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.taxonx;
|
11
|
|
12
|
import java.util.HashMap;
|
13
|
import java.util.Iterator;
|
14
|
import java.util.List;
|
15
|
import java.util.Map;
|
16
|
|
17
|
import org.apache.log4j.Logger;
|
18
|
import org.jdom.Attribute;
|
19
|
import org.jdom.Content;
|
20
|
import org.jdom.Element;
|
21
|
import org.jdom.Namespace;
|
22
|
import org.jdom.Text;
|
23
|
import org.springframework.stereotype.Component;
|
24
|
|
25
|
import eu.etaxonomy.cdm.api.application.CdmApplicationController;
|
26
|
import eu.etaxonomy.cdm.api.service.ICommonService;
|
27
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
28
|
import eu.etaxonomy.cdm.io.common.CdmIoBase;
|
29
|
import eu.etaxonomy.cdm.io.common.ICdmIO;
|
30
|
import eu.etaxonomy.cdm.io.common.IImportConfigurator;
|
31
|
import eu.etaxonomy.cdm.model.common.Language;
|
32
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
33
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
34
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
35
|
import eu.etaxonomy.cdm.model.description.Feature;
|
36
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
37
|
import eu.etaxonomy.cdm.model.description.TextData;
|
38
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
39
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
40
|
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
|
41
|
|
42
|
|
43
|
/**
|
44
|
* @author a.mueller
|
45
|
* @created 29.07.2008
|
46
|
* @version 1.0
|
47
|
*/
|
48
|
@Component
|
49
|
public class TaxonXDescriptionImport extends CdmIoBase<TaxonXImportState> implements ICdmIO<TaxonXImportState> {
|
50
|
private static final Logger logger = Logger.getLogger(TaxonXDescriptionImport.class);
|
51
|
|
52
|
public TaxonXDescriptionImport(){
|
53
|
super();
|
54
|
}
|
55
|
|
56
|
@Override
|
57
|
public boolean doCheck(TaxonXImportState state){
|
58
|
boolean result = true;
|
59
|
logger.warn("Checking for Facts not yet implemented");
|
60
|
//result &= checkArticlesWithoutJournal(bmiConfig);
|
61
|
|
62
|
return result;
|
63
|
}
|
64
|
|
65
|
public Map<Integer, Feature> fillFactCategories(IImportConfigurator config, CdmApplicationController cdmApp){
|
66
|
logger.warn("not yet implemented");
|
67
|
Map<Integer, Feature> featureMap = new HashMap<Integer, Feature>();
|
68
|
// IDescriptionService descriptionService = cdmApp.getDescriptionService();
|
69
|
// ITermService termService = cdmApp.getTermService();
|
70
|
//
|
71
|
// Object source = config.getSource();
|
72
|
return featureMap;
|
73
|
}
|
74
|
|
75
|
private String getDescriptionTitle(TaxonXImportState state){
|
76
|
String result = "Untitled";
|
77
|
Reference ref = state.getModsReference();
|
78
|
if (ref != null){
|
79
|
result = ref.getTitle();
|
80
|
if ( CdmUtils.isEmpty(result)){
|
81
|
result = ref.getTitleCache();
|
82
|
}
|
83
|
}
|
84
|
return result;
|
85
|
}
|
86
|
|
87
|
@Override
|
88
|
public void doInvoke(TaxonXImportState state){
|
89
|
logger.debug("not yet fully implemented");
|
90
|
|
91
|
TaxonXImportConfigurator txConfig = state.getConfig();
|
92
|
Element root = txConfig.getSourceRoot();
|
93
|
Namespace nsTaxonx = root.getNamespace();
|
94
|
|
95
|
//Object source = config.getSource();
|
96
|
|
97
|
logger.info("start make Descriptions ...");
|
98
|
|
99
|
|
100
|
//for testing only
|
101
|
Taxon taxon = getTaxon(txConfig);
|
102
|
if (taxon == null){
|
103
|
logger.warn("Taxon could not be found");
|
104
|
state.setUnsuccessfull();
|
105
|
}
|
106
|
|
107
|
Reference modsReference = state.getModsReference();
|
108
|
if (modsReference == null){
|
109
|
modsReference = state.getConfig().getSourceReference();
|
110
|
}
|
111
|
|
112
|
//unlazyDescription(txConfig, taxon);
|
113
|
TaxonDescription description = TaxonDescription.NewInstance();
|
114
|
description.setTitleCache(getDescriptionTitle(state), true);
|
115
|
if (modsReference != null){
|
116
|
description.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, modsReference, null);
|
117
|
}
|
118
|
|
119
|
Element elTaxonBody = root.getChild("taxonxBody", nsTaxonx);
|
120
|
Element elTreatment = elTaxonBody.getChild("treatment", nsTaxonx);
|
121
|
List<Element> elDivs = elTreatment.getChildren("div", nsTaxonx);
|
122
|
for (Element div : elDivs){
|
123
|
Attribute attrType = div.getAttribute("type", nsTaxonx);
|
124
|
String strType = attrType.getValue();
|
125
|
Feature feature = null;
|
126
|
try {
|
127
|
feature = TaxonXTransformer.descriptionType2feature(strType);
|
128
|
} catch (UnknownCdmTypeException e) {
|
129
|
feature = handleFeatureException(strType, e, txConfig);
|
130
|
}
|
131
|
String text = getText(div);
|
132
|
if (!"".equals(CdmUtils.Nz(text).trim())){
|
133
|
// hibernate throws an exception when a string is longer than approx. 65500 chars.
