Revision e0935f63
Added by Andreas Müller over 4 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraCollectionImport.java | ||
|---|---|---|
| 90 | 90 |
Set<Collection> collectionsToSave = new HashSet<Collection>(); |
| 91 | 91 |
|
| 92 | 92 |
|
| 93 |
Map<String, Collection> collectionMap = partitioner.getObjectMap(NAMESPACE_COLLECTION);
|
|
| 94 |
|
|
| 93 |
@SuppressWarnings("unchecked")
|
|
| 94 |
Map<String, Collection> collectionMap = partitioner.getObjectMap(NAMESPACE_COLLECTION); |
|
| 95 | 95 |
|
| 96 | 96 |
ResultSet rs = partitioner.getResultSet(); |
| 97 | 97 |
|
| ... | ... | |
| 198 | 198 |
@Override |
| 199 | 199 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 200 | 200 |
String nameSpace; |
| 201 |
Class cdmClass; |
|
| 202 | 201 |
Set<String> idSet; |
| 203 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 202 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 204 | 203 |
|
| 205 | 204 |
try{
|
| 206 |
Set<String> collectionIdSet = new HashSet<String>();
|
|
| 205 |
Set<String> collectionIdSet = new HashSet<>(); |
|
| 207 | 206 |
|
| 208 | 207 |
while (rs.next()){
|
| 209 | 208 |
handleForeignKey(rs, collectionIdSet, "partOfFk"); |
| ... | ... | |
| 211 | 210 |
|
| 212 | 211 |
//type specimen map |
| 213 | 212 |
nameSpace = NAMESPACE_COLLECTION; |
| 214 |
cdmClass = Collection.class; |
|
| 215 | 213 |
idSet = collectionIdSet; |
| 216 |
Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 214 |
Map<String, Collection> collectionMap = getCommonService().getSourcedObjectsByIdInSourceC(Collection.class, idSet, nameSpace);
|
|
| 217 | 215 |
result.put(nameSpace, collectionMap); |
| 218 | 216 |
|
| 219 | 217 |
|
| ... | ... | |
| 224 | 222 |
|
| 225 | 223 |
} |
| 226 | 224 |
|
| 227 |
|
|
| 228 |
/* (non-Javadoc) |
|
| 229 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase) |
|
| 230 |
*/ |
|
| 231 | 225 |
@Override |
| 232 | 226 |
protected boolean doCheck(BerlinModelImportState state){
|
| 233 | 227 |
IOValidator<BerlinModelImportState> validator = new AlgaTerraCollectionImportValidator(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraDnaImport.java | ||
|---|---|---|
| 362 | 362 |
@Override |
| 363 | 363 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 364 | 364 |
String nameSpace; |
| 365 |
Class<?> cdmClass; |
|
| 366 | 365 |
Set<String> idSet; |
| 367 | 366 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
| 368 | 367 |
|
| 369 | 368 |
try{
|
| 370 | 369 |
Set<String> taxonIdSet = new HashSet<>(); |
| 371 |
|
|
| 372 | 370 |
Set<String> ecoFactFkSet = new HashSet<>(); |
| 373 |
|
|
| 374 | 371 |
while (rs.next()){
|
| 375 | 372 |
handleForeignKey(rs, taxonIdSet, "taxonId"); |
| 376 | 373 |
handleForeignKey(rs, ecoFactFkSet, "ecoFactId"); |
| ... | ... | |
| 378 | 375 |
|
| 379 | 376 |
//taxon map |
| 380 | 377 |
nameSpace = BerlinModelTaxonImport.NAMESPACE; |
| 381 |
cdmClass = TaxonBase.class; |
|
| 382 | 378 |
idSet = taxonIdSet; |
| 383 |
Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 379 |
Map<String, TaxonBase> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace);
|
|
| 384 | 380 |
result.put(nameSpace, objectMap); |
| 385 | 381 |
|
| 386 | 382 |
|
| 387 | 383 |
//eco fact derived unit map |
| 388 |
nameSpace = AlgaTerraFactEcologyImport.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
|
| 389 |
cdmClass = DerivedUnit.class; |
|
| 384 |
nameSpace = AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
|
| 390 | 385 |
idSet = ecoFactFkSet; |
| 391 |
Map<String, DerivedUnit> derivedUnitMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 386 |
Map<String, DerivedUnit> derivedUnitMap = getCommonService().getSourcedObjectsByIdInSourceC(DerivedUnit.class, idSet, nameSpace);
|
|
| 392 | 387 |
result.put(nameSpace, derivedUnitMap); |
| 393 | 388 |
|
| 394 | 389 |
} catch (SQLException e) {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraEcoFactImport.java | ||
|---|---|---|
| 355 | 355 |
|
| 356 | 356 |
@Override |
| 357 | 357 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 358 |
String nameSpace; |
|
| 359 |
Class<?> cdmClass;
|
|
| 358 |
|
|
| 359 |
String nameSpace;
|
|
| 360 | 360 |
Set<String> idSet; |
| 361 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 361 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 362 | 362 |
|
| 363 | 363 |
try{
|
| 364 |
Set<String> fieldObservationIdSet = new HashSet<String>();
|
|
| 365 |
Set<String> termsIdSet = new HashSet<String>();
|
|
| 366 |
Set<String> collectionIdSet = new HashSet<String>();
|
|
| 364 |
Set<String> fieldObservationIdSet = new HashSet<>(); |
|
| 365 |
Set<String> termsIdSet = new HashSet<>(); |
|
| 366 |
Set<String> collectionIdSet = new HashSet<>(); |
|
| 367 | 367 |
|
| 368 | 368 |
while (rs.next()){
|
| 369 | 369 |
handleForeignKey(rs, fieldObservationIdSet, "DuplicateFk"); |
| ... | ... | |
| 374 | 374 |
} |
| 375 | 375 |
|
| 376 | 376 |
//field observation map for duplicates |
| 377 |
nameSpace = AlgaTerraEcoFactImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE; |
|
| 378 |
cdmClass = FieldUnit.class; |
|
| 377 |
nameSpace = AlgaTerraSpecimenImportBase.ECO_FACT_FIELD_OBSERVATION_NAMESPACE; |
|
| 379 | 378 |
idSet = fieldObservationIdSet; |
| 380 |
Map<String, FieldUnit> fieldObservationMap = (Map<String, FieldUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 379 |
Map<String, FieldUnit> fieldObservationMap = getCommonService().getSourcedObjectsByIdInSourceC(FieldUnit.class, idSet, nameSpace);
|
|
| 381 | 380 |
result.put(nameSpace, fieldObservationMap); |
| 382 | 381 |
|
| 383 | 382 |
//collections |
| 384 | 383 |
nameSpace = AlgaTerraCollectionImport.NAMESPACE_COLLECTION; |
| 385 |
cdmClass = Collection.class; |
|
| 386 | 384 |
idSet = collectionIdSet; |
| 387 |
Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 385 |
Map<String, Collection> collectionMap = getCommonService().getSourcedObjectsByIdInSourceC(Collection.class, idSet, nameSpace);
|
|
| 388 | 386 |
result.put(nameSpace, collectionMap); |
| 389 | 387 |
|
| 390 | 388 |
//sub-collections |
| 391 | 389 |
nameSpace = AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION; |
| 392 |
cdmClass = Collection.class; |
|
| 393 | 390 |
idSet = collectionIdSet; |
| 394 |
Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 391 |
Map<String, Collection> subCollectionMap = getCommonService().getSourcedObjectsByIdInSourceC(Collection.class, idSet, nameSpace);
|
|
| 395 | 392 |
result.put(nameSpace, subCollectionMap); |
| 396 | 393 |
|
| 397 | 394 |
//terms |
| 398 |
nameSpace = AlgaTerraEcoFactImport.TERMS_NAMESPACE;
|
|
| 399 |
cdmClass = FieldUnit.class; //???????? |
|
| 395 |
nameSpace = AlgaTerraSpecimenImportBase.TERMS_NAMESPACE;
|
|
| 396 |
Class<FieldUnit> cdmClass = FieldUnit.class; //????????
