1 |
|
package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;
|
2 |
|
|
3 |
|
import java.sql.ResultSet;
|
4 |
|
import java.sql.SQLException;
|
5 |
|
import java.util.ArrayList;
|
6 |
|
import java.util.Collection;
|
7 |
|
import java.util.HashMap;
|
8 |
|
import java.util.HashSet;
|
9 |
|
import java.util.Iterator;
|
10 |
|
import java.util.List;
|
11 |
|
import java.util.Map;
|
12 |
|
import java.util.Set;
|
13 |
|
import java.util.UUID;
|
14 |
|
import java.util.Map.Entry;
|
15 |
|
|
16 |
|
import org.apache.log4j.Logger;
|
17 |
|
import org.springframework.stereotype.Component;
|
18 |
|
import org.springframework.transaction.TransactionStatus;
|
19 |
|
|
20 |
|
import eu.etaxonomy.cdm.io.common.Source;
|
21 |
|
import eu.etaxonomy.cdm.jaxb.TDWGNamespacePrefixMapper;
|
22 |
|
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
|
23 |
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
24 |
|
import eu.etaxonomy.cdm.model.common.Language;
|
25 |
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
26 |
|
import eu.etaxonomy.cdm.model.common.TermType;
|
27 |
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
28 |
|
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
|
29 |
|
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
|
30 |
|
import eu.etaxonomy.cdm.model.description.Distribution;
|
31 |
|
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
|
32 |
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
33 |
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
34 |
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
35 |
|
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
36 |
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
37 |
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
38 |
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
39 |
|
|
40 |
|
@Component
|
41 |
|
public class FaunaEuropaeaVernacularNamesImport extends FaunaEuropaeaImportBase {
|
42 |
|
private static final Logger logger = Logger.getLogger(FaunaEuropaeaVernacularNamesImport.class);
|
43 |
|
|
44 |
|
private HashMap<String, Reference> sourceMap = new HashMap<String, Reference>();
|
45 |
|
|
46 |
|
@Override
|
47 |
|
protected void doInvoke(FaunaEuropaeaImportState state) {
|
48 |
|
int limit = state.getConfig().getLimitSave();
|
49 |
|
|
50 |
|
if (state.getConfig().isDoVernacularNames()){
|
51 |
|
/* Taxon store for retrieving taxa from and saving taxa to CDM */
|
52 |
|
List<TaxonBase> taxonList = null;
|
53 |
|
/* UUID store as input for retrieving taxa from CDM */
|
54 |
|
Set<UUID> taxonUuids = null;
|
55 |
|
/* Store to hold helper objects */
|
56 |
|
Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuVernacularNamesMap = null;
|
57 |
|
|
58 |
|
|
59 |
|
TransactionStatus txStatus = null;
|
60 |
|
|
61 |
|
createSourceMap(state);
|
62 |
|
|
63 |
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
64 |
|
Source source = fauEuConfig.getSource();
|
65 |
|
|
66 |
|
int i = 0;
|
67 |
|
|
68 |
|
String selectCount =
|
69 |
|
" SELECT count(*) ";
|
70 |
|
|
71 |
|
String selectColumns =
|
72 |
|
" SELECT vernacularNames.*, Taxon.UUID ";
|
73 |
|
|
74 |
|
String fromClause =
|
75 |
|
" FROM vernacularNames INNER JOIN " +
|
76 |
|
" Taxon ON vernacularnames.UUID = Taxon.UUID ";
|
77 |
|
String orderBy = " ORDER BY vernacularNames.UUID";
|
78 |
|
|
79 |
|
String countQuery =
|
80 |
|
selectCount + fromClause;
|
81 |
|
|
82 |
|
String selectQuery =
|
83 |
|
selectColumns + fromClause + orderBy;
|
84 |
|
|
85 |
|
|
86 |
|
|
87 |
|
if(logger.isInfoEnabled()) { logger.info("Start making vernacular names..."); }
