|
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.specimen;
|
|
11
|
|
|
12
|
|
|
13
|
import java.util.ArrayList;
|
|
14
|
import java.util.HashSet;
|
|
15
|
import java.util.List;
|
|
16
|
import java.util.UUID;
|
|
17
|
|
|
18
|
import org.apache.commons.lang.StringUtils;
|
|
19
|
import org.apache.log4j.Logger;
|
|
20
|
|
|
21
|
import eu.etaxonomy.cdm.api.service.IAgentService;
|
|
22
|
import eu.etaxonomy.cdm.api.service.ITermService;
|
|
23
|
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
|
|
24
|
import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;
|
|
25
|
import eu.etaxonomy.cdm.io.taxonx2013.TaxonXImportConfigurator;
|
|
26
|
import eu.etaxonomy.cdm.model.agent.Person;
|
|
27
|
import eu.etaxonomy.cdm.model.agent.Team;
|
|
28
|
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
|
|
29
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
30
|
import eu.etaxonomy.cdm.model.common.LanguageString;
|
|
31
|
import eu.etaxonomy.cdm.model.common.TimePeriod;
|
|
32
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
33
|
import eu.etaxonomy.cdm.model.location.Point;
|
|
34
|
import eu.etaxonomy.cdm.model.location.ReferenceSystem;
|
|
35
|
import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
|
|
36
|
|
|
37
|
/**
|
|
38
|
* @author p.kelbert
|
|
39
|
* @created 20.10.2008
|
|
40
|
* @version 1.0
|
|
41
|
*/
|
|
42
|
public class UnitsGatheringEvent {
|
|
43
|
|
|
44
|
private static final Logger logger = Logger.getLogger(UnitsGatheringEvent.class);
|
|
45
|
private static final boolean DEBUG = false;
|
|
46
|
private final GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
|
|
47
|
|
|
48
|
/*
|
|
49
|
* Constructor
|
|
50
|
* Fill in the locality, coordinates and the collector(s) for the current GatheringEvent
|
|
51
|
* @param app: the CDM Application Controller
|
|
52
|
* @param locality
|
|
53
|
* @param languageIso
|
|
54
|
* @param longitude
|
|
55
|
* @param latitude
|
|
56
|
* @param collectorNames
|
|
57
|
*/
|
|
58
|
public UnitsGatheringEvent(ITermService termService, String locality, String languageIso, Double longitude,
|
|
59
|
Double latitude, String collectorName, String team, SpecimenSynthesysExcelImportConfigurator config){
|
|
60
|
this.setLocality(termService, locality, languageIso);
|
|
61
|
this.setCoordinates(longitude, latitude);
|
|
62
|
if (!collectorName.isEmpty()) {
|
|
63
|
this.setCollector(collectorName, config);
|
|
64
|
}
|
|
65
|
if (!team.isEmpty()) {
|
|
66
|
this.setTeam(team, config);
|
|
67
|
}
|
|
68
|
}
|
|
69
|
//
|
|
70
|
public UnitsGatheringEvent(ITermService termService, String locality, String collectorName, Double longitude,
|
|
71
|
Double latitude, TaxonXImportConfigurator config,IAgentService agentService){
|
|
72
|
if (!StringUtils.isEmpty(locality)) {
|
|
73
|
this.setLocality(termService, locality, null);
|
|
74
|
}
|
|
75
|
this.setCoordinates(longitude, latitude);
|
|
76
|
if (!StringUtils.isEmpty(collectorName)) {
|
|
77
|
this.setCollector(collectorName, config, agentService);
|
|
78
|
}
|
|
79
|
// if (!team.isEmpty()) {
|
|
80
|
// this.setTeam(team, config);
|
|
81
|
// }
|
|
82
|
}
|
|
83
|
|
|
84
|
/*
|
|
85
|
* Constructor
|
|
86
|
* Fill in the locality, coordinates and the collector(s) for the current GatheringEvent
|
|
87
|
* @param app: the CDM Application Controller
|
|
88
|
* @param locality
|
|
89
|
* @param languageIso
|
|
90
|
* @param longitude
|
|
91
|