|
|
| 400 | 397 |
idSet = termsIdSet; |
| 401 |
Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 398 |
//FIXME something not correct here with the classes |
|
| 399 |
Map<String, DefinedTermBase> termMap = (Map)getCommonService().getSourcedObjectsByIdInSourceC(cdmClass, idSet, nameSpace); |
|
| 402 | 400 |
result.put(nameSpace, termMap); |
| 403 | 401 |
|
| 404 | 402 |
} catch (SQLException e) {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraFactEcologyImport.java | ||
|---|---|---|
| 283 | 283 |
@Override |
| 284 | 284 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 285 | 285 |
String nameSpace; |
| 286 |
Class<?> cdmClass; |
|
| 287 | 286 |
Set<String> idSet; |
| 288 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 287 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 289 | 288 |
|
| 290 | 289 |
try{
|
| 291 |
Set<String> taxonIdSet = new HashSet<String>();
|
|
| 292 |
Set<String> extensionFkSet = new HashSet<String>();
|
|
| 293 |
Set<String> referenceIdSet = new HashSet<String>();
|
|
| 290 |
Set<String> taxonIdSet = new HashSet<>(); |
|
| 291 |
Set<String> extensionFkSet = new HashSet<>(); |
|
| 292 |
Set<String> referenceIdSet = new HashSet<>(); |
|
| 294 | 293 |
|
| 295 | 294 |
while (rs.next()){
|
| 296 | 295 |
handleForeignKey(rs, taxonIdSet, "taxonId"); |
| ... | ... | |
| 300 | 299 |
|
| 301 | 300 |
//taxon map |
| 302 | 301 |
nameSpace = BerlinModelTaxonImport.NAMESPACE; |
| 303 |
cdmClass = TaxonBase.class; |
|
| 304 | 302 |
idSet = taxonIdSet; |
| 305 |
Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 303 |
@SuppressWarnings("rawtypes")
|
|
| 304 |
Map<String, TaxonBase> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace); |
|
| 306 | 305 |
result.put(nameSpace, objectMap); |
| 307 | 306 |
|
| 308 | 307 |
//derived unit map |
| 309 |
nameSpace = AlgaTerraFactEcologyImport.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
|
| 310 |
cdmClass = DerivedUnit.class; |
|
| 308 |
nameSpace = AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
|
| 311 | 309 |
idSet = extensionFkSet; |
| 312 |
Map<String, DerivedUnit> derivedUnitMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 310 |
Map<String, DerivedUnit> derivedUnitMap = getCommonService().getSourcedObjectsByIdInSourceC(DerivedUnit.class, idSet, nameSpace);
|
|
| 313 | 311 |
result.put(nameSpace, derivedUnitMap); |
| 314 | 312 |
|
| 315 | 313 |
//reference map |
| 316 | 314 |
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE; |
| 317 |
cdmClass = Reference.class; |
|
| 318 | 315 |
idSet = referenceIdSet; |
| 319 |
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 316 |
Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
|
|
| 320 | 317 |
result.put(nameSpace, referenceMap); |
| 321 | 318 |
|
| 322 | 319 |
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraMorphologyImport.java | ||
|---|---|---|
| 56 | 56 |
*/ |
| 57 | 57 |
@Component |
| 58 | 58 |
public class AlgaTerraMorphologyImport extends AlgaTerraSpecimenImportBase {
|
| 59 |
private static final Logger logger = Logger.getLogger(AlgaTerraMorphologyImport.class); |
|
| 60 | 59 |
|
| 60 |
private static final long serialVersionUID = 5978046406702163690L; |
|
| 61 |
private static final Logger logger = Logger.getLogger(AlgaTerraMorphologyImport.class); |
|
| 61 | 62 |
|
| 62 | 63 |
private static int modCount = 5000; |
| 63 | 64 |
private static final String pluralString = "morpho facts"; |
| ... | ... | |
| 245 | 246 |
} |
| 246 | 247 |
|
| 247 | 248 |
|
| 248 |
|
|
| 249 |
|
|
| 250 | 249 |
private void makeValveFeatures(AlgaTerraImportState state, |
| 251 | 250 |
Map<String, Feature> featureMap2, |
| 252 | 251 |
TermVocabulary<Feature> algaTerraMorphoFeatures2) {
|
| ... | ... | |
| 259 | 258 |
|
| 260 | 259 |
} |
| 261 | 260 |
|
| 262 |
|
|
| 263 | 261 |
private void handleSingleValve(AlgaTerraImportState state, |
| 264 | 262 |
Map<String, Feature> featureMap2, |
| 265 | 263 |
TermVocabulary<Feature> algaTerraMorphoFeatures2, String valveStr) {
|
| ... | ... | |
| 307 | 305 |
|
| 308 | 306 |
|
| 309 | 307 |
@Override |
| 310 |
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
|
|
| 308 |
public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
|
|
| 311 | 309 |
boolean success = true; |
| 312 | 310 |
|
| 313 | 311 |
AlgaTerraImportState state = (AlgaTerraImportState)bmState; |
| 314 |
Set<SpecimenOrObservationBase> objectsToSave = new HashSet<SpecimenOrObservationBase>(); |
|
| 312 |
@SuppressWarnings("rawtypes")
|
|
| 313 |
Set<SpecimenOrObservationBase> objectsToSave = new HashSet<>(); |
|
| 315 | 314 |
|
| 316 | 315 |
ResultSet rs = partitioner.getResultSet(); |
| 317 | 316 |
|
| ... | ... | |
| 483 | 482 |
return ECO_FACT_FIELD_OBSERVATION_NAMESPACE; |
| 484 | 483 |
} |
| 485 | 484 |
|
| 486 |
|
|
| 487 |
|
|
| 488 | 485 |
private void makeParameter(AlgaTerraImportState state, ResultSet rs, DescriptionBase<?> descriptionBase) throws SQLException {
|
| 489 | 486 |
for (int i = 1; i <= 10; i++){
|
| 490 | 487 |
String valueStr = rs.getString(String.format("P%dValue", i));
|
| ... | ... | |
| 524 | 521 |
}else if (isNotBlank(valueStr) || isNotBlank(unitStr) ){
|
| 525 | 522 |
logger.warn("There is value or unit without parameter: " + i);
|
| 526 | 523 |
} |
| 527 |
|
|
| 528 |
|
|
| 529 | 524 |
} |
| 530 |
|
|
| 531 | 525 |
} |
| 532 | 526 |
|
| 533 | 527 |
private String normalizeAndModifyValue(AlgaTerraImportState state, String valueStr, Set<DefinedTerm> valueModifier) {
|
| ... | ... | |
| 575 | 569 |
} |
| 576 | 570 |
} |
| 577 | 571 |
|
| 578 |
|
|
| 579 | 572 |
@Override |
| 580 | 573 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 581 |
String nameSpace; |
|
| 582 |
Class<?> cdmClass;
|
|
| 574 |
|
|
| 575 |
String nameSpace;
|
|
| 583 | 576 |
Set<String> idSet; |
| 584 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 577 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 585 | 578 |
|
| 586 | 579 |
try{
|
| 587 |
Set<String> ecoFactFkSet = new HashSet<String>();
|
|
| 580 |
Set<String> ecoFactFkSet = new HashSet<>(); |
|
| 588 | 581 |
|
| 589 | 582 |
while (rs.next()){
|
| 590 | 583 |
handleForeignKey(rs, ecoFactFkSet, "ecoFactId"); |
| 591 | 584 |
} |
| 592 | 585 |
|
| 593 | 586 |
//eco fact derived unit map |
| 594 |
nameSpace = AlgaTerraFactEcologyImport.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
|
| 595 |
cdmClass = DerivedUnit.class; |
|
| 587 |
nameSpace = AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE; |
|
| 596 | 588 |
idSet = ecoFactFkSet; |
| 597 |
Map<String, DerivedUnit> derivedUnitMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 589 |
Map<String, DerivedUnit> derivedUnitMap = getCommonService().getSourcedObjectsByIdInSourceC(DerivedUnit.class, idSet, nameSpace);
|
|
| 598 | 590 |
result.put(nameSpace, derivedUnitMap); |
| 599 | 591 |
|
| 600 | 592 |
} catch (SQLException e) {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraPictureImport.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 36 | 36 |
|
| 37 | 37 |
|
| 38 | 38 |
/** |
| 39 |
* Import for AlgaTerra images from table
|
|
| 39 |
* Import for AlgaTerra images from table |
|
| 40 | 40 |
* @author a.mueller |
| 41 | 41 |
* @since 18.01.2013 |
| 42 | 42 |
*/ |
| ... | ... | |
| 44 | 44 |
public class AlgaTerraPictureImport extends AlgaTerraImageImportBase {
|
| 45 | 45 |
private static final Logger logger = Logger.getLogger(AlgaTerraPictureImport.class); |
| 46 | 46 |
|
| 47 |
|
|
| 47 |
|
|
| 48 | 48 |
private static int modCount = 5000; |
| 49 | 49 |
private static final String pluralString = "pictures"; |
| 50 |
private static final String dbTableName = "Picture"; //??