|
88 |
|
|
89 |
|
try {
|
90 |
|
ResultSet rs = source.getResultSet(countQuery);
|
91 |
|
rs.next();
|
92 |
|
int count = rs.getInt(1);
|
93 |
|
|
94 |
|
rs = source.getResultSet(selectQuery);
|
95 |
|
|
96 |
|
if (logger.isInfoEnabled()) {
|
97 |
|
logger.info("Number of rows: " + count);
|
98 |
|
logger.info("Count Query: " + countQuery);
|
99 |
|
logger.info("Select Query: " + selectQuery);
|
100 |
|
}
|
101 |
|
|
102 |
|
//int taxonId;
|
103 |
|
|
104 |
|
while (rs.next()) {
|
105 |
|
if ((i++ % limit) == 0) {
|
106 |
|
|
107 |
|
txStatus = startTransaction();
|
108 |
|
taxonUuids = new HashSet<UUID>(limit);
|
109 |
|
fauEuVernacularNamesMap = new HashMap<UUID, FaunaEuropaeaVernacularNamesTaxon>(limit);
|
110 |
|
|
111 |
|
if(logger.isInfoEnabled()) {
|
112 |
|
logger.info("i = " + i + " - vernacular names import transaction started");
|
113 |
|
}
|
114 |
|
}
|
115 |
|
|
116 |
|
//taxonId = rs.getInt("dis_tax_id");
|
117 |
|
String vernameGUID = rs.getString("GUID");
|
118 |
|
String vernacularNameString = rs.getString("verName");
|
119 |
|
//int taxonFk = rs.getInt("taxonFK");
|
120 |
|
int languageFK= rs.getInt("languageFK");
|
121 |
|
String languageCache = rs.getString("languageCache");
|
122 |
|
String taxonUUID= rs.getString("UUID");
|
123 |
|
String verSource = rs.getString("VerSource");
|
124 |
|
UUID currentTaxonUuid = null;
|
125 |
|
|
126 |
|
|
127 |
|
FaunaEuropaeaVernacularName fauEuVernacularName = new FaunaEuropaeaVernacularName();
|
128 |
|
fauEuVernacularName.setGuid(vernameGUID);
|
129 |
|
fauEuVernacularName.setLanguageCache(languageCache);
|
130 |
|
fauEuVernacularName.setLanguageFk(languageFK);
|
131 |
|
fauEuVernacularName.setVernacularName(vernacularNameString);
|
132 |
|
fauEuVernacularName.setSource(verSource);
|
133 |
|
fauEuVernacularName.setTaxonUuid(UUID.fromString(taxonUUID));
|
134 |
|
currentTaxonUuid =UUID.fromString(taxonUUID);
|
135 |
|
if (!taxonUuids.contains(currentTaxonUuid)) {
|
136 |
|
taxonUuids.add(currentTaxonUuid);
|
137 |
|
FaunaEuropaeaVernacularNamesTaxon fauEuVernacularNameTaxon =
|
138 |
|
new FaunaEuropaeaVernacularNamesTaxon(currentTaxonUuid);
|
139 |
|
fauEuVernacularNamesMap.put(currentTaxonUuid, fauEuVernacularNameTaxon);
|
140 |
|
fauEuVernacularNameTaxon = null;
|
141 |
|
} else {
|
142 |
|
if (logger.isTraceEnabled()) {
|
143 |
|
logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
144 |
|
continue;
|
145 |
|
}
|
146 |
|
}
|
147 |
|
|
148 |
|
fauEuVernacularNamesMap.get(currentTaxonUuid).addVernacularName(fauEuVernacularName);
|
149 |
|
|
150 |
|
if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
151 |
|
|
152 |
|
try {
|
153 |
|
commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
|
154 |
|
taxonUuids = null;
|
155 |
|
taxonList = null;
|
156 |
|
fauEuVernacularNamesMap = null;
|
157 |
|
|
158 |
|
} catch (Exception e) {
|
159 |
|
logger.error("Commit of taxa and distributions failed" + e.getMessage());
|
160 |
|
e.printStackTrace();
|
161 |
|
}
|
162 |
|
|
163 |
|
if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}
|
164 |
|
}
|
165 |
|
|
166 |
|
|
167 |
|
}
|
168 |
|
if (taxonUuids != null){
|
169 |
|
try {
|
170 |
|
commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
|
171 |
|
taxonUuids = null;
|
172 |
|
taxonList = null;
|
173 |
|
fauEuVernacularNamesMap = null;
|
174 |
|
} catch (Exception e) {
|
175 |
|
logger.error("Commit of taxa and vernacular names failed");
|
176 |
|
logger.error(e.getMessage());
|
177 |
|
e.printStackTrace();
|
178 |
|
}
|
179 |
|
}
|
180 |
|
rs = null;
|
181 |
|
} catch (SQLException e) {
