|
1
|
/**
|
|
2
|
* Copyright (C) 2009 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.common;
|
|
11
|
|
|
12
|
import java.lang.reflect.InvocationTargetException;
|
|
13
|
import java.lang.reflect.Method;
|
|
14
|
import java.sql.ResultSet;
|
|
15
|
import java.sql.SQLException;
|
|
16
|
import java.util.List;
|
|
17
|
|
|
18
|
import org.apache.log4j.Logger;
|
|
19
|
import org.jdom.Element;
|
|
20
|
import org.jdom.Namespace;
|
|
21
|
|
|
22
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
|
23
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
|
24
|
import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
|
|
25
|
import eu.etaxonomy.cdm.model.common.Annotation;
|
|
26
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
27
|
import eu.etaxonomy.cdm.model.common.IOriginalSource;
|
|
28
|
import eu.etaxonomy.cdm.model.common.ISourceable;
|
|
29
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
|
30
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
31
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
32
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
|
33
|
import eu.etaxonomy.cdm.model.common.TimePeriod;
|
|
34
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
|
35
|
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
|
|
36
|
import eu.etaxonomy.cdm.model.name.NonViralName;
|
|
37
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
38
|
import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
|
|
39
|
/**
|
|
40
|
* @author a.mueller
|
|
41
|
*
|
|
42
|
*/
|
|
43
|
public class ImportHelper {
|
|
44
|
private static final Logger logger = Logger.getLogger(ImportHelper.class);
|
|
45
|
|
|
46
|
public static final boolean OVERWRITE = true;
|
|
47
|
public static final boolean NO_OVERWRITE = false;
|
|
48
|
|
|
49
|
public static final boolean OBLIGATORY = true;
|
|
50
|
public static final boolean FACULTATIVE = false;
|
|
51
|
|
|
52
|
|
|
53
|
|
|
54
|
public static boolean setOriginalSource(ISourceable sourceable, Reference sourceReference, long sourceId, String namespace){
|
|
55
|
return setOriginalSource(sourceable, sourceReference, String.valueOf(sourceId), namespace);
|
|
56
|
}
|
|
57
|
|
|
58
|
/**
|
|
59
|
* Adds an original source object to the identifiable entity.
|
|
60
|
* @param idEntity
|
|
61
|
* @param sourceReference
|
|
62
|
* @param sourceId
|
|
63
|
* @return
|
|
64
|
*/
|
|
65
|
public static boolean setOriginalSource(ISourceable sourceable, Reference sourceReference, String sourceId, String namespace){
|
|
66
|
IOriginalSource<?> originalSource;
|
|
67
|
OriginalSourceType type = OriginalSourceType.Import;
|
|
68
|
if (HibernateProxyHelper.isInstanceOf(sourceable, IdentifiableEntity.class)){
|
|
69
|
originalSource = IdentifiableSource.NewInstance(type, sourceId, namespace, sourceReference, null);
|
|
70
|
}else if (HibernateProxyHelper.isInstanceOf(sourceable, DescriptionElementBase.class)){
|
|
71
|
originalSource = DescriptionElementSource.NewInstance(type, sourceId, namespace, sourceReference, null);
|
|
72
|
}else{
|
|
73
|
throw new ClassCastException("Unknown implementing class for ISourceable "+ sourceable.getClass() + " . Not supported bei ImportHelper.");
|
|
74
|
}
|
|
75
|