|
134
|
// for now we truncate any description text to 65500 characters.
|
135
|
if(text.length() > 65500){
|
136
|
text = text.substring(0, 65500) + "... [text truncated]";
|
137
|
logger.warn("Truncation of text: description for taxon " + taxon.getTitleCache() + " was longer than 65500 characters.");
|
138
|
}
|
139
|
|
140
|
DescriptionElementBase descriptionElement = TextData.NewInstance(text, Language.ENGLISH(), null);
|
141
|
descriptionElement.setFeature(feature);
|
142
|
description.addElement(descriptionElement);
|
143
|
|
144
|
//add reference
|
145
|
if (modsReference != null){
|
146
|
descriptionElement.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, modsReference, null, null, null);
|
147
|
}
|
148
|
}
|
149
|
|
150
|
}
|
151
|
if (description.size() >0){
|
152
|
taxon.addDescription(description);
|
153
|
getTaxonService().save(taxon);
|
154
|
}
|
155
|
return;
|
156
|
}
|
157
|
|
158
|
private Feature handleFeatureException(String strType, UnknownCdmTypeException e, TaxonXImportConfigurator txConfig){
|
159
|
Feature feature = null;
|
160
|
TermVocabulary<Feature> featureVoc = Feature.BIOLOGY_ECOLOGY().getVocabulary();
|
161
|
for (Feature oneFeature : featureVoc.getTerms()){
|
162
|
if (strType.equals(oneFeature.getLabel()) || strType.equals(oneFeature.getRepresentation(Language.DEFAULT() ).getText() )){
|
163
|
feature = oneFeature;
|
164
|
}
|
165
|
}
|
166
|
|
167
|
if (feature == null){
|
168
|
feature = Feature.NewInstance(strType, strType, null);
|
169
|
featureVoc.addTerm(feature);
|
170
|
getTermService().save(feature);
|
171
|
logger.warn(e.getMessage() + ". Feature was added to the feature vocabulary. " + getBracketSourceName(txConfig));
|
172
|
}
|
173
|
return feature;
|
174
|
}
|
175
|
|
176
|
|
177
|
private String getText(Element div){
|
178
|
String result = "";
|
179
|
Iterator<Content> it =div.getDescendants();
|
180
|
while (it.hasNext()){
|
181
|
Content next = it.next();
|
182
|
if (next instanceof Text){
|
183
|
result += ((Text)next).getText();
|
184
|
}
|
185
|
}
|
186
|
return result;
|
187
|
}
|
188
|
|
189
|
private Taxon getTaxon(TaxonXImportConfigurator config){
|
190
|
Taxon result;
|
191
|
// result = Taxon.NewInstance(BotanicalName.NewInstance(null), null);
|
192
|
ICommonService commonService = getCommonService();
|
193
|
|
194
|
String originalSourceId = config.getOriginalSourceId();
|
195
|
String namespace = config.getOriginalSourceTaxonNamespace();
|
196
|
result = (Taxon)commonService.getSourcedObjectByIdInSource(Taxon.class, originalSourceId , namespace);
|
197
|
if (result == null){
|
198
|
logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found");
|
199
|
}
|
200
|
return result;
|
201
|
}
|
202
|
|
203
|
private void unlazyDescription(TaxonXImportConfigurator config, Taxon taxon){
|
204
|
// logger.warn("Preliminary commented"); //used single Transaction for all import instead !
|
205
|
// TransactionStatus txStatus = config.getCdmAppController().startTransaction();
|
206
|
// ITaxonService taxonService = config.getCdmAppController().getTaxonService();
|
207
|
// taxonService.saveTaxon(taxon);
|
208
|
// taxon.getDescriptions().size();
|
209
|
// config.getCdmAppController().commitTransaction(txStatus);
|
210
|
}
|
211
|
|
212
|
/* (non-Javadoc)
|
213
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
214
|
*/
|
215
|
@Override
|
216
|
protected boolean isIgnore(TaxonXImportState state){
|
217
|
return ! state.getConfig().isDoFacts();
|
218
|
}
|
219
|
|
220
|
private String getBracketSourceName(TaxonXImportConfigurator config){
|
221
|
return "(" + config.getSourceNameString() + ")";
|
222
|
}
|
223
|
|
224
|
}
|