1
|
/**
|
2
|
* Copyright (C) 2008 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
|
package eu.etaxonomy.cdm.io.excel.distribution;
|
10
|
|
11
|
import java.io.FileNotFoundException;
|
12
|
import eu.etaxonomy.cdm.common.URI;
|
13
|
import java.util.ArrayList;
|
14
|
import java.util.HashMap;
|
15
|
import java.util.List;
|
16
|
import java.util.Map;
|
17
|
import java.util.Set;
|
18
|
|
19
|
import org.apache.log4j.Logger;
|
20
|
import org.springframework.stereotype.Component;
|
21
|
import org.springframework.transaction.TransactionStatus;
|
22
|
|
23
|
import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorFactory;
|
24
|
import eu.etaxonomy.cdm.api.service.config.IdentifiableServiceConfiguratorImpl;
|
25
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
26
|
import eu.etaxonomy.cdm.common.ExcelUtils;
|
27
|
import eu.etaxonomy.cdm.io.common.CdmImportBase;
|
28
|
import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;
|
29
|
import eu.etaxonomy.cdm.io.excel.common.ExcelImportConfiguratorBase;
|
30
|
import eu.etaxonomy.cdm.io.excel.common.ExcelImportState;
|
31
|
import eu.etaxonomy.cdm.io.excel.common.ExcelRowBase;
|
32
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
33
|
import eu.etaxonomy.cdm.model.description.Distribution;
|
34
|
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
|
35
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
36
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
37
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
38
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
39
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
40
|
|
41
|
/**
|
42
|
* @author a.babadshanjan
|
43
|
* @since 10.11.2008
|
44
|
*/
|
45
|
@Component
|
46
|
public class DistributionImport
|
47
|
extends CdmImportBase<ExcelImportConfiguratorBase, ExcelImportState<ExcelImportConfiguratorBase, ExcelRowBase>> {
|
48
|
|
49
|
private static final long serialVersionUID = 7765309119416657235L;
|
50
|
|
51
|
private static final Logger logger = Logger.getLogger(DistributionImport.class);
|
52
|
|
53
|
/* used */
|
54
|
private static final String EDIT_NAME_COLUMN = "EDIT";
|
55
|
private static final String TDWG_DISTRIBUTION_COLUMN = "TDWG";
|
56
|
private static final String STATUS_COLUMN = "Status";
|
57
|
/* not used */
|
58
|
// private static final String LITERATURE_NUMBER_COLUMN = "Lit.";
|
59
|
// private static final String LITERATURE_COLUMN = "Literature";
|
60
|
// private static final String VERNACULAR_NAME_COLUMN = "Vernacular";
|
61
|
// private static final String HABITAT_COLUMN = "Habitat";
|
62
|
// private static final String CONTROL_COLUMN = "Control";
|
63
|
// private static final String TRANSLATED_COLUMN = "Translated";
|
64
|
// private static final String ISO_DISTRIBUTION_COLUMN = "ISO";
|
65
|
// private static final String NOTES_COLUMN = "Notes";
|
66
|
// private static final String PAGE_NUMBER_COLUMN = "Page";
|
67
|
// private static final String INFO_COLUMN = "Info";
|
68
|
|
69
|
|
70
|
// Stores already processed descriptions
|
71
|
Map<Taxon, TaxonDescription> myDescriptions = new HashMap<Taxon, TaxonDescription>();
|
72
|
|
73
|
@Override
|
74
|
protected void doInvoke(ExcelImportState<ExcelImportConfiguratorBase, ExcelRowBase> state) {
|
75
|
|
76
|
if (logger.isDebugEnabled()) { logger.debug("Importing distribution data"); }
|
77
|
|
78
|
// read and save all rows of the excel worksheet
|
79
|
List<Map<String, String>> recordList;
|
80
|
URI source = state.getConfig().getSource();
|
81
|
try{
|
82
|
recordList = ExcelUtils.parseXLS(source);
|
83
|
} catch (FileNotFoundException e) {
|
84
|
String message = "File not found: " + source;
|
85
|
warnProgress(state, message, e);
|
86
|
logger.error(message);
|
87
|
state.setUnsuccessfull();
|
88
|
return;
|
89
|
}
|
90
|
if (recordList != null) {
|
91
|
Map<String,String> record = null;