sourceable.addSource(originalSource);
|
|
76
|
return true;
|
|
77
|
}
|
|
78
|
|
|
79
|
public static boolean addStringValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName, boolean blankToNull){
|
|
80
|
return addValue(rs, cdmBase, dbAttrName, cdmAttrName, String.class, OVERWRITE, blankToNull);
|
|
81
|
}
|
|
82
|
|
|
83
|
// public static boolean addStringValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName, boolean overwriteNull){
|
|
84
|
// return addValue(rs, cdmBase, dbAttrName, cdmAttrName, String.class, overwriteNull);
|
|
85
|
// }
|
|
86
|
|
|
87
|
public static boolean addBooleanValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName){
|
|
88
|
return addValue(rs, cdmBase, dbAttrName, cdmAttrName, boolean.class, OVERWRITE, false);
|
|
89
|
}
|
|
90
|
|
|
91
|
public static boolean addValue(ResultSet rs, CdmBase cdmBase, String dbAttrName, String cdmAttrName, Class clazz, boolean overwriteNull, boolean blankToNull){
|
|
92
|
Object strValue;
|
|
93
|
try {
|
|
94
|
strValue = rs.getObject(dbAttrName);
|
|
95
|
if (strValue instanceof String && strValue != null){
|
|
96
|
strValue = ((String)strValue).trim();
|
|
97
|
if (blankToNull && strValue.equals("")){
|
|
98
|
strValue = null;
|
|
99
|
}
|
|
100
|
}
|
|
101
|
return addValue(strValue, cdmBase, cdmAttrName, clazz, overwriteNull, OBLIGATORY);
|
|
102
|
}catch (SQLException e) {
|
|
103
|
logger.error("SQLException: " + e);
|
|
104
|
return false;
|
|
105
|
}
|
|
106
|
|
|
107
|
}
|
|
108
|
|
|
109
|
|
|
110
|
public static boolean addXmlStringValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName){
|
|
111
|
return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, String.class, OVERWRITE);
|
|
112
|
}
|
|
113
|
|
|
114
|
public static boolean addXmlStringValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName, boolean overwriteNull){
|
|
115
|
return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, String.class, overwriteNull);
|
|
116
|
}
|
|
117
|
|
|
118
|
public static boolean addXmlBooleanValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName){
|
|
119
|
return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, boolean.class, OVERWRITE);
|
|
120
|
}
|
|
121
|
|
|
122
|
|
|
123
|
public static boolean addXmlValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName, Class clazz, boolean overwriteNull){
|
|
124
|
return addXmlValue(root, cdmBase, xmlElementName, namespace, cdmAttrName, clazz, overwriteNull, OBLIGATORY);
|
|
125
|
}
|
|
126
|
|
|
127
|
public static boolean addXmlValue(Element root, CdmBase cdmBase, String xmlElementName, Namespace namespace, String cdmAttrName, Class clazz, boolean overwriteNull, boolean obligat){
|
|
128
|
Object strValue;
|
|
129
|
strValue = getXmlInputValue(root, xmlElementName, namespace);
|
|
130
|
return addValue(strValue, cdmBase, cdmAttrName, clazz, overwriteNull, obligat);
|
|
131
|
}
|
|
132
|
|
|
133
|
public static boolean addValue(Object sourceValue, CdmBase cdmBase, String cdmAttrName, Class<?> clazz, boolean overwriteNull, boolean obligat){
|
|
134
|
String methodName;
|
|
135
|
// Object strValue;
|
|
136
|
try {
|
|
137
|
if (overwriteNull == NO_OVERWRITE && sourceValue == null ){
|
|
138
|
