Revision 892efc69
Added by Andreas Kohlbecker almost 14 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaRefImport.java | ||
|---|---|---|
| 14 | 14 |
import java.util.Collection; |
| 15 | 15 |
import java.util.HashMap; |
| 16 | 16 |
import java.util.HashSet; |
| 17 |
import java.util.Iterator; |
|
| 17 | 18 |
import java.util.List; |
| 18 | 19 |
import java.util.Map; |
| 19 | 20 |
import java.util.Set; |
| ... | ... | |
| 30 | 31 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
| 31 | 32 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 32 | 33 |
import eu.etaxonomy.cdm.model.common.DescriptionElementSource; |
| 34 |
import eu.etaxonomy.cdm.model.common.OriginalSourceBase; |
|
| 33 | 35 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 34 | 36 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 35 | 37 |
import eu.etaxonomy.cdm.model.description.TextData; |
| ... | ... | |
| 40 | 42 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 41 | 43 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 42 | 44 |
|
| 45 |
import java.util.Map.Entry; |
|
| 46 |
|
|
| 43 | 47 |
|
| 44 | 48 |
/** |
| 45 | 49 |
* @author a.babadshanjan |
| ... | ... | |
| 78 | 82 |
// return false; |
| 79 | 83 |
// } |
| 80 | 84 |
} |
| 81 |
|
|
| 85 |
|
|
| 82 | 86 |
/* (non-Javadoc) |
| 83 | 87 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map) |
| 84 | 88 |
*/ |
| ... | ... | |
| 87 | 91 |
|
| 88 | 92 |
TransactionStatus txStatus = null; |
| 89 | 93 |
List<TaxonBase> taxonList = null; |
| 94 |
List<ReferenceBase> referenceList = null; |
|
| 90 | 95 |
Set<UUID> taxonUuids = null; |
| 91 |
Set<ReferenceBase> references = null;
|
|
| 92 |
Set<TeamOrPersonBase> authors = null;
|
|
| 96 |
Map<Integer, ReferenceBase> references = null;
|
|
| 97 |
Map<String,TeamOrPersonBase> authors = null;
|
|
| 93 | 98 |
Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap = null; |
| 99 |
Map<Integer, UUID> referenceUuids = new HashMap<Integer, UUID>(); |
|
| 100 |
Set<Integer> referenceIDs = null; |
|
| 94 | 101 |
int limit = state.getConfig().getLimitSave(); |
| 95 | 102 |
|
| 96 | 103 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
| ... | ... | |
| 100 | 107 |
boolean success = true; |
| 101 | 108 |
int i = 0; |
| 102 | 109 |
|
| 103 |
String selectCount = |
|
| 110 |
String selectCountTaxRefs =
|
|
| 104 | 111 |
" SELECT count(*) "; |
| 105 | 112 |
|
| 106 |
String selectColumns = |
|
| 113 |
String selectColumnsTaxRefs =
|
|
| 107 | 114 |
" SELECT Reference.*, TaxRefs.*, Taxon.UUID "; |
| 108 | 115 |
|
| 109 |
String fromClause = |
|
| 116 |
String fromClauseTaxRefs =
|
|
| 110 | 117 |
" FROM TaxRefs " + |
| 111 | 118 |
" INNER JOIN Reference ON Reference.ref_id = TaxRefs.trf_ref_id " + |
| 112 | 119 |
" INNER JOIN Taxon ON TaxRefs.trf_tax_id = Taxon.TAX_ID "; |
| 113 | 120 |
|
| 114 |
String orderClause = |
|
| 121 |
String orderClauseTaxRefs =
|
|
| 115 | 122 |
" ORDER BY TaxRefs.trf_tax_id"; |
| 123 |
|
|
| 124 |
String selectCountRefs = |
|
| 125 |
" SELECT count(*) FROM Reference"; |
|
| 126 |
|
|
| 127 |