|
|
| 51 |
|
|
| 50 |
private static final String dbTableName = "Picture"; //?? |
|
| 51 |
|
|
| 52 | 52 |
public AlgaTerraPictureImport(){
|
| 53 | 53 |
super(dbTableName, pluralString); |
| 54 | 54 |
} |
| 55 |
|
|
| 56 |
|
|
| 55 |
|
|
| 56 |
|
|
| 57 | 57 |
/* (non-Javadoc) |
| 58 | 58 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery() |
| 59 | 59 |
*/ |
| 60 | 60 |
@Override |
| 61 | 61 |
protected String getIdQuery(BerlinModelImportState state) {
|
| 62 |
String result = " SELECT p.PictureId "
|
|
| 63 |
+ " FROM Picture p INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk "
|
|
| 62 |
String result = " SELECT p.PictureId " |
|
| 63 |
+ " FROM Picture p INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk " |
|
| 64 | 64 |
+ " WHERE f.FactCategoryFk = 205 AND p.RestrictedFlag = 0 " |
| 65 | 65 |
+ " ORDER BY p.PictureId "; |
| 66 | 66 |
return result; |
| ... | ... | |
| 71 | 71 |
*/ |
| 72 | 72 |
@Override |
| 73 | 73 |
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
| 74 |
String strQuery =
|
|
| 75 |
|
|
| 74 |
String strQuery = |
|
| 75 |
|
|
| 76 | 76 |
" SELECT p.*, f.*, pt.RIdentifier, p.PicturePhrase as FigurePhrase, p.PictureFile as fileName, p.PicturePath as filePath " + |
| 77 |
" FROM Picture p INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk "
|
|
| 78 |
+ " WHERE f.FactCategoryFk = 205 AND ( p.PictureID IN (" + ID_LIST_TOKEN + ") )"
|
|
| 77 |
" FROM Picture p INNER JOIN Fact f ON p.PictureId = f.ExtensionFk LEFT OUTER JOIN PTaxon pt ON f.PTNameFk = pt.PTNameFk AND f.PTRefFk = pt.PTRefFk " |
|
| 78 |
+ " WHERE f.FactCategoryFk = 205 AND ( p.PictureID IN (" + ID_LIST_TOKEN + ") )"
|
|
| 79 | 79 |
+ " ORDER BY p.PictureId, f.factId, pt.RIdentifier "; |
| 80 | 80 |
; |
| 81 | 81 |
return strQuery; |
| ... | ... | |
| 84 | 84 |
/* (non-Javadoc) |
| 85 | 85 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState) |
| 86 | 86 |
*/ |
| 87 |
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
|
|
| 87 |
@Override |
|
| 88 |
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
|
|
| 88 | 89 |
boolean success = true; |
| 89 |
|
|
| 90 |
|
|
| 90 | 91 |
AlgaTerraImportState state = (AlgaTerraImportState)bmState; |
| 91 |
|
|
| 92 |
|
|
| 92 | 93 |
// Set<SpecimenOrObservationBase> specimenToSave = new HashSet<SpecimenOrObservationBase>(); |
| 93 | 94 |
Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>(); |
| 94 |
|
|
| 95 |
|
|
| 95 | 96 |
// Map<String, DerivedUnitBase> ecoFactMap = (Map<String, DerivedUnitBase>) partitioner.getObjectMap(AlgaTerraSpecimenImportBase.ECO_FACT_DERIVED_UNIT_NAMESPACE); |
| 96 |
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
|
|
| 97 |
Map<String, DerivedUnit> specimenMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(AlgaTerraFactEcologyImport.FACT_ECOLOGY_NAMESPACE);
|
|
| 98 |
|
|
| 97 |
Map<String, TaxonBase> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE); |
|
| 98 |
Map<String, DerivedUnit> specimenMap = partitioner.getObjectMap(AlgaTerraFactEcologyImport.FACT_ECOLOGY_NAMESPACE); |
|
| 99 |
|
|
| 99 | 100 |
ResultSet rs = partitioner.getResultSet(); |
| 100 | 101 |
|
| 101 | 102 |
try {
|
| 102 |
|
|
| 103 |
|
|
| 103 | 104 |
int i = 0; |
| 104 | 105 |
|
| 105 | 106 |
//for each reference |
| 106 | 107 |
while (rs.next()){
|
| 107 |
|
|
| 108 |
|
|
| 108 | 109 |
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
|
| 109 |
|
|
| 110 |
|
|
| 110 | 111 |
int pictureId = rs.getInt("PictureID");
|
| 111 | 112 |
int taxonId = rs.getInt("RIdentifier");
|
| 112 | 113 |
int factId = rs.getInt("FactId");
|
| 113 |
|
|
| 114 |
|
|
| 114 |
|
|
| 115 |
|
|
| 115 | 116 |
//TODO etc. Created, Notes, Copyright, TermsOfUse etc. |
| 116 |
|
|
| 117 |
|
|
| 117 | 118 |
try {
|
| 118 |
|
|
| 119 |
|
|
| 119 | 120 |
TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(taxonId)); |
| 120 | 121 |
if (taxonBase == null){
|
| 121 | 122 |
logger.warn("Could not find taxon (" + taxonId +") for picture fact " + factId);
|
| 122 | 123 |
}else if (! taxonBase.isInstanceOf(Taxon.class)){
|
| 123 | 124 |
logger.warn("Taxon is not of class Taxon but " + taxonBase.getClass() + ". RIdentifier: " + taxonId + " PictureId: " + pictureId + ", FactId: "+ factId);
|
| 124 |
|
|
| 125 |
|
|
| 125 | 126 |
}else{
|
| 126 | 127 |
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
| 127 |
|
|
| 128 |
|
|
| 128 | 129 |
Media media = handleSingleImage(rs, taxon, state, partitioner, PathType.Image); |
| 129 |
|
|
| 130 |
|
|
| 130 | 131 |
handlePictureSpecificFields(rs, media, state, specimenMap); |
| 131 |
|
|
| 132 |
taxaToSave.add(taxon);
|
|
| 132 |
|
|
| 133 |
taxaToSave.add(taxon); |
|
| 133 | 134 |
} |
| 134 |
|
|
| 135 |
|
|
| 135 | 136 |
|
| 136 | 137 |
} catch (Exception e) {
|
| 137 | 138 |
logger.warn("Exception in " + getTableName() + ": PictureId " + pictureId + ". " + e.getMessage());
|
| 138 | 139 |
e.printStackTrace(); |
| 139 |
}
|
|
| 140 |
|
|
| 140 |
} |
|
| 141 |
|
|
| 141 | 142 |
} |
| 142 |
|
|
| 143 |
|
|
| 143 | 144 |
// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
|
| 144 | 145 |
|
| 145 | 146 |
logger.warn(pluralString + " to save: " + taxaToSave.size()); |
| 146 |
// getOccurrenceService().save(taxaToSave);
|
|
| 147 |
getTaxonService().save(taxaToSave);
|
|
| 148 |
|
|
| 147 |
// getOccurrenceService().save(taxaToSave); |
|
| 148 |
getTaxonService().save(taxaToSave); |
|
| 149 |
|
|
| 149 | 150 |
return success; |
| 150 | 151 |
} catch (SQLException e) {
|
| 151 | 152 |
logger.error("SQLException:" + e);
|
| ... | ... | |
| 172 | 173 |
} |
| 173 | 174 |
} |
| 174 | 175 |
} |
| 175 |
|
|
| 176 |
|
|
| 176 | 177 |
} |
| 177 | 178 |
|
| 178 | 179 |
|
| 179 | 180 |
@Override |
| 180 | 181 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 181 |
String nameSpace; |
|
| 182 |
Class<?> cdmClass;
|
|
| 182 |
|
|
| 183 |
String nameSpace;
|
|
| 183 | 184 |
Set<String> idSet; |
| 184 | 185 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>(); |
| 185 |
|
|
| 186 |
|
|
| 186 | 187 |
try{
|
| 187 | 188 |
Set<String> taxonIdSet = new HashSet<String>(); |
| 188 | 189 |
Set<String> specimenIdSet = new HashSet<String>(); |
| 189 |
|
|
| 190 |
|
|
| 190 | 191 |
while (rs.next()){
|
| 191 | 192 |
handleForeignKey(rs, taxonIdSet, "RIdentifier"); |
| 192 | 193 |
handleForeignKey(rs, specimenIdSet, "FactFk"); |
| 193 | 194 |
} |
| 194 |
|
|
| 195 |
|
|
| 195 | 196 |
//taxon map |
| 196 | 197 |
nameSpace = BerlinModelTaxonImport.NAMESPACE; |
| 197 |
cdmClass = TaxonBase.class; |
|
| 198 | 198 |
idSet = taxonIdSet; |
| 199 |
Map<String, TaxonBase> taxonMap = (Map<String,TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 199 |
@SuppressWarnings("rawtypes")
|
|
| 200 |
Map<String, TaxonBase> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace); |
|
| 200 | 201 |
result.put(nameSpace, taxonMap); |
| 201 | 202 |
|
| 202 | 203 |
//fact specimen map |
| 203 |
nameSpace = AlgaTerraFactEcologyImport.FACT_ECOLOGY_NAMESPACE; |
|
| 204 |
cdmClass = SpecimenOrObservationBase.class; |
|
| 204 |
nameSpace = AlgaTerraSpecimenImportBase.FACT_ECOLOGY_NAMESPACE; |
|
| 205 | 205 |
idSet = specimenIdSet; |
| 206 |
Map<String, SpecimenOrObservationBase> specimenMap = (Map<String,SpecimenOrObservationBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 206 |
@SuppressWarnings("rawtypes")
|
|
| 207 |
Map<String, SpecimenOrObservationBase> specimenMap = getCommonService().getSourcedObjectsByIdInSourceC(SpecimenOrObservationBase.class, idSet, nameSpace); |
|
| 207 | 208 |
result.put(nameSpace, specimenMap); |
| 208 | 209 |
|
| 209 |
|
|
| 210 |
|
|
| 210 | 211 |
} catch (SQLException e) {
|
| 211 | 212 |
throw new RuntimeException(e); |
| 212 | 213 |
} |
| ... | ... | |
| 225 | 226 |
AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator(); |
| 226 | 227 |
return ! ( config.isDoTypes() && config.isDoImages()) ; |
| 227 | 228 |
} |
| 228 |
|
|
| 229 |
|
|
| 229 | 230 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSiteImagesImport.java | ||
|---|---|---|
| 1 | 1 |
/** |
| 2 | 2 |
* Copyright (C) 2007 EDIT |
| 3 |
* European Distributed Institute of Taxonomy
|
|
| 3 |
* European Distributed Institute of Taxonomy |
|
| 4 | 4 |
* http://www.e-taxonomy.eu |
| 5 |
*
|
|
| 5 |
* |
|
| 6 | 6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
| 7 | 7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
| 8 | 8 |
*/ |
| ... | ... | |
| 19 | 19 |
import org.apache.log4j.Logger; |
| 20 | 20 |
import org.springframework.stereotype.Component; |
| 21 | 21 |
|
| 22 |
import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImageImportBase.PathType; |
|
| 23 | 22 |
import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraTypeImportValidator; |
| 24 | 23 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator; |
| 25 | 24 |
import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState; |
| ... | ... | |
| 39 | 38 |
public class AlgaTerraSiteImagesImport extends AlgaTerraImageImportBase {
|
| 40 | 39 |
private static final Logger logger = Logger.getLogger(AlgaTerraSiteImagesImport.class); |
| 41 | 40 |
|
| 42 |
|
|
| 41 |
|
|
| 43 | 42 |
private static int modCount = 5000; |
| 44 | 43 |
private static final String pluralString = "site images"; |
| 45 |
private static final String dbTableName = "SiteImages"; //??