if (logger.isDebugEnabled()) { logger.debug("no overwrite for NULL-value");}
|
|
139
|
return true;
|
|
140
|
}
|
|
141
|
if (logger.isDebugEnabled()) { logger.debug("addValue: " + sourceValue);}
|
|
142
|
methodName = getSetterMethodName(clazz, cdmAttrName);
|
|
143
|
Method cdmMethod = cdmBase.getClass().getMethod(methodName, clazz);
|
|
144
|
cdmMethod.invoke(cdmBase, sourceValue);
|
|
145
|
return true;
|
|
146
|
} catch (NullPointerException e) {
|
|
147
|
logger.error("NullPointerException: " + e.getMessage());
|
|
148
|
return false;
|
|
149
|
} catch (IllegalArgumentException e) {
|
|
150
|
logger.error("IllegalArgumentException: " + e.getMessage());
|
|
151
|
return false;
|
|
152
|
} catch (IllegalAccessException e) {
|
|
153
|
logger.error("IllegalAccessException: " + e.getMessage());
|
|
154
|
return false;
|
|
155
|
} catch (InvocationTargetException e) {
|
|
156
|
logger.error("InvocationTargetException: " + e.getMessage());
|
|
157
|
return false;
|
|
158
|
}catch (SecurityException e) {
|
|
159
|
logger.error("SecurityException: " + e.getMessage());
|
|
160
|
return false;
|
|
161
|
} catch (NoSuchMethodException e) {
|
|
162
|
if (obligat){
|
|
163
|
logger.error("NoSuchMethod: " + e.getMessage());
|
|
164
|
return false;
|
|
165
|
}else{
|
|
166
|
if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
|
|
167
|
return true;
|
|
168
|
}
|
|
169
|
}
|
|
170
|
|
|
171
|
}
|
|
172
|
|
|
173
|
/**
|
|
174
|
* @param clazz either boolean or other class (for boolean the naming strategy is different !)
|
|
175
|
* @param cdmAttrName
|
|
176
|
* @return
|
|
177
|
// * @throws IllegalArgumentException if a clazz is not yet supported
|
|
178
|
*/
|
|
179
|
public static String getSetterMethodName(Class<?> clazz, String cdmAttrName) {
|
|
180
|
return getSetterPutterMethodName(clazz, cdmAttrName, "set");
|
|
181
|
}
|
|
182
|
|
|
183
|
/**
|
|
184
|
* @param clazz either boolean or other class (for boolean the naming strategy is different !)
|
|
185
|
* @param cdmAttrName
|
|
186
|
* @return
|
|
187
|
// * @throws IllegalArgumentException if a clazz is not yet supported
|
|
188
|
*/
|
|
189
|
public static String getPutterMethodName(Class<?> clazz, String cdmAttrName) {
|
|
190
|
return getSetterPutterMethodName(clazz, cdmAttrName, "put");
|
|
191
|
}
|
|
192
|
|
|
193
|
/**
|
|
194
|
* @param clazz either boolean or other class (for boolean the naming strategy is different !)
|
|
195
|
* @param cdmAttrName
|
|
196
|
* @return
|
|
197
|
// * @throws IllegalArgumentException if a clazz is not yet supported
|
|
198
|
*/
|
|
199
|
private static String getSetterPutterMethodName(Class<?> clazz, String cdmAttrName, String prefix) {
|
|
200
|
String methodName;
|
|
201
|
if (clazz == boolean.class || clazz == Boolean.class){
|
|
202
|
if (cdmAttrName == null || cdmAttrName.length() < 1 ){
|
|
203
|
throw new IllegalArgumentException("boolean CdmAttributeName should have atleast 3 characters");
|
|
204
|
}
|
|
205
|
methodName = prefix + cdmAttrName.substring(2, 3).toUpperCase() + cdmAttrName.substring(3) ;
|
|
206
|
}else {
|
|
207
|
if (cdmAttrName == null || cdmAttrName.length() < 1 ){
|
|
208
|
throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
|
|
209
|
}
|
|