* @param latitude
|
|
92
|
* @param collectorNames
|
|
93
|
*/
|
|
94
|
public UnitsGatheringEvent(ITermService termService, String locality, String languageIso, Double longitude,
|
|
95
|
Double latitude, String elevationText, String elevationMin, String elevationMax, String elevationUnit, String date, List<String> collectorName, List<String> team, Abcd206ImportConfigurator config){
|
|
96
|
this.setLocality(termService, locality, languageIso);
|
|
97
|
this.setCoordinates(longitude, latitude);
|
|
98
|
this.setDate(date);
|
|
99
|
this.setElevation(elevationText, elevationMin, elevationMax, elevationUnit);
|
|
100
|
if (!collectorName.isEmpty()) {
|
|
101
|
List<String> tmp = new ArrayList<String>(new HashSet<String>(collectorName));
|
|
102
|
this.setCollector(tmp.get(0), config);
|
|
103
|
}
|
|
104
|
if (!team.isEmpty()) {
|
|
105
|
List<String> tmpTeam = new ArrayList<String>(new HashSet<String>(team));
|
|
106
|
this.setTeam(StringUtils.join(tmpTeam," & "), config);
|
|
107
|
}
|
|
108
|
}
|
|
109
|
|
|
110
|
public GatheringEvent getGatheringEvent(){
|
|
111
|
return this.gatheringEvent;
|
|
112
|
}
|
|
113
|
|
|
114
|
/**
|
|
115
|
* Set the locality for the current GatheringEvent
|
|
116
|
* @param locality
|
|
117
|
* @param langageIso
|
|
118
|
*/
|
|
119
|
public void setLocality(ITermService termService, String locality, String languageIso){
|
|
120
|
LanguageString loc = null;
|
|
121
|
List<LanguageString> languages = termService.getAllLanguageStrings(0, 0);
|
|
122
|
boolean locFound=false;
|
|
123
|
if ((languageIso == null) || (termService.getLanguageByIso(languageIso) == null)){
|
|
124
|
// if (languageIso != null && termService.getLanguageByIso(languageIso) == null ){
|
|
125
|
// logger.info("unknown iso used for the locality: "+languageIso);
|
|
126
|
// }
|
|
127
|
for (LanguageString ls:languages){
|
|
128
|
if (ls.getText().equalsIgnoreCase(locality)){
|
|
129
|
loc=ls;
|
|
130
|
locFound=true;
|
|
131
|
// System.out.println("REUSE LOCALITY");
|
|
132
|
}
|
|
133
|
}
|
|
134
|
if (!locFound){
|
|
135
|
loc = LanguageString.NewInstance(locality, Language.DEFAULT());
|
|
136
|
termService.saveLanguageData(loc);
|
|
137
|
languages.add(loc);
|
|
138
|
}
|
|
139
|
}else{
|
|
140
|
for (LanguageString ls:languages){
|
|
141
|
if (ls.getText().equalsIgnoreCase(locality) && ls.getLanguage().equals(termService.getLanguageByIso(languageIso))){
|
|
142
|
loc=ls;
|
|
143
|
locFound=true;
|
|
144
|
// System.out.println("REUSE LOCALITY");
|
|
145
|
}
|
|
146
|
}
|
|
147
|
if (!locFound) {
|
|
148
|
loc = LanguageString.NewInstance(locality, termService.getLanguageByIso(languageIso));
|
|
149
|
termService.saveLanguageData(loc);
|
|
150
|
languages.add(loc);
|
|
151
|
}
|
|
152
|
}
|
|
153
|
if (loc == null){logger.warn("PROBLEM LOCALITY");}
|
|
154
|
this.gatheringEvent.setLocality(loc);
|
|
155
|
}
|
|
156
|
|
|
157
|
/*
|
|
158
|
* return the locality associated to the GatheringEvent
|
|
159
|
*/
|
|
160
|
public LanguageString getLocality(){
|
|
161
|
return this.gatheringEvent.getLocality();
|
|
162
|
}
|
|
163
|
|
|
164
|
/*
|
|
165
|
* Set the coordinates for the current GatheringEvent
|
|
166
|
* @param: longitude
|
|
167
|
* @param: latitude
|
|
168
|
*/
|
|
169
|
public void setCoordinates(Double longitude, Double latitude){
|
|
170
|
//create coordinates point
|
|
171
|
if((longitude == null) || (latitude == null)){
|
|
172
|
return;
|
|
173
|
}
|
|