|
|
| 46 |
|
|
| 44 |
private static final String dbTableName = "SiteImages"; //?? |
|
| 45 |
|
|
| 47 | 46 |
public AlgaTerraSiteImagesImport(){
|
| 48 | 47 |
super(dbTableName, pluralString); |
| 49 | 48 |
} |
| 50 |
|
|
| 51 |
|
|
| 49 |
|
|
| 50 |
|
|
| 52 | 51 |
/* (non-Javadoc) |
| 53 | 52 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery() |
| 54 | 53 |
*/ |
| 55 | 54 |
@Override |
| 56 | 55 |
protected String getIdQuery(BerlinModelImportState state) {
|
| 57 |
String result = " SELECT SiteId "
|
|
| 58 |
+ " FROM SiteImages "
|
|
| 56 |
String result = " SELECT SiteId " |
|
| 57 |
+ " FROM SiteImages " |
|
| 59 | 58 |
+ " ORDER BY EcoFactFk "; |
| 60 | 59 |
return result; |
| 61 | 60 |
} |
| ... | ... | |
| 65 | 64 |
*/ |
| 66 | 65 |
@Override |
| 67 | 66 |
protected String getRecordQuery(BerlinModelImportConfigurator config) {
|
| 68 |
String strQuery =
|
|
| 69 |
|
|
| 67 |
String strQuery = |
|
| 68 |
|
|
| 70 | 69 |
" SELECT si.*, si.Comment as FigurePhrase, si.Picture as fileName, si.Path as filePath " + |
| 71 |
" FROM SiteImages si "
|
|
| 72 |
+ " WHERE (si.SiteID IN (" + ID_LIST_TOKEN + ") )"
|
|
| 70 |
" FROM SiteImages si " |
|
| 71 |
+ " WHERE (si.SiteID IN (" + ID_LIST_TOKEN + ") )"
|
|
| 73 | 72 |
+ " ORDER BY EcoFactFk "; |
| 74 | 73 |
; |
| 75 | 74 |
return strQuery; |
| ... | ... | |
| 78 | 77 |
/* (non-Javadoc) |
| 79 | 78 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState) |
| 80 | 79 |
*/ |
| 81 |
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
|
|
| 80 |
@Override |
|
| 81 |
public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
|
|
| 82 | 82 |
boolean success = true; |
| 83 |
|
|
| 83 |
|
|
| 84 | 84 |
AlgaTerraImportState state = (AlgaTerraImportState)bmState; |
| 85 |
|
|
| 85 |
|
|
| 86 | 86 |
Set<SpecimenOrObservationBase> unitsToSave = new HashSet<SpecimenOrObservationBase>(); |
| 87 |
|
|
| 88 |
Map<String, FieldUnit> ecoFactFieldObservationMap = (Map<String, FieldUnit>) partitioner.getObjectMap(AlgaTerraSpecimenImportBase.ECO_FACT_FIELD_OBSERVATION_NAMESPACE);
|
|
| 89 |
|
|
| 87 |
|
|
| 88 |
Map<String, FieldUnit> ecoFactFieldObservationMap = partitioner.getObjectMap(AlgaTerraSpecimenImportBase.ECO_FACT_FIELD_OBSERVATION_NAMESPACE); |
|
| 89 |
|
|
| 90 | 90 |
ResultSet rs = partitioner.getResultSet(); |
| 91 | 91 |
|
| 92 | 92 |
try {
|
| 93 |
|
|
| 93 |
|
|
| 94 | 94 |
int i = 0; |
| 95 | 95 |
|
| 96 | 96 |
//for each reference |
| 97 | 97 |
while (rs.next()){
|
| 98 |
|
|
| 98 |
|
|
| 99 | 99 |
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
|
| 100 |
|
|
| 100 |
|
|
| 101 | 101 |
int figureId = rs.getInt("SiteId");
|
| 102 | 102 |
int ecoFactFk = rs.getInt("EcoFactFk");
|
| 103 |
|
|
| 104 |
|
|
| 103 |
|
|
| 104 |
|
|
| 105 | 105 |
//TODO etc. Created, Notes, Copyright, TermsOfUse etc. |
| 106 |
|
|
| 106 |
|
|
| 107 | 107 |
try {
|
| 108 |
|
|
| 108 |
|
|
| 109 | 109 |
//TODO use deduplicated ecofact |
| 110 | 110 |
FieldUnit fieldObservation = ecoFactFieldObservationMap.get(String.valueOf(ecoFactFk)); |
| 111 |
|
|
| 111 |
|
|
| 112 | 112 |
if (fieldObservation == null){
|
| 113 | 113 |
logger.warn("Could not find eco fact field observation (" + ecoFactFk +") for site image " + figureId);
|
| 114 | 114 |
}else{
|
| 115 |
|
|
| 115 |
|
|
| 116 | 116 |
} |
| 117 |
|
|
| 117 |
|
|
| 118 | 118 |
//field observation |
| 119 | 119 |
Media media = handleSingleImage(rs, fieldObservation, state, partitioner, PathType.Site); |
| 120 |
|
|
| 120 |
|
|
| 121 | 121 |
handleSiteImageSpecificFields(rs, media, state); |
| 122 |
|
|
| 123 |
unitsToSave.add(fieldObservation);
|
|
| 124 |
|
|
| 122 |
|
|
| 123 |
unitsToSave.add(fieldObservation); |
|
| 124 |
|
|
| 125 | 125 |
|
| 126 | 126 |
} catch (Exception e) {
|
| 127 | 127 |
logger.warn("Exception in " + getTableName() + ": SiteId " + figureId + ". " + e.getMessage());
|
| 128 | 128 |
e.printStackTrace(); |
| 129 |
}
|
|
| 130 |
|
|
| 129 |
} |
|
| 130 |
|
|
| 131 | 131 |
} |
| 132 |
|
|
| 132 |
|
|
| 133 | 133 |
// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
|
| 134 | 134 |
|
| 135 | 135 |
logger.warn(pluralString + " to save: " + unitsToSave.size()); |
| 136 |
getOccurrenceService().saveOrUpdate(unitsToSave);
|
|
| 137 |
|
|
| 136 |
getOccurrenceService().saveOrUpdate(unitsToSave); |
|
| 137 |
|
|
| 138 | 138 |
return success; |
| 139 | 139 |
} catch (SQLException e) {
|
| 140 | 140 |
logger.error("SQLException:" + e);
|
| ... | ... | |
| 146 | 146 |
|
| 147 | 147 |
private void handleSiteImageSpecificFields(ResultSet rs, Media media, AlgaTerraImportState state) throws SQLException {
|
| 148 | 148 |
//TODO |
| 149 |
|
|
| 149 |
|
|
| 150 | 150 |
} |
| 151 | 151 |
|
| 152 | 152 |
|
| 153 | 153 |
@Override |
| 154 | 154 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
| 155 |
String nameSpace; |
|
| 156 |
Class<?> cdmClass;
|
|
| 155 |
|
|
| 156 |
String nameSpace;
|
|
| 157 | 157 |
Set<String> idSet; |
| 158 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 159 |
|
|
| 158 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 159 |
|
|
| 160 | 160 |
try{
|
| 161 |
Set<String> ecoFactIdSet = new HashSet<String>();
|
|
| 162 |
|
|
| 161 |
Set<String> ecoFactIdSet = new HashSet<>(); |
|
| 162 |
|
|
| 163 | 163 |
while (rs.next()){
|
| 164 | 164 |
handleForeignKey(rs, ecoFactIdSet, "EcoFactFk"); |
| 165 | 165 |
} |
| 166 |
|
|
| 166 |
|
|
| 167 | 167 |
//field observation map |
| 168 | 168 |
nameSpace = AlgaTerraSpecimenImportBase.ECO_FACT_FIELD_OBSERVATION_NAMESPACE; |
| 169 |
cdmClass = FieldUnit.class; |
|
| 170 | 169 |
idSet = ecoFactIdSet; |
| 171 |
Map<String, FieldUnit> fieldObservationMap = (Map<String,FieldUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 170 |
Map<String, FieldUnit> fieldObservationMap = getCommonService().getSourcedObjectsByIdInSourceC(FieldUnit.class, idSet, nameSpace);
|
|
| 172 | 171 |
result.put(nameSpace, fieldObservationMap); |
| 173 | 172 |
|
| 174 |
|
|
| 173 |
|
|
| 175 | 174 |
} catch (SQLException e) {
|
| 176 | 175 |
throw new RuntimeException(e); |
| 177 | 176 |
} |
| ... | ... | |
| 189 | 188 |
AlgaTerraImportConfigurator config = ((AlgaTerraImportState) bmState).getAlgaTerraConfigurator(); |
| 190 | 189 |
return ! ( config.isDoEcoFacts() && config.isDoImages()) ; |
| 191 | 190 |
} |
| 192 |
|
|
| 191 |
|
|
| 193 | 192 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTaxonRelationImport.java | ||
|---|---|---|
| 98 | 98 |
|
| 99 | 99 |
//reference map |
| 100 | 100 |
String nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE; |
| 101 |
Class<?> cdmClass = Reference.class; |
|
| 102 |
@SuppressWarnings("unchecked")
|
|
| 103 |
Map<String, Reference> refMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 101 |
Class<Reference> cdmClass = Reference.class; |
|
| 102 |
Map<String, Reference> refMap = getCommonService().getSourcedObjectsByIdInSourceC(cdmClass, idSet, nameSpace); |
|
| 104 | 103 |
|
| 105 | 104 |
String classificationName = "Classification - No Name"; |
| 106 | 105 |
|
| ... | ... | |
| 666 | 665 |
|
| 667 | 666 |
private Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForFlatPartition( ResultSet rs) {