210
|
methodName = prefix + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
|
|
211
|
}
|
|
212
|
return methodName;
|
|
213
|
}
|
|
214
|
|
|
215
|
private static boolean valuesAreNull(List<Object> values){
|
|
216
|
for (Object sourceValue : values.toArray()){
|
|
217
|
if (sourceValue != null){
|
|
218
|
return false;
|
|
219
|
}
|
|
220
|
}
|
|
221
|
return true;
|
|
222
|
}
|
|
223
|
|
|
224
|
public static boolean addMultipleValues(List<Object> sourceValues, CdmBase cdmBase, String cdmAttrName, List<Class> classes, boolean overwriteNull, boolean obligat){
|
|
225
|
String methodName;
|
|
226
|
// Object strValue;
|
|
227
|
try {
|
|
228
|
|
|
229
|
if (overwriteNull == NO_OVERWRITE && valuesAreNull(sourceValues)){
|
|
230
|
if (logger.isDebugEnabled()) { logger.debug("no overwrite for NULL-value");}
|
|
231
|
return true;
|
|
232
|
}
|
|
233
|
if (logger.isDebugEnabled()) { logger.debug("addValues: " + sourceValues.toString());}
|
|
234
|
|
|
235
|
|
|
236
|
if (cdmAttrName == null || cdmAttrName.length() < 1 ){
|
|
237
|
throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
|
|
238
|
}
|
|
239
|
methodName = "add" + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
|
|
240
|
|
|
241
|
Class<?>[] classArray = classes.toArray(new Class[0]);
|
|
242
|
Method cdmMethod = cdmBase.getClass().getMethod(methodName, classArray);
|
|
243
|
cdmMethod.invoke(cdmBase, sourceValues.toArray());
|
|
244
|
return true;
|
|
245
|
} catch (NullPointerException e) {
|
|
246
|
logger.error("NullPointerException: " + e.getMessage());
|
|
247
|
return false;
|
|
248
|
} catch (IllegalArgumentException e) {
|
|
249
|
logger.error("IllegalArgumentException: " + e.getMessage());
|
|
250
|
return false;
|
|
251
|
} catch (IllegalAccessException e) {
|
|
252
|
logger.error("IllegalAccessException: " + e.getMessage());
|
|
253
|
return false;
|
|
254
|
} catch (InvocationTargetException e) {
|
|
255
|
logger.error("InvocationTargetException: " + e.getMessage());
|
|
256
|
return false;
|
|
257
|
}catch (SecurityException e) {
|
|
258
|
logger.error("SecurityException: " + e.getMessage());
|
|
259
|
return false;
|
|
260
|
} catch (NoSuchMethodException e) {
|
|
261
|
if (obligat){
|
|
262
|
logger.error("NoSuchMethod: " + e.getMessage());
|
|
263
|
return false;
|
|
264
|
}else{
|
|
265
|
if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
|
|
266
|
return true;
|
|
267
|
}
|
|
268
|
}
|
|
269
|
|
|
270
|
}
|
|
271
|
|
|
272
|
public static boolean addAnnotationFromResultSet(ResultSet rs, String attributeName, AnnotatableEntity cdmBase, Language language){
|
|
273
|
try {
|
|
274
|
String value = rs.getString(attributeName);
|
|
275
|
if (CdmUtils.Nz(value).equals("")){
|
|
276
|
String strAnnotation = attributeName + ": " + value;
|
|
277
|
Annotation annoatation = Annotation.NewInstance(strAnnotation, language);
|
|
278
|
cdmBase.addAnnotation(annoatation);
|
|
279
|
|
|
280
|
}
|
|
281
|
return true;
|
|
282
|
} catch (SQLException e) {
|
|
283
|
logger.warn(e);
|
|
284
|
e.printStackTrace();
|
|
285
|
return false;
|
|
286
|
}
|
|
287
|
}
|
|
288
|
|
|
289
|
|
|
290
|
|
|
291
|
public static Object getXmlInputValue(Element root, String xmlElementName, Namespace namespace){
