refDetailIdSet;
|
327
|
Map<String, Reference> refDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
328
|
result.put(nameSpace, refDetailMap);
|
329
|
|
330
|
} catch (SQLException e) {
|
331
|
throw new RuntimeException(e);
|
332
|
}
|
333
|
return result;
|
334
|
}
|
335
|
|
336
|
/* (non-Javadoc)
|
337
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
338
|
*/
|
339
|
@Override
|
340
|
protected boolean doCheck(BerlinModelImportState state){
|
341
|
IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameRelationImportValidator();
|
342
|
return validator.validate(state);
|
343
|
}
|
344
|
|
345
|
/* (non-Javadoc)
|
346
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
347
|
*/
|
348
|
protected boolean isIgnore(BerlinModelImportState state){
|
349
|
return ! state.getConfig().isDoRelNames();
|
350
|
}
|
351
|
|
352
|
|
353
|
}
|