|
182 |
|
logger.error("SQLException:" + e);
|
183 |
|
state.setUnsuccessfull();
|
184 |
|
}
|
185 |
|
|
186 |
|
if(logger.isInfoEnabled()) { logger.info("End making vernacular names..."); }
|
187 |
|
|
188 |
|
return;
|
189 |
|
}
|
190 |
|
|
191 |
|
}
|
192 |
|
|
193 |
|
@Override
|
194 |
|
protected boolean doCheck(FaunaEuropaeaImportState state) {
|
195 |
|
// TODO Auto-generated method stub
|
196 |
|
return false;
|
197 |
|
}
|
198 |
|
|
199 |
|
@Override
|
200 |
|
protected boolean isIgnore(FaunaEuropaeaImportState state) {
|
201 |
|
// TODO Auto-generated method stub
|
202 |
|
return false;
|
203 |
|
}
|
204 |
|
private void commitTaxaAndVernacularNames(
|
205 |
|
FaunaEuropaeaImportState state,
|
206 |
|
Set<UUID> taxonUuids,
|
207 |
|
Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap,
|
208 |
|
TransactionStatus txStatus) throws Exception {
|
209 |
|
List<TaxonBase> taxonList = prepareTaxaAndVernacularNames(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
|
210 |
|
|
211 |
|
getTaxonService().saveOrUpdate(taxonList);
|
212 |
|
taxonList = null;
|
213 |
|
taxonUuids = null;
|
214 |
|
fauEuTaxonMap = null;
|
215 |
|
commitTransaction(txStatus);
|
216 |
|
|
217 |
|
}
|
218 |
|
|
219 |
|
private List<TaxonBase> prepareTaxaAndVernacularNames(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) throws Exception{
|
220 |
|
|
221 |
|
CommonTaxonName verName = null;
|
222 |
|
|
223 |
|
|
224 |
|
FaunaEuropaeaVernacularNamesTaxon fauEuHelperTaxon;
|
225 |
|
UUID taxonUuid;
|
226 |
|
TaxonDescription taxonDescription;
|
227 |
|
Taxon taxon;
|
228 |
|
for (TaxonBase<?> taxonBase : taxonList) {
|
229 |
|
|
230 |
|
if (taxonBase != null) {
|
231 |
|
|
232 |
|
if (taxonBase instanceof Taxon) {
|
233 |
|
taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
234 |
|
} else {
|
235 |
|
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
236 |
|
if (syn.getAcceptedTaxa().size()>0){
|
237 |
|
taxon = syn.getAcceptedTaxa().iterator().next();
|
238 |
|
}
|
239 |
|
logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
|
240 |
|
+ taxonBase.getClass().getSimpleName() + " using accepted Taxon for vernacular name");
|
241 |
|
continue;
|
242 |
|
}
|
243 |
|
|
244 |
|
|
245 |
|
Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
|
246 |
|
taxonDescription = TaxonDescription.NewInstance();
|
247 |
|
taxon.addDescription(taxonDescription);
|
248 |
|
|
249 |
|
|
250 |
|
taxonUuid = taxonBase.getUuid();
|
251 |
|
fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);
|
252 |
|
|
253 |
|
for (FaunaEuropaeaVernacularName fauEuHelperVernacularName: fauEuHelperTaxon.getVernacularNames()) {
|
254 |
|
|
255 |
|
verName = null;
|
256 |
|
|
257 |
|
/*
|
258 |
|
* UUID uuid = state.getTransformer().getLanguageUuid(languageKey);
|
259 |
|
result = (Language)getTermService().find(uuid);
|
260 |
|
}
|
261 |
|
if (result == null){
|
262 |
|
result = state.getTransformer().getLanguageByKey(languageKey);
|
263 |
|
if (result == null){
|
264 |
|
UUID uuidLanguage;
|
265 |
|
uuidLanguage = state.getTransformer().getLanguageUuid(languageKey);
|
266 |
|
if (uuidLanguage == null){
|
267 |
|
logger.warn("Language not defined: " + languageKey) ;
|
268 |
|
}
|
269 |
|
result = getLanguage(state, uuidLanguage, languageKey, languageKey, null);
|
270 |
|
if (result == null){
|
271 |
|
logger.warn("Language not defined: " + languageKey) ;
|
272 |
|
}
|
273 |
|
}else if (result.getId() == 0){
|
274 |
|
// UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de");
|
275 |
|
UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
276 |
|
TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, result);
|
277 |
|
// TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc);
|
278 |
|
voc.addTerm(result);
|
279 |
|
getTermService().saveOrUpdate(result);
|
280 |
|
state.putLanguage(result);
|
281 |
|
}
|
282 |
|
*
|
283 |
|
*/
|
284 |
|
Language lang = FaunaEuropaeaTransformer.langFK2Language(fauEuHelperVernacularName.getLanguageFk());
|
285 |
|
if (lang == null && fauEuHelperVernacularName.getLanguageFk() == 83){
|
286 |
|
lang = Language.ENGLISH();
|
287 |
|
fauEuHelperVernacularName.setArea("USA");
|
288 |
|
}
|
289 |
|
|
290 |
|
if (lang == null){
|
291 |
|
UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
292 |
|
logger.info("languageFk = " + fauEuHelperVernacularName.getLanguageFk());
|
293 |
|
TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);
|
294 |
|
lang = Language.NewInstance("Dummy", "", "");
|
295 |
|
voc.addTerm(lang);
|
296 |
|
lang =(Language)getTermService().save(lang);
|
297 |
|
FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);
|
298 |
|
}
|
299 |
|
// if (lang.getId() == 0){
|
300 |
|
// UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
301 |
|
// TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);
|
302 |
|
// voc.addTerm(lang);
|
303 |
|
// lang =(Language)getTermService().save(lang);
|
304 |
|
// //FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);
|
305 |
|
// }
|
306 |
|
|
307 |
|
verName = CommonTaxonName.NewInstance(fauEuHelperVernacularName.getVernacularName(), lang);
|
308 |
|
if (fauEuHelperVernacularName.getArea()!= null && fauEuHelperVernacularName.getArea().equals("USA")){
|
309 |
|
verName.setArea(NamedArea.NORTH_AMERICA());
|
310 |
|
}
|
311 |
|
verName.setCreated(null);
|
312 |
|
addOriginalSource(verName, null, null, sourceMap.get(fauEuHelperVernacularName.getSource()));
|
313 |
|
taxonDescription.addElement(verName);
|
314 |
|
|
315 |
|
}
|
316 |
|
}
|
317 |
|
}
|
318 |
|
return taxonList;
|
319 |
|
}
|
320 |
|
|
321 |
|
private void createSourceMap(FaunaEuropaeaImportState state){
|
322 |
|
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
323 |
|
Source source = fauEuConfig.getSource();
|
324 |
|
TransactionStatus txStatus = null;
|
325 |
|
String sourceSelect = "SELECT DISTINCT vernacularNames.VerSource FROM vernacularNames group by vernacularNames.VerSource";
|
326 |
|
try {
|
327 |
|
txStatus =startTransaction();
|
328 |
|
ResultSet rs = source.getResultSet(sourceSelect);
|
329 |
|
Reference sourceRef;
|
330 |
|
String title ;
|
331 |
|
Set<Reference> referncesToSave = new HashSet<Reference>();
|
332 |
|
while (rs.next()) {
|
333 |
|
sourceRef = ReferenceFactory.newGeneric();
|
334 |
|
title = rs.getString("VerSource");
|
335 |
|
sourceRef.setTitle(title);
|
336 |
|
referncesToSave.add(sourceRef);
|
337 |
|
|
338 |
|
}
|
339 |
|
commitReferences(referncesToSave, txStatus);
|
340 |
|
|
341 |
|
}catch (SQLException e) {
|
342 |
|
logger.error("SQLException:" + e);
|
343 |
|
state.setUnsuccessfull();
|
344 |
|
}
|
345 |
|
|
346 |
|
|
347 |
|
}
|
348 |
|
private void commitReferences(Collection<Reference> references, TransactionStatus txStatus) {
|
349 |
|
Map <UUID, Reference> referenceMap =getReferenceService().save(references);
|
350 |
|
Iterator<Entry<UUID, Reference>> it = referenceMap.entrySet().iterator();
|
351 |
|
while (it.hasNext()){
|
352 |
|
Reference<?> ref = it.next().getValue();
|
353 |
|
String refID = ref.getTitle();
|
354 |
|
sourceMap.put(refID, ref);
|
355 |
|
}
|
356 |
|
|
357 |
|
commitTransaction(txStatus);
|
358 |
|
}
|
359 |
|
}
|
|
1 |