174
|
Point coordinates = Point.NewInstance();
|
|
175
|
//add coordinates
|
|
176
|
if (longitude != 0.0) {
|
|
177
|
coordinates.setLongitude(longitude);
|
|
178
|
}
|
|
179
|
if (latitude != 0.0) {
|
|
180
|
coordinates.setLatitude(latitude);
|
|
181
|
}
|
|
182
|
//for proiBiosphere Quentin's data
|
|
183
|
coordinates.setReferenceSystem(ReferenceSystem.WGS84());
|
|
184
|
this.gatheringEvent.setExactLocation(coordinates);
|
|
185
|
|
|
186
|
}
|
|
187
|
|
|
188
|
public void setDate(String date){
|
|
189
|
TimePeriod timeperiod = this.gatheringEvent.getTimeperiod();
|
|
190
|
if(timeperiod==null){
|
|
191
|
timeperiod = TimePeriod.NewInstance();
|
|
192
|
this.gatheringEvent.setTimeperiod(timeperiod);
|
|
193
|
}
|
|
194
|
timeperiod.setFreeText(date);
|
|
195
|
}
|
|
196
|
|
|
197
|
public void setElevation(String elevationText, String elevationMin, String elevationMax, String elevationUnit){
|
|
198
|
if(elevationText!=null){
|
|
199
|
this.gatheringEvent.setAbsoluteElevationText(elevationText);
|
|
200
|
}
|
|
201
|
else{
|
|
202
|
//TODO check for unit at string end
|
|
203
|
String pattern = "\\D";// regex for non-digits
|
|
204
|
if(elevationMin!=null){
|
|
205
|
Integer min = Integer.parseInt(elevationMin.replaceAll(pattern, ""));
|
|
206
|
this.gatheringEvent.setAbsoluteElevation(min);
|
|
207
|
}
|
|
208
|
if(elevationMax!=null){
|
|
209
|
Integer max = Integer.parseInt(elevationMax.replaceAll(pattern, ""));
|
|
210
|
this.gatheringEvent.setAbsoluteElevation(max);
|
|
211
|
}
|
|
212
|
if(elevationUnit!=null){
|
|
213
|
if(!elevationUnit.equals("m")){
|
|
214
|
//TODO convert if necessary
|
|
215
|
}
|
|
216
|
}
|
|
217
|
}
|
|
218
|
}
|
|
219
|
|
|
220
|
/*
|
|
221
|
* Add a NamedArea to the GatheringEvent
|
|
222
|
* @param area: the NamedArea to add
|
|
223
|
*/
|
|
224
|
|
|
225
|
public void addArea(DefinedTermBase area){
|
|
226
|
if (area.isInstanceOf(NamedArea.class)) {
|
|
227
|
this.gatheringEvent.addCollectingArea((NamedArea) area);
|
|
228
|
} else {
|
|
229
|
logger.info("OUPPPPSS :"+area.getClass());
|
|
230
|
}
|
|
231
|
}
|
|
232
|
|
|
233
|
|
|
234
|
|
|
235
|
/*
|
|
236
|
* Create a new collector or collector's team
|
|
237
|
* @param: collectorNames: the list of names to add as collector/collectorTeam
|
|
238
|
* USED - create each time a new Collector
|
|
239
|
*/
|
|
240
|
public void setCollector(String collectorName, SpecimenSynthesysExcelImportConfigurator config){
|
|
241
|
// System.out.println("collectors : "+collectorNames.toString());
|
|
242
|
Person collector;
|
|
243
|
collector = Person.NewInstance();
|
|
244
|
collector.setTitleCache(collectorName, true);
|
|
245
|
if (DEBUG) {
|
|
246
|
System.out.println("getcoll:"+config.getPersons().get(collector.getTitleCache()));
|
|
247
|
}
|
|
248
|
this.gatheringEvent.setCollector(config.getPersons().get(collector.getTitleCache()));
|
|
249
|
|
|
250
|
}
|
|
251
|
|
|
252
|
/*
|
|
253
|
* Create a new collector or collector's team
|
|
254
|
* @param: collectorNames: the list of names to add as collector/collectorTeam
|
|
255
|
* USED - create each time a new Collector
|
|
256
|
*/
|
|
257
|
public void setCollector(String collectorName, TaxonXImportConfigurator config, IAgentService agentService){
|
|
258
|
// System.out.println("collectors : "+collectorNames.toString());
|
|
259
|
Person collector;
|
|
260
|
collector = Person.NewInstance();
|
|
261
|
collector.setTitleCache(collectorName, true);