|
92
|
TransactionStatus txStatus = startTransaction();
|
93
|
|
94
|
for (int i = 0; i < recordList.size(); i++) {
|
95
|
record = recordList.get(i);
|
96
|
analyzeRecord(record);
|
97
|
}
|
98
|
commitTransaction(txStatus);
|
99
|
}
|
100
|
|
101
|
try {
|
102
|
if (logger.isDebugEnabled()) { logger.debug("End distribution data import"); }
|
103
|
|
104
|
} catch (Exception e) {
|
105
|
logger.error("Error closing the application context");
|
106
|
e.printStackTrace();
|
107
|
}
|
108
|
|
109
|
return;
|
110
|
}
|
111
|
|
112
|
|
113
|
/**
|
114
|
* Reads the data of one Excel sheet row
|
115
|
*/
|
116
|
private void analyzeRecord(Map<String,String> record) {
|
117
|
/*
|
118
|
* Relevant columns:
|
119
|
* Name (EDIT)
|
120
|
* Distribution TDWG
|
121
|
* Status (only entries if not native)
|
122
|
* Literature number
|
123
|
* Literature
|
124
|
*/
|
125
|
|
126
|
String editName = "";
|
127
|
List<String> distributionList = new ArrayList<String>();
|
128
|
String status = "";
|
129
|
String literatureNumber = "";
|
130
|
String literature = "";
|
131
|
|
132
|
Set<String> keys = record.keySet();
|
133
|
|
134
|
for (String key: keys) {
|
135
|
|
136
|
String value = record.get(key);
|
137
|
if (!value.equals("")) {
|
138
|
if (logger.isDebugEnabled()) { logger.debug(key + ": '" + value + "'"); }
|
139
|
}
|
140
|
|
141
|
if (key.contains(EDIT_NAME_COLUMN)) {
|
142
|
editName = (String) CdmUtils.removeDuplicateWhitespace(value.trim());
|
143
|
|
144
|
} else if(key.contains(TDWG_DISTRIBUTION_COLUMN)) {
|
145
|
distributionList = CdmUtils.buildList(value);
|
146
|
|
147
|
} else if(key.contains(STATUS_COLUMN)) {
|
148
|
status = (String) CdmUtils.removeDuplicateWhitespace(value.trim());
|
149
|
|
150
|
// } else if(key.contains(LITERATURE_NUMBER_COLUMN)) {
|
151
|
// literatureNumber = (String) CdmUtils.removeDuplicateWhitespace(value.trim());
|
152
|
//
|
153
|
// } else if(key.contains(LITERATURE_COLUMN)) {
|
154
|
// literature = (String) CdmUtils.removeDuplicateWhitespace(value.trim());
|
155
|
//
|
156
|
} else {
|
157
|
//logger.warn("Column " + key + " ignored");
|
158
|
}
|
159
|
}
|
160
|
|
161
|
// Store the data of this record in the DB
|
162
|
if (!editName.equals("")) {
|
163
|
saveRecord(editName, distributionList, status, literatureNumber, literature);
|
164
|
}
|
165
|
}
|
166
|
|
167
|
|
168
|
/**
|
169
|
* Stores the data of one Excel sheet row in the database
|
170
|
*/
|
171
|
private void saveRecord(String taxonName, List<String> distributionList,
|
172
|
String status, String literatureNumber, String literature) {
|
173
|
|
174
|
IdentifiableServiceConfiguratorImpl<TaxonName> config = IdentifiableServiceConfiguratorFactory.getConfigurator(TaxonName.class);
|
175
|
config.setTitleSearchString(taxonName);
|
176
|
config.setMatchMode(MatchMode.BEGINNING);
|
177
|
|
178
|
try {
|
179
|
// get the matching names from the DB
|
180
|
//List<TaxonName> taxonNames = getNameService().findByTitle(config);
|
181
|
List<TaxonName> taxonNames = getNameService().findByName(null, taxonName, null, null, null, null,null,null).getRecords();
|
182
|
if (taxonNames.isEmpty()) {
|
183
|
logger.error("Taxon name '" + taxonName + "' not found in DB");
|
184
|
} else {
|
185
|
if (logger.isDebugEnabled()) { logger.debug("Taxon found"); }
|
186
|
}
|
187
|
|
188
|
// get the taxa for the matching names
|
189
|
for(TaxonName dbTaxonName: taxonNames) {
|
190
|
|
191
|
Set<Taxon> taxa = dbTaxonName.getTaxa();
|
192
|
if (taxa.isEmpty()) {
|
193
|
logger.warn("No taxon found for name '" + taxonName + "'");
|
194
|
} else if (taxa.size() > 1) {
|
195
|
logger.warn("More than one taxa found for name '" + taxonName + "'");
|
196
|
}
|
197
|
|
198
|
for(Taxon taxon: taxa) {
|
199
|
|
200
|
TaxonDescription myDescription = null;
|
201
|
|
202
|
// If we have created a description for this taxon earlier, take this one.