|
| 668 | 667 |
String nameSpace; |
| 669 |
Class cdmClass; |
|
| 670 | 668 |
Set<String> idSet; |
| 671 | 669 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
| 672 | 670 |
|
| 673 | 671 |
try{
|
| 674 | 672 |
Set<String> taxonIdSet = new HashSet<>(); |
| 675 |
Set<String> referenceIdSet = new HashSet<>(); |
|
| 676 | 673 |
// Set<String> classificationIdSet = new HashSet<>(); |
| 677 | 674 |
while (rs.next()){
|
| 678 | 675 |
handleForeignKey(rs, taxonIdSet, "RIdentifier"); |
| ... | ... | |
| 681 | 678 |
|
| 682 | 679 |
//taxon map |
| 683 | 680 |
nameSpace = BerlinModelTaxonImport.NAMESPACE; |
| 684 |
cdmClass = TaxonBase.class; |
|
| 685 | 681 |
idSet = taxonIdSet; |
| 686 |
Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace); |
|
| 682 |
@SuppressWarnings("rawtypes")
|
|
| 683 |
Map<String, TaxonBase> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace); |
|
| 687 | 684 |
result.put(nameSpace, taxonMap); |
| 688 | 685 |
|
| 689 | 686 |
// //tree map |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCommonNameImport.java | ||
|---|---|---|
| 47 | 47 |
*/ |
| 48 | 48 |
@Component |
| 49 | 49 |
public class GlobisCommonNameImport extends GlobisImportBase<Taxon> {
|
| 50 |
private static final Logger logger = Logger.getLogger(GlobisCommonNameImport.class); |
|
| 50 |
|
|
| 51 |
private static final long serialVersionUID = 2462539699442149049L; |
|
| 52 |
private static final Logger logger = Logger.getLogger(GlobisCommonNameImport.class); |
|
| 51 | 53 |
|
| 52 | 54 |
private int modCount = 10000; |
| 53 | 55 |
private static final String pluralString = "common names"; |
| ... | ... | |
| 80 | 82 |
} |
| 81 | 83 |
|
| 82 | 84 |
@Override |
| 83 |
public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
| 85 |
public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
| 84 | 86 |
boolean success = true; |
| 85 | 87 |
|
| 86 |
Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>(); |
|
| 88 |
@SuppressWarnings("rawtypes")
|
|
| 89 |
Set<TaxonBase> objectsToSave = new HashSet<>(); |
|
| 87 | 90 |
|
| 88 |
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 91 |
@SuppressWarnings("unchecked")
|
|
| 92 |
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 89 | 93 |
|
| 90 | 94 |
ResultSet rs = partitioner.getResultSet(); |
| 91 | 95 |
|
| ... | ... | |
| 159 | 163 |
} |
| 160 | 164 |
} |
| 161 | 165 |
|
| 162 |
|
|
| 163 |
private Map<String,Language> languageMap = new HashMap<String,Language>(); |
|
| 166 |
private Map<String,Language> languageMap = new HashMap<>(); |
|
| 164 | 167 |
private Language getLanguage(String isoLang) {
|
| 165 | 168 |
Language result = languageMap.get(isoLang); |
| 166 | 169 |
if (result == null){
|
| ... | ... | |
| 229 | 232 |
@Override |
| 230 | 233 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, GlobisImportState state) {
|
| 231 | 234 |
String nameSpace; |
| 232 |
Class<?> cdmClass; |
|
| 233 | 235 |
Set<String> idSet; |
| 234 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 236 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 235 | 237 |
try{
|
| 236 |
Set<String> taxonIdSet = new HashSet<String>();
|
|
| 238 |
Set<String> taxonIdSet = new HashSet<>(); |
|
| 237 | 239 |
|
| 238 | 240 |
while (rs.next()){
|
| 239 | 241 |
handleForeignKey(rs, taxonIdSet, "IDCurrentSpec"); |
| ... | ... | |
| 241 | 243 |
|
| 242 | 244 |
//taxon map |
| 243 | 245 |
nameSpace = TAXON_NAMESPACE; |
| 244 |
cdmClass = Taxon.class; |
|
| 245 | 246 |
idSet = taxonIdSet; |
| 246 |
Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 247 |
Map<String, Taxon> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class, idSet, nameSpace);
|
|
| 247 | 248 |
result.put(nameSpace, objectMap); |
| 248 | 249 |
|
| 249 | 250 |
|
| ... | ... | |
| 253 | 254 |
return result; |
| 254 | 255 |
} |
| 255 | 256 |
|
| 256 |
|
|
| 257 | 257 |
@Override |
| 258 |
protected boolean doCheck(GlobisImportState state){
|
|
| 258 |
protected boolean doCheck(GlobisImportState state){
|
|
| 259 | 259 |
// IOValidator<GlobisImportState> validator = new GlobisCurrentSpeciesImportValidator(); |
| 260 | 260 |
return true; |
| 261 | 261 |
} |
| ... | ... | |
| 264 | 264 |
protected boolean isIgnore(GlobisImportState state){
|
| 265 | 265 |
return ! state.getConfig().isDoCommonNames(); |
| 266 | 266 |
} |
| 267 |
|
|
| 268 |
|
|
| 269 |
|
|
| 270 |
|
|
| 271 |
|
|
| 272 | 267 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCurrentSpeciesImport.java | ||
|---|---|---|
| 41 | 41 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
| 42 | 42 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 43 | 43 |
|
| 44 |
|
|
| 45 | 44 |
/** |
| 46 | 45 |
* @author a.mueller |
| 47 | 46 |
* @since 20.02.2010 |
| 48 | 47 |
*/ |
| 49 | 48 |
@Component |
| 50 | 49 |
public class GlobisCurrentSpeciesImport extends GlobisImportBase<Taxon> {
|
| 51 |
private static final Logger logger = Logger.getLogger(GlobisCurrentSpeciesImport.class); |
|
| 50 |
|
|
| 51 |
private static final long serialVersionUID = -4392659482520384118L; |
|
| 52 |
private static final Logger logger = Logger.getLogger(GlobisCurrentSpeciesImport.class); |
|
| 52 | 53 |
|
| 53 | 54 |
private int modCount = 10000; |
| 54 | 55 |
private static final String pluralString = "current taxa"; |
| ... | ... | |
| 78 | 79 |
} |
| 79 | 80 |
|
| 80 | 81 |
@Override |
| 81 |
public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
| 82 |
public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
| 82 | 83 |
boolean success = true; |
| 83 | 84 |
|
| 84 |
Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>(); |
|
| 85 |
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 85 |
@SuppressWarnings("rawtypes")
|
|
| 86 |
Set<TaxonBase> objectsToSave = new HashSet<>(); |
|
| 87 |
@SuppressWarnings("unchecked")
|
|
| 88 |
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 86 | 89 |
ResultSet rs = partitioner.getResultSet(); |
| 87 | 90 |
|
| 88 | 91 |
Classification classification = getClassification(state); |
| ... | ... | |
| 230 | 233 |
countryStr = countryStr.substring(1).trim(); |
| 231 | 234 |
} |
| 232 | 235 |
|
| 233 |
|
|
| 234 |
|
|
| 235 | 236 |
countryStr = normalizeCountry(countryStr); |
| 236 | 237 |
|
| 237 | 238 |
NamedArea country = getCountry(state, countryStr); |
| ... | ... | |
| 255 | 256 |
} |
| 256 | 257 |
} |
| 257 | 258 |
|
| 258 |
|
|
| 259 |
|
|
| 260 |
/** |
|
| 261 |
* @param countryStr |
|
| 262 |
* @return |
|
| 263 |
*/ |
|
| 264 | 259 |
private String normalizeCountry(String countryStr) {
|
| 265 | 260 |
String result = countryStr.trim(); |
| 266 | 261 |
if (result.endsWith(".")){
|
| ... | ... | |
| 294 | 289 |
// } |
| 295 | 290 |
} |
| 296 | 291 |
|
| 297 |
|
|
| 298 |
|
|
| 299 |
|
|
| 300 | 292 |
/** |
| 301 | 293 |
* Compares 2 taxa, returns true of both taxa look similar |
| 302 | 294 |
* @param genus |
| ... | ... | |
| 315 | 307 |
return true; |
| 316 | 308 |
} |
| 317 | 309 |
|
| 318 |
|
|
| 319 |
|
|
| 320 |
|
|
| 321 | 310 |
private Taxon getParent(Taxon child, Classification classification) {
|
| 322 | 311 |