String selectColumnsRefs = |
|
| 128 |
" SELECT * FROM Reference order by ref_author"; |
|
| 129 |
|
|
| 116 | 130 |
|
| 117 |
String countQuery = |
|
| 118 |
selectCount + fromClause;
|
|
| 131 |
String countQueryTaxRefs =
|
|
| 132 |
selectCountTaxRefs + fromClauseTaxRefs;
|
|
| 119 | 133 |
|
| 120 |
String selectQuery = |
|
| 121 |
selectColumns + fromClause + orderClause; |
|
| 134 |
String selectQueryTaxRefs = |
|
| 135 |
selectColumnsTaxRefs + fromClauseTaxRefs + orderClauseTaxRefs; |
|
| 136 |
|
|
| 137 |
String countQueryRefs = |
|
| 138 |
selectCountRefs; |
|
| 122 | 139 |
|
| 140 |
String selectQueryRefs = |
|
| 141 |
selectColumnsRefs; |
|
| 142 |
|
|
| 143 |
int count; |
|
| 123 | 144 |
if(logger.isInfoEnabled()) { logger.info("Start making References..."); }
|
| 124 |
|
|
| 145 |
//first add all References to CDM |
|
| 125 | 146 |
try {
|
| 126 |
ResultSet rs = source.getResultSet(countQuery);
|
|
| 127 |
rs.next(); |
|
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int count = rs.getInt(1);
|
|
| 147 |
ResultSet rsRefs = source.getResultSet(countQueryRefs);
|
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| 148 |
rsRefs.next();
|
|
| 149 |
count = rsRefs.getInt(1);
|
|
| 129 | 150 |
|
| 130 |
rs = source.getResultSet(selectQuery);
|
|
| 151 |
rsRefs = source.getResultSet(selectQueryRefs);
|
|
| 131 | 152 |
|
| 132 | 153 |
if (logger.isInfoEnabled()) {
|
| 154 |
logger.info("Get all References...");
|
|
| 133 | 155 |
logger.info("Number of rows: " + count);
|
| 134 |
logger.info("Count Query: " + countQuery);
|
|
| 135 |
logger.info("Select Query: " + selectQuery);
|
|
| 156 |
logger.info("Count Query: " + countQueryRefs);
|
|
| 157 |
logger.info("Select Query: " + selectQueryRefs);
|
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| 136 | 158 |
} |
| 137 |
|
|
| 138 |
while (rs.next()) {
|
|
| 139 |
|
|
| 159 |
|
|
| 160 |
while (rsRefs.next()){
|
|
| 161 |
int refId = rsRefs.getInt("ref_id");
|
|
| 162 |
String refAuthor = rsRefs.getString("ref_author");
|
|
| 163 |
String year = rsRefs.getString("ref_year");
|
|
| 164 |
String title = rsRefs.getString("ref_title");
|
|
| 165 |
|
|
| 166 |
if (year == null){
|
|
| 167 |
try{
|
|
| 168 |
year = String.valueOf((Integer.parseInt(title))); |
|
| 169 |
} |
|
| 170 |
catch(Exception ex) |
|
| 171 |
{
|
|
| 172 |
logger.info("year is empty and " +title + " contains no integer");
|
|
| 173 |
} |
|
| 174 |
} |
|
| 175 |
String refSource = rsRefs.getString("ref_source");
|
|
| 176 |
|
|
| 140 | 177 |
if ((i++ % limit) == 0) {
|
| 141 | 178 |
|
| 142 | 179 |
txStatus = startTransaction(); |
| 143 |
taxonUuids = new HashSet<UUID>(limit); |
|
| 144 |
references = new HashSet<ReferenceBase>(limit); |
|
| 145 |
authors = new HashSet<TeamOrPersonBase>(limit); |
|
| 146 |
fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaReferenceTaxon>(limit); |
|
| 147 |
|
|
| 180 |
references = new HashMap<Integer,ReferenceBase>(limit); |
|
| 181 |
authors = new HashMap<String,TeamOrPersonBase>(limit); |
|
| 182 |
|
|
| 148 | 183 |
if(logger.isInfoEnabled()) {