|
203
|
// Otherwise, create a new description.
|
204
|
// We don't update any existing descriptions in the database at this point.
|
205
|
if (myDescriptions.containsKey(taxon)) {
|
206
|
myDescription = myDescriptions.get(taxon);
|
207
|
} else {
|
208
|
myDescription = TaxonDescription.NewInstance(taxon);
|
209
|
taxon.addDescription(myDescription);
|
210
|
myDescriptions.put(taxon, myDescription);
|
211
|
}
|
212
|
|
213
|
// Status
|
214
|
PresenceAbsenceTerm presenceAbsenceStatus = PresenceAbsenceTerm.NewInstance();
|
215
|
if (status.equals("")) {
|
216
|
presenceAbsenceStatus = PresenceAbsenceTerm.NATIVE();
|
217
|
} else {
|
218
|
presenceAbsenceStatus = PresenceAbsenceTerm.getPresenceAbsenceTermByAbbreviation(status);
|
219
|
}
|
220
|
// TODO: Handle absence case.
|
221
|
// This case has not yet occurred in the excel input file, though.
|
222
|
|
223
|
/* Set to true if taxon needs to be saved if at least one new distribution exists */
|
224
|
boolean save = false;
|
225
|
|
226
|
// TDWG areas
|
227
|
for (String distribution: distributionList) {
|
228
|
|
229
|
/* Set to true if this distribution is a new one*/
|
230
|
boolean ignore = false;
|
231
|
|
232
|
if(!distribution.equals("")) {
|
233
|
NamedArea namedArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(distribution);
|
234
|
TaxonDescription taxonDescription = myDescriptions.get(taxon);
|
235
|
if (namedArea != null) {
|
236
|
// Check against existing distributions and ignore the ones that occur multiple times
|
237
|
Set<DescriptionElementBase> myDescriptionElements = taxonDescription.getElements();
|
238
|
for(DescriptionElementBase descriptionElement : myDescriptionElements) {
|
239
|
if (descriptionElement instanceof Distribution) {
|
240
|
if (namedArea == ((Distribution)descriptionElement).getArea()) {
|
241
|
ignore = true;
|
242
|
if (logger.isDebugEnabled()) {
|
243
|
logger.debug("Distribution ignored: " + distribution);
|
244
|
}
|
245
|
break;
|
246
|
}
|
247
|
}
|
248
|
}
|
249
|
// Create new distribution if not yet exist
|
250
|
if (ignore == false) {
|
251
|
save = true;
|
252
|
Distribution newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
|
253
|
myDescription.addElement(newDistribution);
|
254
|
if (logger.isDebugEnabled()) {
|
255
|
logger.debug("Distribution created: " + newDistribution.toString());
|
256
|
}
|
257
|
}
|
258
|
}
|
259
|
}
|
260
|
}
|
261
|
if (save == true) {
|
262
|
getTaxonService().save(taxon);
|
263
|
if (logger.isDebugEnabled()) { logger.debug("Taxon saved"); }
|
264
|
}
|
265
|
}
|
266
|
}
|
267
|
} catch (Exception e) {
|
268
|
logger.error("Error");
|
269
|
e.printStackTrace();
|
270
|
}
|
271
|
}
|
272
|
|
273
|
|
274
|
@Override
|
275
|
protected boolean doCheck(ExcelImportState<ExcelImportConfiguratorBase, ExcelRowBase> state) {
|
276
|
boolean result = true;
|
277
|
logger.warn("No check implemented for distribution data import");
|
278
|
return result;
|
279
|
}
|
280
|
|
281
|
|
282
|
@Override
|
283
|
protected boolean isIgnore(ExcelImportState<ExcelImportConfiguratorBase, ExcelRowBase> state) {
|
284
|
return false;
|
285
|
}
|
286
|
|
287
|
}
|