if (child == null){
|
| 323 | 312 |
logger.warn("Child is null");
|
| ... | ... | |
| 335 | 324 |
return null; |
| 336 | 325 |
} |
| 337 | 326 |
|
| 338 |
|
|
| 339 |
|
|
| 340 |
|
|
| 341 | 327 |
private Taxon getTaxon(GlobisImportState state, ResultSet rs, String uninomial, String infraGenericEpi, Rank rank, String author, Map<String, Taxon> taxonMap, Integer taxonId) {
|
| 342 | 328 |
if (isBlank(uninomial)){
|
| 343 | 329 |
return null; |
| ... | ... | |
| 379 | 365 |
|
| 380 | 366 |
} |
| 381 | 367 |
|
| 382 |
/* (non-Javadoc) |
|
| 383 |
* @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase) |
|
| 384 |
*/ |
|
| 385 | 368 |
public Taxon createObject(ResultSet rs, GlobisImportState state, Integer taxonId) |
| 386 | 369 |
throws SQLException {
|
| 387 | 370 |
String speciesEpi = rs.getString("dtSpcSpcakt");
|
| ... | ... | |
| 403 | 386 |
return taxon; |
| 404 | 387 |
} |
| 405 | 388 |
|
| 406 |
|
|
| 407 |
|
|
| 408 |
|
|
| 409 | 389 |
@Override |
| 410 | 390 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, GlobisImportState state) {
|
| 411 |
String nameSpace; |
|
| 412 |
Class cdmClass;
|
|
| 391 |
|
|
| 392 |
String nameSpace;
|
|
| 413 | 393 |
Set<String> idSet; |
| 414 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 394 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 415 | 395 |
try{
|
| 416 |
Set<String> taxonIdSet = new HashSet<String>();
|
|
| 396 |
Set<String> taxonIdSet = new HashSet<>(); |
|
| 417 | 397 |
|
| 418 | 398 |
while (rs.next()){
|
| 419 | 399 |
// handleForeignKey(rs, taxonIdSet, "taxonId"); |
| ... | ... | |
| 421 | 401 |
|
| 422 | 402 |
//taxon map |
| 423 | 403 |
nameSpace = TAXON_NAMESPACE; |
| 424 |
cdmClass = Taxon.class; |
|
| 425 | 404 |
idSet = taxonIdSet; |
| 426 |
Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 405 |
Map<String, Taxon> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class, idSet, nameSpace);
|
|
| 427 | 406 |
result.put(nameSpace, objectMap); |
| 428 | 407 |
|
| 429 | 408 |
|
| ... | ... | |
| 433 | 412 |
return result; |
| 434 | 413 |
} |
| 435 | 414 |
|
| 436 |
/* (non-Javadoc) |
|
| 437 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 438 |
*/ |
|
| 439 | 415 |
@Override |
| 440 | 416 |
protected boolean doCheck(GlobisImportState state){
|
| 441 | 417 |
IOValidator<GlobisImportState> validator = new GlobisCurrentSpeciesImportValidator(); |
| 442 | 418 |
return validator.validate(state); |
| 443 | 419 |
} |
| 444 | 420 |
|
| 445 |
|
|
| 446 |
/* (non-Javadoc) |
|
| 447 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 448 |
*/ |
|
| 449 | 421 |
@Override |
| 450 | 422 |
protected boolean isIgnore(GlobisImportState state){
|
| 451 | 423 |
return ! state.getConfig().isDoCurrentTaxa(); |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisImageImport.java | ||
|---|---|---|
| 51 | 51 |
/** |
| 52 | 52 |
* @author a.mueller |
| 53 | 53 |
* @since 20.02.2010 |
| 54 |
* @version 1.0 |
|
| 55 | 54 |
*/ |
| 56 | 55 |
@Component |
| 57 | 56 |
public class GlobisImageImport extends GlobisImportBase<Taxon> {
|
| 58 |
private static final Logger logger = Logger.getLogger(GlobisImageImport.class); |
|
| 57 |
|
|
| 58 |
private static final long serialVersionUID = 5697033145326415146L; |
|
| 59 |
private static final Logger logger = Logger.getLogger(GlobisImageImport.class); |
|
| 59 | 60 |
|
| 60 | 61 |
private int modCount = 1000; |
| 61 | 62 |
|
| ... | ... | |
| 70 | 71 |
super(pluralString, dbTableName, cdmTargetClass); |
| 71 | 72 |
} |
| 72 | 73 |
|
| 73 |
|
|
| 74 |
|
|
| 75 |
|
|
| 76 |
/* (non-Javadoc) |
|
| 77 |
* @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#getIdQuery() |
|
| 78 |
*/ |
|
| 79 | 74 |
@Override |
| 80 | 75 |
protected String getIdQuery() {
|
| 81 | 76 |
String strRecordQuery = |
| ... | ... | |
| 84 | 79 |
return strRecordQuery; |
| 85 | 80 |
} |
| 86 | 81 |
|
| 87 |
|
|
| 88 |
|
|
| 89 |
|
|
| 90 |
/* (non-Javadoc) |
|
| 91 |
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator) |
|
| 92 |
*/ |
|
| 93 | 82 |
@Override |
| 94 | 83 |
protected String getRecordQuery(GlobisImportConfigurator config) {
|
| 95 | 84 |
String strRecordQuery = |
| ... | ... | |
| 101 | 90 |
return strRecordQuery; |
| 102 | 91 |
} |
| 103 | 92 |
|
| 104 |
|
|
| 105 |
|
|
| 106 |
/* (non-Javadoc) |
|
| 107 |
* @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState) |
|
| 108 |
*/ |
|
| 109 | 93 |
@Override |
| 110 |
public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
| 94 |
public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
| 111 | 95 |
boolean success = true; |
| 112 | 96 |
|
| 113 | 97 |
Set<Media> objectsToSave = new HashSet<>(); |
| 114 | 98 |
|
| 115 |
Map<String, DerivedUnit> typeMap = partitioner.getObjectMap(TYPE_NAMESPACE); |
|
| 99 |
@SuppressWarnings("unchecked")
|
|
| 100 |
Map<String, DerivedUnit> typeMap = partitioner.getObjectMap(TYPE_NAMESPACE); |
|
| 116 | 101 |
|
| 117 |
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 118 |
Map<String, TaxonName> specTaxNameMap = partitioner.getObjectMap(SPEC_TAX_NAMESPACE); |
|
| 102 |
@SuppressWarnings("unchecked")
|
|
| 103 |
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE); |
|
| 104 |
@SuppressWarnings("unchecked")
|
|
| 105 |
Map<String, TaxonName> specTaxNameMap = partitioner.getObjectMap(SPEC_TAX_NAMESPACE); |
|
| 119 | 106 |
|
| 120 | 107 |
ResultSet rs = partitioner.getResultSet(); |
| 121 | 108 |
|
| ... | ... | |
| 144 | 131 |
// [file lab2], same as Dateiname04 but less data |
| 145 | 132 |
// Dateipfad |
| 146 | 133 |
|
| 147 |
Set<Media> recordMedia = new HashSet<Media>();
|
|
| 134 |
Set<Media> recordMedia = new HashSet<>(); |
|
| 148 | 135 |
|
| 149 | 136 |
try {
|
| 150 | 137 |
|
| ... | ... | |
| 175 | 162 |
//not type specimen |
| 176 | 163 |
if (specimen == null){
|
| 177 | 164 |
specimen = DerivedUnit.NewPreservedSpecimenInstance(); |
| 178 |
specimen.setTitleCache("Specimen for " + title );
|
|
| 165 |
specimen.setTitleCache("Specimen for " + title, true);
|
|
| 179 | 166 |
String collectionCode = transformCopyright2CollectionCode(copyright); |
| 180 | 167 |
//TODO |
| 181 | 168 |
Collection collection = getCollection(collectionCode); |
| 182 | 169 |
specimen.setCollection(collection); |
| 183 | 170 |
} |
| 184 | 171 |
|
| 185 |
|
|
| 186 | 172 |
//source |
| 187 | 173 |
specimen.addSource(OriginalSourceType.Import, String.valueOf(bildID), IMAGE_NAMESPACE, state.getTransactionalSourceReference(), null); |
| 188 | 174 |
|
| ... | ... | |
| 285 | 271 |
return null; |
| 286 | 272 |
} |
| 287 | 273 |
|
| 288 |
|
|
| 289 |
|
|
| 290 |
|
|
| 291 | 274 |
private String getNameFromFileOs(ResultSet rs) throws SQLException {
|
| 292 | 275 |
String fileOS = rs.getString("file OS");
|
| 293 | 276 |
Pattern pattern = Pattern.compile("(.+)(_.{4}(-.{1,3})?(_Nr\\d{3,4})?_.{2,3}\\.jpg)");
|
| ... | ... | |
| 301 | 284 |
} |
| 302 | 285 |
} |
| 303 | 286 |
|
| 304 |
|
|
| 305 |
|
|
| 306 |
|
|
| 307 | 287 |
private void makeAllMedia(GlobisImportState state, ResultSet rs, Set<Media> recordMedia, Set<Media> objectsToSave) throws SQLException{
|
| 308 | 288 |
//make image path |