|
|
292
|
Object result = null;
|
|
293
|
Element child = root.getChild(xmlElementName, namespace);
|
|
294
|
if (child != null){
|
|
295
|
result = child.getText().trim();
|
|
296
|
}
|
|
297
|
return result;
|
|
298
|
}
|
|
299
|
|
|
300
|
|
|
301
|
public static TimePeriod getDatePublished(String refYear){
|
|
302
|
TimePeriod resultNew;
|
|
303
|
try {
|
|
304
|
resultNew = TimePeriodParser.parseString(refYear);
|
|
305
|
} catch (IllegalArgumentException e) {
|
|
306
|
logger.warn("RefYear could not be parsed: " + refYear);
|
|
307
|
resultNew = null;
|
|
308
|
}
|
|
309
|
return resultNew;
|
|
310
|
}
|
|
311
|
|
|
312
|
//************** EXPORT *******************/
|
|
313
|
|
|
314
|
|
|
315
|
public static<T extends Object> T getValue(CdmBase cdmBase, String cdmAttrName, boolean isBoolean, boolean obligatory){
|
|
316
|
String methodName;
|
|
317
|
T result;
|
|
318
|
try {
|
|
319
|
methodName = getGetterMethodName(cdmAttrName, isBoolean);
|
|
320
|
if (cdmBase.isInstanceOf(NonViralName.class)){
|
|
321
|
cdmBase = CdmBase.deproxy(cdmBase);
|
|
322
|
}
|
|
323
|
Method cdmMethod = cdmBase.getClass().getMethod(methodName);
|
|
324
|
result = (T)cdmMethod.invoke(cdmBase);
|
|
325
|
return result;
|
|
326
|
} catch (NullPointerException e) {
|
|
327
|
logger.error("NullPointerException: " + e.getMessage());
|
|
328
|
return null;
|
|
329
|
} catch (IllegalArgumentException e) {
|
|
330
|
logger.error("IllegalArgumentException: " + e.getMessage());
|
|
331
|
return null;
|
|
332
|
} catch (IllegalAccessException e) {
|
|
333
|
logger.error("IllegalAccessException: " + e.getMessage());
|
|
334
|
return null;
|
|
335
|
} catch (InvocationTargetException e) {
|
|
336
|
logger.error("InvocationTargetException: " + e.getMessage());
|
|
337
|
return null;
|
|
338
|
}catch (SecurityException e) {
|
|
339
|
logger.error("SecurityException: " + e.getMessage());
|
|
340
|
return null;
|
|
341
|
} catch (NoSuchMethodException e) {
|
|
342
|
if (obligatory){
|
|
343
|
logger.error("NoSuchMethod: " + e.getMessage());
|
|
344
|
return null;
|
|
345
|
}else{
|
|
346
|
if (logger.isDebugEnabled()){ logger.debug("NoSuchMethod: " + e.getMessage());}
|
|
347
|
return null;
|
|
348
|
}
|
|
349
|
}
|
|
350
|
|
|
351
|
}
|
|
352
|
|
|
353
|
/**
|
|
354
|
* @param cdmAttrName
|
|
355
|
* @param isBoolean
|
|
356
|
* @return
|
|
357
|
*/
|
|
358
|
public static String getGetterMethodName(String cdmAttrName, boolean isBoolean) {
|
|
359
|
String methodName;
|
|
360
|
if (isBoolean){
|
|
361
|
if (cdmAttrName == null || cdmAttrName.length() < 3 || !( cdmAttrName.startsWith("is") || cdmAttrName.startsWith("use")) ){
|
|
362
|
throw new IllegalArgumentException("boolean CdmAttributeName should have atleast 3 characters and start with 'is' or 'use': " + cdmAttrName);
|
|
363
|
}
|
|
364
|
methodName = cdmAttrName ;
|
|
365
|
}else {
|
|
366
|
if (cdmAttrName == null || cdmAttrName.length() < 1 ){
|
|
367
|
throw new IllegalArgumentException("CdmAttributeName should have atleast 1 character");
|
|
368
|
}
|
|
369
|
methodName = "get" + cdmAttrName.substring(0, 1).toUpperCase() + cdmAttrName.substring(1) ;
|
|
370
|
}
|
|
371
|
return methodName;
|
|
372
|
}
|
|
373
|
|
|
374
|
}
|