|
| 149 | 184 |
logger.info("i = " + i + " - Reference import transaction started");
|
| 150 | 185 |
} |
| 151 | 186 |
} |
| 152 |
|
|
| 153 |
int taxonId = rs.getInt("trf_tax_id");
|
|
| 154 |
int refId = rs.getInt("ref_id");
|
|
| 155 |
String refAuthor = rs.getString("ref_author");
|
|
| 156 |
String year = rs.getString("ref_year");
|
|
| 157 |
String title = rs.getString("ref_title");
|
|
| 158 |
String refSource = rs.getString("ref_source");
|
|
| 159 |
String page = rs.getString("trf_page");
|
|
| 160 |
UUID currentTaxonUuid = null; |
|
| 161 |
if (resultSetHasColumn(rs, "UUID")){
|
|
| 162 |
currentTaxonUuid = UUID.fromString(rs.getString("UUID"));
|
|
| 163 |
} else {
|
|
| 164 |
logger.error("Taxon (" + taxonId + ") without UUID ignored");
|
|
| 165 |
continue; |
|
| 166 |
} |
|
| 167 |
|
|
| 168 |
FaunaEuropaeaReference fauEuReference = new FaunaEuropaeaReference(); |
|
| 169 |
fauEuReference.setTaxonUuid(currentTaxonUuid); |
|
| 170 |
fauEuReference.setReferenceId(refId); |
|
| 171 |
fauEuReference.setReferenceAuthor(refAuthor); |
|
| 172 |
fauEuReference.setReferenceYear(year); |
|
| 173 |
fauEuReference.setReferenceTitle(title); |
|
| 174 |
fauEuReference.setReferenceSource(refSource); |
|
| 175 |
fauEuReference.setPage(page); |
|
| 176 |
|
|
| 177 |
if (!taxonUuids.contains(currentTaxonUuid)) {
|
|
| 178 |
taxonUuids.add(currentTaxonUuid); |
|
| 179 |
FaunaEuropaeaReferenceTaxon fauEuReferenceTaxon = |
|
| 180 |
new FaunaEuropaeaReferenceTaxon(currentTaxonUuid); |
|
| 181 |
fauEuTaxonMap.put(currentTaxonUuid, fauEuReferenceTaxon); |
|
| 182 |
} else {
|
|
| 183 |
if (logger.isTraceEnabled()) {
|
|
| 184 |
logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
|
| 185 |
continue; |
|
| 186 |
} |
|
| 187 |
} |
|
| 188 |
|
|
| 187 |
|
|
| 189 | 188 |
ReferenceBase<?> reference = null; |
| 190 | 189 |
TeamOrPersonBase<Team> author = null; |
| 191 |
ReferenceFactory refFactory = ReferenceFactory.newInstance(); |
|
| 192 |
reference = refFactory.newGeneric(); |
|
| 190 |
//ReferenceFactory refFactory = ReferenceFactory.newInstance(); |
|
| 191 |
reference = ReferenceFactory.newGeneric(); |
|
| 192 |
|
|
| 193 | 193 |
reference.setTitleCache(title); |
| 194 | 194 |
reference.setDatePublished(ImportHelper.getDatePublished(year)); |
| 195 |
author = Team.NewInstance(); |
|
| 196 |
author.setTitleCache(refAuthor); |
|
| 195 |
|
|
| 196 |
if (!authors.containsKey(refAuthor)) {
|
|
| 197 |
if (refAuthor == null) {
|
|
| 198 |
logger.warn("Reference author is null");
|
|
| 199 |
} |
|
| 200 |
author = Team.NewInstance(); |
|
| 201 |
author.setTitleCache(refAuthor); |
|
| 202 |
authors.put(refAuthor,author); |
|
| 203 |
if (logger.isTraceEnabled()) {
|
|
| 204 |
logger.trace("Stored author (" + refAuthor + ")");
|
|
| 205 |
} |
|
| 206 |
//} |
|
| 197 | 207 |
|
| 208 |
} else {
|
|
| 209 |
author = authors.get(refAuthor); |
|
| 210 |
if (logger.isDebugEnabled()) {
|
|
| 211 |
logger.debug("Not imported author with duplicated aut_id (" + refId +
|
|
| 212 |
") " + refAuthor); |
|
| 213 |
} |
|
| 214 |
} |
|