| 309 | 289 |
String pathShort = rs.getString("Dateipfad_kurz");
|
| ... | ... | |
| 413 | 393 |
|
| 414 | 394 |
@Override |
| 415 | 395 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, GlobisImportState state) {
|
| 416 |
String nameSpace; |
|
| 417 |
Class<?> cdmClass;
|
|
| 396 |
|
|
| 397 |
String nameSpace;
|
|
| 418 | 398 |
Set<String> idSet; |
| 419 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 399 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 420 | 400 |
try{
|
| 421 | 401 |
Set<String> currSpecIdSet = new HashSet<>(); |
| 422 | 402 |
Set<String> specTaxIdSet = new HashSet<>(); |
| ... | ... | |
| 430 | 410 |
|
| 431 | 411 |
//specTax map |
| 432 | 412 |
nameSpace = SPEC_TAX_NAMESPACE; |
| 433 |
cdmClass = TaxonName.class; |
|
| 434 | 413 |
idSet = specTaxIdSet; |
| 435 |
Map<String, TaxonName> specTaxNameMap = (Map<String, TaxonName>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 414 |
Map<String, TaxonName> specTaxNameMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonName.class, idSet, nameSpace);
|
|
| 436 | 415 |
result.put(nameSpace, specTaxNameMap); |
| 437 | 416 |
|
| 438 | 417 |
// //taxon map |
| 439 | 418 |
// nameSpace = TAXON_NAMESPACE; |
| 440 |
// cdmClass = Taxon.class; |
|
| 441 | 419 |
// idSet = currSpecIdSet; |
| 442 |
// Map<String, Taxon> taxonMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 420 |
// Map<String, Taxon> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class, idSet, nameSpace);
|
|
| 443 | 421 |
// result.put(nameSpace, taxonMap); |
| 444 | 422 |
|
| 445 | 423 |
|
| 446 | 424 |
//type map |
| 447 |
nameSpace = GlobisSpecTaxImport.TYPE_NAMESPACE; |
|
| 448 |
cdmClass = DerivedUnit.class; |
|
| 425 |
nameSpace = GlobisImportBase.TYPE_NAMESPACE; |
|
| 449 | 426 |
idSet = typeIdSet; |
| 450 |
Map<String, DerivedUnit> typeMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 427 |
Map<String, DerivedUnit> typeMap = getCommonService().getSourcedObjectsByIdInSourceC(DerivedUnit.class, idSet, nameSpace);
|
|
| 451 | 428 |
result.put(nameSpace, typeMap); |
| 452 | 429 |
|
| 453 | 430 |
|
| ... | ... | |
| 468 | 445 |
} |
| 469 | 446 |
} |
| 470 | 447 |
|
| 471 |
/* (non-Javadoc) |
|
| 472 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 473 |
*/ |
|
| 474 | 448 |
@Override |
| 475 | 449 |
protected boolean doCheck(GlobisImportState state){
|
| 476 | 450 |
IOValidator<GlobisImportState> validator = new GlobisImageImportValidator(); |
| 477 | 451 |
return validator.validate(state); |
| 478 | 452 |
} |
| 479 | 453 |
|
| 480 |
|
|
| 481 |
/* (non-Javadoc) |
|
| 482 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 483 |
*/ |
|
| 484 | 454 |
@Override |
| 485 | 455 |
protected boolean isIgnore(GlobisImportState state){
|
| 486 | 456 |
return ! state.getConfig().isDoImages(); |
| 487 | 457 |
} |
| 488 | 458 |
|
| 489 |
|
|
| 490 |
|
|
| 491 |
|
|
| 492 |
/* (non-Javadoc) |
|
| 493 |
* @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doInvoke(eu.etaxonomy.cdm.io.globis.GlobisImportState) |
|
| 494 |
*/ |
|
| 495 | 459 |
@Override |
| 496 | 460 |
protected void doInvoke(GlobisImportState state) {
|
| 497 | 461 |
Reference refGart = ReferenceFactory.newGeneric(); |
| 498 |
refGart.setTitleCache("GART");
|
|
| 462 |
refGart.setTitleCache("GART", true);
|
|
| 499 | 463 |
refGart.setUuid(uuidGartRef); |
| 500 | 464 |
getReferenceService().saveOrUpdate(refGart); |
| 501 | 465 |
super.doInvoke(state); |
| 502 | 466 |
} |
| 503 |
|
|
| 504 |
|
|
| 505 |
|
|
| 506 |
|
|
| 507 |
|
|
| 508 | 467 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisSpecTaxImport.java | ||
|---|---|---|
| 758 | 758 |
return specTypeDepositoryStr; |
| 759 | 759 |
} |
| 760 | 760 |
|
| 761 |
|
|
| 762 |
|
|
| 763 |
|
|
| 764 |
/** |
|
| 765 |
* @param fieldObservation |
|
| 766 |
* @return |
|
| 767 |
*/ |
|
| 768 | 761 |
protected DerivedUnit makeSingleTypeSpecimen(FieldUnit fieldObservation) {
|
| 769 | 762 |
DerivationEvent derivEvent = DerivationEvent.NewInstance(); |
| 770 | 763 |
// derivEvent.setType(DerivationEventType.ACCESSIONING()); |
| ... | ... | |
| 774 | 767 |
return specimen; |
| 775 | 768 |
} |
| 776 | 769 |
|
| 777 |
|
|
| 778 |
|
|
| 779 |
|
|
| 780 |
/** |
|
| 781 |
* @param state |
|
| 782 |
* @return |
|
| 783 |
* @throws SQLException |
|
| 784 |
*/ |
|
| 785 | 770 |
protected FieldUnit makeTypeFieldObservation(GlobisImportState state, |
| 786 | 771 |
ResultSet rs) throws SQLException {
|
| 787 | 772 |
|
| ... | ... | |
| 797 | 782 |
} |
| 798 | 783 |
|
| 799 | 784 |
|
| 800 |
|
|
| 801 |
|
|
| 802 |
/** |
|
| 803 |
* @param name |
|
| 804 |
* @param rs |
|
| 805 |
* @param status |
|
| 806 |
* @param specimen |
|
| 807 |
* @param specTaxId |
|
| 808 |
* @throws SQLException |
|
| 809 |
*/ |
|
| 810 | 785 |
protected void makeTypeDesignation(IZoologicalName name, ResultSet rs, DerivedUnit specimen, Integer specTaxId) throws SQLException {
|
| 811 | 786 |
//type |
| 812 | 787 |
String specType = rs.getString("SpecType");
|
| ... | ... | |
| 819 | 794 |
name.addTypeDesignation(typeDesignation, true); |
| 820 | 795 |
} |
| 821 | 796 |
|
| 822 |
|
|
| 823 |
|
|
| 824 |
|
|
| 825 | 797 |
private SpecimenTypeDesignationStatus getTypeDesigType(String specType, Integer specTaxId) {
|
| 826 | 798 |
if (isBlank(specType) ){
|
| 827 | 799 |
return null; |
| ... | ... | |
| 841 | 813 |
} |
| 842 | 814 |
} |
| 843 | 815 |
|
| 844 |
|
|
| 845 |
|
|
| 846 |
|
|
| 847 |
/** |
|
| 848 |
* @param state |
|
| 849 |
* @param referenceMap |
|
| 850 |
* @param rs |
|
| 851 |
* @param name |
|
| 852 |
* @param specTaxId |
|
| 853 |
* @return |
|
| 854 |
* @throws SQLException |
|
| 855 |
*/ |
|
| 856 | 816 |
private Reference handleNomRef(GlobisImportState state, Map<String, Reference> referenceMap, ResultSet rs, |
| 857 | 817 |
IZoologicalName name, Integer specTaxId) throws SQLException {
|
| 858 | 818 |
//ref |
| ... | ... | |
| 875 | 835 |
return nomRef; |
| 876 | 836 |
} |
| 877 | 837 |
|
| 878 |
|
|
| 879 |
|
|
| 880 |
|
|
| 881 | 838 |
private void validateAcceptedTaxon(Taxon acceptedTaxon, ResultSet rs, Integer specTaxId, Integer acceptedTaxonId) throws SQLException {
|
| 882 | 839 |
if (acceptedTaxon == null){
|
| 883 | 840 |
logger.warn("Accepted taxon is null for taxon taxon to validate. SpecTaxId " + specTaxId + ", accTaxonId: " + acceptedTaxonId);
|
| ... | ... | |
| 894 | 851 |
//TODO |
| 895 | 852 |
} |
| 896 | 853 |
|
| 897 |
|
|
| 898 |
|
|
| 899 |
|
|
| 900 | 854 |
private Synonym getSynonym(GlobisImportState state, ResultSet rs, Integer specTaxId) throws SQLException {
|
| 901 | 855 |
TaxonName name = (TaxonName)makeName(state, rs, specTaxId); |
| 902 | 856 |
|
| ... | ... | |
| 905 | 859 |
return synonym; |
| 906 | 860 |
} |
| 907 | 861 |
|
| 908 |
|
|
| 909 |
|
|
| 910 |
|
|
| 911 | 862 |
/** |
| 912 | 863 |
* @param state |
| 913 | 864 |
* @param rs |
| ... | ... | |
| 942 | 893 |
return name; |
| 943 | 894 |
} |
| 944 | 895 |
|
| 945 |
|
|
| 946 |
|
|
| 947 |
|
|
| 948 | 896 |
private void makeNamePartsAndCache(GlobisImportState state, ResultSet rs, String rank, IZoologicalName name) throws SQLException {
