|
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.io.File;
|
|
13
|
import java.lang.reflect.Method;
|
|
14
|
import java.net.MalformedURLException;
|
|
15
|
import java.net.URL;
|
|
16
|
import java.util.HashSet;
|
|
17
|
import java.util.Set;
|
|
18
|
|
|
19
|
import org.apache.log4j.Logger;
|
|
20
|
|
|
21
|
import eu.etaxonomy.cdm.database.ICdmDataSource;
|
|
22
|
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser;
|
|
23
|
import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelGeneralImportValidator;
|
|
24
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
|
|
25
|
import eu.etaxonomy.cdm.io.common.ImportConfiguratorBase;
|
|
26
|
import eu.etaxonomy.cdm.io.common.ImportStateBase;
|
|
27
|
import eu.etaxonomy.cdm.io.common.Source;
|
|
28
|
import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
|
|
29
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
|
30
|
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
|
|
31
|
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
|
32
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
33
|
|
|
34
|
/**
|
|
35
|
* @author a.mueller
|
|
36
|
* @created 20.03.2008
|
|
37
|
* @version 1.0
|
|
38
|
*/
|
|
39
|
public class BerlinModelImportConfigurator extends ImportConfiguratorBase<BerlinModelImportState> implements IImportConfigurator{
|
|
40
|
private static Logger logger = Logger.getLogger(BerlinModelImportConfigurator.class);
|
|
41
|
|
|
42
|
public static BerlinModelImportConfigurator NewInstance(Source berlinModelSource, ICdmDataSource destination){
|
|
43
|
return new BerlinModelImportConfigurator(berlinModelSource, destination);
|
|
44
|
}
|
|
45
|
|
|
46
|
private PublishMarkerChooser taxonPublishMarker = PublishMarkerChooser.ALL;
|
|
47
|
|
|
48
|
//TODO
|
|
49
|
private static IInputTransformer defaultTransformer = null;
|
|
50
|
|
|
51
|
private boolean doCommonNames = true;
|
|
52
|
|
|
53
|
|
|
54
|
/* Max number of records to be saved with one service call */
|
|
55
|
private int recordsPerTransaction = 1000;
|
|
56
|
|
|
57
|
private Method namerelationshipTypeMethod;
|
|
58
|
private Method uuidForDefTermMethod;
|
|
59
|
private Method userTransformationMethod;
|
|
60
|
private Method nameTypeDesignationStatusMethod;
|
|
61
|
|
|
62
|
private Set<Synonym> proParteSynonyms = new HashSet<Synonym>();
|
|
63
|
private Set<Synonym> partialSynonyms = new HashSet<Synonym>();
|
|
64
|
|
|
65
|
// NameFact stuff
|
|
66
|
private URL mediaUrl;
|
|
67
|
private File mediaPath;
|
|
68
|
private int maximumNumberOfNameFacts;
|
|
69
|
private boolean isIgnore0AuthorTeam = false;
|
|
70
|
|
|
71
|
protected void makeIoClassList(){
|
|
72
|
ioClassList = new Class[]{
|
|
73
|
BerlinModelGeneralImportValidator.class
|
|
74
|
, BerlinModelUserImport.class
|
|
75
|
, BerlinModelAuthorImport.class
|
|
76
|
, BerlinModelAuthorTeamImport.class