| 215 |
|
|
| 216 |
reference.setAuthorTeam(author); |
|
| 217 |
|
|
| 198 | 218 |
ImportHelper.setOriginalSource(reference, fauEuConfig.getSourceReference(), refId, namespace); |
| 199 | 219 |
ImportHelper.setOriginalSource(author, fauEuConfig.getSourceReference(), refId, namespace); |
| 200 | 220 |
|
| 201 | 221 |
// Store reference |
| 202 | 222 |
|
| 203 |
if (!references.contains(refId)) {
|
|
| 223 |
|
|
| 224 |
if (!references.containsKey(refId)) {
|
|
| 225 |
|
|
| 204 | 226 |
if (reference == null) {
|
| 205 | 227 |
logger.warn("Reference is null");
|
| 206 | 228 |
} |
| 207 |
references.add(reference);
|
|
| 229 |
references.put(refId, reference);
|
|
| 208 | 230 |
if (logger.isTraceEnabled()) {
|
| 209 | 231 |
logger.trace("Stored reference (" + refAuthor + ")");
|
| 210 | 232 |
} |
| ... | ... | |
| 212 | 234 |
if (logger.isDebugEnabled()) {
|
| 213 | 235 |
logger.debug("Duplicated reference (" + refId + ", " + refAuthor + ")");
|
| 214 | 236 |
} |
| 215 |
continue; |
|
| 237 |
//continue;
|
|
| 216 | 238 |
} |
| 217 |
|
|
| 218 |
// Store author |
|
| 219 |
|
|
| 220 |
boolean store = true; |
|
| 221 |
if (!authors.contains(refId)) {
|
|
| 222 |
if (refAuthor == null) {
|
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| 223 |
logger.warn("Reference author is null");
|
|
| 239 |
|
|
| 240 |
if (((i % limit) == 0 && i > 1 ) || i == count) {
|
|
| 241 |
|
|
| 242 |
Map <UUID, ReferenceBase> referenceMap =getReferenceService().save(references.values()); |
|
| 243 |
logger.info("i = " + i + " - references saved");
|
|
| 244 |
|
|
| 245 |
Iterator<Entry<UUID, ReferenceBase>> it = referenceMap.entrySet().iterator(); |
|
| 246 |
while (it.hasNext()){
|
|
| 247 |
ReferenceBase ref = it.next().getValue(); |
|
| 248 |
int refID = Integer.valueOf(((OriginalSourceBase)ref.getSources().iterator().next()).getIdInSource()); |
|
| 249 |
UUID uuid = ref.getUuid(); |
|
| 250 |
referenceUuids.put(refID, uuid); |
|
| 224 | 251 |
} |
| 225 |
String storedAuthorTitleCache = null; |
|
| 226 |
for (TeamOrPersonBase<?> storedAuthor : authors) {
|
|
| 227 |
storedAuthorTitleCache = storedAuthor.getTitleCache(); |
|
| 228 |
if (storedAuthorTitleCache.equals(refAuthor)) {
|
|
| 229 |
store = false; |
|
| 230 |
if (logger.isDebugEnabled()) {
|
|
| 231 |
logger.debug("Duplicated author (" + refId + ", " + refAuthor + ")");
|
|
| 232 |
} |
|
| 233 |
break; |
|
| 252 |
references= null; |
|
| 253 |
getAgentService().save((Collection)authors.values()); |
|
| 254 |
|
|
| 255 |
authors = null; |
|
| 256 |
} |
|
| 257 |
|
|
| 258 |
|
|
| 259 |
|
|
| 260 |
} |
|
| 261 |
}catch(SQLException e) {
|
|
| 262 |
logger.error("SQLException:" + e);
|
|
| 263 |
success = false; |
|
| 264 |
} |
|
| 265 |
|
|
| 266 |
|
|
| 267 |
//create the relationships between references and taxa |
|
| 268 |
|
|
| 269 |
Taxon taxon = null; |
|
| 270 |
i = 0; |
|
| 271 |
try{
|
|
| 272 |
ResultSet rsTaxRefs = source.getResultSet(countQueryTaxRefs); |
|
| 273 |
rsTaxRefs.next(); |
|
| 274 |
count = rsTaxRefs.getInt(1); |
|
| 275 |
|
|
| 276 |