package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;
|
|
2 |
|
|
3 |
import java.sql.ResultSet;
|
|
4 |
import java.sql.SQLException;
|
|
5 |
import java.util.ArrayList;
|
|
6 |
import java.util.Collection;
|
|
7 |
import java.util.HashMap;
|
|
8 |
import java.util.HashSet;
|
|
9 |
import java.util.Iterator;
|
|
10 |
import java.util.List;
|
|
11 |
import java.util.Map;
|
|
12 |
import java.util.Set;
|
|
13 |
import java.util.UUID;
|
|
14 |
import java.util.Map.Entry;
|
|
15 |
|
|
16 |
import org.apache.log4j.Logger;
|
|
17 |
import org.springframework.stereotype.Component;
|
|
18 |
import org.springframework.transaction.TransactionStatus;
|
|
19 |
|
|
20 |
import eu.etaxonomy.cdm.io.common.Source;
|
|
21 |
import eu.etaxonomy.cdm.jaxb.TDWGNamespacePrefixMapper;
|
|
22 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
|
|
23 |
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
24 |
import eu.etaxonomy.cdm.model.common.Language;
|
|
25 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
|
26 |
import eu.etaxonomy.cdm.model.common.TermType;
|
|
27 |
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
|
28 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
|
|
29 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
|
|
30 |
import eu.etaxonomy.cdm.model.description.Distribution;
|
|
31 |
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
|
|
32 |
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
33 |
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
34 |
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
35 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
|
36 |
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
37 |
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
38 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
39 |
|
|
40 |
@Component
|
|
41 |
public class FaunaEuropaeaVernacularNamesImport extends FaunaEuropaeaImportBase {
|
|
42 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaVernacularNamesImport.class);
|
|
43 |
|
|
44 |
private HashMap<String, Reference> sourceMap = new HashMap<String, Reference>();
|
|
45 |
|
|
46 |
@Override
|
|
47 |
protected void doInvoke(FaunaEuropaeaImportState state) {
|
|
48 |
int limit = state.getConfig().getLimitSave();
|
|
49 |
|
|
50 |
if (state.getConfig().isDoVernacularNames()){
|
|
51 |
/* Taxon store for retrieving taxa from and saving taxa to CDM */
|
|
52 |
List<TaxonBase> taxonList = null;
|
|
53 |
/* UUID store as input for retrieving taxa from CDM */
|
|
54 |
Set<UUID> taxonUuids = null;
|
|
55 |
/* Store to hold helper objects */
|
|
56 |
Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuVernacularNamesMap = null;
|
|
57 |
|
|
58 |
|
|
59 |
TransactionStatus txStatus = null;
|
|
60 |
|
|
61 |
createSourceMap(state);
|
|
62 |
|
|
63 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
64 |
Source source = fauEuConfig.getSource();
|
|
65 |
|
|
66 |
int i = 0;
|
|
67 |
|
|
68 |
String selectCount =
|
|
69 |
" SELECT count(*) ";
|
|
70 |
|
|
71 |
String selectColumns =
|
|
72 |
" SELECT vernacularNames.*, Taxon.UUID ";
|
|
73 |
|
|
74 |
String fromClause =
|
|
75 |
" FROM vernacularNames INNER JOIN " +
|
|
76 |
" Taxon ON vernacularnames.UUID = Taxon.UUID ";
|
|
77 |
String orderBy = " ORDER BY vernacularNames.UUID";
|
|
78 |
|
|
79 |
String countQuery =
|
|
80 |
selectCount + fromClause;
|
|
81 |
|
|
82 |
String selectQuery =
|
|
83 |
selectColumns + fromClause + orderBy;
|
|
84 |
|
|
85 |
|
|
86 |
|
|
87 |
if(logger.isInfoEnabled()) { logger.info("Start making vernacular names..."); }
|
|
88 |
|
|
89 |
try {
|
|
90 |