|
| 949 | 897 |
String citedFamily = rs.getString("SpecCitedFamily");
|
| 950 | 898 |
String citedGenus = rs.getString("SpecCitedGenus");
|
| ... | ... | |
| 971 | 919 |
|
| 972 | 920 |
@Override |
| 973 | 921 |
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, GlobisImportState state) {
|
| 974 |
String nameSpace; |
|
| 975 |
Class<?> cdmClass;
|
|
| 922 |
|
|
| 923 |
String nameSpace;
|
|
| 976 | 924 |
Set<String> idSet; |
| 977 | 925 |
|
| 978 |
Set<AgentBase> agents = state.getAgents(); |
|
| 926 |
@SuppressWarnings("rawtypes")
|
|
| 927 |
Set<AgentBase> agents = state.getAgents(); |
|
| 979 | 928 |
getAgentService().saveOrUpdate(agents); |
| 980 | 929 |
|
| 981 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
| 930 |
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>(); |
|
| 982 | 931 |
try{
|
| 983 |
Set<String> taxonIdSet = new HashSet<String>();
|
|
| 984 |
Set<String> referenceIdSet = new HashSet<String>();
|
|
| 932 |
Set<String> taxonIdSet = new HashSet<>(); |
|
| 933 |
Set<String> referenceIdSet = new HashSet<>(); |
|
| 985 | 934 |
|
| 986 | 935 |
while (rs.next()){
|
| 987 | 936 |
handleForeignKey(rs, taxonIdSet, "SpecCurrspecID"); |
| ... | ... | |
| 990 | 939 |
|
| 991 | 940 |
//taxon map |
| 992 | 941 |
nameSpace = TAXON_NAMESPACE; |
| 993 |
cdmClass = Taxon.class; |
|
| 994 | 942 |
idSet = taxonIdSet; |
| 995 |
Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 943 |
Map<String, Taxon> objectMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class, idSet, nameSpace);
|
|
| 996 | 944 |
result.put(nameSpace, objectMap); |
| 997 | 945 |
|
| 998 | 946 |
//reference map |
| 999 | 947 |
nameSpace = REFERENCE_NAMESPACE; |
| 1000 |
cdmClass = Reference.class; |
|
| 1001 | 948 |
idSet = referenceIdSet; |
| 1002 |
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
| 949 |
Map<String, Reference> referenceMap = getCommonService().getSourcedObjectsByIdInSourceC(Reference.class, idSet, nameSpace);
|
|
| 1003 | 950 |
result.put(nameSpace, referenceMap); |
| 1004 | 951 |
|
| 1005 | 952 |
//collection map |
| 1006 | 953 |
nameSpace = COLLECTION_NAMESPACE; |
| 1007 | 954 |
List<Collection> listCollection = getCollectionService().list(Collection.class, null, null, null, null); |
| 1008 |
Map<String, Collection> collectionMap = new HashMap<String, Collection>();
|
|
| 955 |
Map<String, Collection> collectionMap = new HashMap<>(); |
|
| 1009 | 956 |
for (Collection collection : listCollection){
|
| 1010 | 957 |
if (isNotBlank(collection.getCode())){
|
| 1011 | 958 |
collectionMap.put(collection.getCode(), collection); |
| ... | ... | |
| 1023 | 970 |
return result; |
| 1024 | 971 |
} |
| 1025 | 972 |
|
| 1026 |
/* (non-Javadoc) |
|
| 1027 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 1028 |
*/ |
|
| 1029 | 973 |
@Override |
| 1030 | 974 |
protected boolean doCheck(GlobisImportState state){
|
| 1031 | 975 |
IOValidator<GlobisImportState> validator = new GlobisSpecTaxaImportValidator(); |
| 1032 | 976 |
return validator.validate(state); |
| 1033 | 977 |
} |
| 1034 | 978 |
|
| 1035 |
|
|
| 1036 |
/* (non-Javadoc) |
|
| 1037 |
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator) |
|
| 1038 |
*/ |
|
| 1039 | 979 |
@Override |
| 1040 | 980 |
protected boolean isIgnore(GlobisImportState state){
|
| 1041 | 981 |
return ! state.getConfig().isDoSpecTaxa(); |
| 1042 | 982 |
} |
| 1043 | 983 |
|
| 1044 |
|
|
| 1045 |
|
|
| 1046 |
|
|
| 1047 | 984 |
@Override |
| 1048 | 985 |
public Reference createObject(ResultSet rs, GlobisImportState state) |
| 1049 | 986 |
throws SQLException {
|
| app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoConabioCommonNamesImport.java | ||
|---|---|---|
| 89 | 89 |
} |
| 90 | 90 |
} |
| 91 | 91 |
|
| 92 |
@SuppressWarnings("unchecked")
|
|
| 93 | 92 |
private void initTaxa() {
|
| 94 | 93 |
if (taxonIdMap == null){
|
| 95 | 94 |
Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet(); |
| 96 |
taxonIdMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(Taxon.class,
|
|
| 95 |
taxonIdMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class,
|
|
| 97 | 96 |
existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE); |
| 98 | 97 |
} |
| 99 | 98 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoConabioDistributionImport.java | ||
|---|---|---|
| 59 | 59 |
return "DistribucionEstatal"; |
| 60 | 60 |
} |
| 61 | 61 |
|
| 62 |
@SuppressWarnings("unchecked")
|
|
| 63 | 62 |
private void initTaxa() {
|
| 64 | 63 |
if (taxonIdMap == null){
|
| 65 | 64 |
Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet(); |
| 66 |
taxonIdMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(Taxon.class,
|
|
| 65 |
taxonIdMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class,
|
|
| 67 | 66 |
existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE); |
| 68 | 67 |
} |
| 69 | 68 |
} |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java | ||
|---|---|---|
| 348 | 348 |
e.printStackTrace(); |
| 349 | 349 |
} |
| 350 | 350 |
//add taxa and their parent taxa |
| 351 |
result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE)); |
|
| 352 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_E, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_E)); |
|
| 353 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_W, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_W)); |
|
| 354 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_K, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_K)); |
|
| 355 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AW, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AW)); |
|
| 356 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AO, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AO)); |
|
| 357 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_R, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_R)); |
|
| 358 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_O, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_O)); |
|
| 359 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_S, (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_S)); |
|
| 351 |
result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE)); |
|
| 352 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_E, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_E)); |
|
| 353 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_W, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_W)); |
|
| 354 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_K, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_K)); |
|
| 355 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AW, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AW)); |
|
| 356 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_AO, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_AO)); |
|
| 357 |
result.put(RedListUtil.CLASSIFICATION_NAMESPACE_R, getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, RedListUtil.CLASSIFICATION_NAMESPACE_R)); |
|
Also available in: Unified diff
adapt some classes to new CommonService.getSourcedObjectSByIdInSourceC and cleanup