rsTaxRefs = source.getResultSet(selectQueryTaxRefs); |
|
| 277 |
|
|
| 278 |
logger.info("Start taxon reference-relationships");
|
|
| 279 |
FaunaEuropaeaReference fauEuReference; |
|
| 280 |
FaunaEuropaeaReferenceTaxon fauEuReferenceTaxon; |
|
| 281 |
while (rsTaxRefs.next()) {
|
|
| 282 |
|
|
| 283 |
|
|
| 284 |
if ((i++ % limit) == 0) {
|
|
| 285 |
|
|
| 286 |
txStatus = startTransaction(); |
|
| 287 |
taxonUuids = new HashSet<UUID>(limit); |
|
| 288 |
referenceIDs = new HashSet<Integer>(limit); |
|
| 289 |
authors = new HashMap<String,TeamOrPersonBase>(limit); |
|
| 290 |
fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaReferenceTaxon>(limit); |
|
| 291 |
|
|
| 292 |
if(logger.isInfoEnabled()) {
|
|
| 293 |
logger.info("i = " + i + " - Reference import transaction started");
|
|
| 234 | 294 |
} |
| 235 | 295 |
} |
| 236 |
if (store == true) {
|
|
| 237 |
authors.add(author); |
|
| 296 |
|
|
| 297 |
|
|
| 298 |
int taxonId = rsTaxRefs.getInt("trf_tax_id");
|
|
| 299 |
int refId = rsTaxRefs.getInt("ref_id");
|
|
| 300 |
String refAuthor = rsTaxRefs.getString("ref_author");
|
|
| 301 |
String year = rsTaxRefs.getString("ref_year");
|
|
| 302 |
String title = rsTaxRefs.getString("ref_title");
|
|
| 303 |
|
|
| 304 |
if (year == null){
|
|
| 305 |
try{
|
|
| 306 |
year = String.valueOf((Integer.parseInt(title))); |
|
| 307 |
} |
|
| 308 |
catch(Exception ex) |
|
| 309 |
{
|
|
| 310 |
logger.info("year is empty and " +title + " contains no integer");
|
|
| 311 |
} |
|
| 312 |
} |
|
| 313 |
String refSource = rsTaxRefs.getString("ref_source");
|
|
| 314 |
String page = rsTaxRefs.getString("trf_page");
|
|
| 315 |
UUID currentTaxonUuid = null; |
|
| 316 |
if (resultSetHasColumn(rsTaxRefs, "UUID")){
|
|
| 317 |
currentTaxonUuid = UUID.fromString(rsTaxRefs.getString("UUID"));
|
|
| 318 |
} else {
|
|
| 319 |
logger.error("Taxon (" + taxonId + ") without UUID ignored");
|
|
| 320 |
continue; |
|
| 321 |
} |
|
| 322 |
|
|
| 323 |
fauEuReference = new FaunaEuropaeaReference(); |
|
| 324 |
fauEuReference.setTaxonUuid(currentTaxonUuid); |
|
| 325 |
fauEuReference.setReferenceId(refId); |
|
| 326 |
fauEuReference.setReferenceAuthor(refAuthor); |
|
| 327 |
fauEuReference.setReferenceYear(year); |
|
| 328 |
fauEuReference.setReferenceTitle(title); |
|
| 329 |
fauEuReference.setReferenceSource(refSource); |
|
| 330 |
fauEuReference.setPage(page); |
|
| 331 |
|
|
| 332 |
if (!taxonUuids.contains(currentTaxonUuid)) {
|
|
| 333 |
taxonUuids.add(currentTaxonUuid); |
|
| 334 |
fauEuReferenceTaxon = |
|
| 335 |
new FaunaEuropaeaReferenceTaxon(currentTaxonUuid); |
|
| 336 |
fauEuTaxonMap.put(currentTaxonUuid, fauEuReferenceTaxon); |
|
| 337 |
} else {
|
|
| 238 | 338 |
if (logger.isTraceEnabled()) {
|
| 239 |
logger.trace("Stored author (" + refAuthor + ")");
|
|
| 339 |
logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
|
| 340 |
//continue; ein Taxon kann mehr als eine Referenz haben |
|
| 240 | 341 |
} |
| 241 | 342 |
} |
| 242 |
|
|
| 243 |
} else {
|
|
| 244 |
if (logger.isDebugEnabled()) {
|
|
| 245 |