ResultSet rs = source.getResultSet(countQuery);
|
|
91 |
rs.next();
|
|
92 |
int count = rs.getInt(1);
|
|
93 |
|
|
94 |
rs = source.getResultSet(selectQuery);
|
|
95 |
|
|
96 |
if (logger.isInfoEnabled()) {
|
|
97 |
logger.info("Number of rows: " + count);
|
|
98 |
logger.info("Count Query: " + countQuery);
|
|
99 |
logger.info("Select Query: " + selectQuery);
|
|
100 |
}
|
|
101 |
|
|
102 |
//int taxonId;
|
|
103 |
|
|
104 |
while (rs.next()) {
|
|
105 |
if ((i++ % limit) == 0) {
|
|
106 |
|
|
107 |
txStatus = startTransaction();
|
|
108 |
taxonUuids = new HashSet<UUID>(limit);
|
|
109 |
fauEuVernacularNamesMap = new HashMap<UUID, FaunaEuropaeaVernacularNamesTaxon>(limit);
|
|
110 |
|
|
111 |
if(logger.isInfoEnabled()) {
|
|
112 |
logger.info("i = " + i + " - vernacular names import transaction started");
|
|
113 |
}
|
|
114 |
}
|
|
115 |
|
|
116 |
//taxonId = rs.getInt("dis_tax_id");
|
|
117 |
String vernameGUID = rs.getString("GUID");
|
|
118 |
String vernacularNameString = rs.getString("verName");
|
|
119 |
//int taxonFk = rs.getInt("taxonFK");
|
|
120 |
int languageFK= rs.getInt("languageFK");
|
|
121 |
String languageCache = rs.getString("languageCache");
|
|
122 |
String taxonUUID= rs.getString("UUID");
|
|
123 |
String verSource = rs.getString("VerSource");
|
|
124 |
UUID currentTaxonUuid = null;
|
|
125 |
|
|
126 |
|
|
127 |
FaunaEuropaeaVernacularName fauEuVernacularName = new FaunaEuropaeaVernacularName();
|
|
128 |
fauEuVernacularName.setGuid(vernameGUID);
|
|
129 |
fauEuVernacularName.setLanguageCache(languageCache);
|
|
130 |
fauEuVernacularName.setLanguageFk(languageFK);
|
|
131 |
fauEuVernacularName.setVernacularName(vernacularNameString);
|
|
132 |
fauEuVernacularName.setSource(verSource);
|
|
133 |
fauEuVernacularName.setTaxonUuid(UUID.fromString(taxonUUID));
|
|
134 |
currentTaxonUuid =UUID.fromString(taxonUUID);
|
|
135 |
if (!taxonUuids.contains(currentTaxonUuid)) {
|
|
136 |
taxonUuids.add(currentTaxonUuid);
|
|
137 |
FaunaEuropaeaVernacularNamesTaxon fauEuVernacularNameTaxon =
|
|
138 |
new FaunaEuropaeaVernacularNamesTaxon(currentTaxonUuid);
|
|
139 |
fauEuVernacularNamesMap.put(currentTaxonUuid, fauEuVernacularNameTaxon);
|
|
140 |
fauEuVernacularNameTaxon = null;
|
|
141 |
} else {
|
|
142 |
if (logger.isTraceEnabled()) {
|
|
143 |
logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
|
144 |
continue;
|
|
145 |
}
|
|
146 |
}
|
|
147 |
|
|
148 |
fauEuVernacularNamesMap.get(currentTaxonUuid).addVernacularName(fauEuVernacularName);
|
|
149 |
|
|
150 |
if (((i % limit) == 0 && i != 1 ) || i == count ) {
|
|
151 |
|
|
152 |
try {
|
|
153 |
commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
|
|
154 |
taxonUuids = null;
|
|
155 |
taxonList = null;
|
|
156 |
fauEuVernacularNamesMap = null;
|
|
157 |
|
|
158 |
} catch (Exception e) {
|
|
159 |
logger.error("Commit of taxa and distributions failed" + e.getMessage());
|
|
160 |
e.printStackTrace();
|
|
161 |
}
|
|
162 |
|
|
163 |
if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}
|
|
164 |
}
|
|
165 |
|
|
166 |
|
|
167 |
}
|
|
168 |
if (taxonUuids != null){
|
|
169 |
try {
|
|
170 |
commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);
|
|
171 |
taxonUuids = null;
|
|
172 |
taxonList = null;
|
|
173 |
fauEuVernacularNamesMap = null;
|
|
174 |
} catch (Exception e) {
|
|
175 |
logger.error("Commit of taxa and vernacular names failed");
|
|
176 |
logger.error(e.getMessage());
|
|
177 |
e.printStackTrace();
|
|
178 |
}
|
|
179 |
}
|
|
180 |
rs = null;
|
|
181 |
} catch (SQLException e) {
|
|
182 |
logger.error("SQLException:" + e);