|
|
77
|
, BerlinModelRefDetailImport.class
|
|
78
|
, BerlinModelReferenceImport.class
|
|
79
|
, BerlinModelTaxonNameImport.class
|
|
80
|
, BerlinModelTaxonNameRelationImport.class
|
|
81
|
, BerlinModelNameStatusImport.class
|
|
82
|
, BerlinModelNameFactsImport.class
|
|
83
|
, BerlinModelTypesImport.class
|
|
84
|
, BerlinModelTaxonImport.class
|
|
85
|
, BerlinModelTaxonRelationImport.class
|
|
86
|
, BerlinModelCommonNamesImport.class
|
|
87
|
, BerlinModelFactsImport.class
|
|
88
|
, BerlinModelOccurrenceImport.class
|
|
89
|
, BerlinModelOccurrenceSourceImport.class
|
|
90
|
, BerlinModelWebMarkerCategoryImport.class
|
|
91
|
, BerlinModelWebMarkerImport.class
|
|
92
|
};
|
|
93
|
}
|
|
94
|
|
|
95
|
|
|
96
|
|
|
97
|
/* (non-Javadoc)
|
|
98
|
* @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getNewState()
|
|
99
|
*/
|
|
100
|
public ImportStateBase getNewState() {
|
|
101
|
return new BerlinModelImportState(this);
|
|
102
|
}
|
|
103
|
|
|
104
|
|
|
105
|
|
|
106
|
/**
|
|
107
|
* @param berlinModelSource
|
|
108
|
* @param sourceReference
|
|
109
|
* @param destination
|
|
110
|
*/
|
|
111
|
private BerlinModelImportConfigurator(Source berlinModelSource, ICdmDataSource destination) {
|
|
112
|
super(defaultTransformer);
|
|
113
|
setNomenclaturalCode(NomenclaturalCode.ICBN); //default for Berlin Model
|
|
114
|
setSource(berlinModelSource);
|
|
115
|
setDestination(destination);
|
|
116
|
}
|
|
117
|
|
|
118
|
|
|
119
|
public Source getSource() {
|
|
120
|
return (Source)super.getSource();
|
|
121
|
}
|
|
122
|
public void setSource(Source berlinModelSource) {
|
|
123
|
super.setSource(berlinModelSource);
|
|
124
|
}
|
|
125
|
|
|
126
|
/* (non-Javadoc)
|
|
127
|
* @see eu.etaxonomy.cdm.io.tcsrdf.IImportConfigurator#getSourceReference()
|
|
128
|
*/
|
|
129
|
public ReferenceBase getSourceReference() {
|
|
130
|
ReferenceFactory refFactory = ReferenceFactory.newInstance();
|
|
131
|
if (sourceReference == null){
|
|
132
|
sourceReference = refFactory.newDatabase();
|
|
133
|
if (getSource() != null){
|
|
134
|
sourceReference.setTitleCache(getSource().getDatabase(), true);
|
|
135
|
}
|
|
136
|
}
|
|
137
|
return sourceReference;
|
|
138
|
}
|
|
139
|
|
|
140
|
|
|
141
|
/* (non-Javadoc)
|
|
142
|
* @see eu.etaxonomy.cdm.io.common.IImportConfigurator#getSourceNameString()
|
|
143
|
*/
|
|
144
|
public String getSourceNameString() {
|
|
145
|
if (this.getSource() == null){
|
|
146
|
return null;
|
|
147
|
}else{
|
|
148
|
return this.getSource().getDatabase();
|
|
149
|
}
|
|
150
|
}
|
|
151
|
|
|
152
|
protected void addProParteSynonym(Synonym proParteSynonym){
|
|
153
|
this.proParteSynonyms.add(proParteSynonym);
|
|
154
|
}
|
|
155
|
|
|
156
|
protected boolean isProParteSynonym(Synonym synonym){
|
|
157
|
return this.proParteSynonyms.contains(synonym);
|
|
158
|
}
|
|
159
|
|
|
160
|