|
|
262
|
Person collector_db = config.getPersons().get(collector.getTitleCache());
|
|
263
|
if (collector_db == null) {
|
|
264
|
UUID uuid = agentService.saveOrUpdate(collector);
|
|
265
|
collector_db=(Person) agentService.find(uuid);
|
|
266
|
}
|
|
267
|
this.gatheringEvent.setCollector(collector_db);
|
|
268
|
|
|
269
|
}
|
|
270
|
|
|
271
|
|
|
272
|
/*
|
|
273
|
* Create a new collector or collector's team
|
|
274
|
* @param: collectorNames: the list of names to add as collector/collectorTeam
|
|
275
|
* USED - create each time a new Collector
|
|
276
|
*/
|
|
277
|
public void setCollector(String collectorName, Abcd206ImportConfigurator config){
|
|
278
|
// System.out.println("collectors : "+collectorNames.toString());
|
|
279
|
Person collector;
|
|
280
|
collector = Person.NewInstance();
|
|
281
|
collector.setTitleCache(collectorName, true);
|
|
282
|
if (DEBUG) {
|
|
283
|
System.out.println("getcoll:"+config.getPersons().get(collector.getTitleCache()));
|
|
284
|
}
|
|
285
|
this.gatheringEvent.setCollector(config.getPersons().get(collector.getTitleCache()));
|
|
286
|
}
|
|
287
|
|
|
288
|
/**
|
|
289
|
* @param tp
|
|
290
|
*/
|
|
291
|
public void setGatheringDate(TimePeriod tp) {
|
|
292
|
this.gatheringEvent.setTimeperiod(tp);
|
|
293
|
}
|
|
294
|
|
|
295
|
/**
|
|
296
|
* @param gatheringTeam
|
|
297
|
*/
|
|
298
|
public void setTeam(String gatheringTeam, SpecimenSynthesysExcelImportConfigurator config) {
|
|
299
|
Team t = new Team();
|
|
300
|
if ((gatheringTeam != null) && !gatheringTeam.isEmpty()) {
|
|
301
|
if ((gatheringTeam.indexOf("et al.") != -1) || (gatheringTeam.indexOf("& al.") != -1) || (gatheringTeam.indexOf(" al.") != -1)){
|
|
302
|
t.setTitleCache(gatheringTeam);
|
|
303
|
} else{
|
|
304
|
String[] tmp1 = gatheringTeam.split(" et ");
|
|
305
|
for (String elt:tmp1){
|
|
306
|
String tmp2[] = elt.split("&");
|
|
307
|
for (String elt2:tmp2) {
|
|
308
|
if (!elt2.trim().isEmpty()) {
|
|
309
|
Person p = Person.NewInstance();
|
|
310
|
p.setTitleCache(elt2);
|
|
311
|
t.addTeamMember(p);
|
|
312
|
}
|
|
313
|
}
|
|
314
|
}
|
|
315
|
}
|
|
316
|
}
|
|
317
|
if (DEBUG) {
|
|
318
|
System.out.println("getteam:"+config.getTeams().get(t.getTitleCache()));
|
|
319
|
}
|
|
320
|
this.gatheringEvent.setCollector(config.getTeams().get(t.getTitleCache()));
|
|
321
|
}
|
|
322
|
|
|
323
|
/**
|
|
324
|
* @param gatheringTeam
|
|
325
|
*/
|
|
326
|
public void setTeam(String gatheringTeam, Abcd206ImportConfigurator config) {
|
|
327
|
Team t = new Team();
|
|
328
|
if ((gatheringTeam != null) && !gatheringTeam.isEmpty()) {
|
|
329
|
if ((gatheringTeam.indexOf("et al.") != -1) || (gatheringTeam.indexOf("& al.") != -1) || (gatheringTeam.indexOf(" al.") != -1)){
|
|
330
|
t.setTitleCache(gatheringTeam);
|
|
331
|
} else{
|
|
332
|
String[] tmp1 = gatheringTeam.split(" et ");
|
|
333
|
for (String elt:tmp1){
|
|
334
|
String tmp2[] = elt.split("&");
|
|
335
|
for (String elt2:tmp2) {
|
|
336
|
if (!elt2.trim().isEmpty()) {
|
|
337
|
Person p = Person.NewInstance();
|
|
338
|
p.setTitleCache(elt2);
|
|
339
|
t.addTeamMember(p);
|
|
340
|
}
|
|
341
|
}
|
|
342
|
}
|
|
343
|
}
|
|
344
|
}
|
|
345
|
if (DEBUG) {
|
|
346
|
System.out.println("getteam:"+config.getTeams().get(t.getTitleCache()));
|
|
347
|
}
|
|
348
|
this.gatheringEvent.setCollector(config.getTeams().get(t.getTitleCache()));
|
|
349
|
}
|
|
350
|
|
|
351
|
|
|
352
|
}
|