|
|
183 |
state.setUnsuccessfull();
|
|
184 |
}
|
|
185 |
|
|
186 |
if(logger.isInfoEnabled()) { logger.info("End making vernacular names..."); }
|
|
187 |
|
|
188 |
return;
|
|
189 |
}
|
|
190 |
|
|
191 |
}
|
|
192 |
|
|
193 |
@Override
|
|
194 |
protected boolean doCheck(FaunaEuropaeaImportState state) {
|
|
195 |
// TODO Auto-generated method stub
|
|
196 |
return false;
|
|
197 |
}
|
|
198 |
|
|
199 |
@Override
|
|
200 |
protected boolean isIgnore(FaunaEuropaeaImportState state) {
|
|
201 |
// TODO Auto-generated method stub
|
|
202 |
return false;
|
|
203 |
}
|
|
204 |
private void commitTaxaAndVernacularNames(
|
|
205 |
FaunaEuropaeaImportState state,
|
|
206 |
Set<UUID> taxonUuids,
|
|
207 |
Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap,
|
|
208 |
TransactionStatus txStatus) throws Exception {
|
|
209 |
List<TaxonBase> taxonList = prepareTaxaAndVernacularNames(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);
|
|
210 |
|
|
211 |
getTaxonService().saveOrUpdate(taxonList);
|
|
212 |
taxonList = null;
|
|
213 |
taxonUuids = null;
|
|
214 |
fauEuTaxonMap = null;
|
|
215 |
commitTransaction(txStatus);
|
|
216 |
|
|
217 |
}
|
|
218 |
|
|
219 |
private List<TaxonBase> prepareTaxaAndVernacularNames(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap, FaunaEuropaeaImportState state) throws Exception{
|
|
220 |
|
|
221 |
CommonTaxonName verName = null;
|
|
222 |
|
|
223 |
|
|
224 |
FaunaEuropaeaVernacularNamesTaxon fauEuHelperTaxon;
|
|
225 |
UUID taxonUuid;
|
|
226 |
TaxonDescription taxonDescription;
|
|
227 |
Taxon taxon;
|
|
228 |
for (TaxonBase<?> taxonBase : taxonList) {
|
|
229 |
|
|
230 |
if (taxonBase != null) {
|
|
231 |
|
|
232 |
if (taxonBase instanceof Taxon) {
|
|
233 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
234 |
} else {
|
|
235 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
236 |
if (syn.getAcceptedTaxa().size()>0){
|
|
237 |
taxon = syn.getAcceptedTaxa().iterator().next();
|
|
238 |
}
|
|
239 |
logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
|
|
240 |
+ taxonBase.getClass().getSimpleName() + " using accepted Taxon for vernacular name");
|
|
241 |
continue;
|
|
242 |
}
|
|
243 |
|
|
244 |
|
|
245 |
Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
|
|
246 |
taxonDescription = TaxonDescription.NewInstance();
|
|
247 |
taxon.addDescription(taxonDescription);
|
|
248 |
|
|
249 |
|
|
250 |
taxonUuid = taxonBase.getUuid();
|
|
251 |
fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);
|
|
252 |
|
|
253 |
for (FaunaEuropaeaVernacularName fauEuHelperVernacularName: fauEuHelperTaxon.getVernacularNames()) {
|
|
254 |
|
|
255 |
verName = null;
|
|
256 |
|
|
257 |
/*
|
|
258 |
* UUID uuid = state.getTransformer().getLanguageUuid(languageKey);
|
|
259 |
result = (Language)getTermService().find(uuid);
|
|
260 |
}
|
|
261 |
if (result == null){
|
|
262 |
result = state.getTransformer().getLanguageByKey(languageKey);
|
|
263 |
if (result == null){
|
|
264 |
UUID uuidLanguage;
|
|
265 |
uuidLanguage = state.getTransformer().getLanguageUuid(languageKey);
|
|
266 |
if (uuidLanguage == null){
|
|
267 |
logger.warn("Language not defined: " + languageKey) ;
|
|
268 |
}
|
|
269 |
result = getLanguage(state, uuidLanguage, languageKey, languageKey, null);
|
|
270 |
if (result == null){
|
|
271 |
logger.warn("Language not defined: " + languageKey) ;
|
|
272 |
}
|
|
273 |
}else if (result.getId() == 0){
|
|
274 |
// UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de");
|
|
275 |
UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
|
276 |
TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, result);
|
|
277 |
// TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc);
|
|
278 |
voc.addTerm(result);
|
|
279 |
getTermService().saveOrUpdate(result);
|
|
280 |
state.putLanguage(result);
|
|
281 |
}
|
|
282 |
*
|
|
283 |
*/
|
|
284 |
Language lang = FaunaEuropaeaTransformer.langFK2Language(fauEuHelperVernacularName.getLanguageFk());
|
|
285 |
if (lang == null && fauEuHelperVernacularName.getLanguageFk() == 83){
|
|
286 |
lang = Language.ENGLISH();
|
|
287 |
fauEuHelperVernacularName.setArea("USA");
|
|
288 |
}
|
|
289 |
|
|
290 |
if (lang == null){
|
|
291 |
UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
|
292 |
logger.info("languageFk = " + fauEuHelperVernacularName.getLanguageFk());
|
|
293 |
TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);
|
|
294 |
lang = Language.NewInstance("Dummy", "", "");
|
|
295 |
voc.addTerm(lang);
|
|
296 |
lang =(Language)getTermService().save(lang);
|
|
297 |
FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);
|
|
298 |
}
|
|
299 |
// if (lang.getId() == 0){
|
|
300 |
// UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084");
|
|
301 |
// TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);
|
|
302 |
// voc.addTerm(lang);
|
|
303 |
// lang =(Language)getTermService().save(lang);
|
|
304 |
// //FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);
|
|
305 |
// }
|
|
306 |
|
|
307 |
verName = CommonTaxonName.NewInstance(fauEuHelperVernacularName.getVernacularName(), lang);
|
|
308 |
if (fauEuHelperVernacularName.getArea()!= null && fauEuHelperVernacularName.getArea().equals("USA")){
|
|
309 |
verName.setArea(NamedArea.NORTH_AMERICA());
|
|
310 |
}
|
|
311 |
verName.setCreated(null);
|
|
312 |
addOriginalSource(verName, null, null, sourceMap.get(fauEuHelperVernacularName.getSource()));
|
|
313 |
taxonDescription.addElement(verName);
|
|
314 |
|
|
315 |
}
|
|
316 |
}
|
|
317 |
}
|
|
318 |
return taxonList;
|
|
319 |
}
|
|
320 |
|
|
321 |
private void createSourceMap(FaunaEuropaeaImportState state){
|
|
322 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
|
|
323 |
Source source = fauEuConfig.getSource();
|
|
324 |
TransactionStatus txStatus = null;
|
|
325 |
String sourceSelect = "SELECT DISTINCT vernacularNames.VerSource FROM vernacularNames group by vernacularNames.VerSource";
|
|
326 |
try {
|
|
327 |
txStatus =startTransaction();
|
|
328 |
ResultSet rs = source.getResultSet(sourceSelect);
|
|
329 |
Reference sourceRef;
|
|
330 |
String title ;
|
|
331 |
Set<Reference> referncesToSave = new HashSet<Reference>();
|
|
332 |
while (rs.next()) {
|
|
333 |
sourceRef = ReferenceFactory.newGeneric();
|
|
334 |
title = rs.getString("VerSource");
|
|
335 |
sourceRef.setTitle(title);
|
|
336 |
referncesToSave.add(sourceRef);
|
|
337 |
|
|
338 |
}
|
|
339 |
commitReferences(referncesToSave, txStatus);
|
|
340 |
|
|
341 |
}catch (SQLException e) {
|
|
342 |
logger.error("SQLException:" + e);
|
|
343 |
state.setUnsuccessfull();
|
|
344 |
}
|
|
345 |
|
|
346 |
|
|
347 |
}
|
|
348 |
private void commitReferences(Collection<Reference> references, TransactionStatus txStatus) {
|
|
349 |
Map <UUID, Reference> referenceMap =getReferenceService().save(references);
|
|
350 |
Iterator<Entry<UUID, Reference>> it = referenceMap.entrySet().iterator();
|
|
351 |
while (it.hasNext()){
|
|
352 |
Reference<?> ref = it.next().getValue();
|
|
353 |
String refID = ref.getTitle();
|
|
354 |
sourceMap.put(refID, ref);
|
|
355 |
}
|
|
356 |
|
|
357 |
commitTransaction(txStatus);
|
|
358 |
}
|
|
359 |
}
|
Fauna Europaea import changes