protected void addPartialSynonym(Synonym partialSynonym){
|
|
161
|
this.partialSynonyms.add(partialSynonym);
|
|
162
|
}
|
|
163
|
|
|
164
|
protected boolean isPartialSynonym(Synonym synonym){
|
|
165
|
return this.partialSynonyms.contains(synonym);
|
|
166
|
}
|
|
167
|
|
|
168
|
/**
|
|
169
|
* @return the mediaUrl
|
|
170
|
*/
|
|
171
|
public URL getMediaUrl() {
|
|
172
|
return mediaUrl;
|
|
173
|
}
|
|
174
|
|
|
175
|
/**
|
|
176
|
* @param mediaUrl the mediaUrl to set
|
|
177
|
*/
|
|
178
|
public void setMediaUrl(URL mediaUrl) {
|
|
179
|
this.mediaUrl = mediaUrl;
|
|
180
|
}
|
|
181
|
|
|
182
|
/**
|
|
183
|
* @return the mediaPath
|
|
184
|
*/
|
|
185
|
public File getMediaPath() {
|
|
186
|
return mediaPath;
|
|
187
|
}
|
|
188
|
|
|
189
|
/**
|
|
190
|
* @param mediaPath the mediaPath to set
|
|
191
|
*/
|
|
192
|
public void setMediaPath(File mediaPath) {
|
|
193
|
this.mediaPath = mediaPath;
|
|
194
|
}
|
|
195
|
|
|
196
|
public void setMediaPath(String mediaPathString){
|
|
197
|
this.mediaPath = new File(mediaPathString);
|
|
198
|
}
|
|
199
|
|
|
200
|
public void setMediaUrl(String mediaUrlString) {
|
|
201
|
try {
|
|
202
|
this.mediaUrl = new URL(mediaUrlString);
|
|
203
|
} catch (MalformedURLException e) {
|
|
204
|
logger.error("Could not set mediaUrl because it was malformed: " + mediaUrlString);
|
|
205
|
}
|
|
206
|
}
|
|
207
|
|
|
208
|
/**
|
|
209
|
* @return the maximumNumberOfNameFacts
|
|
210
|
*/
|
|
211
|
public int getMaximumNumberOfNameFacts() {
|
|
212
|
return maximumNumberOfNameFacts;
|
|
213
|
}
|
|
214
|
|
|
215
|
/**
|
|
216
|
* set to 0 for unlimited
|
|
217
|
*
|
|
218
|
* @param maximumNumberOfNameFacts the maximumNumberOfNameFacts to set
|
|
219
|
*/
|
|
220
|
public void setMaximumNumberOfNameFacts(int maximumNumberOfNameFacts) {
|
|
221
|
this.maximumNumberOfNameFacts = maximumNumberOfNameFacts;
|
|
222
|
}
|
|
223
|
|
|
224
|
/**
|
|
225
|
* If true, an authorTeam with authorTeamId = 0 is not imported (casus Salvador)
|
|
226
|
* @return the isIgnore0AuthorTeam
|
|
227
|
*/
|
|
228
|
public boolean isIgnore0AuthorTeam() {
|
|
229
|
return isIgnore0AuthorTeam;
|
|
230
|
}
|
|
231
|
|
|
232
|
/**
|
|
233
|
* @param isIgnore0AuthorTeam the isIgnore0AuthorTeam to set
|
|
234
|
*/
|
|
235
|
public void setIgnore0AuthorTeam(boolean isIgnore0AuthorTeam) {
|
|
236
|
this.isIgnore0AuthorTeam = isIgnore0AuthorTeam;
|
|
237
|
}
|
|
238
|
|
|
239
|
/**
|
|
240
|
* @return the namerelationshipTypeMethod
|
|
241
|
*/
|
|
242
|
public Method getNamerelationshipTypeMethod() {
|
|
243
|
return namerelationshipTypeMethod;
|
|
244
|
}
|
|
245
|
|
|
246
|
/**
|
|
247
|
* @param namerelationshipTypeMethod the namerelationshipTypeMethod to set
|
|
248
|
*/
|
|
249
|
public void setNamerelationshipTypeMethod(Method namerelationshipTypeMethod) {
|
|
250
|