logger.debug("Not imported author with duplicated aut_id (" + refId +
|
|
| 246 |
") " + refAuthor); |
|
| 343 |
|
|
| 344 |
if (!referenceIDs.contains(refId)) {
|
|
| 345 |
|
|
| 346 |
|
|
| 347 |
referenceIDs.add(refId); |
|
| 348 |
if (logger.isTraceEnabled()) {
|
|
| 349 |
logger.trace("Stored reference (" + refAuthor + ")");
|
|
| 350 |
} |
|
| 351 |
} else {
|
|
| 352 |
if (logger.isDebugEnabled()) {
|
|
| 353 |
logger.debug("Duplicated reference (" + refId + ", " + refAuthor + ")");
|
|
| 354 |
} |
|
| 355 |
//continue; |
|
| 247 | 356 |
} |
| 248 |
} |
|
| 249 |
|
|
| 250 |
fauEuTaxonMap.get(currentTaxonUuid).addReference(fauEuReference); |
|
| 251 |
|
|
| 252 |
Taxon taxon = null; |
|
| 253 |
if (((i % limit) == 0 && i != 1 ) || i == count) {
|
|
| 254 |
|
|
| 357 |
|
|
| 358 |
|
|
| 359 |
fauEuTaxonMap.get(currentTaxonUuid).addReference(fauEuReference); |
|
| 360 |
|
|
| 361 |
|
|
| 362 |
|
|
| 363 |
|
|
| 364 |
if (((i % limit) == 0 && i > 1 ) || i == count) {
|
|
| 365 |
|
|
| 255 | 366 |
try {
|
| 256 |
|
|
| 367 |
|
|
| 257 | 368 |
taxonList = getTaxonService().find(taxonUuids); |
| 258 |
|
|
| 369 |
//get UUIDs of used references |
|
| 370 |
Iterator itRefs = referenceIDs.iterator(); |
|
| 371 |
Set<UUID> uuidSet = new HashSet<UUID>(referenceIDs.size()); |
|
| 372 |
UUID uuid; |
|
| 373 |
while (itRefs.hasNext()){
|
|
| 374 |
uuid = referenceUuids.get(itRefs.next()); |
|
| 375 |
uuidSet.add(uuid); |
|
| 376 |
} |
|
| 377 |
referenceList = getReferenceService().find(uuidSet); |
|
| 378 |
references = new HashMap<Integer, ReferenceBase>(limit); |
|
| 379 |
for (ReferenceBase ref : referenceList){
|
|
| 380 |
references.put(Integer.valueOf(((OriginalSourceBase)ref.getSources().iterator().next()).getIdInSource()), ref); |
|
| 381 |
} |
|
| 259 | 382 |
for (TaxonBase taxonBase : taxonList) {
|
| 260 |
|
|
| 383 |
|
|
| 261 | 384 |
// Create descriptions |
| 262 |
|
|
| 385 |
|
|
| 263 | 386 |
if (taxonBase == null) {
|
| 264 | 387 |
if (logger.isDebugEnabled()) {
|
| 265 |
logger.debug("TaxonBase is null (" + currentTaxonUuid + ")");
|
|
| 388 |
logger.debug("TaxonBase is null ");
|
|
| 266 | 389 |
} |
| 267 | 390 |
continue; |
| 268 | 391 |
} |
| ... | ... | |
| 273 | 396 |
if (acceptedTaxa.size() > 0) {
|
| 274 | 397 |
taxon = syn.getAcceptedTaxa().iterator().next(); |
| 275 | 398 |
} else {
|
| 276 |
// if (logger.isDebugEnabled()) {
|
|
| 399 |
// if (logger.isDebugEnabled()) {
|
|
| 277 | 400 |
logger.warn("Synonym (" + taxonBase.getUuid() + ") does not have accepted taxa");
|
| 278 |
// }
|
|
| 401 |
// }
|
|
| 279 | 402 |
} |
| 280 | 403 |
} else {
|
| 281 | 404 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
| 282 | 405 |
} |
| 283 |
|
|
| 406 |
|
|
| 284 | 407 |
if (taxon != null) {
|
| 285 | 408 |
TaxonDescription taxonDescription = null; |
| 286 | 409 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
| ... | ... | |
| 290 | 413 |
taxonDescription = TaxonDescription.NewInstance(); |
| 291 | 414 |
taxon.addDescription(taxonDescription); |
| 292 | 415 |
} |
| 293 |
|
|
| 294 |
|
|
| 416 |
|
|
| 417 |
|
|
| 295 | 418 |