this.namerelationshipTypeMethod = namerelationshipTypeMethod;
|
|
251
|
}
|
|
252
|
|
|
253
|
/**
|
|
254
|
* @return the taxonPublishMarker
|
|
255
|
*/
|
|
256
|
public BerlinModelTaxonImport.PublishMarkerChooser getTaxonPublishMarker() {
|
|
257
|
return taxonPublishMarker;
|
|
258
|
}
|
|
259
|
|
|
260
|
/**
|
|
261
|
* @param taxonPublishMarker the taxonPublishMarker to set
|
|
262
|
*/
|
|
263
|
public void setTaxonPublishMarker(
|
|
264
|
BerlinModelTaxonImport.PublishMarkerChooser taxonPublishMarker) {
|
|
265
|
this.taxonPublishMarker = taxonPublishMarker;
|
|
266
|
}
|
|
267
|
|
|
268
|
|
|
269
|
|
|
270
|
/**
|
|
271
|
* @return the uuidForDefTermMethod
|
|
272
|
*/
|
|
273
|
public Method getUuidForDefTermMethod() {
|
|
274
|
return uuidForDefTermMethod;
|
|
275
|
}
|
|
276
|
|
|
277
|
/**
|
|
278
|
* @param uuidForDefTermMethod the uuidForDefTermMethod to set
|
|
279
|
*/
|
|
280
|
public void setUuidForDefTermMethod(Method uuidForDefTermMethod) {
|
|
281
|
this.uuidForDefTermMethod = uuidForDefTermMethod;
|
|
282
|
}
|
|
283
|
|
|
284
|
/**
|
|
285
|
* @return the userTransformationMethod
|
|
286
|
*/
|
|
287
|
public Method getUserTransformationMethod() {
|
|
288
|
return userTransformationMethod;
|
|
289
|
}
|
|
290
|
|
|
291
|
/**
|
|
292
|
* @param userTransformationMethod the userTransformationMethod to set
|
|
293
|
*/
|
|
294
|
public void setUserTransformationMethod(Method userTransformationMethod) {
|
|
295
|
this.userTransformationMethod = userTransformationMethod;
|
|
296
|
}
|
|
297
|
|
|
298
|
|
|
299
|
|
|
300
|
/**
|
|
301
|
* @return the nameTypeDesignationStatusMethod
|
|
302
|
*/
|
|
303
|
public Method getNameTypeDesignationStatusMethod() {
|
|
304
|
return nameTypeDesignationStatusMethod;
|
|
305
|
}
|
|
306
|
|
|
307
|
|
|
308
|
/**
|
|
309
|
* @param nameTypeDesignationStatusMethod the nameTypeDesignationStatusMethod to set
|
|
310
|
*/
|
|
311
|
public void setNameTypeDesignationStatusMethod(
|
|
312
|
Method nameTypeDesignationStatusMethod) {
|
|
313
|
this.nameTypeDesignationStatusMethod = nameTypeDesignationStatusMethod;
|
|
314
|
}
|
|
315
|
|
|
316
|
/**
|
|
317
|
* @return the limitSave
|
|
318
|
*/
|
|
319
|
public int getRecordsPerTransaction() {
|
|
320
|
return recordsPerTransaction;
|
|
321
|
}
|
|
322
|
|
|
323
|
/**
|
|
324
|
* @param limitSave the limitSave to set
|
|
325
|
*/
|
|
326
|
public void setRecordsPerTransaction(int recordsPerTransaction) {
|
|
327
|
this.recordsPerTransaction = recordsPerTransaction;
|
|
328
|
}
|
|
329
|
|
|
330
|
|
|
331
|
public boolean isDoCommonNames() {
|
|
332
|
return doCommonNames;
|
|
333
|
}
|
|
334
|
|
|
335
|
|
|
336
|
/**
|
|
337
|
* @param doCommonNames
|
|
338
|
*/
|
|
339
|
public void setDoCommonNames(boolean doCommonNames) {
|
|
340
|
this.doCommonNames = doCommonNames;
|
|
341
|
|
|
342
|
}
|
|
343
|
|
|
344
|
|
|
345
|
|
|
346
|
|
|
347
|
}
|