UUID taxonUuid = taxonBase.getUuid(); |
| 296 | 419 |
FaunaEuropaeaReferenceTaxon fauEuHelperTaxon = fauEuTaxonMap.get(taxonUuid); |
| 297 |
|
|
| 420 |
ReferenceBase citation; |
|
| 421 |
String microCitation; |
|
| 422 |
DescriptionElementSource originalSource; |
|
| 423 |
Synonym syn; |
|
| 298 | 424 |
for (FaunaEuropaeaReference storedReference : fauEuHelperTaxon.getReferences()) {
|
| 299 |
|
|
| 425 |
|
|
| 300 | 426 |
TextData textData = TextData.NewInstance(Feature.CITATION()); |
| 301 | 427 |
|
| 302 |
ReferenceBase citation = storedReference.getCdmReference();
|
|
| 303 |
String microCitation = storedReference.getPage();
|
|
| 304 |
DescriptionElementSource originalSource = DescriptionElementSource.NewInstance(null, null, citation, microCitation, null, null);
|
|
| 428 |
citation = references.get(storedReference.getReferenceId());
|
|
| 429 |
microCitation = storedReference.getPage(); |
|
| 430 |
originalSource = DescriptionElementSource.NewInstance(null, null, citation, microCitation, null, null); |
|
| 305 | 431 |
if (isSynonym){
|
| 306 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
| 432 |
syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
| 307 | 433 |
originalSource.setNameUsedInSource(syn.getName()); |
| 308 | 434 |
} |
| 309 | 435 |
textData.addSource(originalSource); |
| ... | ... | |
| 314 | 440 |
if(logger.isInfoEnabled()) {
|
| 315 | 441 |
logger.info("i = " + i + " - Transaction committed");
|
| 316 | 442 |
} |
| 317 |
|
|
| 318 |
// save taxa, references, and authors
|
|
| 443 |
|
|
| 444 |
// save taxa |
|
| 319 | 445 |
getTaxonService().save(taxonList); |
| 320 |
getReferenceService().save(references); |
|
| 321 |
getAgentService().save((Collection)authors); |
|
| 322 |
|
|
| 446 |
|
|
| 447 |
|
|
| 323 | 448 |
taxonUuids = null; |
| 324 | 449 |
references = null; |
| 325 |
authors = null; |
|
| 326 | 450 |
taxonList = null; |
| 327 | 451 |
fauEuTaxonMap = null; |
| 452 |
referenceIDs = null; |
|
| 453 |
referenceList = null; |
|
| 454 |
uuidSet = null; |
|
| 328 | 455 |
commitTransaction(txStatus); |
| 329 |
|
|
| 456 |
|
|
| 330 | 457 |
} catch (Exception e) {
|
| 331 |
logger.warn("An exception occurred when creating reference with id " + refId +
|
|
| 332 |
". Reference could not be saved."); |
|
| 458 |
logger.warn("An exception occurred when creating reference, reference could not be saved.");
|
|
| 333 | 459 |
} |
| 334 | 460 |
} |
| 335 |
} |
|
| 461 |
} |
|
| 462 |
rsTaxRefs.close(); |
|
| 336 | 463 |
} catch (SQLException e) {
|
| 337 | 464 |
logger.error("SQLException:" + e);
|
| 338 | 465 |
success = false; |
| 339 | 466 |
} |
| 467 |
|
|
| 340 | 468 |
if(logger.isInfoEnabled()) { logger.info("End making references ..."); }
|
| 341 |
|
|
| 469 |
|
|
| 342 | 470 |
return success; |
| 343 | 471 |
} |
| 344 | 472 |
|
| 473 |
|
|
| 474 |
|
|
| 475 |
|
|
| 476 |
|
|
| 345 | 477 |
|
| 346 | 478 |
/* (non-Javadoc) |
| 347 | 479 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
Also available in: Unified diff
merging /branches/cdmlib/SPRINT-Chichorieae1/ to trunk